June 02, 2009

Patterns of natural selection and phenotype convergence in FUT2

This paper shows an example of convergent evolution in humans, in which similarity in an observable trait is explained by different underlying gene variants. Another example of this phenomenon is convergent evolution of skin color with depigmentation of Caucasoids and Mongoloids relative to the African ancestral form occurred due to different mutations, or lactase persistence where the ability to digest milk evolved independently in Europe and Africa.

Molecular Biology and Evolution doi:10.1093/molbev/msp108

A natural history of FUT2 polymorphism in humans

Anna Ferrer-Admetlla et al.

Abstract

Because pathogens are powerful selective agents, host cell surface molecules used by pathogens as identification signals can reveal the signature of selection. Most of them are oligosaccharides, synthesized by glycosyltransferases. One known example is balancing selection shaping ABO evolution as a consequence of both, A and B antigens being recognized as receptors by some pathogens, and anti-A and/or anti-B natural antibodies produced by hosts conferring protection against the numerous infectious agents expressing A and B motifs. These antigens can also be found in tissues other than blood if there is activity of another enzyme, FUT2, a fucosyltransferase responsible for ABO biosynthesis in body fluids. Homozygotes for null variants at this locus present the non-secretor phenotype (se), since they can not express ABO antigens in secretions. Multiple independent mutations have been shown to be responsible for the non-secretor phenotype, which is coexisting with the secretor phenotype in most populations. In this study, we have resequenced the coding region of FUT2 in 732 individuals from 39 worldwide human populations. We report a complex pattern of natural selection acting on the gene. While frequencies of secretor and non-secretor phenotypes are similar in different populations, the point mutations at the base of the phenotypes are different, with some variants showing a long history of balancing selection among Eurasian and African populations, and one recent variant showing a fast spread in East Asia, likely due to positive selection. Thus a convergent phenotype composition has been achieved through different mutations with different evolutionary histories.

Link

Modern humans not Neandertals made the Aurignacian

The absence of complete Homo sapiens remains in conjunction with Aurignacian industries have led some to raise the issue of who the originators of the Aurignacian were: modern humans or Neandertals who were present in Europe at that time. A new paper puts the isolated dental remains through a statistical analysis, and comes up with the conclusion that modern humans are very likely to have been behind the Aurignacian.

Journal of Human Evolution doi:10.1016/j.jhevol.2009.02.003

Who made the Aurignacian and other early Upper Paleolithic industries?

Shara E. Bailey et al.

Abstract

The Aurignacian is typically taken as a marker of the spread of anatomically modern humans into Europe. However, human remains associated with this industry are frustratingly sparse and often limited to teeth. Some have suggested that Neandertals may, in fact, be responsible for the Aurignacian and the earliest Upper Paleolithic industries. Although dental remains are frequently considered to be taxonomically undiagnostic in this context, recent research shows that Neandertals possess a distinct dental pattern relative to anatomically modern humans. Even so, it is rare to find mandibles or maxillae that preserve all or most of their teeth; and, the probability of correctly identifying individuals represented by only a few teeth or a single tooth is unknown.

We present a Bayesian statistical approach to classifying individuals represented exclusively by teeth into two possible groups. The classification is based on dental trait frequencies and sample sizes for ‘known’ samples of 95 Neandertals and 63 Upper Paleolithic modern humans. In a cross validation test of the known samples, 89% of the Neandertals and 89% of the Upper Paleolithic modern humans were classified correctly. We then classified an ‘unknown’ sample of 52 individuals: 34 associated with Aurignacian or other (non-Châtelperronian) early Upper Paleolithic industries, 15 associated with the Châtelperronian, and three unassociated. Of the 34 early Upper Paleolithic-associated individuals, 29 were assigned to modern humans, which is well within the range expected (95% of the time 26–33) with an 11% misclassification rate for an entirely modern human sample. These results provide some of the strongest evidence that anatomically modern humans made the Aurignacian and other (non-Châtelperronian) early Upper Paleolithic industries.

Link

June 01, 2009

Y chromosomes from 7th c. Ergolding (Bavaria, Germany)

From the paper:
Men from the grave 244 (marked 244A to 244F) were buried together into a single wooden burial chamber. Individuals found in the western part of the chamber (244A, 244B, and 244C) lied straight on the back, body-by-body, and all 3 men were buried with swords, spears, shields, and spurs, like heavily armored mounted warriors (9). Historic value of the artifacts found in the grave 244 makes this place one of the richest Bavarian burial sites from the late-Merowig period (9). The grave 244 dates to the period around 670 AD. The eastern part of the burial chamber with the individuals 244D, 244E, and 244F was robbed and therefore no valuable artifacts
were found.
The haplotypes are on p. 291 of the paper. Two men probably belonged to haplogroup G2a, and four men to haplogroup R1b. The R1b men were probably patrilineally related, and two of them, (244A/244B) based on their autosomal profiles were probably full siblings.

Someone ought to re-run the haplotypes in ysearch and also the autosomal profiles using something like OmniPop. Feel free to comment/link if you do.

Added to the Ancient Y chromosome studies compendium.

Croat Med J. 2009 Jun;50(3):286-95.

Kinship and y-chromosome analysis of 7th century human remains: novel DNA extraction and typing procedure for ancient material.

Vanek D, Saskova L, Koch H.

Daniel Vanek, Forensic DNA Service, Janovskeho 18, 170 00 Prague 7, Czech Republic, daniel.vanek@DNA.com.cz.

Aim. To develop novel DNA extraction and typing procedure for DNA identification of the 7th century human remains, determine the familiar relationship between the individuals, estimate the Y-chromosome haplogroup, and compare the Y-chromosome haplotype with the contemporary populations. Methods. DNA from preserved femur samples was extracted using the modified silica-based extraction technique. Polymerase chain reaction amplification was performed using human identification kits MiniFiler, Identifiler, and Y-filer and also laboratory-developed and validated Y-chromosome short tandem repeat (STR) pentaplexes with short amplicons. Results. For 244A, 244B, 244C samples, full autosomal DNA profiles (15 STR markers and Amelogenin) and for 244D, 244E, 244F samples, MiniFiler profiles were produced. Y-chromosome haplotypes consisting of up to 24 STR markers were determined and used to predict the Y-chromosome haplogroups and compare the resulting haplotypes with the current population. Samples 244A, 244B, 244C, and 244D belong to Y-chromosome haplogroup R1b and the samples 244E and 244F to haplogroup G2a. Comparison of ancient haplotypes with the current population yielded numerous close matches with genetic distance bellow 2. Conclusion. Application of forensic genetics in archaeology enables retrieving new types of information and helps in data interpretation. The number of successfully typed autosomal and Y-STR loci from ancient specimens in this study is one of the largest published so far for aged samples.

Link

May 30, 2009

Multifaceted origin of cattle revealed by DNA (Achilli et al. 2009)

PLoS ONE doi:10.1371/journal.pone.0005753

The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome

Alessandro Achilli et al.

Abstract

A Neolithic domestication of taurine cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of taurine cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.

Link

May 29, 2009

Ancient mtDNA and craniometric evolution of Amerindians

This paper shows that while the mtDNA gene pool of Amerindians did not undergo substantial change since the Holocene (haplogroups B, C, D were detected in the ancient samples, all of them common today), their cranial morphology changed from a more generalized to a more Mongoloid pattern.

In my opinion, the fact that Amerindians evolved in a Mongoloid direction may suggest one of three things:
  1. proto-Mongoloid traits were present as tendencies in the founding population, and they evolved in parallel in the Americas and in East Asia
  2. proto-Mongoloid traits were absent in the founding population, and they evolved independently in the Americas
  3. proto-Mongoloid traits were absent in the founding population, but they were added by limited gene flow from Asia
Even in Asia itself, except for isolated finds in Siberia, the first full-blown Mongoloids emerge in the Holocene. The Mongoloid type even spread to the south of the continent, which was formerly occupied by populations more similar to Australo-Melanesians.

Why the type became so successful remains to be seen; adaptive explanations for a rounder skull, flatter face, and heavy eyelids have been proposed as responses to extreme arctic cold, but why would similar phenotypes be selected for in regions of less extreme climate?

Sexual selection might play a role, although it would be difficult to establish over such a large area.

My guess is that various aspects of the Mongoloid pattern existed in low frequency or as isolated tendencies across East Eurasia and America. As populations grew during the Holocene, these traits spread in a wider range. Naturally, in the periphery, their blending was incomplete, with different quasi-Mongoloid types emerging there, e.g., prominent-nosed, round-headed Amerindians vs. flat-nosed, long-headed Proto-Uralics.

Thus, ancestral Amerindians either already had, or later received -by limited gene flow- a set of Mongoloid traits from Asia, which were selected for the same reasons as they did in Asia, but the "bottleneck" of the Bering did not allow them to receive the full package of traits.

PLoS ONE doi:10.1371/journal.pone.0005746

Discrepancy between Cranial and DNA Data of Early Americans: Implications for American Peopling

S. Ivan Perez et al.

Abstract

Currently, one of the major debates about the American peopling focuses on the number of populations that originated the biological diversity found in the continent during the Holocene. The studies of craniometric variation in American human remains dating from that period have shown morphological differences between the earliest settlers of the continent and some of the later Amerindian populations. This led some investigators to suggest that these groups—known as Paleomericans and Amerindians respectively—may have arisen from two biologically different populations. On the other hand, most DNA studies performed over extant and ancient populations suggest a single migration of a population from Northeast Asia. Comparing craniometric and mtDNA data of diachronic samples from East Central Argentina dated from 8,000 to 400 years BP, we show here that even when the oldest individuals display traits attributable to Paleoamerican crania, they present the same mtDNA haplogroups as later populations with Amerindian morphology. A possible explanation for these results could be that the craniofacial differentiation was a local phenomenon resulting from random (i.e. genetic drift) and non-random factors (e.g. selection and plasticity). Local processes of morphological differentiation in America are a probable scenario if we take into consideration the rapid peopling and the great ecological diversity of this continent; nevertheless we will discuss alternative explanations as well.

Link

Brain structure and IQ

PLoS Comput Biol doi:10.1371/journal.pcbi.1000395

Brain Anatomical Network and Intelligence

Yonghui Li et al.

Abstract

Intuitively, higher intelligence might be assumed to correspond to more efficient information transfer in the brain, but no direct evidence has been reported from the perspective of brain networks. In this study, we performed extensive analyses to test the hypothesis that individual differences in intelligence are associated with brain structural organization, and in particular that higher scores on intelligence tests are related to greater global efficiency of the brain anatomical network. We constructed binary and weighted brain anatomical networks in each of 79 healthy young adults utilizing diffusion tensor tractography and calculated topological properties of the networks using a graph theoretical method. Based on their IQ test scores, all subjects were divided into general and high intelligence groups and significantly higher global efficiencies were found in the networks of the latter group. Moreover, we showed significant correlations between IQ scores and network properties across all subjects while controlling for age and gender. Specifically, higher intelligence scores corresponded to a shorter characteristic path length and a higher global efficiency of the networks, indicating a more efficient parallel information transfer in the brain. The results were consistently observed not only in the binary but also in the weighted networks, which together provide convergent evidence for our hypothesis. Our findings suggest that the efficiency of brain structural organization may be an important biological basis for intelligence.

Link

May 28, 2009

Ancient mtDNA from Pompeii

From the paper:
The aim of this study was to investigate family relationships among the inhabitants of Cajus Iulius Polybius’ house. In addition, the mtDNA haplogroup attribution of these individuals was considered.

...

Regarding the mtDNA haplogroups, individuals 3A, 3B, 2A, 2B, 2C, 3D most likely belong to haplogroup T2b (Malyarchuk & Derenko, 1999; Pike, 2006; Richards et al., 2000), which in modern Italians ranges between 4.4 and 4.7% (A. Torroni, personal communication). The polymorphisms in positions 16294 and 16304 detected in individuals 3A, 3B, 2A, 2B, 2C, 3D in haplogroup T2b are often associated with the polymorphism at nucleotide 16296 (Pike, 2006; Richards et al., 2000). The absence of this mutation in our individuals is probably due to the instability of this nucleotide in haplogroup T2b (Malyarchuk & Derenko, 1999; Richards et al., 2000; Pike, 2006).

...

Individual 1A, besides the polymorphism at position 16399 in HVS1, shows a sequence identical to rCRS at position 7028 hence we might assume that he most likely belongs to haplogroup H (Torroni et al., 1996). Individual 1B, showing polymorphisms at positions 16292 and 16298 and a sequence identical to rCRS at positions 73 and 4580, most likely belongs to haplogroup HV0 (Achilli et al., 2007; Pierron et al., 2008).

...

For individual 5,6A, who shows a polymorphism at positions 16391 and 73, and for 5,6B who shares the rCRS in HVS1 and at position 73, we can conclude that while individual 5,6A cannot be attributed to haplogroup H, individual 5,6B most likely can be (Torroni et al., 1996).
Some pictures from the house of Polybius.

Annals of Human Genetics
doi:10.1111/j.1469-1809.2009.00520.x

Ancient DNA and Family Relationships in a Pompeian House

Giovanni Di Bernardo et al.

Abstract

Archaeological, anthropological and pathological data suggest that thirteen skeletons found in a house at the Pompeii archaeological site, dated to 79 A.D., belong to one family. To verify this and to identify the relationships between these individuals, we analyzed DNA extracted from bone specimens. Specifically, hypervariable segment 1 (HVS1) of the human mitochondrial DNA (mtDNA) control region was amplified in two overlapping polymerase chain reactions and the sequences were compared to the revised Cambridge Reference Sequence. As independent controls, other polymorphic sites in HVS1, HVS2 and in the coding region were analyzed. We also amplified some short tandem repeats of the thirteen specimens. This study revealed that six of the thirteen individuals are indeed closely related.

Link

Heterozygosity and heart-related quantitative traits

Annals of Human Genetics doi:10.1111/j.1469-1809.2009.00514.x

Association between SNP Heterozygosity and Quantitative Traits in the Framingham Heart Study

Didahally R. Govindaraju et al.

Abstract

Associations between multilocus heterozygosity and fitness traits, also termed heterozygosity and fitness correlations (HFCs), have been reported in numerous organisms. These studies, in general, indicate a positive relationship between heterozygosity and fitness traits. We studied the association between genome-wide heterozygosity at 706 non-synonymous and synonymous SNPs and 19 quantitative traits, including morphological, biochemical and fitness traits in the Framingham Heart Study. Statistically significant association was found between heterozygosity and systolic and diastolic blood pressures as well as left ventricular diameter and wall thickness. These results suggest that heterozygosity may be associated with traits, such as blood pressure that closely track environmental variations. Balancing selection may be operating in the maintenance of heterozygosity and the major components of blood pressure and hypertension. Genome wide SNP heterozygosity may be used to understand the phenomenon of dominance as well as the evolutionary basis of many quantitative traits in humans.

Link

May 27, 2009

The first Korean genome

An interesting bit:
In addition, the comparison of indels between SJK and YH (Table 4) showed that the two genomes shared the same type of indels by 99.5% on the same genomic loci (SJK and HuRef shared 86.2%, SJK and Watson shared 87.8%, SJK and NA18507 shared 93.6%).

So -based on indels- the Korean and Chinese individuals are ~24 times less distant to each other than the Korean is to James Watson (a European descendant) and ~13 times less distant to each other than the Korean was to NA18507 (a Nigerian). Table 4 in the paper has all the detailed numbers.

Figure 2 shows the overlap -number of SNPs- between various full genomes available.


Consider (E): 1.2 million SNPs are shared by the Korean and Venter/Watson; ~0.5 million are shared by the Korean and Venter (but not Watson) and the Korean and Watson (but not Venter), i.e., they transcend racial lines.

But, another ~0.5 million is shared by Venter and Watson, but not the Korean. A subset of these may be shared by accident for these three individuals (i.e., another Korean might also possess some of them). Another subset may be shared by Venter and Watson and most other Caucasoids; another subset may be shared by Venter and Watson, presumably due to their common Western European ancestry (or shared other minor ancestry), and so on.

As we sample more full genomes, we will be able to zero in on the pan-human SNPs, which represent shared human genetic diversity, as well as SNPs limited to races, subraces, ethnic groups, regions, ..., individuals.

This is an open access paper, so you can read it for yourselves.

Genome Research doi:10.1101/gr.092197.109

The first Korean genome sequence and analysis: Full genome sequencing for a socio-ethnic group

Sung-Min Ahn et al.

Abstract

We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel SNPs that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: 1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venter's, 46.94% against Watson's, and 44.17% against the Yoruba genomes), 2) 99.5% (22,495 out of 22,605) of short indels (less than 4 bp) discovered on the same loci had the same size and type as YH, and 3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.

Link

Evidence of leprosy in India (~2,000BC)

Anthropology.net points me to this new paper. I recommend that post for more details on the study.

PLoS ONE doi:10.1371/journal.pone.0005669

Ancient Skeletal Evidence for Leprosy in India (2000 B.C.)

Gwen Robbins et al.

Abstract

Background

Leprosy is a chronic infectious disease caused by Mycobacterium leprae that affects almost 250,000 people worldwide. The timing of first infection, geographic origin, and pattern of transmission of the disease are still under investigation. Comparative genomics research has suggested M. leprae evolved either in East Africa or South Asia during the Late Pleistocene before spreading to Europe and the rest of the World. The earliest widely accepted evidence for leprosy is in Asian texts dated to 600 B.C.

Methodology/Principal Findings

We report an analysis of pathological conditions in skeletal remains from the second millennium B.C. in India. A middle aged adult male skeleton demonstrates pathological changes in the rhinomaxillary region, degenerative joint disease, infectious involvement of the tibia (periostitis), and injury to the peripheral skeleton. The presence and patterning of lesions was subject to a process of differential diagnosis for leprosy including treponemal disease, leishmaniasis, tuberculosis, osteomyelitis, and non-specific infection.

Conclusions/Significance

Results indicate that lepromatous leprosy was present in India by 2000 B.C. This evidence represents the oldest documented skeletal evidence for the disease. Our results indicate that Vedic burial traditions in cases of leprosy were present in northwest India prior to the first millennium B.C. Our results also support translations of early Vedic scriptures as the first textual reference to leprosy. The presence of leprosy in skeletal material dated to the post-urban phase of the Indus Age suggests that if M. leprae evolved in Africa, the disease migrated to India before the Late Holocene, possibly during the third millennium B.C. at a time when there was substantial interaction among the Indus Civilization, Mesopotamia, and Egypt. This evidence should be impetus to look for additional skeletal and molecular evidence of leprosy in India and Africa to confirm the African origin of the disease.

Link

May 25, 2009

MHC-dissimilar mating in Brazil

This seems to parallel previous findings on European Americans.

Opposites attract -- how genetics influences humans to choose their mates
Vienna, Austria: New light has been thrown on how humans choose their partners, a scientist will tell the annual conference of the European Society of Human Genetics today (Monday May 25). Professor Maria da Graça Bicalho, head of the Immunogenetics and Histocompatibility Laboratory at the University of Parana, Brazil, says that her research had shown that people with diverse major histocompatibility complexes (MHCs) were more likely to choose each other as mates than those whose MHCs were similar, and that this was likely to be an evolutionary strategy to ensure healthy reproduction.

Females' preference for MHC dissimilar mates has been shown in many vertebrate species, including humans, and it is also known that MHC influences mating selection by preferences for particular body odours. The Brazilian team has been working in this field since 1998, and decided to investigate mate selection in the Brazilian population, while trying to uncover the biological significance of MHC diversity.

The scientists studied MHC data from 90 married couples, and compared them with 152 randomly-generated control couples. They counted the number of MHC dissimilarities among those who were real couples, and compared them with those in the randomly-generated 'virtual couples'. "If MHC genes did not influence mate selection", says Professor Bicalho, "we would have expected to see similar results from both sets of couples. But we found that the real partners had significantly more MHC dissimilarities than we could have expected to find simply by chance."

Within MHC-dissimilar couples the partners will be genetically different, and such a pattern of mate choice decreases the danger of endogamy (mating among relatives) and increases the genetic variability of offspring. Genetic variability is known to be an advantage for offspring, and the MHC effect could be an evolutionary strategy underlying incest avoidance in humans and also improving the efficiency of the immune system, the scientists say.

The MHC is a large genetic region situated on chromosome 6, and found in most vertebrates. It plays an important role in the immune system and also in reproductive success. Apart from being a large region, it is also an extraordinarily diverse one.

"Although it may be tempting to think that humans choose their partners because of their similarities", says Professor Bicalho, "our research has shown clearly that it is differences that make for successful reproduction, and that the subconscious drive to have healthy children is important when choosing a mate."

The scientists believe that their findings will help understanding of conception, fertility, and gestational failures. Research has already shown that couples with similar MHC genes had longer intervals between births, which could imply early, unperceived miscarriages. "We intend to follow up this work by looking at social and cultural influences as well as biological ones in mate choice, and relating these to the genetic diversity of the extended MHC region", says Professor Bicalho.

"We expect to find that cultural aspects play an important role in mate choice, and certainly do not subscribe to the theory that if a person bears a particular genetic variant it will determine his or her behaviour. But we also think that the unconscious evolutionary aspect of partner choice should not be overlooked. We believe our research shows that this has an important role to play in ensuring healthy reproduction, by helping to ensure that children are born with a strong immune system better able to cope with infection."


I had previously posted some more abstracts from ESHG 2009. Here is the abstract from this study:

New evidences about MHC-based patterns of mate choice
M. Bicalho, J. da Silva, J. M. Magalhães, W. Silva;

Major Histocompatibility Complex (MHC) genes code for cell surface proteins, which plays an important role in immune recognition. In the late 1970s, Yamazaki observed that inbred mice were more likely to mate with partners having MHC dissimilar genes. Females’ preference for MHC dissimilar mates was also observed in other vertebrate species, including humans. It has been shown that MHC influences mating selection mediated by preferences based on body odor. What’s the functional significance of these findings, if some? It was assumed that through olfactory cues MHC-related evolved as a strategy to maximize the offspring MHC heterozygosity. Parents with dissimilar MHCs could provide their offspring with a better chance to ward infections off because their immune system genes are more diverse. MHC genotype might be used to signal relatedness and immune response genotypes through.

We investigated whether husband-wife couples (n=90) obtained from LIGH’s database were more MHC-similar/dissimilar in comparison to random couples generated from the same database (n=55 000) as to collect evidence of MHC influence in MHC-based patterns of mate choice.

The individuals HLA typing (Class I and Class II) was performed by PCR-SSP or PCR-rSSOP using a commercial kit ( One Lambda Inc., Canoga Park. CA, USA).

Our results and comparisons ( p= 0,014) suggest that couples seem to be formed by individuals with less HLA similarity, corroborating the hypothesis that HLA antigens, especially Class I, may influence mate selection and marriages in humans.

May 24, 2009

European admixture and Body Mass Index in African Americans

While a larger portion of African ancestry in African Americans is associated with higher probability of obesity, a larger portion of African ancestry in a particular locus actually reduced the probability of obesity. This underscores the importance of not relying on first-order approximations (racial identity) when more detailed information is available.

From the paper:
We have carried out admixture mapping analyses to search for genomic regions associated with BMI. This pooled analysis of samples from 14 studies is the largest admixture scan reported to date. In more than 15,000 individuals, we identified a locus on chromosome 5 where greater local European ancestry was associated with higher levels of BMI (P = 5.8×10−7), and two regions on chromosome X where greater local European ancestry was associated with lower levels of BMI (both P<5.0×10−6). Each of these three associations was above and beyond the contribution of genome-wide European ancestry, and each reached genome-wide significance.

...

The inverse correlation between BMI and percentage of European ancestry estimated on the genome-wide scale confirmed the results from previous studies of smaller sample size and fewer markers [29],[30]. However, while genome-wide ancestry is likely correlated with local ancestry, it cannot fully capture ancestry information at each locus as there exists variation across the genome in the effects of locus-specific ancestry on obesity. In particular, local European ancestry at 5q13.3 was positively associated with BMI, providing the first evidence of a genome-wide significant ancestry association being in the opposite direction to the overall epidemiological association.
PLoS Genetics doi:10.1371/journal.pgen.1000490

Admixture Mapping of 15,280 African Americans Identifies Obesity Susceptibility Loci on Chromosomes 5 and X

Ching-Yu Cheng et al.

Abstract

The prevalence of obesity (body mass index (BMI) ≥30 kg/m2) is higher in African Americans than in European Americans, even after adjustment for socioeconomic factors, suggesting that genetic factors may explain some of the difference. To identify genetic loci influencing BMI, we carried out a pooled analysis of genome-wide admixture mapping scans in 15,280 African Americans from 14 epidemiologic studies. Samples were genotyped at a median of 1,411 ancestry-informative markers. After adjusting for age, sex, and study, BMI was analyzed both as a dichotomized (top 20% versus bottom 20%) and a continuous trait. We found that a higher percentage of European ancestry was significantly correlated with lower BMI (ρ = −0.042, P = 1.6×10−7). In the dichotomized analysis, we detected two loci on chromosome X as associated with increased African ancestry: the first at Xq25 (locus-specific LOD = 5.94; genome-wide score = 3.22; case-control Z = −3.94); and the second at Xq13.1 (locus-specific LOD = 2.22; case-control Z = −4.62). Quantitative analysis identified a third locus at 5q13.3 where higher BMI was highly significantly associated with greater European ancestry (locus-specific LOD = 6.27; genome-wide score = 3.46). Further mapping studies with dense sets of markers will be necessary to identify the alleles in these regions of chromosomes X and 5 that may be associated with variation in BMI.

Link

May 23, 2009

Y chromosome population structure in Arabian peninsula

On the left, the MDS plot of genetic distances in studied populations and others from the literature. The haplotypes are available in free supplementary material (pdf). Someone ought to feed these to Whit Athey's haplogroup predictor to get estimates of the haplogroup composition of the Arabian populations.

Hum Hered 2009;68:45-54 (DOI: 10.1159/000210448)

Local Population Structure in Arabian Peninsula Revealed by Y-STR Diversity

Farida Alshamali et al.

Abstract

Genetic studies have been underway on Arabian Peninsula populations because of their pivotal geographic location for population migration and times of occurrence. To assist in better understanding population dynamics in this region, evidence is presented herein on local population structure in the Arabian Peninsula, based on Y-STR characterisation in four Arabian samples and its comparison in a broad geographical scale. Our results demonstrate that geography played an important role in shaping the genetic structure of the region around the Near-East. Populations are grouped regionally but none of these groups is significantly differentiated from others and all groups merge in the Near-East, in keeping with this important migration corridor for the human species. Focusing on the Arabian Peninsula, we show that Dubai and Oman share genetic affinities with other Near-Eastern populations, while Saudi Arabia and Yemen show a relative distinctive isolated background. Those two populations may have been kept relatively separated from migration routes, maybe due to their location in a desert area.

Link

May 22, 2009

Macedonia Evidence initiative

A very worthwhile effort. From the About section of the website:

Classical Scholars from around the world, well known for their expertise in the history of Greece are presenting, examining, and discussing the historical evidence.

The first few scholars were motivated by the article in the Archaeology magazine, and the letter Stephen G. Miller, Ph.D sent in response, which Archaeology did not publish.

Since then, the list of scholars that have examined the evidence has been growing and 222 scholars have undersigned the letter to President Barak Obama.

If you want to contribute to the discussion, please contact us at: SavingAlexander@macedonia-evidence.org.

The text of the letter:

Dear President Obama,

We, the undersigned scholars of Graeco-Roman antiquity, respectfully request that you intervene to clean up some of the historical debris left in southeast Europe by the previous U.S. administration.

On November 4, 2004, two days after the re-election of President George W. Bush, his administration unilaterally recognized the “Republic of Macedonia.” This action not only abrogated geographic and historic fact, but it also has unleashed a dangerous epidemic of historical revisionism, of which the most obvious symptom is the misappropriation by the government in Skopje of the most famous of Macedonians, Alexander the Great.

We believe that this silliness has gone too far, and that the U.S.A. has no business in supporting the subversion of history. Let us review facts. (The documentation for these facts [here in boldface] can be found attached and at: http://macedonia-evidence.org/documentation.html)

The land in question, with its modern capital at Skopje, was called Paionia in antiquity. Mts. Barnous and Orbelos (which form today the northern limits of Greece) provide a natural barrier that separated, and separates, Macedonia from its northern neighbor. The only real connection is along the Axios/Vardar River and even this valley “does not form a line of communication because it is divided by gorges.”

While it is true that the Paionians were subdued by Philip II, father of Alexander, in 358 B.C. they were not Macedonians and did not live in Macedonia. Likewise, for example, the Egyptians, who were subdued by Alexander, may have been ruled by Macedonians, including the famous Cleopatra, but they were never Macedonians themselves, and Egypt was never called Macedonia.

Rather, Macedonia and Macedonian Greeks have been located for at least 2,500 years just where the modern Greek province of Macedonia is. Exactly this same relationship is true for Attica and Athenian Greeks, Argos and Argive Greeks, Corinth and Corinthian Greeks, etc.

We do not understand how the modern inhabitants of ancient Paionia, who speak Slavic – a language introduced into the Balkans about a millennium after the death of Alexander – can claim him as their national hero. Alexander the Great was thoroughly and indisputably Greek. His great-great-great grandfather, Alexander I, competed in the Olympic Games where participation was limited to Greeks.

Even before Alexander I, the Macedonians traced their ancestry to Argos, and many of their kings used the head of Herakles - the quintessential Greek hero - on their coins.

Euripides – who died and was buried in Macedonia– wrote his play Archelaos in honor of the great-uncle of Alexander, and in Greek. While in Macedonia, Euripides also wrote the Bacchai, again in Greek. Presumably the Macedonian audience could understand what he wrote and what they heard.

Alexander’s father, Philip, won several equestrian victories at Olympia and Delphi, the two most Hellenic of all the sanctuaries in ancient Greece where non-Greeks were not allowed to compete. Even more significantly, Philip was appointed to conduct the Pythian Games at Delphi in 346 B.C. In other words, Alexander the Great’s father and his ancestors were thoroughly Greek. Greek was the language used by Demosthenes and his delegation from Athens when they paid visits to Philip, also in 346 B.C. Another northern Greek, Aristotle, went off to study for nearly 20 years in the Academy of Plato. Aristotle subsequently returned to Macedonia and became the tutor of Alexander III. They used Greek in their classroom which can still be seen near Naoussa in Macedonia.

Alexander carried with him throughout his conquests Aristotle’s edition of Homer’s Iliad. Alexander also spread Greek language and culture throughout his empire, founding cities and establishing centers of learning. Hence inscriptions concerning such typical Greek institutions as the gymnasium are found as far away as Afghanistan. They are all written in Greek.

The questions follow: Why was Greek the lingua franca all over Alexander’s empire if he was a “Macedonian”? Why was the New Testament, for example, written in Greek?

The answers are clear: Alexander the Great was Greek, not Slavic, and Slavs and their language were nowhere near Alexander or his homeland until 1000 years later. This brings us back to the geographic area known in antiquity as Paionia. Why would the people who live there now call themselves Macedonians and their land Macedonia? Why would they abduct a completely Greek figure and make him their national hero?

The ancient Paionians may or may not have been Greek, but they certainly became Greekish, and they were never Slavs. They were also not Macedonians. Ancient Paionia was a part of the Macedonian Empire. So were Ionia and Syria and Palestine and Egypt and Mesopotamia and Babylonia and Bactria and many more. They may thus have become “Macedonian” temporarily, but none was ever “Macedonia”. The theft of Philip and Alexander by a land that was never Macedonia cannot be justified.

The traditions of ancient Paionia could be adopted by the current residents of that geographical area with considerable justification. But the extension of the geographic term “Macedonia” to cover southern Yugoslavia cannot. Even in the late 19th century, this misuse implied unhealthy territorial aspirations.

The same motivation is to be seen in school maps that show the pseudo-greater Macedonia, stretching from Skopje to Mt. Olympus and labeled in Slavic. The same map and its claims are in calendars, bumper stickers, bank notes, etc., that have been circulating in the new state ever since it declared its independence from Yugoslavia in 1991. Why would a poor land-locked new state attempt such historical nonsense? Why would it brazenly mock and provoke its neighbor?

However one might like to characterize such behavior, it is clearly not a force for historical accuracy, nor for stability in the Balkans. It is sad that the United States of America has abetted and encouraged such behavior.

We call upon you, Mr. President, to help - in whatever ways you deem appropriate - the government in Skopje to understand that it cannot build a national identity at the expense of historic truth. Our common international society cannot survive when history is ignored, much less when history is fabricated.

The Frequently Asked Questions are worth reading too.

May 21, 2009

Female mice prefer outbred males

BMC Evol Biol. 2009 May 16;9(1):104. [Epub ahead of print]

Females prefer the scent of outbred males: good-genes-as-heterozygosity?

Ilmonen P, Stundner G, Thosz M, Penn DJ.

ABSTRACT: BACKGROUND: There is increasing interest to determine the relative importance of non-additive genetic benefits as opposed to additive ones for the evolution of mating preferences and maintenance of genetic variation in sexual ornaments. The 'good-genes-as-heterozygosity' hypothesis predicts that females should prefer to mate with more heterozygous males to gain more heterozygous (and less inbred) offspring. Heterozygosity increases males' sexual ornamentation, mating success and reproduction success, yet few experiments have tested whether females are preferentially attracted to heterozygous males, and none have tested whether females' own heterozygosity influences their preferences. Outbred females might have the luxury of being more choosey, but on the other hand, inbred females might have more to gain by mating with heterozygous males. We manipulated heterozygosity in wild-derived house mice (Mus musculus musculus) through inbreeding and tested whether the females are more attracted to the scent of outbred versus inbred males, and whether females' own inbreeding status affects their preferences. We also tested whether infecting both inbred and outbred males with Salmonella would magnify females' preferences for outbred males. RESULTS: Females showed a significant preference for outbred males, and this preference was slightly more pronounced among inbred females. We found no evidence that Salmonella infection increased the relative attractiveness of outbred versus inbred males; however, we found no evidence that inbreeding affected males' disease resistance in this study. CONCLUSIONS: Our findings support the idea that females are more attracted to outbred males, and they suggest that such preferences may be stronger among inbred than outbred females, which is consistent with the 'good-genes-as-heterozygosity' hypothesis. It is unclear whether this odour preference reflects females' actual mating preferences, though it suggests that future studies should consider females' as well as males' heterozygosity. Our study has implications for efforts to understand how mate choice can provide genetic benefits without eroding genetic diversity (lek paradox), and also conservation efforts to determine the fitness consequences of inbreeding and the maintenance of genetic diversity in small, inbred populations.

Link

May 20, 2009

Review paper on Y-chromosome haplogroup E-M35 (Lancaster 2009)

This is quite useful as a reference for those interested in E-M35 and its many subclades.

A quick comment on p. 53 where Sicily is discussed and the prevalence of R1b and I1 in the West is mentioned in the context of Phoenicians who settled in West Sicily.

Haplogroup I1 is probably to a large degree due to the Normans whose capital was in Palermo (NW Sicily). R1b on the other hand may have been added by the Normans, but may also be due to the pre-Greek populations of Sicily, such as the Sicani who were (after Herodotus) of Iberian origin.

Journal of Genetic Genealogy Volume 5, Number 1, Spring, 2009

Y Haplogroups, Archaeological Cultures and Language Families: A Review of the Possibility of Multidisciplinary Comparisons Using the Case of Haplogroup E-M35

Andrew Lancaster

Abstract

Archaeology, comparative linguistics and population genetics all have something to add to speculation about early human migrations, and the three disciplines often make reference to each other in broad terms. But, in reality, the results are often disappointingly indecisive. This article explores the case of Y haplogroup E-M35 (E1b1b1), which has so far mainly only been mentioned in a passing way in archaeological and linguistic debate, but which, it shall be shown, shows great promise as more detailed about it's phylogenetic structure, and its regional distribution becomes available each year.

Link (pdf)