Disease genes are ancient genes

A very interesting paper, which shows that genes that cause human disease tend to be those which appeared earlier in evolution on Earth, rather than in the mammalian lineage. Perhaps, ancient genes are very important for the proper functioning of an organism (they managed to survive the longest, so they must be doing something important), and hence dysfunctions caused by them would have a major negative effect.

Molecular Biology and Evolution, doi:10.1093/molbev/msn214

An ancient evolutionary origin of genes associated with human genetic diseases

Tomislav Domazet-Loo and Diethard Tautz

Abstract

Several thousand genes in the human genome have been linked to a heritable genetic disease. The majority of these appear to be non-essential genes (i.e. are not embryonically lethal when inactivated) and one could therefore speculate that they are late additions in the evolutionary lineage towards humans. Contrary to this expectation, we find that they are in fact significantly over-represented among the genes that have emerged during the early evolution of the metazoa. Using a phylostratigraphic approach, we have studied the evolutionary emergence of such genes at 19 phylogenetic levels. The majority of disease genes was already present in the eukaryotic ancestor and the second largest number has arisen around the time of evolution of multicellularity. Conversely, genes specific to the mammalian lineage are highly underrepresented. Hence, genes involved in genetic diseases are not simply a random subset of all genes in the genome, but are biased towards ancient genes.

Link

Female life expectancy vs. Female Birth Rate

Evolution and Human Behavior doi:10.1016/j.evolhumbehav.2008.08.002

Sex difference in life span affected by female birth rate in modern humans

Alexei A. Maklakov

Abstract

Sex differences in life span are common in different taxa, including primates, but not well understood. Theory and comparative evidence suggest that differential costs of reproduction between the sexes may explain the differences in sex-biased mortality across large taxonomic groups. The level of sex-specific reproductive effort may thus affect the difference in life span across populations. Modern humans (Homo sapiens), generally show the typical mammalian pattern of male-biased mortality. Here, I asked whether the differences in female birth rates between countries affect the sex difference in life span. I used the data on male and female life span and female birth rate in different countries from publicly available databases, while controlling for geographic and economic factors. The analysis suggests that female birth rate explains 17% of the variation in relative sex differences in life span across countries. Low female birth rate results in females living relatively longer than males. These data suggest that a simple biological factor—female birth rate—may explain a significant part of the variation in sex differences in life span across human populations.

Link

Y chromosomes of the Ruling Dynasty of the Nso' in Cameroon

From the paper:

The groups are (1) the won nto', descendants of a fon down to the third or fourth generation; (2) the duy, descendants of a fon who ruled more than three or four generations ago together with, according to Chem-Langhëë and Fanso (1997), some members of commoner lineages whose heads are descendants of princesses and members of associated patriclans or clan segments, allegedly founded by immigrant royals, that provide state counselors; (3) the nshiylav, subjects born or recruited2 into palace service (patrilineally inherited); and (4) the mtaar, commoners (patrilineally inherited). Although the majority of the Nso' are self-identifying Christians of the Roman Catholic denomination, the fon has, through the generations, maintained a polygynous household, which in 2005 numbered over 70 women.3

...

The most common NRY haplogroup in the won nto' was Y*(xBR,A3b2), with a frequency of 55.6% ( ; table 1). This haplogroup was also found at a frequency of 17.6% in the duy. Furthermore, all Y*(xBR,A3b2) chromosomes had the same microsatellite haplotype (14-12-20-11-14-14; ... For convenience only we refer to Y*(xBR,A3b2) and the associated microsatellite haplotype as the won nto' modal haplotype (WMH); it had ten representatives, while the next most frequent haplotype in the won nto' had only two. The modal NRY haplogroup in the non–won nto' social classes was E3a, with a diverse range of NRY types at the microsatellite haplotype level

...

A principal coordinates analysis plot (fig. 2) based on a pairwise FST distance matrix calculated using NRY haplogroup frequencies (see table F1 for genetic distances and associated P values) clearly distanced the won nto' from both the other Nso' social classes and other ethnic groups, demonstrating that high frequencies of Y*(xBR,A3b2) are not typical of Grassfields and Tikar Plain NRY profiles. Accordingly, because Y*(xBR,A3b2) is typical of a hunter-gatherer population and the WMH is the most likely candidate to be the NRY type of the father of the first Nso' fon, the NRY data favor the oral tradition that the princess married an indigenous Visale, from whom all subsequent fons descend.

Current Anthropology doi: 10.1086/590119

Sex-Specific Genetic Data Support One of Two Alternative Versions of the Foundation of the Ruling Dynasty of the Nso' in Cameroon

Krishna R. Veeramah et al.

Abstract

Sex-specific genetic data favor a specific variant of the oral history of the kingdom of Nso' (a Grassfields city-state in Cameroon) in which the royal family traces its descent from a founding ancestress who married into an autochthonous hunter-gatherer group. The distributions of Y chromosome and mitochondrial DNA variation in the Nso' in general and in the ruling dynasty in particular are consistent with specific Nso' marriage practices, suggesting strict conservation of the royal social class along agnatic lines. This study demonstrates the efficacy of using genetics to augment other sources of information (e.g., oral histories, archaeology, and linguistics) when seeking to recover the histories of African peoples.

Link

Integrated detection of SNPs and Copy number variation

While SNPs are single-letter changes in the genetic code, copy number variation (CNV) involves the multiplication (or deletion) of entire chunks of DNA. While in a SNP, the allele is a single letter (e.g., C or T), in CNVs, the allele is an integer number of how many copies of the particular chunk of DNA an individual has. What this paper shows is that most human CNVs don't appear to be "fresh" changes but rather old "frozen" changes that are linked to specific SNPs or combinations of SNPs. Practically, this means that a CNV allele can be inferred fairly accurately by looking at SNPs in the region of the chromosome where it occurs.

Nature Genetics 40, 1166 - 1174 (2008)

Integrated detection and population-genetic analysis of SNPs and copy number variation

Steven A McCarroll et al.

Abstract

Dissecting the genetic basis of disease risk requires measuring all forms of genetic variation, including SNPs and copy number variants (CNVs), and is enabled by accurate maps of their locations, frequencies and population-genetic properties. We designed a hybrid genotyping array (Affymetrix SNP 6.0) to simultaneously measure 906,600 SNPs and copy number at 1.8 million genomic locations. By characterizing 270 HapMap samples, we developed a map of human CNV (at 2-kb breakpoint resolution) informed by integer genotypes for 1,320 copy number polymorphisms (CNPs) that segregate at an allele frequency >1%. More than 80% of the sequence in previously reported CNV regions fell outside our estimated CNV boundaries, indicating that large (>100 kb) CNVs affect much less of the genome than initially reported. Approximately 80% of observed copy number differences between pairs of individuals were due to common CNPs with an allele frequency >5%, and more than 99% derived from inheritance rather than new mutation. Most common, diallelic CNPs were in strong linkage disequilibrium with SNPs, and most low-frequency CNVs segregated on specific SNP haplotypes.

Link

More ASHG 2008 abstracts

The previous batch is here.

Analysis of East Asia Genetic Substructure: Population Differentiation and PCA Clusters Correlate with Geographic Distribution

Accounting for genetic substructure within European populations has been important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to other continental populations an understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation(Fst) and Principal Components Analyses(PCA) are examined using >200K genotypes from multiple populations of East Asian ancestry(total 298 subjects). The population groups included those from the Human Genome Diversity Panel[Cambodian(CAMB), Yi, Daur, Mongolian(MGL), Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, and Xibo], HapMap(CHB and JPT), and East Asian or East Asian American subjects of Vietnamese(VIET), Korean(KOR), Filipino(FIL) and Chinese ancestry. Paired Fst(Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups(CHB/KOR, 0.0019; CHB/JPT, 00651; CHB/VIET, 0.0065) with larger separation with FIL(CHB/FIL, 0.014). Low levels of differentiation were also observed between DAI and VIET(0.0045) and between VIET and CAMB(0.0062). Similarly, small Fsts were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan. For example, the four For PCA, the first two PCs showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations.corner groups were JPT, FIL, CAMB and MGL with the CHB forming the center group, and KOR was between CHB and JPT. Other small ethnic groups were also in rough geographic correlation with their putative origins. These studies have also enabled the selection of a subset of East Asian substructure ancestry informative markers(EASTASAIMS) that may be useful for future genetic association studies in reducing type 1 errors and in identifying homogeneous groups.

Worldwide Population Structure using SNP Microarray Genotyping

We genotyped 348 individuals sampled from 24 populations world-wide using the Affymetrix 250k NspI microarray chip. For context, we added matching genotypes from 210 HapMap individuals for a total of 250,823 loci genotyped in 543 individuals from 28 populations. We included populations from India and Daghestan to provide detail between the genetic poles of Western Europe, East Asia, and sub-Sahara Africa. With so many markers, principal components analyses reveal genetic differentiation between almost all identified populations in our sample. Northern and southern European populations (FST = 0.004, p <0.01) are statistically distinguishable, as are upper and lower caste groups in India (FST = 0.005, p <0.01). All individuals are accurately classified into continental groups, and even between closely-related populations, genetic- and self-classifications conflict for only a minority of individuals (e.g. ~2% between upper and lower Indian castes; k-means clustering.) As expected, the HapMap CHB+JPT, CEU, and YRI samples are most similar to our east Asian, west European, and African samples, respectively. The HapMap CEU samples and our northern European ancestry samples were both collected from Utah. Although individual samples cannot be reliably classified into their collection of origin, the groups are statistically distinguishable despite their high similarity (FST = 0.0005, n.s.). Our Japanese group is also statistically distinguishable from the HapMap JPT group (FST = 0.006, p <0.01), and in this comparison, most samples can be correctly classified. With such large numbers of genotypes, significant differences can be found even between very similar population samplings. Our results provide guidelines for researchers in selecting suitable control populations for case-control studies.

Frequency distribution and selection in 4 pigmentation genes in Europe

Pigmentation is one of the more obvious forms of variation in humans, particularly in Europeans where one sees more within group variation in hair and eye pigmentation than in the rest of the world. We studied 4 genes (SLC24A5, SLC45A2, OCA2 and MC1R) that are believed to contribute to the pigment phenotypes in Europeans. SLC24A5 has a single functional variant that leads to lighter skin pigmentation. Data on 83 populations worldwide (including 55 from our lab) show the variant (at rs1426654) has almost reached fixation in Europe, Southwest Asia, and North Africa, has moderate to high frequencies (.2-.9) throughout Central Asia, and has frequencies of .1-.3 in East and South Africa. The variant is essentially absent elsewhere. SLC45A2 also has a single functional variant (at rs16891982) associated with light skin pigmentation in Europe. Data on 84 populations worldwide show the light skin allele is nearly fixed in Northern Europe but has lower frequencies in Southern Europe, the Middle East and Northern Africa. In Central Asia the frequency of the SLC45A2 variant declines more quickly than the SLC24A5 variant. It is absent in both East and South Africa. In OCA2 we typed 4 SNPs (rs4778138, rs4778241, rs7495174, rs12913832) with a haplotype associated with blue eyes in Europeans. This haplotype shows a Southeastern to Northwestern pattern in Europe with frequencies of .25 (.05 homozygous) in the Adygei to .85 (.75 homozygous) in the Danes. In MC1R we typed 5 SNPs (rs3212345, rs3212357, rs3212363, C_25958294_10, rs7191944) that cover the entire MC1R gene and found a predominantly European haplotype that ranges in frequency from .35 to .65 in Europe, reaching its highest levels in Southwest Asia and Northwestern Europe. Extended Haplotype Heterozygosity (EHH) and normalized Haplosimilarity (nHS) show evidence of selection at SLC24A5 in not only our European and Southwest Asian populations but also our East African populations. Neither SLC45A2 or OCA2 showed evidence of selection in either test. MC1R did not show evidence of selection for our European specific haplotype but we did see some evidence both upstream and downstream in our nHS test in Europe.

Using principal components analysis to identify candidate genes for natural selection.

Genetic markers that differentiate populations are excellent candidates for natural selection due to local adaptation, and may shed light into physiological pathways that underlie disorders with varying frequencies around the world. Principal Components Analysis (PCA) has emerged as a powerful tool for the characterization and analysis of the structure of genomewide datasets. In prior work, we described an algorithm that can be used to select small subsets of genetic markers (SNPs) that correlate well with population structure, as captured by PCA. Our method can be used to detect SNPs that differentiate individuals from different geographic regions, or even neighboring subpopulations. We set out to explore the nature and properties of the genes where population-differentiating SNPs reside, by analyzing the publicly available Human Genome Diversity Panel dataset (650,000 SNPs for 1,043 individuals, 51 populations). Applying our SNP selection algorithms, we chose small subsets of SNPs that almost perfectly reproduce worldwide population structure as identified by PCA. We determined SNP panels both for population differentiation within seven geographic regions, as well as around the globe. We then explored the hypothesis that the selected SNPs attained their current worldwide allele frequency patterns as a response to the pressure of natural selection. Comparing our lists to recently published reports, we found a significant overlap with other genomewide scans for selection, thus validating our hypothesis. For example, EDAR (involved in the development of hair follicles) harbors the most differentiating SNPs in our world-wide panels. SNPs located in genes that are involved in skin and eye pigmentation (OCA2, MYO5C, HERC1, HERC2) are also among the top population differentiating markers. In East Asia, SNPs residing at the ADH cluster appear among the most important SNPs for population structure, while, in Europe, the same is true for genes that are involved in immune response to pathogens (CR1, DUOX2, TLR, and HLA). Finally, a comprehensive gene ontology analysis is presented.

Central Asian patrilineal populations

On the same topic as the preceding post. I would add that a major cause for the higher informativeness of the human Y-chromosome is the fact that most of the presently dominant lineages in the world are fairly recent, and hence there has been less time for random diffusion of patrilineages on the map to wipe out pre-established patterns of Y-chromosomes associated with archaeologically or historically dominant patriarchal groups.

In the standard model, males are more static, and females more mobile, because they may move fairly long distances to settle in their husband's residence. This factor is counterbalanced, I think, by the excess organized migration of surplus males in societies where there is socio-economic/reproductive inequality.

Thus, the constant individualistic short-range migration of women, coupled with their greater reproductive equality, over long periods of time, evens out the distribution of mtDNA lineages, with the resulting distribution further obscured by (climate-related) selective factors acting on human mtDNA. On the contrary, the Y-chromosome landscape is established by patrilocal males staying by and defending their hearths, but is occasionally punctuated by long-range collective migration of patrilineally related males.

PLoS Genetics doi:10.1371/journal.pgen.1000200

Sex-Specific Genetic Structure and Social Organization in Central Asia: Insights from a Multi-Locus Study

Laure Ségurel et al.

Abstract

In the last two decades, mitochondrial DNA (mtDNA) and the non-recombining portion of the Y chromosome (NRY) have been extensively used in order to measure the maternally and paternally inherited genetic structure of human populations, and to infer sex-specific demography and history. Most studies converge towards the notion that among populations, women are genetically less structured than men. This has been mainly explained by a higher migration rate of women, due to patrilocality, a tendency for men to stay in their birthplace while women move to their husband's house. Yet, since population differentiation depends upon the product of the effective number of individuals within each deme and the migration rate among demes, differences in male and female effective numbers and sex-biased dispersal have confounding effects on the comparison of genetic structure as measured by uniparentally inherited markers. In this study, we develop a new multi-locus approach to analyze jointly autosomal and X-linked markers in order to aid the understanding of sex-specific contributions to population differentiation. We show that in patrilineal herder groups of Central Asia, in contrast to bilineal agriculturalists, the effective number of women is higher than that of men. We interpret this result, which could not be obtained by the analysis of mtDNA and NRY alone, as the consequence of the social organization of patrilineal populations, in which genetically related men (but not women) tend to cluster together. This study suggests that differences in sex-specific migration rates may not be the only cause of contrasting male and female differentiation in humans, and that differences in effective numbers do matter.

Link

Polygyny in human evolution

This paper suggests that polygyny has been a feature of our species for most of its history. They arrive at this conclusion by comparing genetic variation in autosomal DNA and X chromosomes.

Autosomal DNA spends an equal amount of time in male and female bodies, while X chromosomes spend twice as long in female than in male bodies. In a polygynous society, many males don't have offspring while most women do. Hence, genetic variation in X chromosomes has a higher chance to arise (more bodies=>more mutations) and to be maintained (more bodies=>less drift).

This ties in quite nicely with my recent suggestion on reproductive inequality for human Y-chromosomes.

Related story in the New Scientist.

Hammer's team discovered more genetic differences in the X chromosome than would be expected if equal numbers of males and females tended to mate, over human history. The only explanation for this pattern is widespread, long-lasting polygyny, he says.

His team's analysis reflects all of human history, and modern monogamy has not even left a blip in our genomes. "I don't know how long monogamy has been with us," Hammer says. "It seems it hasn't been around long, evolutionarily."

PLoS Genetics doi:10.1371/journal.pgen.1000202

Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity

Sex-Biased Evolutionary Forces Shape Genomic Patterns of Human Diversity et al.

Abstract

Comparisons of levels of variability on the autosomes and X chromosome can be used to test hypotheses about factors influencing patterns of genomic variation. While a tremendous amount of nucleotide sequence data from across the genome is now available for multiple human populations, there has been no systematic effort to examine relative levels of neutral polymorphism on the X chromosome versus autosomes. We analyzed ~210 kb of DNA sequencing data representing 40 independent noncoding regions on the autosomes and X chromosome from each of 90 humans from six geographically diverse populations. We correct for differences in mutation rates between males and females by considering the ratio of within-human diversity to human-orangutan divergence. We find that relative levels of genetic variation are higher than expected on the X chromosome in all six human populations. We test a number of alternative hypotheses to explain the excess polymorphism on the X chromosome, including models of background selection, changes in population size, and sex-specific migration in a structured population. While each of these processes may have a small effect on the relative ratio of X-linked to autosomal diversity, our results point to a systematic difference between the sexes in the variance in reproductive success; namely, the widespread effects of polygyny in human populations. We conclude that factors leading to a lower male versus female effective population size must be considered as important demographic variables in efforts to construct models of human demographic history and for understanding the forces shaping patterns of human genomic variability.

Link

ASHG 2008 abstracts

Just a sample of abstracts that I found interesting from the upcoming meeting of the American Society of Human Genetics.

Strong linkage disequilibrium for the frequent GJB2 35delG mutation in the Greek population.

Up to forty percent of autosomal recessive, congenital, severe to profound hearing impairment cases result from mutations in the GJB2 gene. The 35delG mutation accounts for the majority of mutations detected in Caucasian populations and represents one of the most frequent disease mutations identified so far. Some previous studies have assumed that the high frequency of the 35delG mutation reflects the presence of a mutational hot spot, whilst other studies support the theory of a common founder. Greece is amongst the countries presenting the highest frequency of the 35delG mutation (3.5%), and a recent study raised the hypothesis of the origin of this mutation in ancient Greece. We genotyped 60 Greek deafness patients homozygous for the 35delG mutation for six single nucleotide polymorphisms (SNPs) and two microsatellite markers, mapping within or flanking the GJB2 gene, as compared to 60 Greek hearing controls. A strong linkage disequilibrium was found between the 35delG mutation and the DNA markers at distances of 34 kb on the centromeric and 90 kb on the telomeric side of the gene, respectively. A comparison of the present findings with those of a previous study from Belgium, UK and USA, demonstrated a common haplotype reflecting the common founder. Our study supports the hypothesis of a founder effect and we further propose that ethnic groups of Greek ancestry could have propagated the 35delG mutation, as evidenced by historical data beginning from the 15th century BC.

Detection of population substructure among Jews and a north/south gradient within Ashkenazi Jews using 32 STR markers.

Understanding and detecting population substructure are critical issues. Using 32 autosomal STR markers and the program STRUCTURE we demonstrated differentiation between Ashkenazi (AJ) (N=135) and Sephardic (SJ) (N=226) Jewish populations in the form of Northern and Southern European genetic components (AJ north 73%, south 22%, SJ north 32%, south 61%) and a significant relationship between latitude of grandparental country of origin (GCO) and percent north/south genetic component in AJ. Notably, we revealed substructure among Jews (and among European Americans (EA)) using a small STR panel, only when additional samples representing major continental populations (African American, EA, Asian) were included in analyses. Further, negative RIS (-0.035) indicates recent admixture in individuals with both SJ and AJ parents (N=38). RIS is a measure of inbreeding adapted from FIS for STR markers. Negative RIS indicates allelic variation within individuals greater than expected under random mating, i.e., excess heterozygosity due to outbreeding. Although geographic patterns are seen in the average north/south percent assignment values between groups as defined by AJ or SJ, grandparental world region of origin, or GCO, within each group there is high variability among individual assignment values. Thus, even based on data from a small marker set, AJ is not a homogeneous population. The north/south gradient in AJ may be a reflection of the pre-existing north/south gradient in European host populations (recently shown in other studies using large numbers of SNPs) with which Jews admixed slowly. We also demonstrate the utility of including purported parental populations when attempting to detect population substructure within closely related populations.

Mutation meltdown of mitochondrial DNA and Neanderthal extinction.

There is emerging evidence that mitochondrial DNA (mtDNA) plays and integral role in the evolution of the human species. Although contentious, recent phylogenetic studies of modern humans implicate genetic variation of mitochondrial DNA (mtDNA) as a major factor underpinning the climatic adaptation of across the globe. Greater sequence diversity in the MTATP6 gene in arctic populations led to the idea that specific mtDNA polymorphisms cause subtle uncoupling of the respiratory chain, with the subsequent generation of additional heat being adaptive in northern climes. Our knowledge of mtDNA and its affect on adaptability may help us to understand how modern humans have survived their early ancestors. Here, we characterise the mtDNA of one of these extinct hominids. Neanderthals are the closest hominid relatives of modern humans, who up until 30,000 years ago coexisted in Europe and western Asia. Recently, over 1Mb of DNA was successfully extracted and characterised from the Vi-80 Neanderthal fossil. We reanalysed 2,705 base pairs of mtDNA in order to examine the hypothesis that mitochondrial dysfunction contributed to the Neanderthals demise. We identified thirty-two nucleotide differences from the modern human mtDNA reference sequence and by treating the Vi-80 as a diagnostic sample leads us to the conclusion that sequence variants that are highly likely to be artifacts, and a large proportion of the remaining mutations could be due to nuclear pseudogene amplification. We did identify a potentially deleterious variation; however more study may be needed to ascertain the effect of mitochondrial dysfunction on Neanderthal survival.

Early Siberian Maternal Lineages in the Tubalar of Northeastern Altai Inferred from High-Resolution Mitochondrial DNA Analysis

At the hight of the last glaciation (~18 kya) Siberians were confined to the southern strongholds, which were areas of continuous occupation, and where immediate ancestors of the Uralic, Kettic and Altaian language groups differentiated. To better understand the evolutionary relationships between the earlier and contemporary Siberians, we focused on the northern Altaic prehistory preserved in the mtDNA diversity of the Tubalar, until recently representing a typical hunting-gathering population. The present study includes 139 Tubalar. All mtDNAs were subjected to high-resolution SNP analysis, followed by complete sequencing of selected mtDNA samples. We showed that the core of the Tubalar genetic makeup proved to be a mixture of west (H8, U4b, U5a1, and X2e) and east Eurasian (A and B1) haplogroups derived from macrohaplogroup N, and Siberian derivatives of the macrohaplogroup M identifiable by subhaplogroup-specific mutations. For example, among the 36 Tubalar mtDNA samples that belong to haplogroup D, 10 (28%) harbored diagnostic markers of the subhaplogroup D3a2a shared with the Chukchi and Eskimos. This finding verified at the complete sequence level we attributed to ancient link between early Siberians, who underwent pronounced differentiation in the Altai-Sayan region, and some of the Eskimo tribes. A comparison of the mtDNA data generated through the course of this study with published complete sequences has contributed essentially to parsimonious phylogenetic structure of mtDNA evolution in west Siberia. Specifically, northeastern Altai appears to be a good candidate for the ancestral homeland of the haplogroup U4b, which is apparently ancient European. For some haplogroups, such as X2e, the relatively recent arrival to the Altai region is more likely.

Sex-specific gene flow between Pygmy and non-Pygmy populations

Cultural traditions and preferences may drive sex-specific gene flow among human populations. We have examined sex-specific gene flow between Mbuti Pygmies, a hunter-gather population, and surrounding agriculturist groups, the Alur, Hema, and Nande, which all reside in Central Africa. We used 18 lineage-defining Y chromosome SNPs and HVS1 mitochondrial DNA sequence information to examine patterns of gene flow among these groups. Mbuti Pygmy males have more diverse Y chromosome lineages (Mbuti Pygmy [n = 28]: = 0.229; Alur [n = 10]: 0.193; Hema [n = 18]: 0.178; Nande [n = 15]: 0.090) and slightly less mtDNA diversity than neighboring groups (0.020, 0.023, 0.025, 0.022 in Mbuti Pygmy, Alur, Hema, and Nande groups, respectively). The majority of Mbuti Pygmy males have a Y haplotype characteristic of Mbuti Pygmies (B2b); however, more than 30% of Pygmy males exhibit Y haplotypes associated with Bantu-speaking agricultural populations (E3a lineage). Conversely, no agriculturist males exhibit Y haplogroups associated with Mbuti Pygmy populations but instead have derived Y haplogroups characteristic of Bantu agriculturalists (E2, E3a). Pairwise FST was calculated among all populations using Y haplogroup frequency and HVS1 mtDNA sequence data. YDNA and mtDNA FST values between Mbuti Pygmy and non-Pygmy groups (Alur, Hema, and Nande) were 0.278, 0.355, and 0.217 (for YDNA) and 0.088, 0.239 and 0.217 (for mtDNA), respectively. A Mantel test between pairwise FST matrices showed no significant correlation ((r = 0.27; p 0.35), which indicates that patterns of genetic differentiation differ between Y chromosome SNPs and mtDNA sequence patterns. These results also suggest no emigration of Mbuti Pygmy Y chromosomes into surrounding groups but immigration of non-Mbuti Pygmy Y chromosomes into the Mbuti Pygmy population.

Population Structure in Mongolia from a Mitochondrial DNA Perspective.

Mongolia has experienced a complex series of demographic movements over the past 10-20 millennia that have shaped the patterns of its modern human genetic variation. However, modern populations in Mongolia have not been extensively studied for DNA diversity, nor has the genetic contribution of Mongolians to the gene pools of contemporary populations in Southeast Asia and Oceania been fully resolved. Archaeological evidence from as early as the late Neolithic suggests the presence of both West and East Eurasian cultures in this region. Later demographic movements involving the emergence of the Mongolian and later Manchu Empires have further convoluted Mongolias population structure. To clarify the complex population history of Mongolia, we analyzed variation in the mtDNAs of 190 individuals from several Mongolian ethnic groups, including the Uriankhai, Zakhchin, Derbet, Khoton and Khalkha. We screened all samples for phylogenetically informative coding region SNPs and sequenced HVSI to assess control region variation in them. Our data suggest that the mtDNA diversity present in our population is consistent with the general pattern of variation observed in East Asia, with the most frequent haplogroups being C, D and G. Haplogroup variation in Mongolian ethnic groups reveals considerable maternal diversity with a predominance of basal M types. Interestingly, the Mongolians also possessed West Eurasian haplogroups, such as H, J and K, which are not commonly observed in East Asia, even at low frequencies. The main ethnic group in Mongolia, the Khalkha, was highly variable with respect to mtDNA haplotypes in comparison with the other ethnic groups, and clearly distinct from the Khoton and Zakhchin, as evidenced by distance measures. Overall, these data provide insights into the origins and affinities of these populations, their relationships with East Asian groups and neighboring Turkic speaking groups, including indigenous Altaians, and their possible role in the peopling of the Americas.

Allocation of YSTR Microvariant Alleles to Y-Chromosome Binary Haplogroups.

Y-chromosome short tandem repeat (YSTR) loci are used extensively in studies of population substructure, temporality of population dynamics, and forensic identification. The occurrence of non-consensus YSTR alleles, such as unusually short alleles or partial insertion/deletion events (microvariants), have been used successfully as indicators of common ancestry among YSTR haplotypes, exposing further levels of phylogenetic substructure with restricted geographic distributions. However, the high variability of STR loci can potentially lead to false associations due to homoplasy (ie, recurrent mutation). Thus, YSTR haplotypes are best interpreted within the context of the binary marker defined Y-chromosome phylogeny. To identify YSTR microvariant alleles potentially useful for elucidating further phylogenetic substructure within binary haplogroups, we have assessed the haplogroup affiliation of microvariant alleles found at informative frequencies in public YSTR databases for the following YSTR loci: DYS385, DYS392, DYS441, DYS446, DYS447, DYS449 and DYS464. We report haplogroup affiliations for each variant allele and geographic origins of representative samples.

L1c2a, the (African) Haplogroup With The Longest Mitochondrial Genome!

Haplotypes derived from the maternally-inherited mitochondrial DNA (mtDNA) control region are often employed as a first step in determining phylogenetic-relevant samples that could be selected for additional coding region testing. Using the currently defined world mtDNA haplogroup tree, researchers can assign these haplotypes to specific branches, paying particular attention to novel mutations that could assist in identifying new subclades. During a recent survey of the nearly 58000 mtDNA control region haplotypes currently present in the publicly accessible Sorenson Molecular Genealogy Foundation database, we observed a small number of mtDNAs (n=16) characterized by the presence of unusually long insertions of up to 200 bases. A small subset of these particularly long mtDNA haplotypes shared an identical insertion of 15 bases. Genealogical analysis combined with haplogroup prediction confirmed that these haplotypes shared a common African origin. Additionally, based on the pedigree data gathered, we determine the donors were not closely related. Moreover, through the analysis of complete mtDNA sequences, we conclude that the newly defined haplogroup is most likely of recent origin. As reported in this study, insertions of more than 10 bps are quite rare in the general population and in the published literature, thus providing an interesting case work in population and possibly future disease studies.

Mitochondrial DNA footprints in modern Mongolia.

Although Mongolia is one of the most sparsely populated countries in the world, it is located at a pivotal crossroad between the four corners of Asia (including the well-known Silk Road) and has been characterized throughout history by events that greatly added to its current cultural and ethnic diversity. Among these, perhaps one of the most significant happening was the ambitious expansion strategy employed by Mongolias most prominent personality, Genghis Khan, whose empire eventually stretched across all of modern-day China, a portion of modern Russia, Southern Asia, Eastern Europe and the Middle East. In 2007, through a well-planned collection effort, researchers at the Sorenson Molecular Genealogy Foundation and the National University of Mongolia were able to gather over 3,000 DNA samples, informed consents, and genealogical data throughout the country of Mongolia, including samples from 21 distinct tribal or ethnic populations. All the samples were sequenced for the three hypervariable segments of the mitochondrial DNA (mtDNA) control region to assess the genetic composition of modern Mongolia. The most common mtDNA haplotypes are typical of haplogroup C, which is frequent throughout Eastern Asia. However, nearly 40% of the observed mtDNA lineages are of Western Eurasian origin, including a significant frequency (~7%) of haplogroup H - the most common in Europe. The high prevalence of Western Eurasian lineages could be a remnant from Genghis Khans conquering efforts, trade and cultural exchanges along the Silk Route. To assess the extent of recent gene flow that could account for the elevated levels of Eurasian haplogroups within Mongolian populations, we have examined genealogical data of samples representative of Western Eurasian haplogroups.

Y chromosome microsatellite haplotypes in the Hutterite founders.

The current population of >12,000 Schmiedeleut Hutterites are descendants of 38 male founders who were born between 1700 and 1830 in Europe. Only 12 of these founders, each with a unique surname, have living male descendants related through male-only lineages. DNA samples were available in our laboratory for 75 male descendants of 11 of the 12 founders, accounting for 673 independent paternal meioses. We genotyped 9 microsatellite loci, which included a mean of 6.8 (range 2-23) males per lineage to evaluate potential relationships between the founders. Fourteen different haplotypes were identified, with an average of 3.5 (range 1-8) pairwise differences between haplotypes. All descendants within each of 9 lineages had identical Y haplotypes. Descendents of two of these lineages, 2 and 10, had the same haplotype despite different surnames, suggesting possible relatedness between the founders of these two lineages. Descendants of two lineages, 6 and 11, each carried three distinct haplotypes. Within each of these lineages the haplotypes differed from the ancestral haplotype by one repeat size at two loci. Additional male descendants in lineages 6 and 11 were then genotyped for the discrepant microsatellites, confirming the presence of three Y haplotypes each in lineages 6 and 11. The one mutation arose at each of four loci: DYS388, DYS389II, DYS390, DYS393. Three mutations were gains of one repeat; it was not possible to determine if the fourth mutation was a gain or loss of one repeat. The ancestral haplotypes in these two lineages are identical at four microsatellite loci; the alleles at the other five loci differ by one repeat size. The average mutation rate at these 9 loci was 0.00066 (95% CI 0.00015-0.0013), similar to other estimates. These data suggest that the founders of lineages 2 and 10 may have been related through paternal lines and that surnames do not strictly correspond to unique Y chromosomes. Moreover, certain ancestral haplotypes (i.e., those in lineages 6 and 11) may be more prone to mutation. Supported by NIH grants HD21244 and HL085197.

Genetic History of human populations of East African inferred from mtDNA and Y chromosome analyses.

Evidence from genetic, paleobiological, and archaeological studies suggest that Africa, especially East Africa, is most likely to be the cradle of the modern human species. Despite this fact, very little is currently known about genetic diversity in African populations in general, and East African populations in particular. Genetic data demonstrate that the patterns of genetic variation in East African populations are complex. All four major language families spoken in Africa (Afro-Asiatic, Nilo-Saharan, Niger-Kordofanian, and Khoisan) are found in the region. As part of a large study of population genetic diversity of East and Northeast Africa, we examined Y chromosome genetic diversity (to ascertain paternal lineages) as well as mitochondrial genetic diversity (to ascertain maternal lineages) in 1200 - 1500 individuals from ~ 40 Tanzanian, Sudanese, and Kenyan populations. For the Y chromosome analysis, we genotyped 60 UEPs (analyzed in a hierarchical manner to construct haplotypes) in a total of ~1500 male individuals. In order to infer ages of lineages and migration patterns, we further genotyped the individuals for 16 Y chromosome microsatellites. For the mtDNA analysis, we sequenced the mitochondrial D-loop in a total of 1200 individuals from the same populations, and for 200 individuals, we did complete mitochondrial genome sequencing. We compare our results with published results of studies from other parts of Africa and the Middle East. Our results indicate that East African populations have some of the most ancestral Y chromosome and mtDNA lineages in Africa, suggesting that they may have been an ancient source of dispersion throughout Africa. Additionally, we find evidence for ancient geneflow between East Africa and the Middle East. We also ascertained the effect of the Bantu-expansion and signature of recent migration of Cushitic-speaking groups originating from Ethiopia on peopling of East Africa.

Analysis of mtDNA and Y-chromosome haplogroups in Mexican Mestizos and Amerindian groups.

The Mexican population is mainly conformed by Mestizos, individuals with a genetic background consisting of Amerindian, European and African contributions. Genetic heterogeneity in Mexicans results from a complex demographic history that started with the peopling of North and Central America about 15,000 yrs ago, including the settlement of at least 60 different indigenous groups in Mexico, regional differences in admixture dynamics after colonization by Spaniards in the XVI century, epidemics and migration. Y chromosome-specific and mitcohondrial (mt) DNA polymorphisms are useful to help understand the genetic structure and history of human populations, due to their uniparental inheritance and lack of recombination. In order to refine the portrait of genetic variability derived from the Mexican Genome Diversity Project, we are characterizing maternal and paternal lineages participating in admixture. For this we included genotypic data from 163 mt SNPs and 123 Y chromosome SNPs present in the Illumina Human1M chip of 450 individuals, 300 mestizos from six states located in different regions: Northern, Central and Southern; and 150 individuals from different Amerindian groups (Tepehuanes, Zapotecos and Mayas). With this information, we are measuring genetic diversity using Fst and AMOVA analysis. Admixture analysis includes average and individual ancestral contribution estimates using autosomal SNPs. Initial results show that in our Mestizo sample, 88% of the mt haplogroups are Amerindian (A, B, C or D), and the rest includes European and African lineages. We have identified differences in proportions of each haplogroup in both Mestizos and Amerindians. Knowledege about the distribution of mt and Y-chromosome haplogroups in Mexican Mestizos and Amerindian groups, will generate valuable information to better understand genetic relationships between Mexicans and other Latin American populations. In addition, it may contribute to strengthen analysis in association studies of common complex diseases.

The origin of Native Americans from a mitochondrial DNA viewpoint.

America, the last continent to be colonized by modern humans, is characterized by an extraordinary linguistic and cultural diversity. Until recently, it was generally believed that starting around 13,500 years ago, the first Paleo-Indians arrived from Beringia, passing through an interior ice-free corridor in western North America, and spread rapidly all the way to Tierra del Fuego. Today, we realize that the peopling of the Americas involved a much more complex process. As for the maternally transmitted mitochondrial DNA (mtDNA), it has been clear since the early nineties that Native Americans could be traced back to four major maternal lineages (haplogroups) of Asian affinity. These were initially named A, B, C and D, and are now termed A2, B2, C1 and D1. More than 95% of living Native Americans belong to these four haplogroups, which can be considered pan-American, because they are shared by North, Central and South American populations. Later, five additional maternal lineages were discovered and named X2a, D2, D3, C4c, and D4h3. These less common or rare haplogroups are restricted only to some Native American populations or geographic areas and bring the overall number of Native American mtDNA lineages to nine. Our comprehensive overview of the four pan-American branches of the mtDNA tree suggests a scenario with a human entry and spread into the Americas from Beringia about 20,000 years ago, and preliminary data raise the possibility that the uncommon five Native American haplogroups might have marked additional migratory events from Asia or Beringia. Overall, through a combined analysis of modern and ancient Native American mtDNA, we are making an effort for reconstructing the complex pre-Columbian history at both macro- and micro-geographic levels.

Identifying genes affecting normal variation in human facial features using admixed populations.

Seven selection-nominated candidate genes (COL11A1, LMNA, FGFR1, FGFR2, TRPS, BRAF, FLNA) known to be involved in Mendelian craniofacial dysmorphologies and to have high allele frequency differences between West African and European populations were tested for admixture linkage to normal facial feature traits. The sample consists of 254 subjects (n=131 African Americans, n=123 Brazilians) of West African and European genetic ancestry. Each individual was genotyped at 176 ancestry informative markers (AIMs), which allowed for proportional estimation of genetic ancestry from four parental populations and adjustments for admixture stratification.
3D images of faces were acquired using the 3dMDface imaging system. 3D coordinate data were collected from 22 landmarks placed on each image using the 3dMDPatient software. The 231 possible pairwise landmark distances were scaled to the geometric mean and then analyzed using Euclidean Distance Matrix Analysis.
We used both ANOVA and ADMIXMAP to control for admixture stratification and to test for associations between the 231 pairwise landmark distances and 183 AIMs, using sex, height and BMI as covariates. We used a four-population model (West African, European, East Asian, and Native American).
There is a strong concordance between the ANOVA and ADMIXMAP results. Many landmark distances, particularly on the mouth and nose, were significantly associated with genetic ancestry. Additionally, three of the candidate genes show no effects on pairwise landmark distances while four show distinct patterns of association. For example, FGFR2 is associated primarily with the length of the face. These results represent the first identification of the first genes affecting normal variation in facial features.

Ethnicity-Confirmed Genetic Structure in New Hampshire.

Genetic population structure is known to result from shared ancestry. Though there have been several studies of genetic structure within and among different geographic regions and ethnic groups, little is known of the genetic structure of highly admixed US populations or whether the structure is concordant with self-reported ancestry. In this study, 1529 single nucleotide polymorphisms (SNPs) from 864 healthy control individuals from New Hampshire were measured as part of a bladder cancer epidemiology study. The SNPs were from approximately 500 cancer susceptibility genes scattered throughout the genome. Of these, 960 Tag SNPs were used to cluster individuals using the Structure algorithm for between 2 and 5 subpopulations. Subtle genetic structure was found, suggesting the appropriate number of subpopulations to be either 4 or 5 (FSTs 4 populations: 0.0377, 0.0399, 0.0363, 0.0340; 5 populations: 0.0452, 0.0536, 0.0585, 0.0534, 0.0521). We coded the individuals self-reported ancestries in a genotype fashion (i.e. 0= not reporting that ancestry, 1= reporting part that ancestry, 2= reporting only that ancestry) and conducted a Spearmans rank correlation between each ancestry and the structure q value, which represents the proportion of an individual that originated from a certain genetic subpopulation. Those of Russian, Polish and Lithuanian ancestry most consistently clustered together. The ancestry results support either 4 or 5 subpopulations. In order to investigate linkage disequilibrium (LD), the complete set of SNPs from the 7 most densely genotyped genes were used to make haploview plots between the different groups. The results vary by gene, though for one gene in particular, GHR, the results are very different for 4 subpopulations. These results suggest that despite New Hampshires admixture and presumed homogeneity, there are 4 or 5 distinct genetic subgroups within the population that can be linked to self-reported ancestry and display differences in patterns of LD.

Inference of human demographic parameters using haplotype patterns from genome-wide SNP data.

Accurate inference of human demographic history from genetic data is essential for identification of single nucleotide polymorphism (SNP) association with disease and for inference of natural selection. Haplotype diversity and haplotype sharing carry additional demographic information to that obtainable from SNP frequency spectra, and so we propose a novel method using haplotype summary statistics to fit demographic models to genome-wide SNP data. We divide the genome into 0.25 cM windows and for each we tabulate the number of distinct haplotypes and the frequency of the most common haplotype. We summarize the data by the genome-wide joint distribution of these two statistics. Coalescent simulations are then used to evaluate whether different demographic models are compatible with the observed data. Application of our method to simulated data shows that our method can reliably infer parameters from complex demographic models (such as bottlenecks) and is relatively robust to the levels of SNP ascertainment bias found in many genome-wide datasets. We have applied our method to data collected by the International HapMap Consortium and find that a bottleneck model best fits the CEU population. We have also analyzed a large dataset consisting of Affymetrix 500k data from ~2,900 individuals with ancestry from Taiwan, Japan, India, Mexico and many European countries. Since this dataset includes ~2,300 European individuals, we are able to study haplotype patterns at a fine scale within Europe. Interestingly, we find that within Europe there is a south-to-north gradient with decreasing levels of haplotype diversity moving north, consistent with south to north migrations. We also find that the southwestern European sample has higher haplotype diversity than the southeastern European sample. Additionally, a higher proportion of haplotypes are shared between the southwestern European sample and the Yoruba sample than between southeastern European sample and the Yoruba sample. These two patterns are consistent with recent admixture across the Mediterranean from Northern Africa.

Genome wide analysis and heritability estimation of intelligence in the International Multi-centre ADHD Genetics (IMAGE) study.

Attention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder characterised by symptoms of inattention, hyperactivity and impulsivity. There is growing evidence of heterogeneity in its etiology, pathophysiology and clinical expression. One approach to resolving heterogeneity involves the identification of endophenotypes, intervening variables that might mediate pathways between specific genes and clinical phenotype. IQ is a candidate endophenotype for ADHD. Genome-wide linkage analyses of full scale IQ and IQ subscales were performed in the International Multi-centre ADHD Genetics (IMAGE) study including 1094 families with 1094 DSM-IV combined type ADHD probands and their 1441 siblings (unselected for ADHD status). IQ was measured using five subscales of the WISC-IIIR scale. The full scale prorated IQ score and the five subscales were used as quantitative traits for linkage analysis. 5,407 autosomal SNPs were used to run multipoint regression-based linkage analyses using MERLIN. The h2 estimates from the IQ subscales and the full IQ score ranged from 31% to 100%. Three suggestive linkage signals were found (LOD scores 2, p values 0.001) on chromosomes 7, 9 and 14 for three different subscales. Previously, two regions on chromosomes 7 and 14 were reported as being associated or linked to IQ. Our results, though only suggestive, suggest the presence of additional genetic variants contributing to the variance of IQ in ADHD.

Population structure in Japan with 140k SNPs

After the many recent studies on fine-scale genetic ancestry in Europe, a new paper investigates population structure in Japan using 140k SNPs. From the paper:

Our present study has clearly shown, on the basis of analysis of genome-wide SNP genotypes that most Japanese individuals fall into two main clusters: the Hondo cluster and the Ryukyu cluster. Our results also show that local regions in Honshu Island (the largest island of Japan) are still genetically differentiated, even though human migration within Japan has become rather frequent in the past 100 years or so. Our finding that the individuals from Tohoku were less related to Han-Chinese individuals than were the individuals from Kinki and Kyushu suggests that the individuals in Tohoku were less affected by immigrants from the Asian continent than were the individuals in Kinki. The immigrants who came to Japan from the Asian continent through the Korean Peninsula may have entered Japan from northern Kyushu, the Japan Sea side of Kinki or Chugoku.

American Journal of Human Genetics doi: doi:10.1016/j.ajhg.2008.08.019

Japanese Population Structure, Based on SNP Genotypes from 7003 Individuals Compared to Other Ethnic Groups: Effects on Population-Based Association Studies

Yumi Yamaguchi-Kabata et al.

Abstract

Because population stratification can cause spurious associations in case-control studies, understanding the population structure is important. Here, we examined Japanese population structure by “Eigenanalysis,” using the genotypes for 140,387 SNPs in 7003 Japanese individuals, along with 60 European, 60 African, and 90 East-Asian individuals, in the HapMap project. Most Japanese individuals fell into two main clusters, Hondo and Ryukyu; the Hondo cluster includes most of the individuals from the main islands in Japan, and the Ryukyu cluster includes most of the individuals from Okinawa. The SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were found in the HLA region in chromosome 6. The nonsynonymous SNPs with the greatest frequency differences between the Hondo and Ryukyu clusters were the Val/Ala polymorphism (rs3827760) in the EDAR gene, associated with hair thickness, and the Gly/Ala polymorphism (rs17822931) in the ABCC11 gene, associated with ear-wax type. Genetic differentiation was observed, even among different regions in Honshu Island, the largest island of Japan. Simulation studies showed that the inclusion of different proportions of individuals from different regions of Japan in case and control groups can lead to an inflated rate of false-positive results when the sample sizes are large.

Link

Varki et al. (2008) on Human Uniqueness in Nature Reviews Genetics

From the paper:

Remarkable similarities of known human and chimpanzee protein sequences initially led to the suggestion that significant differences might be primarily in gene and protein expression, rather than protein structure6. Further analysis of alignable non-coding sequences affirmed this ~1% difference. However, the subsequent identification of non-alignable sequences that were due to small- and large-scale segmental deletions and duplications21–23 showed that the overall difference between the two genomes is actually ~4%.

...

Why are coding-sequence changes in brain genes under a larger degree of purifying selection than in other tissues? The reason for this is not immediately clear as a wide range of brain function supports life to reproductive age in humans.

...

But this notion, which is based on single nucleotide changes in protein-coding sequence, has to be reconciled with the CNV data, because CNVs in humans seem to be enriched among genes involved in neurodevelopmental processes.

...

However, connecting such genes involved in disorders of human cognition to the specific phenotypes undergoing selection poses significant challenges. A salient example involves two genes, abnormal spindle homologue microcephaly associated (ASPM) and microcephalin (MCPH1), the adaptive evolution of these genes in humans was claimed to be related to normal variation in brain size, on the basis of the fact that Mendelian mutations in each results in microcephaly in humans152,153. However, not all investigators have found evidence for the adaptive evolution of ASPM or MCPH1 (ref. 154). Also, neither gene is likely to contribute significantly
to normal variation in human brain size155. This case illustrates the challenges of interpreting genetic data in the face of complex phenotypes, especially those that are poorly understood.

Nature Reviews Genetics doi:10.1038/nrg2428

Human uniqueness: genome interactions with environment, behaviour and culture

Ajit Varki et al.

Abstract

What makes us human? Specialists in each discipline respond through the lens of their own expertise. In fact, 'anthropogeny' (explaining the origin of humans) requires a transdisciplinary approach that eschews such barriers. Here we take a genomic and genetic perspective towards molecular variation, explore systems analysis of gene expression and discuss an organ-systems approach. Rejecting any 'genes versus environment' dichotomy, we then consider genome interactions with environment, behaviour and culture, finally speculating that aspects of human uniqueness arose because of a primate evolutionary trend towards increasing and irreversible dependence on learned behaviours and culture — perhaps relaxing allowable thresholds for large-scale genomic diversity.

Link

Deshpande et al. (2008) on Out of Africa

This is an important new paper which adds some complexity to the Out of Africa theory. Much existing work has focused on a "tree-like" story of the emergence of modern humans, with an African source population at the root, and other populations being less diverse the further they are (geographically) from the source.

This new model is not limited on colonization, i.e., the movement of a subset of a territory's population into a new uninhabited territory, but also on "lateral" gene exchange between pre-established populations.

From the paper:

Unlike previous models, ours separated colonization events from the continued exchange of people between occupied territories. Our estimates of the exchange rate between neighbouring populations were very low (below 0.01), with carrying capacities ranging from approximately 600 to 1200. Assuming that the census size is three times this effective population size, we derive a census size of approximately 1800–3600 people in each deme. Since each deme has dimensions of 125x125 km, this corresponds to a population density of approximately 0.11–0.23 persons m^-2, well within the range for hunter–gatherers referred to by Liu et al. (2006).

Related: Geographic and genetic distance in human populations, A Geographically Explicit Genetic Model of Worldwide Human-Settlement History

Proceedings of the Royal Society B doi: 10.1098/rspb.2008.0750

A serial founder effect model for human settlement out of Africa

Omkar Deshpande, Serafim Batzoglou, Marcus W. Feldman, L. Luca Cavalli-Sforza

Abstract

The increasing abundance of human genetic data has shown that the geographical patterns of worldwide genetic diversity are best explained by human expansion out of Africa. This expansion is modelled well by prolonged migration from a single origin in Africa with multiple subsequent serial founding events. We discuss a new simulation model for the serial founder effect out of Africa and compare it with results from previous studies. Unlike previous models, we distinguish colonization events from the continued exchange of people between occupied territories as a result of mating. We conduct a search through parameter space to estimate the range of parameter values that best explain key statistics from published data on worldwide variation in microsatellites. The range of parameters we use is chosen to be compatible with an out-of-Africa migration at 50–60Kyr ago and archaeo–ethno–demographic information. In addition to a colonization rate of 0.09–0.18, for an acceptable fit to the published microsatellite data, incorporation into existing models of exchange between neighbouring populations is essential, but at a very low rate. A linear decay of genetic diversity with geographical distance from the origin of expansion could apply to any species, especially if it moved recently into new geographical niches.

Link

The Byzantine origin of clinical geriatrics

Wien Med Wochenschr. 2008;158(17-18):471-80.

[Why should Byzantium be considered as a cradle of clinical geriatrics?]

Lapin A.

Abstract

Generally, roots of today's medical ethics are thought to have sprouted from antiquity and from classical Hebraic consciousness, while the origin of hospital medicine and institutional nursing of the elderly was assumed in Middle Age and in modern times, respectively. But even between these two periods, notably in Byzantium (324-1453) there were many famous physicians working with surprising skills in many disciplines such as surgery and ophthalmology. The most important achievement of that time, however, was in public health care. Following the Christian ideal of philanthropy, numerous hospitals (nosokomeia), hospices (xenodocheia) and asylums for the elderly (gerokomeia) of a remarkable organisation and professionalism were founded in many cities of the Byzantine Empire. Concerning the elderly patients, interesting findings were obtained concerning ageing process (eschatogeria), geriatric symptoms, multimorbidity, marasm and typically occurring diseases. Interesting approaches were realized with regard to the nursing care, diet and recommended life style for the elderly. By the end of the Byzantium Empire in 1453 and due to the different cultural development in the West, which was sometimes marked by conflicts between church and science and by the regulations of medicine, the knowledge about the Byzantine health care was almost lost. It survived, however, only in hospitals of occidental monastic orders, which brought their experience from East-Mediterranean area. Their hospitals were than a base for modern health care and for geriatrics.

Link

mtDNA haplogroups and Parkinson's

J Neural Transm. 2008 Sep 23. [Epub ahead of print]

Mitochondrial DNA haplogroups and subhaplogroups are associated with Parkinson's disease risk in a Polish PD cohort.

Gaweda-Walerych K, Maruszak A, Safranow K, Bialecka M, Klodowska-Duda G, Czyzewski K, Slawek J, Rudzinska M, Styczynska M, Opala G, Drozdzik M, Canter JA, Barcikowska M, Zekanowski C.

mtDNA common variation is inconsistently reported to modify the risk of Parkinson's disease (PD). We evaluated the impact of the mitochondrial haplogroups, subhaplogroups, coding and non-coding single-nucleotide polymorphisms on PD risk in 241 PD patients and 277 control subjects. After stratification by gender, we found that haplogroup J (OR 0.19; 95% CI 0.069-0.53; P = 0.0014) was associated with a lower PD risk in males. Unexpectedly, subhaplogroup analysis based on the control region (CR) polymorphisms demonstrated that subcluster K1a was more prevalent in healthy controls, while K1c was more frequent in PD patients (P = 0.025 and P = 0.011, respectively; two-tailed Fisher's exact test). Additionally, we confirmed the hypothesis that sublineages (U4 + U5a1 + K+J1c + J2), previously proposed to partially uncouple oxidative phosphorylation (OXPHOS), decrease PD risk (P = 0.027, chi(2) with Yates' correction). The putative protective effect of uncoupling mtDNAs against PD might result from decreased production of reactive oxygen species. We propose that stratification into subhaplogroups or by gender could be necessary to reveal the involvement of specific mtDNA sublineages in PD pathogenesis.

Link

Nutrition behind Flynn effect?

The Flynn effect is the improvement of IQ scores over time, with people born more recently tending to score higher than the average of previous generations. This paper suggests that better nutrition of pregnant women and infants is behind this phenomenon.

Intelligence doi: doi:10.1016/j.intell.2008.07.008

What has caused the Flynn effect? Secular increases in the Development Quotients of infants

Richard Lynn

Abstract

Results of five studies show that during the second half of the twentieth century there were increases in the Development Quotients (DQs) of infants in the first two years of life. These gains were obtained for the Bayley Scales in the United States and Australia, and for the Griffiths Test in Britain. The average of 19 data points is a DQ gain of approximately 3.7 DQ points per decade. Similar gains of approximately 3.9 IQ points per decade have been present among preschool children aged 4–6 years. These gains are about the same as the IQ gains of school age students and adults on the Wechsler and Binet tests. This suggests that the same factor has been responsible for all these secular gains. This rules out improvements in education, greater test sophistication, etc. and most of the other factors that have been proposed to explain the Flynn effect. It is proposed that the most probable factor has been improvements in pre-natal and early post-natal nutrition.

Link

Facial masculinity and testosterone levels correlated (after a win)

Proceedings of the Royal Society B doi: 10.1098/rspb.2008.0990

Testosterone responses to competition in men are related to facial masculinity

Nicholas Pound et al.

Abstract

Relationships between androgens and the size of sexually dimorphic male traits have been demonstrated in several non-human species. It is often assumed that a similar relationship exists for human male faces, but clear evidence of an association between circulating testosterone levels and the size of masculine facial traits in adulthood is absent. Here we demonstrate that, after experimentally determined success in a competitive task, men with more a masculine facial structure show higher levels of circulating testosterone than men with less masculine faces. In participants randomly allocated to a ‘winning’ condition, testosterone was elevated relative to pre-task levels at 5 and 20min post-task. In a control group of participants allocated to a ‘losing’ condition there were no significant differences between pre- and post-task testosterone. An index of facial masculinity based on the measurement of sexually dimorphic facial traits was not associated with pre-task (baseline) testosterone levels, but was associated with testosterone levels 5 and 20min after success in the competitive task. These findings indicate that a man's facial structure may afford important information about the functioning of his endocrine system.

Link

Neanderthals' trips to the sea in search of food

Another data point for Neanderthal behavioral complexity; this paper shows that Neanderthals made forays to the sea to exploit marine food resources. UPDATE: John Hawks comments.

PNAS doi: 10.1073/pnas.0805474105

Neanderthal exploitation of marine mammals in Gibraltar

C. B. Stringer et al.

Abstract

Two coastal sites in Gibraltar, Vanguard and Gorham's Caves, located at Governor's Beach on the eastern side of the Rock, are especially relevant to the study of Neanderthals. Vanguard Cave provides evidence of marine food supply (mollusks, seal, dolphin, and fish). Further evidence of marine mammal remains was also found in the occupation levels at Gorham's Cave associated with Upper Paleolithic and Mousterian technologies [Finlayson C, et al. (2006) Nature 443:850–853]. The stratigraphic sequence of Gibraltar sites allows us to compare behaviors and subsistence strategies of Neanderthals during the Middle Paleolithic observed at Vanguard and Gorham's Cave sites. This evidence suggests that such use of marine resources was not a rare behavior and represents focused visits to the coast and estuaries.

Link

Stonehenge was built in 2,300BC and may have been a healing center

There have been quite a few stories on Stonehenge lately. Now, the BBC reports on the results of new carbon dating:

Archaeologists have pinpointed the construction of Stonehenge to 2300 BC - a key step to discovering how and why the mysterious edifice was built.

The radiocarbon date is said to be the most accurate yet and means the ring's original bluestones were put up 300 years later than previously thought.

and new interpretations about its function:

Professors Darvill and Wainwright believe that Stonehenge was a centre of healing - a "Neolithic Lourdes", to which the sick and injured travelled from far and wide, to be healed by the powers of the bluestones.

They note that "an abnormal number" of the corpses found in tombs nearby Stonehenge display signs of serious physical injury and disease.

And analysis of teeth recovered from graves show that "around half" of the corpses were from people who were "not native to the Stonehenge area".

Such a prominent edifice need not have a single function. Healing cults tend to form around important religious sites irrespective of their original purpose.

There is a BBC Timewatch documentary on this which will air on Sep 27; a couple of video clips are on the BBC site. Apparently, the scientists suggest that the bluestones were put up ~2,300BC, while the trilithons were put up ~2,100BC. The monument started to enter its phase of decline and neglect ~1,900BC.

Interestingly, as pointed out in the clip, the new date for the erection of Stonehenge coincides with the burial date for the Amesbury archer.

Comparison of different methods for estimating admixture

Yann Klimentidis links to this new paper.

American Journal of Epidemiology doi:10.1093/aje/kwn224

Comparison of Statistical Methods for Estimating Genetic Admixture in a Lung Cancer Study of African Americans and Latinos

Melinda C. Aldrich et al.

Abstract

A variety of methods are available for estimating genetic admixture proportions in populations; however, few investigators have conducted detailed comparisons using empirical data. The authors characterized admixture proportions among self-identified African Americans (n = 535) and Latinos (n = 412) living in the San Francisco Bay Area who participated in a lung cancer case-control study (1998–2003). Individual estimates of genetic ancestry based on 184 informative markers were obtained from a Bayesian approach and 2 maximum likelihood approaches and were compared using descriptive statistics, Pearson correlation coefficients, and Bland-Altman plots. Case-control differences in individual admixture proportions were assessed using 2-sample t tests and logistic regression analysis. Results indicated that Bayesian and frequentist approaches to estimating admixture provide similar estimates and inferences. No difference was observed in admixture proportions between African-American cases and controls, but Latino cases and controls significantly differed according to Amerindian and European genetic ancestry. Differences in admixture proportions between Latino cases and controls were not unexpected, since cases were more likely to have been born in the United States. Genetic admixture proportions provide a quantitative measure of ancestry differences among Latinos that can be used in analyses of genetic risk factors.

Link

John Hawks stars in the "Neanderthal Code"!

Ok, "stars" may be a bit too much, but judging from the videos on the National Geographic site, he seems to have quite a big role in the documentary:

I feel like the defense attorney for the Neanderthals sometimes. I am trying to see the ways that they overlapped with us, and trying to add complexity to the story, because any story that involves things happening over a continent over thousands of years, it's got to be complicated.

I don't have a very strong opinion on Neanderthal-sapiens relations, but I must acknowledge that in Prof. Hawks, everyone's favorite Paleolithic mystery men (and women) have found one of their most eloquent defenders.

Ian Tattersall also appears (probably on the Out of Africa corner of the ring).

Most anthropologists today seem to be somewhere between the replacement and assimilation model of human origins, with Wolpoff's multi-regional model still in the running, and Coon's "candelabra" model mostly abandoned.

This is one debate that has raged for decades, and depends on the interpretation of a handful of old skeletons, and of the new DNA evidence about Neanderthals.

I will probably be watching the Neanderthal Code and making further comments in the coming week.

UPDATE Here is the 10-page article from the October 2008 issue of National Geographic.

Carl Zimmer article on Intelligence (and some thoughts on nature/nurture and IQ)

Carl Zimmer blogs about his Scientific American article on Intelligence. From the article:

It was with great delight that Plomin got his hands on microarrays that could detect 500,000 genetic markers--hundreds of times more than he had previously used. He and his colleagues got cheek swabs from 7,000 children, isolated their DNA, and ran it through the microarrays. And once more the results were disappointing.

“I’m not willing to say that we have found genes for intelligence,” Plomin declares, “because there have been so many false positives. They’re such small effects that you’re going to have to replicate them in many studies to feel very confident about them.”

I had blogged about this study when it came out. I repeat my comments from 2006 which are still valid today:

It appears that the hunt for genes affecting intelligence is not going well. I can't say that I'm surprised, because I have always maintained that intelligence is an emergent property of a set of co-operating genes during development in a particular environment and I don't anticipate that the geno-centric approach will take us closer to understanding it.

Intelligence, and -I believe- other complex traits are like complex dishes with many ingredients. The ingredients themselves (e.g., salt, lettuce, or chicken) are themselves unremarkable, but it is the way that they are put together and turned on and off by internal and external stimuli (the pot, the temperature, time, etc.) that makes a good dish.

I have expressed the same view in the recent entry on genome-wide association studies:

This Lego-block paradigm is based on the notion that most of our alleles are commodity "building blocks"; if they are brought together harmoneously, they produce positive results. The occasional allele may have a large effect, and some alleles fit better together than others. Yet, most of the success or failure of a construction depends on how the components fit together, and not what they are.

From the Carl Zimmer article:

Researchers have made images of their developing brains once a year, and Shaw has focused much of his attention on what the pictures reveal about the growth of the cortex, the outer rind of the brain where the most sophisticated information processing takes place.

...

In all children the cortex gets thicker as new neurons grow and produce new branches. Then the cortex thins out as branches are pruned. But in some parts of the cortex, Shaw found, development took a different course in children with different levels of intelligence. “The superclever kids started off very thin,” Shaw says. “They got really relatively thicker, but in adolescence they got thinner again very quickly.”

I had blogged about this study in 2006; check out that blog entry to see the thickness curves of cortex in development.

At the dawn of the genetics era, physical anthropologists' ideas that intelligence was correlated with the brain's observable properties were often ridiculed. And, yet neuronatomical correlates are pretty much the only game in town when it comes to giving a prediction (admittedly a very coarse one) of a person's IQ

That doesn't mean that genes don't play a role in intelligence; they do, and it's a sizeable one. But that role is hidden in a gene-gene and gene-environment interaction web of thousands of factors, where the individual components aren't really important, but the way they are put together are.

This realization also leads one to question genetic fetishists' conclusions about environmental influences on IQ.

It is true that scientists have looked at a lot of possible environmental influences on IQ and have come up short on significant environmental factors that can boost a person's IQ. There is simply very limited evidence that any particular environment can achieve this --sort of really bad influences such as malnutrition or some infectious diseases in childhood. And, yet we know that part of the variation of IQ is due to environmental influences. What gives?

What scientists have looked at are recognizable, "obvious", environmental influences (parenting style, schooling, etc.), which are analogous to the "common variants" in genetics.

Just as a microarray-based genome-wide association study has no clue about the rare family-level gene complexes and disease factors, so studies of environmental influences have no clue about the rare family/school/peer group micro-environments affecting a person's development.

Thus, the failure to find strong environmental influences on IQ doesn't strengthen the nature side of the nature-nurture divide, just as the failure to find strong genetic influences on IQ doesn't strengthen the nurture side.

The truth is, that Intelligence is an emergent property of a complex web of genetic and non-genetic interactions.

A human being is like a black box with zillions of inputs, some of them genetic, others environmental. We know that the box's output, e.g. its IQ score on a test is related to its inputs; but the relationship isn't linear and tidy: you can try different inputs from here to eternity, but you won't be able to figure out what the output is.

As I wrote in my post on height and body mass index, real progress will come about only when we finally look into the box:

Real progress will only come about with more developmental and functional studies, i.e. studies that actually look at what genes do in the body.

Figuring out how humans "work" is easier said than done. But, I believe, there is no shortcut.

Google trumps MitoMap for identifying mtDNA mutations

Hum Mutat. 2008 Sep 17. [Epub ahead of print]

Exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches.

Bandelt HJ, Salas A, Taylor RW, Yao YG.

Given its relative ease, screening the entire mitochondrial DNA (mtDNA) for heteroplasmic or novel homoplasmic mutations has become part of the routine diagnostic workup for the molecular geneticist confronted with a disease case exhibiting clinical and biochemical features of mitochondrial dysfunction. "Novelty" of a given mtDNA variant is most often equated with nonregistration in the extensive MITOMAP database (www.mitomap.org). This practice has led to a number of spurious findings and wrong conclusions concerning the pathogenic status of specific mtDNA mutations, especially in the absence of proper evaluation and pathogenicity scoring. We demonstrate by way of real cases targeting the mt-tRNA(Cys) (MT-TC) gene and a stretch within the MT-ND3 gene, that a straightforward Google search can identify twice as many previously observed mutations than any MITOMAP query could achieve. Further, we reassess the recent rediscovery of m.15287T>C by listing all known occurrences and, where possible, providing the haplogroup context, shedding new light on the potential pathogenicity status of m.15287T>C.

Link

Political orientation and physiological response

I have often noticed when I turn on the TV and there is a political discussion going on with speakers I don't recognize, that it's often possible to guess (better than chance) the participants' side. Whether it's appearance, clothing, or mannerisms, there may be subtle clues that our minds have come to associate with particular political attitudes. For that to be possible, however, political orientation should be made manifest in some way. In this paper, it is shown that people who are startled more easily tend to be more right-wing in the American political spectrum. It would be interesting to repeat this experiment in other countries. (I'll post the abstract when I see it -- posted)

UPDATE (Sep 19): John Hawks posts a long and skeptical commentary on the study, which should be read by anyone interested in the subject.

Political attitudes are predicted by physiological traits

HOUSTON -- (Sept. 16, 2008) -- Is America's red-blue divide based on voters' physiology? A new paper in the journal Science, titled "Political Attitudes Are Predicted by Physiological Traits," explores the link.

Rice University's John Alford, associate professor of political science, co-authored the paper in the Sept. 19 issue of Science.

Alford and his colleagues studied a group of 46 adult participants with strong political beliefs. Those individuals with "measurably lower physical sensitivities to sudden noises and threatening visual images were more likely to support foreign aid, liberal immigration policies, pacifism and gun control, whereas individuals displaying measurably higher physiological reactions to those same stimuli were more likely to favor defense spending, capital punishment, patriotism and the Iraq War," the authors wrote.

Science Vol. 321. no. 5896, pp. 1667 - 1670
DOI: 10.1126/science.1157627

Political Attitudes Vary with Physiological Traits

Douglas R. Oxley et al.

Although political views have been thought to arise largely from individuals' experiences, recent research suggests that they may have a biological basis. We present evidence that variations in political attitudes correlate with physiological traits. In a group of 46 adult participants with strong political beliefs, individuals with measurably lower physical sensitivities to sudden noises and threatening visual images were more likely to support foreign aid, liberal immigration policies, pacifism, and gun control, whereas individuals displaying measurably higher physiological reactions to those same stimuli were more likely to favor defense spending, capital punishment, patriotism, and the Iraq War. Thus, the degree to which individuals are physiologically responsive to threat appears to indicate the degree to which they advocate policies that protect the existing social structure from both external (outgroup) and internal (norm-violator) threats.

Link

Y chromosomes from the Pyrenees

Once again, this paper uses the inappropriate 0.00069/locus/generation mutation rate, hence all its age estimates are wrong. I wonder who the first scientist will be to say that the Emperor has no clothes; the practice of uncritically using a mutation rate derived under totally inapplicable demographic assumptions will eventually be noticed.

From the paper:

However comparing the average STR variances of the R1b1b2c (0.243), R1b1b2d (0.207) and I2a2 (0.278) lineages considered in this study and given the replicated estimates pointing to a Mesolithic time frame for the origin, diversification and diffusion of the I2a2 clade (Rootsi et al. 2004), the temporal interpretation here provided for R1b1b2c seems reliable.

Reliable indeed. Even with the wrong mutation rate these lineages can't be pushed to the Paleolithic. Better estimates for them are: R1b1b2c: ~1,350BC; R1b1b2d: ~850BC; I2a2: ~1,800BC.

From the paper:

However, the time to the most-recent common ancestor (TMRCA) of the Pyrenean R1b1b2d lineages was here estimated at 7383 ± 1477 years ago, which is consistent with an early dispersion of R1b1b2d all over the Pyrenees and subsequent dissemination outside the mountain range from the Neolithic era onwards. The much younger age estimated by Hurles et al. (1999) for the SRY2627 mutation can, nevertheless, be explained by the mutation rate used (2.1×10−3, for microsatellites), which does not take into account evolutionary considerations (see Zhivotovsky et al. 2006).

Hurles was right; the authors should follow their own advice and see Zhivotovsky et al. 2006. They will realize that their 0.00069/locus/generation is derived for a demographic scenario in which a lineage originating 7383 years ago has only ~150 living descendants, an underestimation of several orders of magnitude.

From the paper:

The Y lineages representative of what might have been a pre-Neolithic male genetic composition in Iberia, were those bearing the Palaeolithic mutations M269, including its Mesolithic derived branches R1b1b2c-M153 and R1b1b2d-SRY2627, plus those falling in the I clade defined by the Mesolithic M170.

It's as if time has frozen and scientists are doomed to forever repeat what other scientists have said before them.

Annals of Human Genetics doi: 10.1111/j.1469-1809.2008.00478.x

In search of the Pre- and Post-Neolithic Genetic Substrates in Iberia: Evidence from Y-Chromosome in Pyrenean Populations

A. M. López-Parra et al.

Abstract

The male-mediated genetic legacy of the Pyrenean population was assessed through the analysis of 12 Y-STR and 27 Y-SNP loci in a sample of 169 males from 5 main geographical areas in the Spanish Pyrenees: Cinco Villas (Western Pyrenees), Jacetania and Valle de Arán (Central Pyrenees) and Alto Urgel and Cerdaña (Eastern Pyrenees). In the Iberian context, the Pyrenean samples present some specificities, being characterizeded by a high proportion of chromosomes R1b1b2-M269 (including the usually uncommon R1b1b2d-SRY2627 and R1b1b2c-M153 types) or I2a2-M26 and low proportions of other haplogroups. Our results indicate that an old pre-Neolithic substrate is preponderant in populations of the whole Pyrenean fringe. However, AMOVA revealed a high level of substructure within Pyrenean populations, partially explained by drift effects as well as by the signature of an ancient genetic differentiation between Western and Eastern Pyrenees.

Link

Mark Stoneking review on Human Origins

Nothing really new in this paper, but the figure of the different models of human evolution is interesting. I have issues with the model of Assimilation shown, however, since only Europeans are shown as assimilating pre-existing populations (Neanderthals). There have been suggestions in the past that other human populations may have interacted with their own local inhabitants, e.g., erecti in Asia.

I also have issues with Stoneking's caricature of Carleton Coon's "candelabra" model. Saying that this model is not tenable today is one thing, but ascribing racist motivations behind it is another:

The candelabra model was most prominently associated with the anthropologist Carleton Coon (1904–1981), and fell out of favour when he used it to promote racist views. According to Coon, the transformation to modern humans occurred first

in Europeans, and hence they have had the most time to evolve from their ‘primitive’ ancestry, whereas Africans were the last to transform into modern humans and therefore have had the least amount of time to shed their primitive ancestry—and in case you were wondering, Carleton Coon was of European ancestry.

There is actually no good reason to ascribe racist motivations to Coon's model of human origins. It was simply an interpretation of the evidence (such as it was in his day). Coon's suggestion that different races crossed the sapiens threshold at different times did not imply superiority and inferiority. While he almost certainly believed in inherent differences between the races (as most scientists in his day did, and many still do), his views were definitely not based on an idea of Africans as having less time to evolve.

EMBO Reports 9, S1, S46–S50 (2008)

Human origins. The molecular perspective

Mark Stoneking

Abstract

Link

The face of Dante Alighieri

Journal of Archaeological Science doi:10.1016/j.jas.2008.09.006

THE FACE OF THE POET DANTE ALIGHIERI RECONSTRUCTED BY
VIRTUAL MODELLING AND FORENSIC ANTHROPOLOGY TECHNIQUES

Stefano Benazzi et al.

Abstract

This paper describes the multi-disciplinary approach to reconstruct the face of Dante Alighieri (1265-1321). Since the Dante’s sepulchre will be opened in 2021, the reconstructive process is based on morphological and metric data collected on the poet’s cranium during the formal identification of his remains in 1921 by the anthropologist Fabio Frassetto, as well as on the resulting plaster model. Starting from this plaster model and a morphologically compatible reference mandible, since the original mandible was never found, a 3D digital model of the complete skull was obtained by reverse engineering and virtual modelling techniques. The most important aspect in this work was the method of virtual modelling proposed for the ex novo generation of the mandible. The physical model of the skull (cranium + mandible) was then produced by means of a rapid prototyping system. This model was finally used to recreate Dante’s face via traditional facial reconstruction techniques currently used in forensic anthropology.

Link

Support for "large" Troy at the time of the Trojan War

See also the Historicity of the Trojan War and The eclipse of 1178BC and the return of Odysseus to Ithaca

Discovery of Bronze-Age `Refrigerators' Expands Homer's Troy :

Sept. 17 (Bloomberg) -- The remains of two outsized earthenware pots, a ditch and evidence of a gate dating back more than 3,000 years are changing scholars' perceptions about the city of Troy at the time Homer's ``Iliad'' was set.

The discoveries this year show that Troy's lower town was much bigger in the late Bronze Age than previously thought, according to Ernst Pernicka, the University of Tubingen professor leading excavations on the site in northwestern Turkey.

His team has uncovered a trench 1.4 kilometers long, 4 meters wide and 2 meters deep. The full length of the trench, which probably encircled the city and served a defensive purpose, may be as much as 2.5 kilometers, Pernicka said in an interview in his office in Mannheim, Germany. Troy may have been as big as 40 hectares, with a population as high as 10,000, he estimates.

...

The discovery of the trench around the lower town vindicates Pernicka's predecessor, Manfred Korfmann, who faced accusations from a fellow German scholar that he was misleading the public in his interpretation of the ditch, which might have been for drainage. After Korfmann died in 2005, Pernicka took over his work and aims to publish the results of 20 years of digging and research.

...

What archaeology has shown is that Troy's golden era ended in 1180. Where preceding Trojans had used potters' wheels for about 1,000 years, ceramics found on the site show the technology was lost with the arrival of a new people, probably from the Balkans, who reverted to hand-made pots. The newcomers also built their houses in a completely different style.

Origins of Venice

How the barbarians drove Romans to build Venice:

Historians agree that the explanation is that Venice was founded on the islands by refugees from Roman cities such as Ravenna, Padua and Aquileia as they fled from invasions, first by Attila the Hun in the 5th century and then, a century later, by the Lombards, as the final remnants of the Roman Empire crumbled.

However, Paolo Mozzi, a researcher at the University of Padua geography department, said high-definition satellite photographs had revealed the ruins of an extensive town much closer to present day Venice at Altino – known in Roman times as Altinum – a little more than seven miles north of the city, close to Marco Polo airport.

“The hypothesis is that as Altinum also succumbed to the Barbarian invasions, the inhabitants fled farther down to the lagoon to build Venice on the islands, using some of the stones from their city,” he said. At its height, he said, Altinum had been an important trading and seafaring centre on the Adriatic, before it was overrun by Attila in the mid-5th century.

Vikings abroad in search of women

Viking Age Triggered by Shortage of Wives?:

Sept. 17, 2008 -- During the Viking Age from the late eighth to the mid-eleventh centuries, Scandinavians tore across Europe attacking, robbing and terrorizing locals. According to a new study, the young warriors were driven to seek their fortunes to better their chances of finding wives.

The odd twist to the story, said researcher James Barrett, is that it was the selective killing of female newborns that led to a shortage of Scandinavian women in the first place, resulting later in intense competition over eligible women.

...

Soren Sindbaek, assistant professor of medieval and Renaissance archaeology at Denmark's University of Aarhus, told Discovery News that the new paper "is very right in pointing out the inadequacy" of former explanations for the Viking Age.

"We need indeed to seek for an individual, social motivation behind the fact that a large number of young men chose to set out on extremely risky voyages in hopes of acquiring wealth and esteem in foreign lands," Sindbaek said.

Erratum on my Y-STR variance work (which, surprisingly further supports its central thesis)

I realized today that there was a central error in my assumptions today on the entire Y-STR series. This error related to the condition I used to detect whether a man was also a Most Recent Common Ancestor:

Lineages start with one man, and over the generations grow (or shrink) in size as men have (or fail to have) sons. Previously, I considered that there was a new MRCA in the lineage if the number of descendants in one generation was reduced to 1 man.

So, for example let these be the number of patrilineal descendants in the first few generations:

Generation	# of descendants
0	1 (Patriarch)
1	3
2	4
3	6
4	3
5	1
6	3
7	2

I concluded that the "Patriarch" (at generation 0) was not the MRCA (correct) and that the new MRCA was the single surviving man in generation 5 (not necessarily correct).

It is true that at generation 5, the man becomes the new MRCA, since no other patrilineal cousins of his exist at that time.

BUT, it is also possible for e.g., one of the 3 men of generation 6 to be an MRCA. All it takes is for the next generation (7) to be produced entirely by him.

So: the single survivor at generation 5 has three sons in generation 6, thus he is temporarily the MRCA. However, only one of his three sons produces the two men of generation 7, and thus this son becomes the new MRCA.

In retrospect this is an obvious mistake to make, and is the result of using a sufficient condition for an MRCA (the lineage reduced to one man) which is not however necessary for a man to be an MRCA.

What are the consequences?

I will be issuing a bug fix for the Y-chromosome Microsatellite Genealogy Simulator over the next few days. But, it's interesting to see how this error affects the story I've been defending throughout the posts in the Y-STR series, namely that Y-STR variance accumulates at near the germline mutation rate for large observable present-day haplogroups.

For any particular lineage, the MRCA I calculated so far was no younger, and sometimes older than the real one. Consequently, Y-STR variance has accumulated at an even faster rate since the time of the real MRCA, even closer to the germline rate.

At this point I am not in a position of determining how big this effect will be, and I will repeat and report some of my earlier experiments. A few exploratory runs so far, have revealed a small but not insignificant increase in the effective mutation rate.

Stay tuned...

UPDATE #1

I carried out some experiments to see how different in age are the previously calculated "MRCA" and the real MRCA. To differentiate between the two, I will call the previous "MRCA" as a "Near Extinction" event, where a lineage is reduced to one man in one generation. The real MRCA is simply a man of the lineage who produces the entire next generation.

As I mentioned in the very first post of this series, at the MRCA, variance is reset to 0; thus variance is of no use to determine the length of time that has elapsed between the Patriarch and the MRCA. This time can be estimated, however, from demographic considerations.

g	m	TMRCA	s.d	TNearExtinct	s.d
50	1	40	16	43	13
50	1.05	44	10	46	9
100	1	86	26	91	22
100	1.05	95	10	97	7

It can be seen that (i) the TMRCA is fairly close to the TNearExtinct, and they are both fairly close to the Patriarch, whose time is g. This closeness (in relative terms) increases as both g and m (the average number of sons/man) increase. Both TMRCA and TNearExtinct can be quite variable, as evidenced by their respective s.d.'s, but this variability decreases as m increases.

UPDATE #2

I have repeated my experiments on the effective mutation rate. You can compare the results directly, but it's obvious that the discrepancy exists somewhat only for m=1 and the results are almost identical otherwise. Thus, the problem identified in this erratum does not appear to affect by much all my past inferences about TMRCA and its relationship to Y-STR variance.

g	m	Size	Var	ASD	μ/wv	μ/wa
50	1.00	32	0.043	0.058	2.9	2.2
50	1.01	41	0.047	0.062	2.6	2.0
50	1.02	53	0.052	0.068	2.4	1.8
50	1.03	72	0.057	0.072	2.2	1.7
50	1.04	98	0.061	0.077	2.1	1.6
50	1.05	135	0.065	0.080	1.9	1.6
50	1.10	813	0.086	0.099	1.5	1.3
100	1.00	58	0.081	0.106	3.1	2.4
100	1.01	99	0.097	0.123	2.6	2.0
100	1.02	185	0.118	0.147	2.1	1.7
100	1.03	360	0.135	0.163	1.9	1.5
100	1.04	757	0.153	0.180	1.6	1.4
50	1.00	31	0.043	0.058	2.9	2.2
50	1.01	41	0.048	0.063	2.6	2.0
50	1.02	54	0.052	0.067	2.4	1.9
50	1.03	73	0.058	0.074	2.2	1.7
50	1.04	97	0.064	0.081	2.0	1.5
50	1.05	134	0.065	0.081	1.9	1.5
50	1.10	813	0.085	0.098	1.5	1.3
100	1.00	58	0.082	0.108	3.0	2.3
100	1.01	99	0.101	0.130	2.5	1.9
100	1.02	184	0.120	0.151	2.1	1.7
100	1.03	362	0.135	0.163	1.9	1.5
100	1.04	749	0.154	0.181	1.6	1.4
100	1.05	1593	0.168	0.193	1.5	1.3
200	1.00	111	0.162	0.208	3.1	2.4
200	1.01	347	0.228	0.280	2.2	1.8
200	1.02	1443	0.293	0.342	1.7	1.5
200	1.03	7132	0.350	0.391	1.4	1.3
200	1.04	38123	0.387	0.421	1.3	1.2
400	1.00	212	0.300	0.377	3.3	2.7
400	1.01	2767	0.589	0.670	1.7	1.5
400	1.02	78149	0.768	0.825	1.3	1.2

Reconstruction of female Neanderthal

This is a very early prototype of things that may be possible in the future. The DNA-based evidence was limited to pigmentation, as far as I can tell. Unfortunately, as with other complex traits, there has been a limited crop of useful genes identified for observable human traits.

No need for such DNA evidence is -of course- needed to reconstruct skeletal structure, since the skeletal structure is pretty much the only part of a person's appearance that survives along Paleolithic time scales.

However, there is wide room for progress in inferring both pigmentation (there have been successes here, but the problem is by no means completely solved), as well as non-surviving traits such as muscular development, hair texture, etc.

Apparently, there is also a National Geographic documentary to accompany this.

Off topic: doesn't she resemble somewhat Vincent from Beauty and the Beast?

PHOTO IN THE NEWS: DNA-Based Neanderthal Face Unveiled:

September 17, 2008—Meet Wilma—named for the redheaded Flintstones character—the first model of a Neanderthal based in part on ancient DNA evidence.

Artists and scientists created Wilma (shown in a photo released yesterday) using analysis of DNA from 43,000-year-old bones that had been cannibalized. Announced in October 2007, the findings had suggested that at least some Neanderthals would have had red hair, pale skin, and possibly freckles.

Lactase persistence allele is clinal in Great Britain

Lactase non-persistence seems to be more important in the south and east of Great Britain.

European Journal of Human Genetics doi: 10.1038/ejhg.2008.156

Lactase persistence-related genetic variant: population substructure and health outcomes

George Davey Smith et al.

Abstract

Lactase persistence is an autosomal-dominant trait that is common in European-derived populations. A basic tendency for lactase persistence to increase from the southeast to the northwest across European populations has been noted, but such trends within countries have not been extensively studied. We genotyped the C/T-13910 variant (rs4988235) that constitutes the putatively causal allele for lactase persistence (T allele representing persistence) in a general population sample of 3344 women aged 60–79 years from 23 towns across Britain. We found an overall frequency of 0.253 for the C (lactase non-persistence) allele, but with considerable gradients of decreasing frequency from the south to the north and from the east to the west of Britain for this allele. Daily sunlight was positively related to C (non-persistence) allele prevalence. However, sunlight exposure and latitude are strongly correlated, and it was not possible to identify which is the primary factor statistically underlying the distribution of lactase persistence. The C/T-13910 variant (rs4988235) was not related to drinking milk or bone health (although drinking milk itself was protective of bone health), and was essentially unrelated to a wide range of other lifestyle, health and demographic characteristics. One exception was general health being rated as being poor or fair, for which there was an odds ratio of 1.38 (1.04, 1.84) for women homozygous for the C allele; on adjustment for latitude and longitude of place of birth, this attenuated to 1.19 (0.87, 1.64). The lactase persistence variant could contribute to the examination of data for the existence of, and then statistical control for, population substructure in genetic association studies.

Link

Three-stage colonization model for Americas reconsidered

I had blogged about this model before. From the earlier paper:

Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth ≈40,000 and ≈15,000 years ago separated by a long period of population stability.

This model was now criticized by Fagundes et al. who discovered that the early stage of the model was an artifact of the inclusion of mtDNA sequences of non-American origin:

Our results refute the specific details of the “three-stage model”, since the early stage of expansion into Beringia followed by a long period of stasis could not be reproduced in any mtDNA data set cleaned from non-Native American haplotypes.

This is acknowledged by the authors of the three-stage model in Mulligan et al:

We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e. ~40,000 years ago) expansion signal we had proposed for the proto-Amerind population.

The authors do however claim that:

Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of the Americas and the processes of colonization.

What's the lesson from all this? Many of the conclusions drawn by geneticists are very sensitive to data outliers: 9 out of 77 sequences that shouldn't have been included was enough to provide support for the 40kya stage of growth, which was now revealed to be spurious.

Clustering humans: on biological boundaries

From the paper:

Nevertheless beyond such a treacherous ideology, we need boundaries, since we need clusters both to achieve group-oriented diagnostics and therapeutics, and to grasp the evolution of Homo sapiens. Of course these clusters must be named in some way. To be honest nothing prevents us from continuing to use the word ‘race’ for them, especially now that we have understood the real epistemological status of this notion and the methodological path used to determine its content. Unfortunately ‘race’ is a too ideologically and historically committed term, and it would be wise not to use it. The history of human culture has showed us that even if words are not dangerous, the humans who use them can be extremely dangerous.

The problem with this view is that by not using the word "race", the wrong impression is given, namely that "races do not exist", rather than the intended one that "things that we could call races exist, but we prefer not to name them because some bad people do so, and have done so in the past".

A secondary consequence is that by avoiding the use of the word "race" and its terminology, or replacing it with "ethnic group", "continental population", or "cluster", we make communication more difficult, e.g., because "ethnic group" is a social-political-cultural as well as biological concept, races do not map perfectly to geographically circumscribed continents, and "clusters" can be defined in a number of different ways without necessarily the property of "exhibiting genetic similarity reflecting common descent" that is characteristic of biological race.

Thirdly, even if "race" is a dangerous word, does any one believe that people's attitudes towards each other will magically change if they stop using racial terminology? Will a person's prejudices evaporate into thin air if it becomes impolite to speak of human races? On the contrary, existing prejudices will most likely go underground, and all sorts of incorrect notions about it will proliferate as scientists refuse to acknowledge its existence.

If we look back to the age before the emergence of race classification in Homo sapiens in the 18th century, we will see that there was plenty of opportunity for prejudice and conflict. So, rather than thinking that the identification of human races leads to prejudice, we should think that prejudice leads to an abuse of the race concept, just as it leads to an abuse of other religious, linguistic, or social concepts to justify itself. Does the fact that dangerous people use religious differences suggest that we should abandon classification of mankind's religious belief systems?

Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, Volume 39, Issue 1, March 2008, Pages 163-170

Clustering humans: on biological boundaries

Ludovica Lorussoa, and Giovanni Boniolo

Abstract

We inquire into the notions of ‘boundary’ and ‘cluster’ in the fields of medical genetics, pharmacogenetics, and population genetics. First we show that the two notions are not well discussed in literature. Then we propose a promising explication of them, in which we argue that clustering is always ‘property laden’, that is, fundamentally dependent on decisions about the properties to be taken into account. In particular we suggest three different kinds of properties (main properties, investigating properties, and catalyzing properties) that have a role in these decisions. That is, we conclude that boundaries and clusters among humans depend on our way of considering nature. Concepts of ‘race’ and ‘ethnic group’ are discussed too, since they are the most used clusters among humans.

Link

Genographic project paper on human mtDNA mutation rates

This is a fairly technical paper which should be of interest for those interested in uniparental markers and their age estimation.

Genetics doi: 10.1534/genetics.108.091116

Maximum Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA from Partial Phylogenetic Classification

Saharon Rosset et al.

Abstract

The mitochondrial DNA hyper-variable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates of mutation rates among nucleotide sites in this region are essential. We have developed a novel maximum-likelihood methodology for estimating site-specific mutation rates from partial phylogenetic information, such as haplogroup association. The resulting estimation problem is a generalized linear model, with a non-standard link function. We develop inference and bias correction tools for our estimates and a hypothesis testing approach for site independence. We demonstrate our methodology using 16,609 HVS-I samples from the Genographic Project. Our results suggest that mutation rates among nucleotide sites in HVS-I are highly variable. The 16,400--16,500 region exhibits significantly lower rates compared to other regions, suggesting potential functional constraints. Several loci identified in the literature as possible termination associated sequences (TAS) do not yield statistically slower rates than the rest of HVS-I, casting doubt on their functional importance. Our tests do not reject the null hypothesis of independent mutation rates among nucleotide sites, supporting the use of site-independence assumption for analyzing HVS-I. Potential extensions of our methodology include its application to estimation of mutation rates in other genetic regions, like Y-chromosome short tandem repeats.

Link

Why genome-wide association studies don't really work (and how human evolution really happens)

In case you are skeptical about my gloomy assessment of the power of genome-wide association studies, here is Nicholas Wade in today's New York Times, profiling David Goldstein (via john hawks):

This idea, called the common disease/common variant hypothesis, drove major developments in biology over the last five years. Washington financed the HapMap, a catalog of common genetic variation in the human population. Companies like Affymetrix and Illumina developed powerful gene chips for scanning the human genome. Medical statisticians designed the genomewide association study, a robust methodology for discovering true disease genes and sidestepping the many false positives that have plagued the field.

But David B. Goldstein of Duke University, a leading young population geneticist known partly for his research into the genetic roots of Jewish ancestry, says the effort to nail down the genetics of most common diseases is not working. “There is absolutely no question,” he said, “that for the whole hope of personalized medicine, the news has been just about as bleak as it could be.”

...

The reason for this disappointing outcome, in his view, is that natural selection has been far more efficient than many researchers expected at screening out disease-causing variants. The common disease/common variant idea is largely wrong. What has happened is that a multitude of rare variants lie at the root of most common diseases, being rigorously pruned away as soon as any starts to become widespread.

I would only add that the common variant idea is probably wrong for neutral or positive traits as well. While negative traits are culled from the gene pool by purifying selection, advantageous traits (muscularity, beauty, intelligence, etc.) are positively selected.

But, what is selected? Surely, "a multitude of rare variants" can't exist for positive traits: most mutation is deleterious; the good stuff doesn't appear de novo very often. In my opinion, by and large, it is not common variants behind these traits. Rather, it is fortuitous combinations of unexceptional alleles.

This Lego-block paradigm is based on the notion that most of our alleles are commodity"building blocks"; if they are brought together harmoneously, they produce positive results. The occasional allele may have a large effect, and some alleles fit better together than others. Yet, most of the success or failure of a construction depends on how the components fit together, and not what they are.

I had previously made the point that evolution doesn't require mutation, selection, or drift but can be effected by the self-segregation of individuals into geographical or social niches for which they are better adapted. Differential reproduction of the semi-segregated geographical or social groups (i.e. group selection) then ensues.

There has doubtlessly been recent selection in humans, particularly because of feedback from the changed environments humans created for ourselves.

But, individuals don't differ from each other primarily because of genes that have undergone population-wide selection. Rather, we differ from each other first because we belong to a specific hierarchy of groups (race, subrace, ethnic group, etc.) and foremost because we have inherited a particular combination of alleles, our "family lego shape" from our parents.

Why I won't be testing with 23andMe (yet)

Since the announcement of the price reduction of the 23andMe service, I had a couple of readers e-mail me, asking whether I thought it was worth it. My response was to do their own research to figure out whether the information they would learn would be worth the asking price.

Here is why, despite the much lowered price, I am not convinced.

What is a 23andMe test worth to you?

The 23andMe test gives you four types of information:

• The frivolous, e.g., Bitter Taste perception.
• The obvious, e.g., Hair Color.
• The medical, e.g., Type 2 Diabetes.
• The ancestral.

The frivolous kind is perhaps a good and safe topic for conversation (as opposed, e.g., to Schizophrenia) but its value is obviously not $400.

The obvious kind tells you something that you already know about yourself; it only confirms that you have the genes for your known phenotype. Again, this is not useful information, unless perhaps your spouse orders a test too: then, you could sometimes calculate the chances of your children presenting a phenotype for simple quasi-Mendelian traits. 

The medical kind is potentially useful. It is for this kind of information that you should research the traits on offer, to see if (i) they interest you, and (ii) there are strong associations for them. The truth is, however, as I pointed out recently that for all their hype, genome-wide association studies have produced meagre results. Your family medical history and lifestyle are much more likely to affect your health than the common variants genotyped in the current generation of microarrays. But, by all means, do your own research, since a trait that interests you may be one for which strong associations have been found.

Finally, the ancestral information is potentially useful, since recent papers have shown that multi-100K SNP genome-wide testing can produce fine-scale ancestral inference, even in relative homogeneous populations such as Europeans. However, as of this writing, you won't get this type of information, but rather a simple 4-group global admixture estimate, as well as a measure of your similarity to the Human Genome Diversity Panel populations. For anyone whose known genealogical ancestry isn't complex, this information will not be novel.

23andMe have also apparently included some fairly detailed SNP typing that place you in the Y-chromosome (if you are male) and mtDNA phylogeny, giving you a detailed haplogroup assessment. Even if this information wasn't known to me, this part of the test would not be tempting, since haplogroup assignment reveals only very coarse information. Almost certainly, you would want to follow up with a Y-STR panel or mtDNA full-genome sequence, which would allow you to meaningfully compare yourself with the many others that have tested so far; but that is not an option with 23andMe.

What is a 23andMe test worth to 23andMe?

23andMe have definitely emphasized the "coolness" factor of getting DNA tested. It has definitely generated a lot of publicity, and getting tested is marketed as a social prestige marker. 

However, the "coolness" factor isn't enough to sell tests. It is not known how many have been sold so far, but there are indications that not many is close to the truth:

• No one cuts the price by 60% if there is solid demand for a product. Prices for Y-STR tests haven't dropped by nearly as much in 5+ years, since there is a real demand for them by genetic genealogists.
• People have a Gattaca-view of genetic testing, and are afraid of the information it may reveal. It has been said that 23andMe has downplayed the significance of the associations they report to keep regulators off their backs, but a more significant reason may be to entice reluctant consumers to test.

One would think that a company selling genetic tests would stress the importance of the genetic information, but this is clearly not the case. To its credit, 23andMe doesn't oversell the actual science, which as I mentioned above, isn't all that revealing. 

This NY Times story gives a useful hint:

Ms. Wojcicki and Linda Avey, the company’s other founder, say their chief goal is to advance science by compiling a database of genetic information that medical researchers can tap (while protecting customers’ anonymity). Customers cannot opt out of having their information anonymously shared, but they can refuse to participate in surveys focusing on specific traits.

This is also why the Coriell Institute is offering genotyping for free. 

It is simply a problem of body count. Progress has been hampered by small sample sizes. Collecting and genotyping large samples is hampered both by strict ethics rules that publically-funded medical researchers must adhere to, and also by the actual cost of sample-collection and genotyping.

23andMe's goal isn't to be a service provider to consumers. Their goal is to entice regular people to pay the cost of genotyping, while at the same time helping it build its huge "database of genetic information."

Just as a TV station doesn't exist for providing news and entertainment to an audience, but provides news and entertainment so it can sell ads and make money, so 23andMe doesn't exist to sell genetic information to consumers, but sells genetic information to build and exploit its genetic database.

What it would take to make me a customer

There is nothing wrong with 23andMe's strategy: its goal is to advance science (and make money doing it) by offering genetic information to consumers. This is a potentially win-win situation for both. However, as I explained above, the information one can expect from the test today isn't all that special.

Since I don't want to be a naysayer, here is what it would take to convince me to test with 23andMe:

-- Fine-scale ancestry analysis --

The science has progressed to a point where this is possible. We now know that distinct subgroups can be discerned within all the major continental races. The latest research revealed an additional insight: it doesn't take a large samples to place individuals on the map fairly accurately. Even countries with less than 5 sampled individuals found their way to the "correct" geographical spot. 

The corrolary of the above observation is that a global-level sampling of human genetic diversity can be done at a reasonable cost. Leveraging existing samples, and adding mini-samples from many unstudied locations can lead to powerful ancestry analysis, which can be gradually and continuously refined as more samples are collected (both on the "field" and using customers of unmixed localized heritage)

23andMe's partnership with ancestry.com suggests that they take this segment of their market seriously. So, when and if they offer a test which provides ancestral information beyond the obvious, I will be tempted to test with them.

Ideal craniofacial height / standing height = 1/7-1/8.5, (plus instructions to test your own)

Here is how to test your own craniofacial height / standing height ratio. Take a picture of yourself facing the camera, looking forward. A good rule of thumb is for the bottom of your eye socket to align with your earhole; you can use a side mirror to practice your posture before you take the shot. Obviously, you shouldn't wear shoes, and you should arrange your hair in a way that it doesn't "stand up". Your mouth shouldn't be open or your jaw loose; just have a natural expression. Also, make sure that the camera is a few meters away from you; the more, the better (as long as you can produce a picture with enough resolution for measurement). Use a self-timer or have your friend take the picture.

Once you have the picture in your computer, measure:

• craniofacial height CFH: from top of your head to bottom of your chin.
  
• standing height SH: from top of your head to the point on the floor where your heels touch.
  

Now divide CFH/SH and you have your own ratio: congrats! You can take SH/CFH to see how this is expressed as a fraction.

What is your craniofacial height / standing height
	Less than 1/8
	Between 1/8 and 1/7.5
	More than 1/7.5
Free polls from Pollhost.com

From the paper:

It is generally acknowledged that the work of Polycleitus in the fifth century BC was used by other sculptors as demonstrating the ‘ideal’ proportions of a man. The craniofacial height to standing height proportion of the available marble copies of the Doryphorus is 1/7.5.

In the late fourth century BC, the prolific sculptor Lysippos is thought to have established a new canon using eight heads to standing height. This is evident from inspection of the Roman marble copy of the Apollo Belvedere in the Vatican Museum.

The Roman architect Vitruvius based his guidelines on the Classical Greek sculptors. He described the facial height to standing height proportion of 1/10, which corresponds to a craniofacial height to standing height proportion of 1/8.

The scientifically enquiring minds of the Renaissance were no longer interested in blindly following the Classical ‘ideal’, and began to study human anatomy and record human proportions. Adapting the work of Vitruvius with his own research, Leonardo da Vinci provided the Renaissance canons of proportion. He described the ‘ideal’ craniofacial height to standing height proportion as 1/8. Durer later described the ‘ideal’ man of ‘Eight head-lengths’.

The results of this study lend support to the use of a proportional ratio between the Classical ideal of 1/7.5 and the Renaissance ideal of 1/8.

...

The craniofacial height to standing height proportion may be calculated from the original anthropometric data provided by Farkas2. From this original anthropometric data, the craniofacial height to standing height proportion in young adult males (age range 19–25 years) was found to be 1/7.7 (range 1/7.4 to 1/8.1), and in young adult females (age range 19–25 years) was found to be 1/7.6 (range 1/7.2 to 1/7.9) (Table 1).

The results of this study, based on lay and clinician judgements of attractiveness, generally validate the anthropometric data. In this study it was found that a proportion of 1/7.5 was perceived as the most attractive, with 1/8 a close second. The images regarded as most attractive by the participants had a mean craniofacial height to standing height proportion of 1/7.8 (min=1/7 and max=1/8.5). The mean rank preference score was found to be minimal for a craniofacial height to standing height proportion of 1/8 and increased when the craniofacial height to standing height proportion moved away from 1/8 in either direction (Table 8).

Int J Oral Maxillofac Surg. 2008 Sep 6. [Epub ahead of print]

The influence of craniofacial to standing height proportion on perceived attractiveness.

Naini FB, Cobourne MT, McDonald F, Donaldson AN.

Department of Orthodontics, St George's Hospital, United Kingdom.

An idealised male image, based on Vitruvian Man, was created. The craniofacial height was altered from a proportion of 1/6 to 1/10 of standing height, creating 10 images shown in random order to 89 observers (74 lay people; 15 clinicians), who ranked the images from the most to the least attractive. The main outcome was the preference ranks of image attractiveness given by the observers. Linear regressions were used to assess what influences the choice for the most and the least attractive images, followed by a multivariate rank ordinal logistic regression to test the influence of age, gender, ethnicity and professional status of the observer. A craniofacial height to standing height proportion of 1/7.5 was perceived as the most attractive (36%), followed by a proportion of 1/8 (26%). The images chosen as most attractive by more than 10% of observers had a mean proportion of 1/7.8(min=1/7; max=1/8.5). The images perceived as most unattractive had a proportion of 1/6 and 1/10. The choice of images was not influenced by the age, gender, ethnicity or professional status of the observers. The ideal craniofacial height to standing height proportion is in the range 1/7 to 1/8.5. This finding should be considered when planning treatment to alter craniofacial or facial height.

Link

Social perception of obesity

Caption for figure:

1. Lean (L - narrow shoulders, thin torso and extremities, knee and elbow joints thicker than thy and arm diameter). 2. Muscular (M – Broad shoulders, curved extremities, chest and abdominal muscles shown, thy and arm diameters greater than knee and elbow joints). 3. Slightly fat and feminine (F – rounded shoulders, cylindrical extremities). Each of the three body forms was represented with (designated by +) and without (−) abdominal obesity as shown in rows. The sequence of these figures was randomized during the test and the figures were labeled serially by alphabets.

From the paper:

hysical characters were associated with the appropriate body forms as expected. The physical traits strong, rough and tough and physically aggressive were associated with the muscular non-obese [M−] figure. Lethargic was associated with F+. Disease prone was significantly associated with L− on the one hand and F+ on the other indicating that people negatively associate both the extremes with health. The trait swift was also strongly associated with L−. The traits that are not obviously physical were also strongly associated with certain body forms. Brave, conscious about looks, influential, dominating, status conscious, modern and confident were associated with M−; physical risk avoider, money minded, political, rich, stupid, selfish and greedy were associated most strongly with F+; friendly, intelligent, methodical, business risk avoider, successful, loving, kind, and honest were associated with F−; and L− was the commonest choice for swift, physical risk avoider, talkative and the trait depressed was associated with L+ [table 1].

Link to Table 1.

PLoS ONE doi: 10.1371/journal.pone.0003187

Obesity as a Perceived Social Signal

Manasee Mankar et al.

Abstract

Fat accumulation has been classically considered as a means of energy storage. Obese people are theorized as metabolically ‘thrifty’, saving energy during times of food abundance. However, recent research has highlighted many neuro-behavioral and social aspects of obesity, with a suggestion that obesity, abdominal obesity in particular, may have evolved as a social signal. We tested here whether body proportions, and abdominal obesity in particular, are perceived as signals revealing personality traits. Faceless drawings of three male body forms namely lean, muscular and feminine, each with and without abdominal obesity were shown in a randomized order to a group of 222 respondents. A list of 30 different adjectives or short descriptions of personality traits was given to each respondent and they were asked to allocate the most appropriate figure to each of them independently. The traits included those directly related to physique, those related to nature, attitude and moral character and also those related to social status. For 29 out of the 30 adjectives people consistently attributed specific body forms. Based on common choices, the 30 traits could be clustered into distinct ‘personalities’ which were strongly associated with particular body forms. A centrally obese figure was perceived as “lethargic, greedy, political, money-minded, selfish and rich”. The results show that body proportions are perceived to reflect personality traits and this raises the possibility that in addition to energy storage, social selection may have played some role in shaping the biology of obesity.

Link

Y chromosomes of Bayash Romani

Once again, the 0.00069/locus/generation rate is used in this paper, and hence its estimated ages are wrong. The given Y-STR variance for haplogroup H1a in Table 2 is 0.06, which corresponds to an age of ~800 years.

It's interesting though, that Zhivotovsky is a co-author of this paper which states that:

A recent refinement of E1b1b1a-M78 by novel biallelic markers indicates that its subhaplogroup E1b1b1a2-V13 is the most common in Europe (Cruciani et al., 2007). In fact, E1b1b1a2-V13 originated in Western Asia about 11 KYA and expanded in Southeastern Europe about 4.5 KYA, not in connection with the spread of agriculture as traditionally assumed, but rather at the beginning of the Balkan Bronze age, as a consequence of the in situ population increase in the already populated territory (Cruciani et al., 2007).

and he was a co-author of King et al. (2008) which stated that:

The calculated expansion time of haplogroup E3b1a2-V13 in mainland Greece is 8,600 y BP at Nea Nikomedeia and 9,200 y BP at Lerna/Franchthi Cave and is consistent with the late Mesolithic/initial Neolithic horizon. These dates exceed those reported previously for Europe (Cruciani et al., 2007) that date to the Bronze Age. This discrepancy arises mainly because of differences in the choice of mutation rate used.

Peter Underhill was also a co-author of the latter study, and also of the recent paper on Sicily which used germline mutation rates and:

The estimate of Time to Most Recent Common Ancestor is about 2380 years before present, which broadly agrees with the archaeological traces of the Greek classic era.

Mesolithic - Early Bronze Age - classical Greek. Three completely different ages using three different mutation rates: a mutation rate 3.6x slower than the germline rate => Mesolithic. A mutation rate 2.4 to 2.8x slower => Early Bronze Age. A germline mutation rate => classical Greek.

My most recent take. I'll be much surprised if E-V13 turns out to be anything other than 2nd millennium BC in the Balkans.

American Journal of Physical Anthropology doi: 10.1002/ajpa.20933

Dissecting the molecular architecture and origin of Bayash Romani patrilineages: Genetic influences from South-Asia and the Balkans

Irena Martinovi Klari et al.

Abstract

The Bayash are a branch of Romanian speaking Roma living dispersedly in Central, Eastern, and Southeastern Europe. To better understand the molecular architecture and origin of the Croatian Bayash paternal gene pool, 151 Bayash Y chromosomes were analyzed for 16 SNPs and 17 STRs and compared with European Romani and non-Romani majority populations from Europe, Turkey, and South Asia. Two main layers of Bayash paternal gene pool were identified: ancestral (Indian) and recent (European). The reduced diversity and expansion signals of H1a patrilineages imply descent from closely related paternal ancestors who could have settled in the Indian subcontinent, possibly as early as between the eighth and tenth centuries AD. The recent layer of the Bayash paternal pool is dominated by a specific subset of E1b1b1a lineages that are not found in the Balkan majority populations. At least two private mutational events occurred in the Bayash during their migrations from the southern Balkans toward Romania. Additional admixture, evident in the low frequencies of typical European haplogroups, J2, R1a, I1, R1b1b2, G, and I2a, took place primarily during the early Bayash settlement in the Balkans and the Romani bondage in Romania. Our results indicate two phenomena in the Bayash and analyzed Roma: a significant preservation of ancestral H1a haplotypes as a result of considerable, but variable level of endogamy and isolation and differential distribution of less frequent, but typical European lineages due to different patterns of the early demographic history in Europe marked by differential admixture and genetic drift.

Link

mtDNA haplogroup M2 in India

BMC Evolutionary Biology doi: 10.1186/1471-2148-8-230

The earliest settlers' antiquity and evolutionary history of Indian populations: evidence from M2 mtDNA lineage

Satish Kumar et al.

Abstract

Background

The "out of Africa" model postulating single "southern route" dispersal posits arrival of "Anatomically Modern Human" to Indian subcontinent around 66–70 thousand years before present (kyBP). However the contributions and legacy of these earliest settlers in contemporary Indian populations, owing to the complex past population dynamics and later migrations has been an issue of controversy. The high frequency of mitochondrial lineage "M2" consistent with its greater age and distribution suggests that it may represent the phylogenetic signature of earliest settlers. Accordingly, we attempted to re-evaluate the impact and contribution of earliest settlers in shaping the genetic diversity and structure of contemporary Indian populations; using our newly sequenced 72 and 4 published complete mitochondrial genomes of this lineage.

Results

The M2 lineage, harbouring two deep rooting subclades M2a and M2b encompasses approximately one tenth of the mtDNA pool of studied tribes. The phylogeographic spread and diversity indices of M2 and its subclades among the tribes of different geographic regions and linguistic phyla were investigated in detail. Further the reconstructed demographic history of M2 lineage as a surrogate of earliest settlers' component revealed that the demographic events with pronounced regional variations had played pivotal role in shaping the complex net of populations phylogenetic relationship in Indian subcontinent.

Conclusion

Our results suggest that tribes of southern and eastern region along with Dravidian and Austro-Asiatic speakers of central India are the modern representatives of earliest settlers of subcontinent. The Last Glacial Maximum aridity and post LGM population growth mechanised some sort of homogeneity and redistribution of earliest settlers' component in India. The demic diffusion of agriculture and associated technologies around 3 kyBP, which might have marginalized hunter-gatherer, is coincidental with the decline of earliest settlers' population during this period.

Link

Political orientation and IQ

There are tons of debates whether left- or right-wing people are more intelligent. This paper shows that context matters, and political orientation can be predictive of intelligence.

From the paper:

Second, there was also much evidence to support Hypothesis 3, the notion of a curvilinear relationship with political extremists commanding greater cognitive resources than those in the political center 

Not too surprising for anyone who pays attention to political campaigns. Also:

First, there was substantial support for Hypothesis 1 concerning a negative, linear relationship between conservatism and cognitive ability: conservative gender role attitudes and self-descriptions predicted SAT-V and ACT.

and:

Although conducted at a different level of analysis than Study 1, Study 2 yielded some support for Hypothesis 1: In states with high political involvement, there was a linear and positive relationship between state-IQ and the proportion of Democrats in the state legislature. This finding represents a conceptual replication of important aspects of Study 1. At the same time, Study 2 also replicated an unanticipated finding in Study 1, namely, that some conservative leanings were related to higher cognitive ability. In Study 2, this finding was quite robust, but was confined to states with comparatively low political involvement. Unfortunately, Study 2 did not allow the examination of different kinds of conservative leanings, but relied on the proportion of Democratic lawmakers in a state’s legislatures. Similarly, Study 2 did not permit the examination of different aspects of cognitive ability; thus, it remains open whether observed effects were largely driven by verbal ability, as suggested by Study 1.

Personality and Individual Differences doi: doi:10.1016/j.paid.2008.08.003

Is there a relationship between political orientation and cognitive ability? A test of three hypotheses in two studies

Markus Kemmelmeier

Abstract

Two studies tested one linear and two curvilinear hypotheses concerning the relationship between political conservatism-liberalism and cognitive ability. Study 1, focusing on students at a selective US university (n = 7279), found support for the idea that some dimensions of conservatism are linked to lower verbal ability, whereas other dimensions are linked to higher verbal ability. There was also strong support for political extremists both on the left and right being higher in verbal ability than centrists. Study 2 employed aggregate data pertaining to the 50 US states and demonstrated that conservatism was linked to lower cognitive ability in states with high political involvement, but found conservatism to be correlated with higher average ability in states with low political involvement. The discussion addresses potential implications and criticisms of this research.

Link

How superstitions can be favored by evolution

Superstitious behaviour assigns importance to events that aren't likely to influence the future, e.g., "I saw a black cat, so I'll have a lousy day."

Superstitions are something that doesn't have an obvious adaptive value: if you make such irrational associations between events, you are not more likely to anticipate some future event.

Hamilton's rule, the foundation of kin selection theory, links together the "cost" that an organism is willing to pay with the "benefit" that he will heap.

Pascal's wager, on the other hand, aims to show that a very large payoff ("eternal life") is worth the price ("belief in god") even if one assigns a small probability to the event "god exists".

What this paper shows is that a strategy of making associations between events, even though some of them are superstitious and irrational (i.e. there is no causal relationship) may be selected by evolution.

A good way to see why is to think of three human types:

• The "super-rationalist" overanalyzes everything, and wants to be convinced of a causal relationship before taking a decision. 
• The "madman" sees connection between all sorts of events, most of which are unconnected.
• The "average Joe" has a lower rationality threshold than the super-rationalist, thus often making decisions based on superstitious associations.

The "super-rationalist" will be right more often than the other two types, but his meticulousness may be a waste of energy and opportunity; the "madman" will be chasing shadows, going this way or that on a whim. The "average Joe" may fare better overall, since his willingness to bet on flimsier evidence will sometimes lead him to a large payoff.

Proceedings of the Royal Society B DOI 10.1098/rspb.2008.0981

The evolution of superstitious and superstition-like behaviour


Kevin R. Foster, Hanna Kokko

Abstract

Superstitious behaviours, which arise through the incorrect assignment of cause and effect, receive considerable attention in psychology and popular culture. Perhaps owing to their seeming irrationality, however, they receive little attention in evolutionary biology. Here we develop a simple model to define the condition under which natural selection will favour assigning causality between two events. This leads to an intuitive inequality—akin to an amalgam of Hamilton's rule and Pascal's wager—-that shows that natural selection can favour strategies that lead to frequent errors in assessment as long as the occasional correct response carries a large fitness benefit. It follows that incorrect responses are the most common when the probability that two events are really associated is low to moderate: very strong associations are rarely incorrect, while natural selection will rarely favour making very weak associations. Extending the model to include multiple events identifies conditions under which natural selection can favour associating events that are never causally related. Specifically, limitations on assigning causal probabilities to pairs of events can favour strategies that lump non-causal associations with causal ones. We conclude that behaviours which are, or appear, superstitious are an inevitable feature of adaptive behaviour in all organisms, including ourselves.

Link

Mediterranean diet reduces risk of dying, heart disease, cancer, Parkinson's, and Alzheimer's

The article is freely available.

BMJ 2008;337:a1344

Adherence to Mediterranean diet and health status: meta-analysis

Francesco Sofi et al.

Abstract

Objective To systematically review all the prospective cohort studies that have analysed the relation between adherence to a Mediterranean diet, mortality, and incidence of chronic diseases in a primary prevention setting.
Design Meta-analysis of prospective cohort studies.

Data sources English and non-English publications in PubMed, Embase, Web of Science, and the Cochrane Central Register of Controlled Trials from 1966 to 30 June 2008.

Studies reviewed Studies that analysed prospectively the association between adherence to a Mediterranean diet, mortality, and incidence of diseases; 12 studies, with a total of 1 574 299 subjects followed for a time ranging from three to 18 years were included.

Results The cumulative analysis among eight cohorts (514 816 subjects and 33 576 deaths) evaluating overall mortality in relation to adherence to a Mediterranean diet showed that a two point increase in the adherence score was significantly associated with a reduced risk of mortality (pooled relative risk 0.91, 95% confidence interval 0.89 to 0.94). Likewise, the analyses showed a beneficial role for greater adherence to a Mediterranean diet on cardiovascular mortality (pooled relative risk 0.91, 0.87 to 0.95), incidence of or mortality from cancer (0.94, 0.92 to 0.96), and incidence of Parkinson’s disease and Alzheimer’s disease (0.87, 0.80 to 0.96).

Conclusions Greater adherence to a Mediterranean diet is associated with a significant improvement in health status, as seen by a significant reduction in overall mortality (9%), mortality from cardiovascular diseases (9%), incidence of or mortality from cancer (6%), and incidence of Parkinson’s disease and Alzheimer’s disease (13%). These results seem to be clinically relevant for public health, in particular for encouraging a Mediterranean-like dietary pattern for primary prevention of major chronic diseases.

Link

Men find women more attractive in the winter

... but the effect seems to be limited to their bodies, not their faces. The researchers' explanation is that during the summer, men are exposed to more women's bodies, and hence have "higher standards."

It'd be interesting to do a study comparing the relative attractiveness of women who met their spouses in the summer vs. winter.

Perception. 2008;37(7):1079-85.

Men's attraction to women's bodies changes seasonally.

Pawlowski B, Sorokowski P.

Humans exhibit seasonal variation in hormone levels, behaviour, and perception. Here we show that men's assessments of women's attractiveness change also seasonally. In five seasons (from winter 2004 to winter 2005) 114 heterosexual men were asked to assess the attractiveness of the same stimuli: photos of a female with three different waist-to-hip ratios; photos of female breasts, and photos of average-looking faces of young women. For each season, the scores given to the stimuli of the same category (body shape, breast, and face) were combined. Friedman's test revealed significant changes for body shape and breast attractiveness assessments across the seasons, but no changes for face ratings. The highest scores for attractiveness were given in winter and the lowest in summer. We suggest that the observed seasonality is related to the well-known 'contrast effect'. More frequent exposure to women's bodies in warmer seasons might increase men's attractiveness criteria for women's body shape and breasts.

Link

Major Histocompatibility Complex and Mate Selection in Africans and Europeans

This is a very important study posted in the freely available PLoS Genetics. The Major Histocompatibility Complex (MHC) has been implicated in attractiveness, and has even been made the focus of dna-based dating.

Unlike many other human traits, say nose length, where people tend to mate with others like themselves, the opposite has been suggested for the MHC. The reasoning goes, that MHC is related to disease-resistance, and couples dissimilar in it will produce heterozygous children that will be more capable of fighting disease.

To test this hypothesis, scientists looked at how dissimilar spouses actually are in the MHC, comparing it with their genome-wide dissimilarity: the question is, do they differ in the MHC more or less than they do across the entire genome.

The answer was surprising. African spouses tended to be similar to each other -compared to random African individuals- indicating that there was a tendency for people to marry those genetically close to them. However, no significant pattern emerged for the MHC, i.e., they didn't tend to marry those who were either similar or dissimilar to them.

Europeans spouses, on the other hand, were more dissimilar to each other in the MHC than random individuals, and more dissimilar in the MHC than in the rest of the genome. So, this is strong evidence for assortative mating of MHC-dissimilar Europeans, but not MHC-dissimilar Africans.

Here is the authors' explanation:

On the other hand, Yoruba couples exhibited a significant genome-wide signature of assortative mating, which is likely to result from socio-demographic processes specific to this population. The Yoruba are still organized in paternal lineages, which are exogamous units [32] and C. Adebamowo, personal communication. Although we do not have specific ethnological data collected with the Yoruba samples to explain our observations, a process in which matrimonial exchanges between genealogically related lineages are more frequent than matrimonial exchanges between genealogically unrelated lineages could have left such a genome-wide signature. On the contrary, for the MHC region, no significant pattern of similarity/dissimilarity was observed, at either the molecular level or the serological level. Several hypotheses can be proposed to explain this observation: firstly, it is possible either that the MHC is not involved in mate choice in this population, or that social factors are relatively more important than the MHC and that the sample size here does not allow detection of MHC effect on mate choice.

In other words, the genetic similarity between Yoruban spouses may be the result of population structure, in which individuals mate within social units, rather than with individuals from the entire population.

On the other hand, the unimportance of the MHC for Yoruban mating can be attributed to either its unimportance for Yorubans, or to the fact that "social factors" rather than "good chemistry" play a bigger role in mate choice. A test on other African populations with different social patterns would, perhaps, resolve this puzzle.

PLoS Genetics doi: 0.1371/journal.pgen.1000184

Is Mate Choice in Humans MHC-Dependent?

Raphaëlle Chaix et al.

Abstract

In several species, including rodents and fish, it has been shown that the Major Histocompatibility Complex (MHC) influences mating preferences and, in some cases, that this may be mediated by preferences based on body odour. In humans, the picture has been less clear. Several studies have reported a tendency for humans to prefer MHC-dissimilar mates, a sexual selection that would favour the production of MHC-heterozygous offspring, who would be more resistant to pathogens, but these results are unsupported by other studies. Here, we report analyses of genome-wide genotype data (from the HapMap II dataset) and HLA types in African and European American couples to test whether humans tend to choose MHC-dissimilar mates. In order to distinguish MHC-specific effects from genome-wide effects, the pattern of similarity in the MHC region is compared to the pattern in the rest of the genome. African spouses show no significant pattern of similarity/dissimilarity across the MHC region (relatedness coefficient, R = 0.015, p = 0.23), whereas across the genome, they are more similar than random pairs of individuals (genome-wide R = 0.00185, p<10−3). We discuss several explanations for these observations, including demographic effects. On the other hand, the sampled European American couples are significantly more MHC-dissimilar than random pairs of individuals (R = −0.043, p = 0.015), and this pattern of dissimilarity is extreme when compared to the rest of the genome, both globally (genome-wide R = −0.00016, p = 0.739) and when broken into windows having the same length and recombination rate as the MHC (only nine genomic regions exhibit a higher level of genetic dissimilarity between spouses than does the MHC). This study thus supports the hypothesis that the MHC influences mate choice in some human populations.

Link

The effective mutation rate with multiple Y-STRs

The relationship between Y-STR variance Var and time in generations g is:

Var = wg

This equation has two unknowns: g, the time to the Most Recent Common Ancestor, and w, the unknown effective mutation rate. Thus, to estimate g we must first estimate w.

What I have argued in my posts of the Y-STR Series is that w is "close" to μ, the germline mutation rate. However, "close" means "on average close". For any particular genealogy and random sequence of mutations within that genealogy, it may be  fairly different from its expected value. Thus, a particular group may accumulate variance at a much lower rate or even faster than μ.

I have carried out some simulations with nm-marker haplotypes, to see how w, or more precisely w/μ (the effective rate expressed in units of the germline rate) behaves. As always, results are averaged over 10,000 runs. The number of generations was kept at g=150 and the individual marker mutation rate at μ=0.0025/locus/generation.

m	nm	E[w/μ]	s.d.	Group size
1.000	1	0.31	0.47	82
1.000	6	0.31	0.26	82
1.000	11	0.31	0.23	81
1.000	16	0.31	0.22	83
1.025	1	0.58	0.52	900
1.025	6	0.58	0.28	892
1.025	11	0.59	0.24	902
1.025	16	0.58	0.22	885
1.075	1	0.84	0.33	434347
1.075	6	0.84	0.16	438545
1.075	11	0.84	0.13	439894
1.075	16	0.84	0.12	432672

The table has five columns:

• m: the growth constant; each man has m sons on average according to a Poisson process
• nm: the number of Y-STR loci
• E[w/μ]: the mean effective mutation rate
• s.d.: the standard deviation of the effective mutation rate
• Group size: the average number of present-day descendants
  

It's obvious, as in the previous experiments, that a fairly fast growth constant (m=1.075) is necessary to create a haplogroup with a large number of present-day descendants (~435k), and for such a group, the effective mutation rate is 0.84μ.

As nm, the number of markers, increases, the s.d. of the effective rate decreases. But, note: the difference between nm=11 and nm=16 is miniscule. A large number of markers is welcome when available, but no substantial gain is to be expected in terms of accuracy, beyond 10-20 markers.

These results illustrate vividly that large haplogroups behave more "regularly" than small ones. For m=1 and with 16 markers it is w=0.31 (s.d.=0.22), whereas for m=1.075 it is w=0.84 (s.d.=0.12). So, while for the small group, the standard deviation is 71% of the expected value, for the large group it is only 14%.

Thus, for large groups likely to be made the object of a population study, not only is the effective mutation rate close to the germline rate, but its variability is also greatly reduced.

Interclade Age Estimation

I have also carried out simulations using the interclade method, considering a pair of haplotypes whose common ancestor is g=150 generations in the past.

nm		Estimated Age		s.d.
		(times g)
1		1.01		1.91
6		1.01		0.76
11		1.00		0.55
16		0.99		0.45

This method produces an unbiased estimate but it is obvious that it is a very noisy one, much more than in the previous case. Even for nm=67 markers (not shown in table), the standard deviation remains at 0.22.

The above experiment considered only a pair of haplotypes. This is a worst-case scenario. In a best-case scenario, two groups (A and B) of Y-chromosomes coalesce to ancestors who lived immediately after the common ancestor of both groups, and each group expanded at a very fast rate. In such a case, each pair of haplotypes (one from group A and one from group B) is approximately independent of any other pair.

Unfortunately, it's impossible to determine whether or not such a scenario is valid, since it would entail determining the age of the two groups, i.e. the very thing we are trying to estimate, as well as the population demography of each group.

I did carry an experiment with 10 completely independent pairs (rather than 1) coalescing to the common ancestor. The results are listed below:

nm		Estimated Age		s.d.
		(times g)
1		1.01		0.57
6		0.98		0.22
11		1.00		0.17
16		1.01		0.15

Unlike the simple variance-based method, the interclade method can be used only when two groups can be shown to coalesce to a common ancestor (e.g. haplogroups D and E to a common YAP-bearing ancestor).

Its accuracy depends on (i) a large number of markers used, (ii) the two groups founded soon after their common ancestor, and then expanding rapidly, to approximate a star phylogeny. Without these assumptions (which can't be verified easily), its performance is actually not superior to that of a simple variance method.

Genes for Height and Body Mass Index; and, the limits of association studies

Quite often I find that the most interesting stuff in a paper isn't in its main content:

Simplistically speaking linkage studies are geared for relatively rare alleles with large effects within families (that may be of little effect in the population), whereas association studies are designed to detect common genetic effects that have smaller effects. In the case of rare monogenic disease, multiple rare variants at linked loci (allelic heterogeneity) seem to be the rule not the exception.42 For common polygenic disease and quantitative traits this question is still unanswered – there are examples for both common43 and rare alleles,44 and theoretical and empirical studies suggest a role for both rare and common variants.45

...

The modest LOD scores we observed for BMI despite the large study sample likely
reflects the heterogeneity of our study populations, and may suggest that there are relatively few common loci with strong effects for BMI across these populations.

This is a very important (and under-appreciated) issue. People have a genetic predisposition to be fat or thin; we are certain of as much. But what kinds of genes are responsible for this?

Under the "Common loci" explanation, in a population there is a limited number of genes which affect one's weight: if you get the "fat" genes you are likely to be fat, if you get the "thin" ones, you are likely to be thin.

An association study boils down to looking at people's genes and trying to correlate them with the trait of interest, e.g. their body mass index.

But, to discover such an association, people must be "fat" or "thin" because of the same genes. These genes must thus be "common" in the population.

If on the other hand, people are thin or fat because of family-specific genes, i.e. uncommon genes that are limited to families and are "uncommon" in the population, an association study can't detect them: it will notice that there are "fat" and "thin" people, but won't be able to find a common genetic pattern distinguishing the two.

A family-based linkage study, on the other hand, looks at the genes inherited by children from a parent. If, e.g. a fat father and thin mother have a fat daughter and a thin son, it pays off to see which genes were inherited by the daughter from the father: chances are, some of them may be the rare family-specific genes responsibly for her weight.

What this study has found is that rare rather than common loci are responsible for body mass index. In other words, people have a predisposition to be fat or thin mainly not because of genes that abound in the population, but because of rare genes common in a family.

If you have been paying attention in the last few years, you'd have noticed that genetic effects of discovered loci in association studies for quantitative traits have been rather underwhelming, explaining a very small (rarely more than 10%, usually less) percentage of the variation.

There are two reasons for this: first, many genes are responsible for each trait, but, more importantly, that a lot (in my opinion most) of the variation for quantitative traits is due to rare variants that can't be discovered by association studies.

The implications of this realization are manifold, but here are two:

• Companies such as 23andme and decodeme who offer personal genome scans aren't likely to offer any really interesting information to consumers any time soon. On the one hand, for legal reasons, they are unlikely to dabble into Mendelian traits that have big and dramatic effects on consumers' health. On the other, they can't figure out which particular family-inherited genes have a major impact on their customers' health (unless multiple family members get tested at several $100 each). Thus, they have to make do with the common alleles discovered in association studies that have minor effects. No wonder prices are dropping.
• Real progress will only come about with more developmental and functional studies, i.e. studies that actually look at what genes do in the body. Note, that in an association study, you don't really need to know what effect a particular allele has: if you discover a statistically significant correlation between its presence and a phenotype, you're done. But, to make progress, we have to understand how phenotypes are produced. Then, instead of estimating that a person will be obese because he carries particular gene found to have an association with obesity in population samples, we will be able to tell what effects the genes will actually have in his body. Naturally, this is easier said than done.

European Journal of Human Genetics doi: 10.1038/ejhg.2008.152

Genome-wide linkage screen for stature and body mass index in 3.032 families: evidence for sex- and population-specific genetic effects

Sampo Sammalisto et al.

Abstract

Stature (adult body height) and body mass index (BMI) have a strong genetic component explaining observed variation in human populations; however, identifying those genetic components has been extremely challenging. It seems obvious that sample size is a critical determinant for successful identification of quantitative trait loci (QTL) that underlie the genetic architecture of these polygenic traits. The inherent shared environment and known genetic relationships in family studies provide clear advantages for gene mapping over studies utilizing unrelated individuals. To these ends, we combined the genotype and phenotype data from four previously performed family-based genome-wide screens resulting in a sample of 9.371 individuals from 3.032 African-American and European-American families and performed variance-components linkage analyses for stature and BMI. To our knowledge, this study
represents the single largest family-based genome-wide linkage scan published for stature and BMI to date. This large study sample allowed us to pursue population- and sex-specific analyses as well. For stature, we found evidence for linkage in previously reported loci on 11q23, 12q12, 15q25 and 18q23, as well as 15q26 and 19q13, which have not been linked to stature previously. For BMI, we found evidence for two loci: one on 7q35 and another on 11q22, both of which have been previously linked to BMI in multiple populations. Our results show both the benefit of (1) combining data to maximize the sample size and (2) minimizing heterogeneity by analyzing subgroups where within-group variation can be reduced and suggest that the latter may be a more successful approach in genetic mapping.

Link

Non-local Neolithic cattle remains near Stonehenge

The non-local origin of the cattle emphasizes the importance of the site, as it could draw prosperous cattle-owning visitors from afar. Together with the recent story on the Stonehenge fence, and its status as an elite burial ground, it appears that this was an important nexus of religious activity.

Stone-age pilgrims 'held barbecues at Stonehenge'

Analysis of animal remains found near to Stonehenge has shown that cattle were brought to the area from as far away as Wales or even the Scottish Highlands.

Scientists tested the chemical fingerprint of cattle teeth found at Durrington Walls, a Neolithic monument built 500 years before Stonehenge.

They found that far from being local, the animals could only have been reared in areas of Wales or Scotland, which have high levels of the chemical element strontium in the soil.

...

Dr Jane Evans, from the British Geological Survey who carried out the research, said: "It looks like people were driving cattle to the area from a significant distance away.

"The area must have been an important place for rituals and gatherings long before the first stones were laid at Stonehenge itself.

"People are coming from considerable distances and dispersion in order to have feasts and were bringing their own food supplies for what must have been a kind of bring your own beef barbecue."

Neanderthals grew fast, matured later (?)

I haven't read this paper, but it's difficult to see how any statistically meaningful inference about the Neanderthal population can be derived from one neonate and two infants. Not only is the sample small, but after all it represents Neanderthals who died at an early age. Perhaps their mothers weren't large or nurturing enough to care for them...

See related story at National Geographic.

PNAS doi: 10.1073/pnas.0803917105

Neanderthal brain size at birth provides insights into the evolution of human life history

Marcia S. Ponce de León et al.

Abstract

From birth to adulthood, the human brain expands by a factor of 3.3, compared with 2.5 in chimpanzees [DeSilva J and Lesnik J (2006) Chimpanzee neonatal brain size: Implications for brain growth in Homo erectus. J Hum Evol 51: 207–212]. How the required extra amount of human brain growth is achieved and what its implications are for human life history and cognitive development are still a matter of debate. Likewise, because comparative fossil evidence is scarce, when and how the modern human pattern of brain growth arose during evolution is largely unknown. Virtual reconstructions of a Neanderthal neonate from Mezmaiskaya Cave (Russia) and of two Neanderthal infant skeletons from Dederiyeh Cave (Syria) now provide new comparative insights: Neanderthal brain size at birth was similar to that in recent Homo sapiens and most likely subject to similar obstetric constraints. Neanderthal brain growth rates during early infancy were higher, however. This pattern of growth resulted in larger adult brain sizes but not in earlier completion of brain growth. Because large brains growing at high rates require large, late-maturing, mothers [Leigh SR and Blomquist GE (2007) in Campbell CJ et al. Primates in perspective; pp 396–407], it is likely that Neanderthal life history was similarly slow, or even slower-paced, than in recent H. sapiens.

Link

Neolithic feasting in Pre-Pottery Neolithic, and the significance of cattle

Journal of Anthropological Archaeology doi:10.1016/j.jaa.2008.06.002

Transformations in an early agricultural society: Feasting in the southern Levantine Pre-Pottery Neolithic

Katheryn C. Twiss

Abstract

Feasting is a powerful and transformative phenomenon. Societies are both integrated and differentiated through feasting; identities are both enacted and altered; and ideologies are inculcated. This paper uses ethnographic data to establish criteria for the archaeological recognition of prehistoric feasting. These criteria are then used to assess the changing evidence for feasting across the southern Levantine Pre-Pottery Neolithic (ca. 10,200–7500 BP/9700–6250 cal BC), with the aim of shedding light on changes in social organization across the transition to agriculture.

During most of the Pre-Pottery Neolithic, the extent and scale of feasting expanded as sociopolitical complexity increased. Towards the end of the period, however, populations dispersed and feasting probably declined. Feasts were simultaneously integrative and competitive, ameliorating scalar stress even as they offered opportunities for individual or household competition. Feasts may also have played a key role in conferring ideological prominence on Neolithic cattle, and perhaps even contributed to their adoption as domesticates.

Link

Crop domestication didn't happen overnight or in one place

From the paper:

Recently, archaeobotanical evidence has overturned the rapid transition model that crop domestication was initiated and completed in a brief period at the Pleistocene/Holocene boundary (see Fig. 1). All three stages of the domestication process have been extended in timescale. Large plant assemblages have provided evidence for wild-cereal gathering as old as 23,000 years B.P. at Ohalo II (29), some 10,000 years earlier than previously thought. Evidence of predomestication cultivation has been established from 13,000–12,500 years B.P. (30, 31), during the Younger Dryas. Within the predomestication period, there appear to have been numerous beginnings of agriculture, with different species hailing from different localities rather than in a single Neolithic Package (32). The final stage of the domestication process in which the domestication syndrome traits are fixed has also been found to be a slow process; Tanno and Willcox (33, 34) argue that the tough-rachis mutant took over 3,000 years of cultivation to reach fixation and the syndrome traits themselves appeared in slow sequence, not together over a short period.

The apparent protracted process of domestication from plants of multiple origins is apparently at odds with the genetic data suggesting that domestication plants are monophyletic, the result of a single domestication event in a definite place. But:

The outcome of the final scenario of a single origin was most surprising because these simulations were slower than multipleorigin ones to reach monophyly. Consequently, we reach the superficially counterintuitive conclusion that, when viewed through multilocus systems, multiple-origin crops are actually more likely to result in monophyly than single-origin ones. In fact, it is quite reasonable to suppose that this conclusion might be the case. The underlying reason is that cultivated crops that originate from a single wild population are more similar to their wild progenitor population than an amalgamated cultivated population that will have additional genetic contributions from other wild sources: Crops of multiple origins are, from the outset, more differentiated from their wild sources than crops of a single origin.

From a press release:

Dr Robin Allaby says:

"This picture of protracted development of crops has major implications for the understanding of the biology of the domestication process and these strike chords with other areas of evolutionary biology."

"This lengthy development should favour the close linkage of domestication syndrome trait genes which may become much more important because linked genes will not be broken up by gene flow – and this makes trait selection and retention easier. Interestingly, as more crop genomes become mapped, the close linkage of two or more domestication syndrome genes has been reported on several occasions."

"This process has similarities to the evolution of 'supergenes' in which many genes cluster around a single locus to contribute to one overall purpose."

"We now need to move this research area to a new level. Domestication was a complex process and can now be viewed more legitimately as the paragon of evolutionary process that Darwin originally recognized. There are many interacting factors involved that we know about operating on a wide range of levels from the gene to the farmer and climate – the challenge is to integrate them into a single story."

PNAS - September 16, 2008 - vol. 105 - no. 37

The genetic expectations of a protracted model for the origins of domesticated crops

Robin G. Allaby et al.

Abstract

Until recently, domestication has been interpreted as a rapid process with little predomestication cultivation and a relatively rapid rise of the domestication syndrome. This interpretation has had a profound effect on the biological framework within which investigations into crop origins have been carried out. A major underlying assumption has been that artificial selection pressures were substantially stronger than natural selection pressures, resulting in genetic patterns of diversity that reflect genetic independence of geographic localities. Recent archaeobotanical evidence has overturned the notion of a rapid transition, resulting in a protracted model that undermines these assumptions. Conclusions of genome-wide multilocus studies remain problematic in their support of a rapid-transition model by indicating that domesticated crops appear to be associated by monophyly with only a single geographic locality. Simulations presented here resolve this conflict, indicating that the results observed in such studies are inevitable over time at a rate that is largely influenced by the long-term population size. Counterintuitively, multiple origin crops are shown to be more likely to produce monophyletic clades than crops of a single origin. Under the protracted transition, the importance of the rise of the domestication syndrome becomes paramount in producing the patterns of genetic diversity from which crop origins may be deduced. We identify four different interacting levels of organization that now need to be considered to track crop origins from modern genetic diversity, making crop origins a problem that could be addressed through system-based approaches.

Link

Female bosses cause distress to female (but not male) employees

This paper shows that women with a female supervisor or female/male supervisors suffer distress and ill health. Men, on the other hand fare best when they have a female/male supervisor team. Feel free to post your own horror stories from the workplace.

Journal of Health and Social Behavior, Volume 49, Number 3, September 2008 , pp. 286-300(15)

Relational Demography in the Workplace and Health: An Analysis of Gender and the Subordinate-Superordinate Role-Set

Schieman, Scott; McMullen, Taralyn

Abstract

Using data from a 2005 national survey of working adults in the United States, we examine the effects of the gender composition of the superordinate-subordinate role-set on mental and physical health measures. Subordinates' and superordinates' genders are important determinants. Men who work in gender-mixed superordinate contexts (i.e., with one male and one female superior) report lower levels of distress and physical symptoms than men who work with one male superior. Women who work with one male superior report less distress and fewer physical symptoms compared to women who work with one female superior or in gender-mixed superordinate contexts. With a few exceptions, these observations generally hold net of occupation, job sector, and an array of work-related conditions. We discuss the implications of these findings in light of predictions derived from the similarity-attraction and role congruity theories. We also outline ways that theoretical development in relational demography can be refined by a more specific focus on the demographic characteristics—especially gender—of the superordinate-subordinate role-set.

Link

Price reduction of 23andme service

The Spittoon blogs about a great reduction in the price of the 23andme service.

With the introduction of v2, our next-generation analytical platform, 23andMe customers will have access to an even more powerful set of SNPs we use to probe their unique genetic composition. And thanks to advances by Illumina, the provider of our genetic analysis technology, that information will now be available at the reduced price of $399.

I am skeptical that Illumina has made any great "advances" in the less than one year since the launch of the 23andme service. From the press release:

The price reduction is largely made possible following technological advancements by Illumina — a leading provider of genetic analysis technologies — to its DNA Analysis Beadchips, which 23andMe uses to genotype customers. The new Beadchip, called the HumanHap550-Quad+, makes use of a four-sample format. 23andMe also has added improved custom content to the new Beadchip, which will include a broader range of Single Nucleotide Polymorphism (SNP) variations and rare mutations not found on the previous Beadchip, thereby providing more relevant data on published associations, as well as maternal and paternal ancestry.

I think that this is part of a strategy (by either Illumina to sell more chips, or 23andme to sell more tests, or both). The previous $1,000 price tag made the test pretty much a luxury item, as it reveals generally mild associations, which are important at the population level, but not so much for the individual. The new pricing probably aims to tempt more "regular people" to the personal genomics market.

23andme has put a lot of emphasis on 23andwe, which aims to discover new associations in the company's customers by correlating the results of "customer-surveys" with the genomic data. 23andwe is probably very important in the long-term as a source of revenue, since the discovered associations may have commercial utility. But, to discover them, the company needs to expand its customer base, so that statistically significant associations will emerge.

Market economics dictates that more customers will now opt for the test, and I hope some of them will try my EURO-DNA-CALC.

Masculine vs. Feminine Walk

Walk this way? Masculine motion seems to come at you, while females walk away

You can tell a lot about people from the way they move alone: their gender, age, and even their mood, earlier studies have shown. Now, researchers reporting in the September 9th issue of Current Biology, a Cell Press publication, have found that observers perceive masculine motion as coming toward them, while a characteristically feminine walk looks like it's headed the other way.

Such studies are done by illuminating only the joints of model walkers and asking observers to identify various characteristics about the largely ambiguous figures.

"It's a really interesting thing," said Rick van der Zwan of Southern Cross University in Australia. "If you look at someone with just their joints illuminated when they aren't moving, it's difficult to tell what it is you are looking at. But as soon as they move, instantaneously, you can tell that it's a person and perceive their nature. You can tell if it's a boy or a girl, young or old, angry or happy.… You can discern all these qualities about their state, affect, and actions with no cues at all about what they look like—with no form at all, just motion."

Many previous studies of biological motion perception have relied on male figures as models, van der Zwan said. One of those earlier studies had noticed an interesting phenomenon: even though you can't really tell whether a so-called point-light figure is facing toward you or away, people seemed to perceive those figures always as facing in their direction.

Now, van der Zwan and his colleagues show that this isn't always true.

In their study, they allowed people to observe point-light figures representing a continuum from an extremely "girly girl" to a "hulking male." At the halfway point in between was a gender-neutral walker that observers judged as male half the time and female half the time.

Their results showed that walking male figures did indeed appear to face toward you. Female figures, on the other hand, seemed as though they faced away. The results are the first to show a link between the perception of gender from biological motion cues and the perception of orientation.

That same pattern emerged regardless of the gender of the person watching, a finding that van der Zwan considers an important clue about the behavior.

"Our data suggest that biological motion is an important cue for social organisms trying to operate in environments where other cues as to the actions or intentions of other organisms may be ambiguous," the researchers wrote. "Whilst the precise role of local cues in mediating these effects requires further explication, it is tempting to speculate that the orientation biases reported here reflect the development of perceptual mechanisms that weigh in the probable cost of misinterpreting the actions and intentions of others. For example, a male figure that is otherwise ambiguous might best be perceived as approaching to allow the observer to prepare to flee or fight. Similarly, for observers, and especially infants, the departure of females might signal also a need to act, but for different reasons."

I wonder what these different reasons are. A hint from our closest relatives:

Although chimpanzees virtually never adopt face-to-face positions, bonobos do so in one out of three copulations in the wild.

The "infant" explanation probably relates to a tendency to cry when a mother is perceived as leaving.

It will be interesting to see if ethnicity/race/social class can also be perceived by walking style. 

See also Walking speed in different cities.

Current Biology doi:10.1016/j.cub.2008.06.054

Correlated changes in perceptions of the gender and orientation of ambiguous biological motion figures

Anna Brooks et al.

The sensitivity of the mammalian visual system to biological motion cues has been shown to be general and acute [1], [2] and [3]. Human observers, in particular, can deduce higher-order information, such as the orientation of a figure (which way it is facing), its gender, emotional state, and even personality traits, on the basis only of sparse motion cues. Even when the stimulus information is confined to point lights attached to the major joints of an actor (so-called point-light figures), observers can use information about the way the actor is moving to tell what they are doing, whether they are a male or female, and how they are feeling [4], [5] and [6]. Here we report the novel finding that stimulus manipulations that made such walkers appear more female also had the effect of making the walkers appear more often as if they were walking away from rather than towards observers. Using frontal-view (or rear-view) point-light displays of human walkers, we asked observers to judge whether they seemed to be walking towards or away from the viewing position. Independent of their own gender, observers reliably reported those figures they perceived to be male as looking like they were approaching (as reported in [7]), but those they perceived to be female as walking away. Furthermore, figures perceived to be gender-neutral also appeared more often, although not exclusively, to be walking towards observers.

Link

Balancing selection and homosexuality

The idea in this paper is that the genetic factors leading one to be homosexual also lead one to have higher mating success if he turns out to be heterosexual.

The use of "lifetime number of opposite sex sexual partners" as a stand-in for reproductive success is fairly problematic. It seems more likely that a couple that marries young with limited pre-marital experience will have a higher number of children than individuals who spend a lot of time having sex with multiple people (not to mention the risk to one's health from such behavior).

In my own opinion (see Beautiful Wives and Gay Sons) homosexuality is rooted in a side-effect of the expression of femininity-- or masculinity-enhancing traits in individuals of the wrong gender: if, e.g., a couple has an excess of "feminine" DNA between them, it may produce reproductively successful daughters but sons at higher risk for homosexuality. These genes are more successful (than average) in female bodies, and less than average in male ones: thus they are maintained in the gene pool.

There is a good case to be made, however, for a link between homosexuality and promiscuity. A certain lack of inhibition may be linked to the expression of the homosexual phenotype; this may explain why homosexuals tend to have more partners than average compared to heterosexuals. 

Evolution and Human Behavior doi: 10.1016/j.evolhumbehav.2008.07.002

Genetic factors predisposing to homosexuality may increase mating success in heterosexuals

Brendan P. Zietsch et al.

Abstract

There is considerable evidence that human sexual orientation is genetically influenced, so it is not known how homosexuality, which tends to lower reproductive success, is maintained in the population at a relatively high frequency. One hypothesis proposes that while genes predisposing to homosexuality reduce homosexuals' reproductive success, they may confer some advantage in heterosexuals who carry them. However, it is not clear what such an advantage may be. To investigate this, we examine a data set where a large community-based twin sample (N=4904) anonymously completed a detailed questionnaire examining sexual behaviors and attitudes. We show that psychologically masculine females and feminine men are (a) more likely to be nonheterosexual but (b), when heterosexual, have more opposite-sex sexual partners. With statistical modelling of the twin data, we show that both these relationships are partly due to pleiotropic genetic influences common to each trait. We also find a trend for heterosexuals with a nonheterosexual twin to have more opposite-sex partners than do heterosexual twin pairs. Taken together, these results suggest that genes predisposing to homosexuality may confer a mating advantage in heterosexuals, which could help explain the evolution and maintenance of homosexuality in the population.

Link

mtDNA of Mongolians

While I agree that the Mongol Empire played a major role in the admixture of Caucasoids and Mongoloids, we have very clear evidence now that the two races had been mixing in Central Asia long before that time.

J Hum Genet.

Genetic imprint of the Mongol: signal from phylogeographic analysis of mitochondrial DNA

Cheng B, Tang W, He L, Dong Y, Lu J, Lei Y, Yu H, Zhang J, Xiao C.

Abstract

Mitochondrial deoxyribonucleic acid (DNA) from 201 unrelated Mongolian individuals in the three different regions was analyzed. The Mongolians took the dominant East Asian-specific haplogroups, and some European-prevalent haplogroups were detected. The East Asians-specific haplogroups distributed from east to west in decreasing frequencies, and the European-specific haplogroups distributed conversely. These genetic data suggest that the Mongolian empire played an important role in the maternal genetic admixture across Mongolians and even Central Asian populations, whereas the Silk Road might have contributed little in the admixture between the East Asians and the Europeans.

Link

Reconstructing the ancestral allele value in a Y-STR locus

Sengupta et al. (2006) proposed using the median observed allele in a Y-STR locus as an estimate of the ancestral allele in that locus.

The average squared distance using the median allele tends to be lower (on average) than if the real ancestral allele was used. So, while the equation ASD = μg is appropriate if the real ancestral allele is used (where μ is the mutation rate and g the number of generations since the MRCA), if the median allele is used, then ASD=w_ag is appropriate where w_a is the effective mutation rate.

Unfortunately this effective rate depends on population history, becoming close to the germline rate μ if the haplogroup attains a large size early on after the MRCA. As I have argued in many recent posts, for the large observed modern haplogroups, it is very likely that the effective rate should be close to the germline rate; yet, the discrepancy between the two introduces an element of uncertainty in the calculation of TMRCA (=g)

Naturally, it's obvious to ask: how often does the median allele equal the real ancestral allele? In my simulations, I set g to 10, 100, or 300 generations, and the growth constant m to 1 or 1.02. I expected the median allele to equal the ancestral allele more often for a younger group (less time for it to get obfuscated by the passage of time), and also for a more rapidly expanding group (a more star-like pattern of expansion).

g	m	% Correct
10	1	98.1
100	1	83.0
300	1	61.0
10	1.02	98.3
100	1.02	86.5
300	1.02	79.6

This intuition is essentially correct. It is for younger, and more rapidly expanding groups that the ancestral allele is estimated most accurately.

It is also worthwhile to see how using other methods of estimating ancestral alleles (e.g. building a rooted haplotype tree) would perform. I have only personally carried out experiments where the modal (most frequent) allele is used.

Using the modal allele tends to be a right guess slightly more often than the median one, giving a less biased estimate of the age. However, when the modal allele fails, it fails spectacularly: the median allele is conservative, being right in the middle of the observed alleles, whereas the modal allele may be observed for either a very small or very high number of repeats, which may be a long way off from the ancestral value in each particular case. Hence, the modal allele leads to age estimates with a higher variance.

Hence, I am in favor of the use of the median allele as an estimator of the ancestral one.

Appendix: age estimates using median or real ancestral allele

Below are the age estimates (ASD/μ) using either the median or the (unknown) ancestral allele.

		Age	Age
g	m	(median allele)	(ancestral allele)
10	1	5.4	10.3
100	1	42	99.7
300	1	114.9	302
10	1.02	5.6	10.3
100	1.02	56.8	100
300	1.02	233.1	297.5

How bottlenecks affect Y-STR variance (not much)

Continuing my investigation of how Y-STR variance changes over time (most recent entry), I wanted to see how a bottleneck affects Y-STR variance. An ice age, a plague, a major war or military defeat are all possible causes of a massive reduction in population size, with an associated loss of STR variance.

To study this, I modified my code, so that rather than having a unique growth constant m, there may be multiple segments during which growth is governed by a different constant. In particular, I simulated a period of g=99 generations with m=1 or m=1.05, but in the last (100th) generation, I set m to 0.5, 0.1, 0.01, representing a bottleneck equivalent to the loss of half, nine tenths, or ninety nine hundreds of the haplogroup population; I will call these "mild", "severe", or "extreme" bottleneck.

In the following table I list the observed reduction in Y-STR variance compared to the case where there is no bottleneck. As usual, the results are averaged over 10,000 runs.

		Change in Variance (%)
m	Mild	Severe	Extreme
1	-1.9	-2.03	-15.86
1.05	1.6	0.55	-4.98

As expected, variance decreases more in an extreme bottleneck, but not as sharply as one might expect. Indeed, if the long-term trend is positive (m=1.05), the expected variance of surviving groups may even increase after a bottleneck. What gives?

During a bottleneck, two things happen:

• Y-STR variance within individual lineages decreases, as e.g. rare alleles are lost, however:
  
• Low-frequency lineages (which usually have lower Y-STR variance) are more likely to be lost, i.e. to become extinct during the bottleneck.
  

Thus, while all lineages suffer a loss of Y-STR variance during a bottleneck, the loss of low-frequency lineages means that, lineages that survive after a bottleneck may on average, even have higher Y-STR variance than the ones before it.

Predictably, larger groups (created at m=1.05) experience less severe effects during a bottleneck. Note, also that in this simulation, haplogroups did not even grow to very large sizes (only ~1,600 men for m=1.05 and no bottleneck); thus, real-world haplogroups will probably be even less susceptible to bottlenecks.

Conclusion

Bottlenecks don't seem to reduce Y-STR variance dramatically, especially for large haplogroups. So, while they are a potential mechanism for reducing the effective mutation rate, by periodically removing variance, their efficacy is limited.

Indeed, bottlenecks not only reduce Y-STR diversity but also haplogroup abundance. Thus, in order to achieve the same present-day haplogroup abundance, growth in the post-bottleneck eras must proceed even faster than if no bottleneck had occurred, with a therefore higher effective rate during those rebound periods.

In conclusion, while dramatic bottlenecks at a time when human population sizes were small, e.g., the Ice Ages during the Paleolithic, may have effectively reduced Y-STR variance of surviving lineages, this effect seems to have been unimportant in large human populations emerging from the Neolithic onwards.

Ethnic nationalism reappraised

Jerry Z. Muller has an interesting article in Foreign Affairs, titled Us and Them: The Enduring Power of Ethnic Nationalism, in which he argues that the reason why Europe has enjoyed such a long period of peace after World War II was the fact that post-war states were largely ethnically homogeneous. Thus, he argues, peace was not so much the result of European nations' "overcoming" their nationalism, but rather its fulfillment, i.e. the creation of nation states dominated by a single ethnic group.

It's a fairly interesting piece, touching among other things on the resurgence of nationalism after the Cold War in the few places in Europe (e.g. the former Yugoslavia and Soviet Union) where national and ethnic borders did not coincide, the distinction between ethnic and civic nationalism, and the challenges that ethnic nationalism faces in an age of immigration.

The fence around Stonehenge

Revealed: The 5,000-year-old, 20ft-high fence which hid Stonehenge from its nosy Stone Age neighbours

Tourists who complain about the fence put up around Stonehenge in the Seventies should spare a thought for their Neolithic ancestors... they couldn’t even see the site because of a huge wooden barrier.

Archaeologists have found traces of the 20ft-high timber fence that snaked almost two miles across Salisbury Plain and hid sacred ceremonies from unworthy locals more than 5,000 years ago.

...

‘The most plausible explanation is that it was built at huge cost to the community to screen the environs of Stonehenge from view. Basically, we think it was to keep the lower classes from seeing what exactly their rulers and the priestly class were doing.

This seems to be consistent with the idea that Stonehenge was used as an elite burial ground, and unlike the recent Stonehenge Decoded documentary, where the monument was presented more or less as a voluntary community building project/ritual space.

Dhaskalio Kavos cult site in the Aegean Bronze Age

See previous post on Excavation on Keros aims to solve riddle of Cycladic figurines. In the picture Colin Renfrew with some of the broken statuettes (from this Vima story of a couple years ago)

Symbolic past of early Aegeans revealed at Dhaskalio Kavos site

A rocky islet and a nearby hillside have yielded evidence of one of Greece’s oldest and most enigmatic ritual sites. Imported stones and fragmented marble statuettes show that Dhaskalio and Kavos were “a symbolic central place for the Early Bronze Age” in the Aegean, according to Professor Colin Renfrew.

Kavos is a stony, scrub-covered slope on the Cycladic island of Keros. Forty-five years ago Professor Renfrew, then a PhD student at Cambridge, found extensive looting there, with fragments of marble bowls and the famous Cycladic folded-arm figurines scattered across the surface.

...

The Kavos fragments “must have been deposited in the course of ceremonies which were clearly of pan-Cycladic significance. Dhaskalio Kavos can now be regarded as a symbolic central place, the first such regional centre to have been discovered from the Aegean Early Bronze Age,” Professor Renfrew reports. On the Dhaskalio islet, “it is striking that no marble figurines of the standard folded-arm form were found, despite their frequency in the special deposit.”

Phallic figurines from Israel

Phallic Figurines Found in Israel Stone Age Burials

Prehistoric graves with an unusual abundance of phallic figurines and oddly arranged human remains have been found in Israel, archaeologists announced recently.

Near Nazerat (Nazareth), the Stone Age site, called Kfar HaHoresh, dates to between 8,500 and 6,750 B.C.

...

Archaeologists have primarily found female symbolic figurines in other burials of this time period.

"At Kfar HaHoresh, all the gender-oriented symbolism seems to be male," Goring-Morris said. "Researchers in the past have put more emphasis on the 'mother goddess' of agriculture."

Some weird bits of interpretation:

Also the shift in men's role from hunters to more settled herders and farmers may have reduced their status and self-image, Goring-Morris said. This may have led the prehistoric people to bury young male adults at Kfar HaHoresh with animals as a way of honoring their past lives as hunters.

It's not as if the transition to farming/herder happened overnight, so that there would be such "longing" for the men's past lives as hunters. In any case, hunting was never really replaced by farming, but lost its importance in the economic activity of early Neolithic society.

And:

"If you have the skull of your grandfather or grandmother on the mantelpiece at home, this could be your legal document that you were the owner of the house or had certain legal rights, passed from one generation to the next."

Skull as legal document is just plain weird.

Oldest skeleton in Americas in underwater cave of Mexico

Oldest Skeleton in Americas Found in Underwater Cave?

Deep inside an underwater cave in Mexico, archaeologists may have discovered the oldest human skeleton ever found in the Americas.

Dubbed Eva de Naharon, or Eve of Naharon, the female skeleton has been dated at 13,600 years old. If that age is accurate, the skeleton—along with three others found in underwater caves along the Caribbean coast of the Yucatán Peninsula—could provide new clues to how the Americas were first populated.

...

Clues from the skeletons' skulls hint that the people may not be of northern Asian descent, which would contradict the dominant theory of New World settlement. That theory holds that ancient humans first came to North America from northern Asia via a now submerged land bridge across the Bering Sea (see an interactive map of ancient human migration).

"The shape of the skulls has led us to believe that Eva and the others have more of an affinity with people from South Asia than North Asia," González explained.

Early Native Americans seem to have had higher diversity in appearance than later ones, but this does not really indicate waves of migration from different sources. See Craniofacial shape variation and Native American origins

This model takes into account a founder population occupying Beringia during the last glaciation characterized by high craniofacial diversity, founder mtDNA and Y-chromosome lineages and some private autosomal alleles. After a Beringian population expansion, which could have occurred concomitant with their entry into America, more recent circumarctic gene flow would have enabled the dispersion of northeast Asian-derived characters and some particular genetic lineages from East Asia to America and vice versa.

This is not specific to the Americas: the familiar traits of the three major human races (Caucasoids, Mongoloids, and Negroids) were in existence for a long time before their first attestation. It is a process of diversity-reducing selection, and integration of traits of different origins that has led to the crystallization of the present-day types during the Holocene. 

Toumai not 7-million years old

Wikipedia on Sahelanthropus tchadensis.

Finder of key hominid fossil disputes 7-million-year dating

Brunet appeared to have scored a knockout blow in February this year, when radiological measurements estimated that the soil where Toumai was found was between 6.8 million and 7.2 million years old.

...

But the man who discovered Toumai, Alain Beauvilain, of the University of Paris at Nanterre, has now publicly challenged this estimate.

...

But Beauvilain, a Chadian fossil expert of long standing, says that, contrary to Brunet's assertions that the fossil had been "unearthed," the cranium was found loose on the sand.

People tend to pick spouses who resemble their opposite-sex parent

NOTE [29 Jan 09] Apparently this paper has been retracted.

In this paper, it is shown that men are more similar to their wife's father than to a random man from the population, and similarly women are more similar to their husband's father.

This was assessed both by using observers' ratings of likeness between two individuals, but also by examining the correlations between facial features.

Spouses' features were correlated with each other, with the most important correlation being in the nose length/face height ratio (r=0.728), suggesting that men with prominent noses tend to marry similar women.

The most important correlation between a woman's father and her husband was also in this ratio (r=0.72).

The most important correlation between a man's mother and his wife was in the jaw width/face width ratio (the zygo-gonial index), with r=0.928. Quite strong correlations were also found for the inverse facial index (face length/face width, r=0.786) and the lip fullness/lip width (r=0.676).

Proceedings of the Royal Society B DOI 10.1098/rspb.2008.1021

Facialmetric similarities mediate mate choice: sexual imprinting on opposite-sex parents

Tamas Bereczkei, Gabor Hegedus, Gabor Hajnal

Abstract

Former studies have suggested that imprinting-like processes influence the shaping of human mate preferences. In this study, we provide more direct evidence for assessing facial resemblance between subjects' partner and subjects' parents. Fourteen facial proportions were measured on 312 adults belonging to 52 families, and the correlations between family members were compared with those of pairs randomly selected from the population. Spouses proved to be assortatively mated in the majority of measured facial proportions. Significant correlations have been found between the young men and their partner's father (but not his mother), especially on facial proportions belonging to the central area of the face. Women also showed resemblance to their partner's mother (but not to their father) in the facial characteristics of their lower face. Replicating our previous studies, facial photographs of participants were also matched by independent judges who ascribed higher resemblance between partners, and subjects and their partners' opposite-sex parents, compared with controls. Our results support the sexual imprinting hypothesis which states that children shape a mental template of their opposite-sex parents and search for a partner who resembles that perceptual schema. The fact that only the facial metrics of opposite-sex parents showed resemblance to the partner's face tends to rule out the role of familiarity in shaping mating preferences. Our findings also reject several other rival hypotheses. The adaptive value of imprinting-related human mating is discussed, and a hypothesis is made of why different facial areas are involved in males' and females' search for resemblance.


Link

Nerik: Hittite holy city

Hittites' holy city Nerik to emerge

Late in the second millennium B.C., as the Hittites were experimenting with bronze, they built a holy city called Nerik near the Black Sea, according to evidence being slowly gathered by archeologists.

Today, excavators at the Oymaağaç mound in the Black Sea city of Samsun's Vezirköprü district are reveling in their potential find, believing the evidence is mounting and Oymaağaç will be unveiled as the holder of Nerik.

...

According to Zimmermann, the most prominent findings to date at the Oymaağaç dig, which started two years ago and was expected to finish in 10 years, were the fragments of cuneiform tablets. He said they were the northernmost written sources found in Hittite Anatolia. Also, he said they had found a number of bullae, which are lumps of clay molded around a cord and stamped with a seal to prevent tampering with the contents of a container, from the Hittite imperial period in the late second millennium.

AVPR1A and pair bonding in humans

From the press release:

Hasse Walum and his colleagues made use of data from The Twin and Offspring Study in Sweden, which includes over 550 twins and their partners or spouses. The gene under study codes for one of the receptors for vasopressin, a hormone found in the brains of most mammals. The team found that men who carry one or two copies of a variant of this gene  allele 334  often behave differently in relationships than men who lack this gene variant.

The incidence of allele 334 was statistically linked to how strong a bond a man felt he had with his partner. Men who had two copies of allele 334 were also twice as likely to have had a marital or relational crisis in the past year than those who lacked the gene variant. There was also a correlation between the mens gene variant and what their respective partners thought about their relationship.

The same gene was previously implicated in Creative Dance personality. Gene Expression has more.

PNAS doi: 10.1073/pnas.0803081105

Genetic variation in the vasopressin receptor 1a gene (AVPR1A) associates with pair-bonding behavior in humans

Hasse Walum et al.

Abstract

Pair-bonding has been suggested to be a critical factor in the evolutionary development of the social brain. The brain neuropeptide arginine vasopressin (AVP) exerts an important influence on pair-bonding behavior in voles. There is a strong association between a polymorphic repeat sequence in the 5′ flanking region of the gene (avpr1a) encoding one of the AVP receptor subtypes (V1aR), and proneness for monogamous behavior in males of this species. It is not yet known whether similar mechanisms are important also for human pair-bonding. Here, we report an association between one of the human AVPR1A repeat polymorphisms (RS3) and traits reflecting pair-bonding behavior in men, including partner bonding, perceived marital problems, and marital status, and show that the RS3 genotype of the males also affects marital quality as perceived by their spouses. These results suggest an association between a single gene and pair-bonding behavior in humans, and indicate that the well characterized influence of AVP on pair-bonding in voles may be of relevance also for humans.

Link

Selection in NAT2 in 12 human populations

Label of the figure:

Each pie represents the percentage of the slow (white), intermediate (grey), and fast (black) acetylators in the extended panel, inferred from genotype data as described in Materials and Methods. Inset: map showing the frequency of slow (white) and fast (black) haplotypes as inferred based on biochemical data [6].

Table S1 has the population frequencies. From the paper:

From a phylogeographic perspective, the consistency of the networks across different populations means that all the major haplotypes had originated prior to the differentiation of the study populations. However, the out-of-Africa bottleneck predicts lower diversity levels in non-African compared to African populations, and this is not observed at the NAT2 locus. There is no marked tendency of any of the derived NAT2 haplotypes to be continent-specific.

...

Several features of the data generated by us and by others [8], [10]–[12] suggest that selection acted on multiple slow-causing variants.


...

In conclusion, our data favour the hypothesis that a selective pressure drove at least three slow-causing variants to the frequencies observed today, but do not allow us to discriminate between balancing selection and directional selection on multiple standing variants.

PLoS ONe doi: 10.1371/journal.pone.0003136

Multiple Advantageous Amino Acid Variants in the NAT2 Gene in Human Populations

Francesca Luca et al.

Abstract

Background
Genetic variation at NAT2 has been long recognized as the cause of differential ability to metabolize a wide variety of drugs of therapeutic use. Here, we explore the pattern of genetic variation in 12 human populations that significantly extend the geographic range and resolution of previous surveys, to test the hypothesis that different dietary regimens and lifestyles may explain inter-population differences in NAT2 variation.

Methodology/Principal Findings
The entire coding region was resequenced in 98 subjects and six polymorphic positions were genotyped in 150 additional subjects. A single previously undescribed variant was found (34T>C; 12Y>H). Several aspects of the data do not fit the expectations of a neutral model, as assessed by coalescent simulations. Tajima's D is positive in all populations, indicating an excess of intermediate alleles. The level of between-population differentiation is low, and is mainly accounted for by the proportion of fast vs. slow acetylators. However, haplotype frequencies significantly differ across groups of populations with different subsistence.

Conclusions/Significance
Data on the structure of haplotypes and their frequencies are compatible with a model in which slow-causing variants were present in widely dispersed populations before major shifts to pastoralism and/or agriculture. In this model, slow-causing mutations gained a selective advantage in populations shifting from hunting-gathering to pastoralism/agriculture. We suggest the diminished dietary availability of folates resulting from the nutritional shift, as the possible cause of the fitness increase associated to haplotypes carrying mutations that reduce enzymatic activity.

Link

Milk and culture

Significance Of Milk In Development Of Culture To Be Studied:

ScienceDaily (Sep. 4, 2008) — The capacity to drink and tolerate milk may have been of tremendous importance for the cultural development of Europe. In a major EU project, being launched today and coordinated by Uppsala University in Sweden, researchers will now study when and where this capacity emerged and what it entailed.

...

“The oldest pottery shards shown to contain milk were found in southeastern Europe, more precisely in what today is northeastern Greece. We believe that the mutation once grew common there and then became fundamental to the development of agrarian culture,” says Anders Götherstam, who will be coordinating the project.

See also the recent post on Earliest evidence for milk. In Northern Greece, milk has been detected in Stavroupoli (5.7ky BC) and Makriyalos (5.2ky BC)

Via Gene Expression

Genomic ancestry of Mexicans

Individuals in an admixed population inherit a fraction of their genomic ancestry from the contributing ancestral groups, with individual chromosomal segments inherited from each of them (as e.g. 23andme's ancestry painting shows)

In this paper, researchers discovered that in particular regions of the genome, Mexicans, who are a 3-way mixture of Europeans, Amerindians, and Sub-Saharan Africans, tend to have lower than average African ancestry, or higher-than-average European ancestry.

This indicates that these regions have been under selection, which has managed, in the few centuries or so since the arrival of Europeans and Africans in the New World to (dis)favor particular chunks of DNA.

From the paper:

Admixture in the present day Mexican American population has occurred over the past 500 years, during the post-Columbian era of the New World. As noted before (FBPP Investigators 2002), this Latino population is composed primarily of European and Native American ancestry, with a modest amount of African ancestry. Our overall estimates of average Native American (39%), European (57%) and African (4%) ancestry in this population from Starr County, Texas are quite similar to what was observed for a sample of Mexicans from Mexico City by Wang et al. (2008), with corresponding proportions of 40, 57 and 3%, respectively.

...

Our results are different from those presented by Tang et al. (2007) in a study of ancestral admixture in Puerto Ricans. Those authors found evidence for excess African ancestry on chromosome 6p and excess Native American ancestry on chromosomes 8q and 11q. Despite both being Latino populations, Mexicans and Puerto Ricans are actually quite distinct regarding their genetic as well a social and demographic histories. On average, Mexicans are primarily European and Native American in ancestry, with a modest African contribution (Tang et al. 2006); by contrast, Puerto Ricans have substantial African ancestry and more modest Native American ancestry (Tang et al. 2007). It is intriguing to consider the possibility that different environmental exposures operated on these populations with distinct genetic admixtures to produce differing patterns of selection. Both populations were subjected to prevalent endemic infectious diseases in the years following the Spanish conquest, a time when selection may have operated in the formation of these new admixed populations.

Human Genetics doi: 10.1007/s00439-008-0541-5

Genome-wide distribution of ancestry in Mexican Americans

Analabha Basu et al

Abstract Migrations to the new world brought together individuals from Europe, Africa and the Americans. Inter-mating between these migrant and indigenous populations led to the subsequent formation of new admixed populations, such as African and Latino Americans. These unprecedented events brought together genomes that had evolved independently on different continents for tens of thousands of years and presented new environmental challenges for the indigenous and migrant populations, as well as their offspring. These circumstances provided novel opportunities for natural selection to occur that could be reflected in deviations at specific locations from the genome-wide ancestry distribution. Here we present an analysis examining European, Native American and African ancestry based on 284 microsatellite markers in a study of Mexican Americans from the Family Blood Pressure Program. We identified two genomic regions where there was a significant decrement in African ancestry (at 2p25.1, p < 10−8 and 9p24.1, p < 2 × 10−5) and one region with a significant increase in European ancestry (at 1p33, p < 2 × 10−5). These locations may harbor genes that have been subjected to natural selection after the ancestral mixing giving rise to Mexicans.

Link

Neuroanatomical correlates of intelligence

Intelligence doi:10.1016/j.intell.2008.07.002

Neuroanatomical correlates of intelligence

Eileen Luders et al.

Abstract

With the advancement of image acquisition and analysis methods in recent decades, unique opportunities have emerged to study the neuroanatomical correlates of intelligence. Traditional approaches examining global measures have been complemented by insights from more regional analyses based on pre-defined areas. Newer state-of-the-art approaches have further enhanced our ability to localize the presence of correlations between cerebral characteristics and intelligence with high anatomic precision. These in vivo assessments have confirmed mainly positive correlations, suggesting that optimally increased brain regions are associated with better cognitive performance. Findings further suggest that the models proposed to explain the anatomical substrates of intelligence should address contributions from not only (pre)frontal regions, but also widely distributed networks throughout the whole brain.

Link

No modern behavioral "package" in Pleistocene Sahul

Wikipedia on Sahul Shelf.
Journal of Human Evolution Volume 55, Issue 2, August 2008, Pages 187-222

The revolution that didn't arrive: A review of Pleistocene Sahul

Phillip J. Habgood and Natalie R. Franklin

Abstract

There is a “package” of cultural innovations that are claimed to reflect modern human behaviour. The introduction of the “package” has been associated with the Middle-to-Upper Palaeolithic transition and the appearance in Europe of modern humans. It has been proposed that modern humans spread from Africa with the “package” and colonised not only Europe but also southern Asia and Australia (McBrearty and Brooks, 2000; Mellars, 2006a). In order to evaluate this proposal, we explore the late Pleistocene archaeological record of Sahul, the combined landmass of Australia and Papua New Guinea, for indications of these cultural innovations at the earliest sites. It was found that following initial occupation of the continent by anatomically and behaviourally modern humans, the components were gradually assembled over a 30,000-year period. We discount the idea that the “package” was lost en route to Sahul and assess the possibility that the “package” was not integrated within the material culture of the initial colonising groups because they may not have been part of a rapid colonisation process from Africa. As the cultural innovations appear at different times and locations within Sahul, the proposed “package” of archaeologically visible traits cannot be used to establish modern human behaviour. Whilst the potential causal role of increasing population densities/pressure in the appearance of the “package” of modern human behaviour in the archaeological record is acknowledged, it is not seen as the sole explanation because the individual components of the “package” appear at sites that are widely separated in space and time.

Link

Romans and AIDS resistance

Via the Herald:

Scientists believe the invading Romans caused the loss of a genetic shield that makes some people resistant to infection by the Aids virus, HIV.

The gene variant, called CCR5-Delta32, impairs the ability of HIV to enter white blood cells.

People with the mutation are not as easily infected by the virus and take longer to develop full-blown Aids.

Generally, only Europeans and western Asians carry the variant, which becomes less widespread as you move south.

More than 15% of people in some parts of northern Europe have CCR5-Delta32, compared with fewer than 4% of Greeks.

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He does not think the Romans spread a different version of the gene into their colonies by breeding with the natives.

A more likely explanation, he believes, is that they introduced a fatal disease to which carriers of the CCE5-Delta32 variant were unusually susceptible.

New Scientist magazine reported: "As the Romans moved north, this disease killed people with the variant.

It's hard to envision a disease that would be limited to the territory of the Roman Empire. The Roman frontier was fluid, with both Romans trading beyond it, and barbarians moving into Roman territory; it's hard to imagine how a disease could be "contained" within the territory of the Empire. Moreover, I don't really see a good candidate for a really dramatic Empire-wide epidemic, which would surely have been noticed by historians.

Via the BBC:

In countries inside the borders of the empire for longer periods, such as Spain, Italy and Greece, the frequency of the CCR5-delta32 gene, which offers some protection against HIV, is between 0% and 6%.

Countries at the fringe of the empire, such as Germany, and modern England, the rate is between 8% and 11.8%, while in countries never conquered by Rome, the rate is greater than this.

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However, some researchers believe that infections may have played a role - but in reverse -increasing rather than decreasing the frequency of the variant.

Researchers at the University of Liverpool suggested that the variant may have offered protection against pandemics such as the Black Death which swept Europe on a regular basis during and after the Roman era.

These, said the Liverpool researchers, were illnesses which may have been lethal to people without the gene variant, raising its frequency from one in 20,000 people to approximately 10% in Northern Europe.

Infection, Genetics and Evolution doi:10.1016/j.meegid.2008.08.007

Is the European spatial distribution of the HIV-1-resistant CCR5-Delta32 allele formed by a breakdown of the pathocenosis due to the historical Roman expansion?

Eric Faure and Manuela Royer-Carenzi

We studied the possible effects of the expansion of ancient Mediterranean civilizations during the five centuries before and after Christ on the European distribution of the mutant allele for the chemokine receptor gene CCR5 which has a 32-bp deletion (CCR5-Delta32). There is a strong evidence for the unitary origin of the CCR5-Delta32 mutation, this it is found principally in Europe and Western Asia, with generally a north-south downhill cline frequency. Homozygous carriers of this mutation show a resistance to HIV-1 infection and a slower progression towards AIDS. However, HIV has clearly emerged too recently to have been the selective force on CCR5. Our analyses showed strong negative correlations in Europe between the allele frequency and two historical parameters, i.e. the first colonization dates by the great ancient Mediterranean civilizations, and the distances from the Northern frontiers of the Roman Empire in its greatest expansion. Moreover, other studies have shown that the deletion frequencies in both German Bronze Age and Swedish Neolithic populations were similar to those found in the corresponding modern populations, and this deletion has been found in ancient DNA of around 7000 years ago, suggesting that in the past, the deletion frequency could have been relatively high in European populations. In addition, in West Nile virus pathogenesis, CCR5 plays an antimicrobial role showing that host genetic factors are highly pathogen-specific. Our results added to all these previous data suggest that the actual European allele frequency distribution might not be due to genes spreading, but to a negative selection resulting in the spread of pathogens principally during Roman expansion. Indeed, as gene flows from colonizers to European native populations were extremely low, the mutational changes might be associated with vulnerability to imported infections. To date, the nature of the parasites remains unknown; however, zoonoses could be incriminated.

Link

Long-legged Chinese women have more children

Evolution and Human Behavior doi:10.1016/j.evolhumbehav.2008.06.003

Are longer legs associated with enhanced fertility in Chinese women?

Richard Fielding et al.

Abstract

Female height impacts fertility differently in western and nonwestern cultures. Leg length or relatively longer legs comprise key components of height and possibly indicates mate value. We examined the associations between height, its components, and reproductive outcomes in a large Chinese cohort. Multivariable regression was used to assess the association of height, leg length (standing minus sitting height) and relatively longer legs with number of offspring in a cross-sectional sample of 9998 Chinese people aged at least 50 years from Phase 2 of the Guangzhou Biobank Cohort Study recruited in 2005–2006. Older and less educated respondents had more children. Adjusted for age, childhood socioeconomic status (SES), and education, women with longer legs had more offspring; however, there was no such association in men. When stratified by childhood SES (reported parental material possessions), longer legs and relatively longer legs were most strongly associated with more offspring in women from poorer backgrounds. Fertility was specifically associated with longer legs and relatively longer legs in women only. The difference in the association of leg length to number of offspring by childhood SES suggests a preference advantage rather than a physiological advantage in being taller. However, these benefits were specific to reproductive success in women and particularly women from poorer backgrounds suggesting that social factors may have facilitated fertility.

Link

Launch of Google Chrome and first impressions

Just downloaded Google Chrome, the new browser from Google. First impressions: launches fast, the usual comfortable and minimalistic Google interface style, no need to install any plugins for flash video or pdfs. If you are used to Firefox shortcuts, many of them are the same (e.g. to start and close tabs, or to change the text size). Features I like: (i) when you open a new tab, you see your "most visited sites" so you can quickly go to a page you like, (ii) when you increase or decrease text size, images don't scale (I didn't like this feature in Firefox 3.0) (iii) you can search your browsing history, which seems more useful than trying e.g. to re-create a search engine query that led you to a particular page. (iv) view page source opens in a new tab rather than a new window; very useful if you hate multiple open windows, (v) each tab is its own process, so I guess if one of them hangs, you can kill it individually without losing all your other open tabs; not sure how you can figure out which process in your task manager corresponds to which tab, however. Not sure when it will crash (it's still in beta), but so far it's looking great

Updte: A nice demo video which covers a lot of the features of the browser:

Female attractiveness not linked to higher reproductive success in rural Poland

Coll Antropol. 2008 Jun;32(2):457-60.

Is female attractiveness related to final reproductive success?

Pawlowski B, Boothroyd LG, Perrett DI, Kluska S.

In order to test the assumption that female attractiveness relates to reproductive success, photographs of 47 rural Polish women taken in their youth were rated for attractiveness, and BMI at age 18 was recorded; these measures of attractiveness were then compared with their subsequent life histories. Facial attractiveness did not relate to number of children or grandchildren. It also did not relate to age of marriage or husband's education. It did relate to number of marriages and husband's height. BMI at age 18 did not relate significantly to any of the outcome variables. These results suggest that although more attractive women may have married higher quality (taller) husbands and may in ancestral population have achieved greater reproductive success this way, there is no evidence in a modern, European Catholic society for their having greater reproductive success.

Link

YAP in 25 ethnic groups from Yunnan China

YAP defines haplogroup DE of the human Y-chromosome phylogeny, which joins together the haplogroup E, found in Negroids and Caucasoids, with haplogroup D, found mainly among Mongoloids, including the archaic Ainu, but also non-Mongoloid populations such as the Andaman Islanders.

The YAP frequencies listed here are, in all probability mostly of haplogroup D.

Sci China C Life Sci. 2003 Apr;46(2):135-140.

The geographic polymorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan, China.

Shi H, Dong Y, Li W, Yang J, Li K, Zan R, Xiao C.

The genetic polymorphisms of Y chromosome at YAP locus in 25 ethnic groups (33 populations) of China were analyzed in a total of 1294 samples. The average YAP+ frequency of the 33 populations was 9.2%, coinciding with published data of Chinese populations. Primi has the highest YAP+ frequency (72.3%), which is also the highest YAP+ among all the eastern Asian populations studied. The YAP+ occurred in 17 populations studied including Tibetan (36.0%), Naxi (37.5% and 25.5%), Zhuang (21.3%), Jingpo (12.5%), Miao (11.8%), Dai (11.4%, 10.0%, 3.3% and 2.0%), Yi (8.0%), Bai of Yunnan (6.7% and 6.0%), Mongol of Inner Mongolia (4.3%), Tujia of Hunan (2.6%), Yao (2.2%) and Nu (1.8%). The other 15 populations are YAP-including Lahu (2 populations), Hani, Achang, Drung, Lisu, Sui, Bouyei, Va, Bulang, Deang, Man and Hui and Mongol of Yunnan and Bai of Hunan. The YAP+ frequencies varied among the different ethnic groups studied, and even different among the same ethnic group living in different geographic locations. Using the genetic information, combined with the knowledge of ethnology, history and archaeology, the origin and prehistoric migrations of the ethnic groups in China, especially in Yunnan Province were discussed.

Link

Geography and Genetic structure in Europe (again)

A new letter in Nature has appeared online with an almost identical conclusion with the Current Biology paper I blogged about earlier. The new study included 3,192 individuals from POPRES, genotyped with the Affymetrix 500K chip.

The newer study included a wider sampling of populations, including Cypriots, Turks, and Eastern Slavs among others. Hence, the correspondence with the map of Europe is even stronger than before.

While in the previous study PC2 separated the Finns from the rest, the wider sampling, especially of Eastern Europeans now causes a clearer separation along the east-west axis. Note that PC2 in this study is not the same as PC2 in the previous one, as can be easily seen by e.g., (i) the fact thatPortugal and Spain are correctly placed to the west of Great Britain, and (ii) the fact that the Finnish score is about the same as that of Greeks and Yugoslavs in this study. In any case, Finland is represented by a single individual.

This underscores the often-forgotten fact that PCs are calculated from the available data and thus depend on the included populations. The inclusion of Eastern Europeans (esp. Eastern Slavs and Balts) in this study has now made the strong east-west differentiation in Europe, the most salient feature on the second PC. Unfortunately no higher PCs are presented.

From the paper:

The direction of the PC1 axis and its relative strength may reflect a special role for this geographic axis in the demographic history of Europeans (as first suggested in ref. 10). PC1 aligns north-northwest/ south-southeast (NNW/SSE, 216 degrees) and accounts for approximately twice the amount of variation as PC2 (0.30% versus 0.15%, first eigenvalue54.09, second eigenvalue52.04).

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More robust evidence for the importance of a roughly NNW/SSE axis in Europe is that, in these same data, haplotype diversity decreases from south to north (A.A. et al., submitted).

The only deviation from geography seems to be the Slovakian individual:

There is only one obvious outlier, which is Slovakia; however Slovakia is represented in our data set by only one individual, and based on the individual’s position in PC1-PC2 space it’s possible this outlier may actually have had Italian, rather than Slovakian ancestry.

and the Russians:

The Russian Federation is less-striking as an outlier, and appears to lie too far “west” genetically, which may be a result of small sample size (n = 6) or simply that the Russians sampled here have ancestry from a location further west than the proxy location for Russia (Moscow) would suggest.

As for the Greeks (GR), once again, they are placed between Italians and their northern neighbors, with Albanians (AL), a pre-Slavic Balkan population especially close, followed by Slavomacedonians ("MK") and Bulgarians (BG). This is especially impressive given the small sample sizes (8 for Greece to 2 for Bulgaria). It appears that even individual members of ethnic groups "find their way" to the appropriate place of the map.

The Way Ahead

Both this and the previous paper have made it abundantly clear that, even in Europe, where genetic differentiation is very limited and populations are arrayed in a cline, it is possible to determine the rough geographical or ethnic origin of an unknown individual. Even for closely related groups where the precise origin can't be determined (e.g. Spanish vs. Portuguese), we can at least exclude with high probability most other European groups.

The applications of this are obvious: criminal or victim DNA can be pinpointed on the map. The ethnic origin of undocumented persons (e.g. illegal immigrants) can be ascertained with some confidence. Adoptees or persons of unknown ultimate origins (such as many inhabitants of the New World) may be able to trace their ancestry to something more than they could guess by looking at the mirror.

Indeed, while 500K markers are used in this analysis, it will turn out that fewer markers will carry most of the power of distinguishing between ethnic and geographical groups: you only have to examine 500K of them to harvest the useful ones.

This opens wide possibilities for ancestry testing; such testing previously gave one fairly obvious information ("you're 99% European") and cost a substantial amount. It will soon be possible, using a specialized panel of the most informative markers to create ancestry testing that is both affordable and informative.

The identification of ethnic differences in autosomal DNA also allows us to look at history from a new perspective, as the ethnic origins of skeletal material from the past will be ascertained with a precision unmatched by biological anthropology.

Of course, for the distant past, problems with obtaining authentic ancient DNA will remain, as well as the fact that accelerating human evolution may have changed allele frequencies or introduced new alleles into populations. Nonetheless, there is hope for real progress.

The real impediment will not be, in my opinion, technical, but rather psychological/political. The realization that not only major continental races, but also ethnic groups are biological entitites goes against the prevailing politically correct orthodoxy. According to this orthodoxy, European nations are artificial cultural constructions whose members share a "myth" of common origins; they are "constructed" products of the last few centuries; ethnic identification is a subjective notion of self-identity, rather than an objective notion of ancestry and homeland.

It now appears that while European nations are not races, they are, nonetheless, biological populations, occupying specific positions along the Caucasoid genetic continuum, and distinguishable from most other European nations, if not always their immediate neighbors.

Nature advance online publication 31 August 2008 | doi:10.1038/nature07331

Genes mirror geography within Europe

John Novembre et al.

Understanding the genetic structure of human populations is of fundamental interest to medical, forensic and anthropological sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation and suggest the potential to use large samples to uncover variation among closely spaced populations1, 2, 3, 4, 5. Here we characterize genetic variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between genetic and geographic distances; indeed, a geographical map of Europe arises naturally as an efficient two-dimensional summary of genetic variation in Europeans. The results emphasize that when mapping the genetic basis of a disease phenotype, spurious associations can arise if genetic structure is not properly accounted for. In addition, the results are relevant to the prospects of genetic ancestry testing6; an individual's DNA can be used to infer their geographic origin with surprising accuracy—often to within a few hundred kilometres.

Link