Literature review of Sub-Saharan African IQ

Intelligence doi:10.1016/j.intell.2009.05.002

A systematic literature review of the average IQ of sub-Saharan Africans

Jelte M. Wicherts et al.

Abstract

On the basis of several reviews of the literature, Lynn [Lynn, R., (2006). Race differences in intelligence: An evolutionary analysis. Augusta, GA: Washington Summit Publishers.] and Lynn and Vanhanen [Lynn, R., & Vanhanen, T., (2006). IQ and global inequality. Augusta, GA: Washington Summit Publishers.] concluded that the average IQ of the Black population of sub-Saharan Africa lies below 70. In this paper, the authors systematically review published empirical data on the performance of Africans on the following IQ tests: Draw-A-Man (DAM) test, Kaufman-Assessment Battery for Children (K-ABC), the Wechsler scales (WAIS & WISC), and several other IQ tests (but not the Raven's tests). Inclusion and exclusion criteria are explicitly discussed. Results show that average IQ of Africans on these tests is approximately 82 when compared to UK norms. We provide estimates of the average IQ per country and estimates on the basis of alternative inclusion criteria. Our estimate of average IQ converges with the finding that national IQs of sub-Saharan African countries as predicted from several international studies of student achievement are around 82. It is suggested that this estimate should be considered in light of the Flynn Effect. It is concluded that more psychometric studies are needed to address the issue of measurement bias of western IQ tests for Africans.

Link

mtDNA of Native Mexicans

Human Genetics doi:10.1007/s00439-009-0693-y

Linguistic and maternal genetic diversity are not correlated in Native Mexicans

Karla Sandoval et al.

Abstract

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.

Link

Craniofacial norms of Malays

Singapore Med J. 2009 May;50(5):525-8.

Craniofacial anthropometric norms of Malays

Ngeow WC, Aljunid ST.

INTRODUCTION: This study was undertaken to establish the craniofacial anthropometric norms of young adult Malaysian Malays. METHODS: The study group consisted of convenient samples of 100 healthy volunteers (aged 18-25 years), with an equal number of female and male subjects who had no history of mixed racial parentage. 22 linear measurements were taken twice from 22 landmarks over six craniofacial regions. RESULTS: The Malays shared many similar sizes of measurements with the Singaporean Chinese. Their left eye fissure length and mouth width (ch-ch) were almost identical for both genders. However, Malay females had an upper lip height (sn-sto) (left) and ear width (pra-pa) similar to Singaporean Chinese females. Six other measurements, viz. the head width (eu-eu), head circumference (on-op), face height (n-gn), lower face height (sn-gn), (left) eye fissure height (ps-pi), cutaneous upper lip height (sn-ls) and cutaneous upper lip height (ls-sto), were 0.4-4.3 mm less in the Malays. Measurements for another four parameters, viz. the length of the head (g-op), biocular width (ex-ex), lower vermillion height (sto-li) and (left) ear length (sa-sba), were 0.5-3.6 mm higher in the Malays. Only three measurements were obviously different; the height of the head (v-n) and intercanthal width (en-en), were lower, and the protrusion of the nasal tip (sn-prn) was higher in the Malays. CONCLUSION: These findings suggest that three features, i.e. the height of the head (v-n), intercanthal width (en-en) and protrusion of the nasal tip (sn-prn) may be useful in differentiating a Malay face from a Singaporean Chinese one.

Link

Lactase persistence in Greece and Italy

From the paper:

Furthermore, they indicate the existence of a genetic heterogeneity in Italy, in accordance with previous studies on classical markers (Piazza et al., 1988) and Y-chromosome (Capelli et al., 2007; see also Francalacci and Sanna, 2008). On the contrary, a substantial homogeneity was detected among Greek groups (Supporting Information Table S3), which is congruent with the only previous genetic study conducted in Greece on a multiregional scale (Di Giacomo et al., 2003).

The occurrence of lactase persistence in Greece and Southern Italy is virtually the same, which is not very surprising given the origins of the latter population.

American Journal of Human Biology Volume 21 Issue 2, Pages 217 - 219, doi:10.1002/ajhb.20851

Tracing the distribution and evolution of lactase persistence in Southern Europe through the study of the T_-13910 variant

Paolo Anagnostou et al.

Abstract

We investigated the occurrence and intra-allelic variability of the T-13910 variant located upstream of the lactase gene in 965 individuals from 20 different locations of Italy and Greece. The T-13910 frequency ranges from 0.072 (Sardinia) to 0.237 (North-East Italy), with a statistically significant difference between North-East Italians and other Italian populations. The comparison of the lactose tolerance predicted by T-13910 and that assessed by other studies using physiological tests shows a one-way statistically significant discrepancy that could be due to sampling differences. However, the possible role of other genetic factors underlying lactase persistence is worth exploring. The time of the most recent common ancestor and departures from neutrality of the T-13910 allele were assessed using three microsatellite loci. Time estimates were found to be congruent with the appearance of dairy farming in Southern Europe and the occurrence of a single introgression event. Robust signals of selection can be observed in North-East Italy only. We discuss the possible role of cultural traits and genetic history in determining these observed micro-evolutionary patterns.

Link

MAOA and gang membership/weapon use

Comprehensive Psychiatry doi:10.1016/j.comppsych.2009.03.010

Monoamine oxidase A genotype is associated with gang membership and weapon use

Kevin M. Beaver et al.

Abstract

Context

A functional polymorphism in the promoter region of the monoamine oxidase A (MAOA) gene has been found to be associated with a broad range of antisocial phenotypes, including physical violence. At the same time, it is well known that gang members represent some of the most serious violent offenders. Even so, no research has ever examined the association between MAOA and gang membership.

Objectives

The aim of this study is to examine the association between MAOA and gang membership and between MAOA and weapon use.

Design

We examined the effects of MAOA by using a molecular genetic association research design.

Setting

A nonclinical sample was used in this study.

Participants

Participants were drawn from the National Longitudinal Study of Adolescent Health (1155 females, 1041 males).

Main Outcome Measures

The outcome measures of this study are gang membership and weapon use.

Results

The low MAOA activity alleles conferred an increased risk of joining a gang and using a weapon in a fight for males but not for females. Moreover, among male gang members, those who used weapons in a fight were more likely to have a low MAOA activity allele when compared with male gang members who do not use weapons in a fight.

Conclusions

Male carriers of low MAOA activity alleles are at risk for becoming a gang member and, once a gang member, are at risk for using weapons in a fight.

Link

YHRD updated germline mutation rates

YHRD has updated with new mutation rates for Y-STR loci. This is an invaluable resource, as it pools mutation rates from all published studies to produce an overall rate based on a large sample. 

As I have argued elsewhere, uncertainty about the mutation rate is one of the major sources of uncertainty about age estimates of Y-chromosome common ancestors. Hopefully more researchers will start using these rates (as e.g., Di Gaetano et al. did) rather than those picked from single papers of the literature, especially "evolutionary" ones.

Geography and human adaptation (Coop et al. 2009)

From the paper:

More generally, alleles that strongly differentiate the French from both the Han and Yoruba (Figure 3D) are typically present at high frequency across all of Europe, the Middle East and South Asia (an area defined here as “west Eurasia”), and at low frequency elsewhere. This pattern of sharing across the west Eurasian populations is highly consistent with observations from random markers showing that the populations in west Eurasia form a single cluster in some analyses of worldwide population structure [40]. Allele frequencies at high- FST SNPs in two central Asian populations, the Uygur and Hazara, tend to be intermediate between west Eurasia and east Asia, consistent with observations that these populations have recent mixed ancestry between west Eurasia and east Asia [38],[40],[66].

From Figure 3: "frequency distributions for 50 of the most extreme SNPs genome-wide in the following pairs of comparisons: (A, B): SNPs for which Yoruba are highly differentiated from both Han and French; (C, D): French are differentiated from Yoruba and Han; (E, F): Han are differentiated from Yoruba and French."

From the paper:

Our results therefore suggest that local adaptation is tightly constrained by the ancestral relationships and migration rates among populations. It seems likely that selection in humans is generally not divergent enough to generate large frequency differences at individual loci between population pairs that are either recently separated, or regularly exchange migrants [53],[54]. Furthermore, populations may be too mobile, or their identities too fluid, to experience very localized pressures consistently over the several thousand years that may be required for large allele frequency changes.

However in contrast, it seems that selected alleles may not spread effectively between broad geographic regions (see Figure 3, Supplementary Figure 15 in Text S1 and [21]). Perhaps this is because populations usually adapt to similar selection pressures by parallel mutation [18],[23],[25] rather than by the spread of migrants between regions [72],[73].

UPDATE (June 5)

From the public release:

In recent years, geneticists have identified a handful of genes that have helped human populations adapt to new environments within just a few thousand years—a strikingly short timescale in evolutionary terms. However, the team found that for most genes, it can take at least 50,000-100,000 years for natural selection to spread favorable traits through a human population. According to their analysis, gene variants tend to be distributed throughout the world in patterns that reflect ancient population movements and other aspects of population history. "We don't think that selection has been strong enough to completely fine-tune the adaptation of individual human populations to their local environments," says co-author Jonathan Pritchard. "In addition to selection, demographic history -- how populations have moved around -- has exerted a strong effect on the distribution of variants."

To determine whether the frequency of a particular variant resulted from natural selection, Pritchard and his colleagues compared the distribution of variants in parts of the genome that affect the structure and regulation of proteins to the distribution of variants in parts of the genome that do not affect proteins. Since these neutral parts of the genome are less likely to be affected by natural selection, they reasoned that studying variants in these regions should reflect the demographic history of populations.

The researchers found that many previously identified genetic signals of selection may have been created by historical and demographic factors rather than by selection. When the team compared closely related populations they found few large genetic differences. If the individual populations' environments were exerting strong selective pressure, such differences should have been apparent.

Selection may still be occurring in many regions of the genome, says Pritchard. But if so, it is exerting a moderate effect on many genes that together influence a biological characteristic. "We don't know enough yet about the genetics of most human traits to be able to pick out all of the relevant variation," says Pritchard. "As functional studies go forward, people will start figuring out the phenotypes that are associated with selective signals," says lead author Graham Coop. "That will be very important, because then we can figure out what selection pressures underlie these episodes of natural selection."

Gene Expression has a long post on this study.

PLoS Genetics doi:10.1371/journal.pgen.1000500

The Role of Geography in Human Adaptation

Graham Coop et al.

Abstract

Various observations argue for a role of adaptation in recent human evolution, including results from genome-wide studies and analyses of selection signals at candidate genes. Here, we use genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of putatively selected alleles at a range of geographic scales. We find that the average allele frequency divergence is highly predictive of the most extreme FST values across the whole genome. On a broad scale, the geographic distribution of putatively selected alleles almost invariably conforms to population clusters identified using randomly chosen genetic markers. Given this structure, there are surprisingly few fixed or nearly fixed differences between human populations. Among the nearly fixed differences that do exist, nearly all are due to fixation events that occurred outside of Africa, and most appear in East Asia. These patterns suggest that selection is often weak enough that neutral processes—especially population history, migration, and drift—exert powerful influences over the fate and geographic distribution of selected alleles.

Link

Regional population structure in Iceland (Price et al. 2009)

In 2008 Ethnicity Struck Back, but in 2009, it already seems we're well on our way to finding the structure within ethnic groups themselves, as was possible in Sardinia and Estonia.

A new paper shows that such structure exists in Iceland, a population often used for association studies, because of its presumed homogeneity.

Individuals with most of their ancestry from one of several regions tend to cluster together in the PCA plot (top), but "random" individuals with ancestry from many regions tend to be all over the map. 

From the paper:

The ancestry predictions were correct for 47% of samples, correct to within a distance of one region for 74% of samples, and correct to within a distance of two regions for 93% of samples. The accuracy increased to 58% (87% to within one region, 97% to within two regions) when restricting to the 98 (of 250) samples with at least 16 of 32 ancestors from a single region.

Figure 3 shows the Icelandic populations in the context of Scotland and Norway. From the paper:

Based on the available data, the optimal linear combination yielded an estimate of 64% Norse and 36% Scottish ancestry, with a standard error of less than 2%.  [...] For each region, the estimate of Norse ancestry was between 62% and 65%, with a standard error of less than 2% (except region 1, for which we obtained 61% with a standard error of less than 3%).

Admixture took place so long ago, that it has spread evenly across Iceland, with no regions being particularly "Norse" or "Scottish" in ancestry. But, while the ancestral components are regionally the same, it is clear from the accuracy of region estimates that the various populations of Icelanders have not been panmictic, and thus some barriers to gene flow even in this very homogeneous population has allowed for the emergence of regional structure.

Finally:

A consequence of the recent origin of the genetic differences between Icelandic subpopulations is that allele frequency differences follow the null distribution predicted by neutral drift. Thus, there is little risk of false positive associations due to population stratification in disease association studies, despite the fact that there are genuine differences between regions.

PLoS Genetics doi:10.1371/journal.pgen.1000505

The Impact of Divergence Time on the Nature of Population Structure: An Example from Iceland

Alkes Price et al.

Abstract

The Icelandic population has been sampled in many disease association studies, providing a strong motivation to understand the structure of this population and its ramifications for disease gene mapping. Previous work using 40 microsatellites showed that the Icelandic population is relatively homogeneous, but exhibits subtle population structure that can bias disease association statistics. Here, we show that regional geographic ancestries of individuals from Iceland can be distinguished using 292,289 autosomal single-nucleotide polymorphisms (SNPs). We further show that subpopulation differences are due to genetic drift since the settlement of Iceland 1100 years ago, and not to varying contributions from different ancestral populations. A consequence of the recent origin of Icelandic population structure is that allele frequency differences follow a null distribution devoid of outliers, so that the risk of false positive associations due to stratification is minimal. Our results highlight an important distinction between population differences attributable to recent drift and those arising from more ancient divergence, which has implications both for association studies and for efforts to detect natural selection using population differentiation.

Link

Population density and cultural complexity (Powell et al. 2009)

From ScienceDaily:

High population density leads to greater exchange of ideas and skills and prevents the loss of new innovations. It is this skill maintenance, combined with a greater probability of useful innovations, that led to modern human behaviour appearing at different times in different parts of the world.

In the study, the UCL team found that complex skills learnt across generations can only be maintained when there is a critical level of interaction between people. Using computer simulations of social learning, they showed that high and low-skilled groups could coexist over long periods of time and that the degree of skill they maintained depended on local population density or the degree of migration between them. Using genetic estimates of population size in the past, the team went on to show that density was similar in sub-Saharan Africa, Europe and the Middle-East when modern behaviour first appeared in each of these regions. The paper also points to evidence that population density would have dropped for climatic reasons at the time when modern human behaviour temporarily disappeared in sub-Saharan Africa.

Science doi:10.1126/science.1170165

Late Pleistocene Demography and the Appearance of Modern Human Behavior

Adam Powell et al.

Abstract

The origins of modern human behavior are marked by increased symbolic and technological complexity in the archaeological record. In western Eurasia this transition, the Upper Paleolithic, occurred about 45,000 years ago, but many of its features appear transiently in southern Africa about 45,000 years earlier. We show that demography is a major determinant in the maintenance of cultural complexity and that variation in regional subpopulation density and/or migratory activity results in spatial structuring of cultural skill accumulation. Genetic estimates of regional population size over time show that densities in early Upper Paleolithic Europe were similar to those in sub-Saharan Africa when modern behavior first appeared. Demographic factors can thus explain geographic variation in the timing of the first appearance of modern behavior without invoking increased cognitive capacity.

Link

mtDNA haplogroup U5b3 (Pala et al. 2009)

As always, time estimates depend on the mutation rate used:

Because the mutation rate of Mishmar et al.37 is probably an overestimate, mainly caused by partial saturation of some synonymous mutations,40 and that of Kivisild et al.39 represents an underestimate,41 we used the intermediate global coalescence time of modern human mtDNA recently proposed by Perego et al.42 as a reference point for the internal calibration of both approaches. Accordingly, we converted the haplogroup sequence divergences into time estimates by using averaged time calibrations corresponding to 4610 years per coding-region substitution and 7650 years per synonymous transition (Table 1). With this approach, the coalescence time estimates for the entire U5b3 are between 10.1 ky and 8.1 ky.

See Time dependency of the human mtDNA evolutionary mutation rate for some discussion of mutation rates and archaeological correlations, and the newer paper on Purifying selection and the mtDNA clock.

American Journal of Human Genetics doi:10.1016/j.ajhg.2009.05.004

Mitochondrial Haplogroup U5b3: A Distant Echo of the Epipaleolithic in Italy and the Legacy of the Early Sardinians

Maria Pala et al.

Abstract

There are extensive data indicating that some glacial refuge zones of southern Europe (Franco-Cantabria, Balkans, and Ukraine) were major genetic sources for the human recolonization of the continent at the beginning of the Holocene. Intriguingly, there is no genetic evidence that the refuge area located in the Italian Peninsula contributed to this process. Here we show, through phylogeographic analyses of mitochondrial DNA (mtDNA) variation performed at the highest level of molecular resolution (52 entire mitochondrial genomes), that the most likely homeland for U5b3a haplogroup present at a very low frequency across Europewas the Italian Peninsula. In contrast to mtDNA haplogroups that expanded from other refugia, the Holocene expansion of haplogroup U5b3 toward the North was restricted by the Alps and occurred only along the Mediterranean coasts, mainly toward nearby Provence (southern France). From there, 7,0009,000 years ago, a subclade of this haplogroup moved to Sardinia, possibly as a result of the obsidian trade that linked the two regions, leaving a distinctive signature in the modern people of the island. This scenario strikingly matches the age, distribution, and postulated geographic source of a Sardinian Y chromosome haplogroup (I2a2-M26), a paradigmatic case in the European context of a founder event marking both female and male lineages.

Link

Purifying selection and the mtDNA clock (Soares et al. 2009)

This paper deals with the problem of a time-varying mutation rate due to purifying selection, i.e., the removal of harmful variation from the mtDNA gene pool.

From the paper:

Thus, it estimates the coalescence time of the mtDNA tree overall at ~160,000 kya, L3 (the clade that evolved within Africa and gave rise to the three major non-African haplogroups—sometimes termed ‘‘macrohaplogroups’’— M, N, and R) at 65 kya, and M, N, and R themselves at 40–50 kya.

...

In any event, L3 probably expanded ~70 kya, possibly associated with an improvement of the climatic conditions around that time after a long period of drought.103 There are no ‘‘pre-M’’ or ‘‘pre-N’’ clades extant either within or outside Africa, so the out-of-Africa event could be as early as the coalescence time of L3. These data render an outof- Africa dispersal prior to the Toba eruption in Sumatra at ~74 kya less likely.

...

the age of haplogroup M in India, at 49.4 (39.0; 60.2) kya, is significantly lower than in East Asia, at 60.6 (47.3; 74.3) kya (both are lower in r but the proportional
difference is similar; see Table 3).

...

Europe was first settled by modern humans ~45 kya, and it is believed that one of the branches of U, U5 or a genetically close ancestor to U5, arose among the first settlers. The ML estimate of haplogroup U5 is 36.0 (25.3; 47.2) kya, and lower with r at 30.7 (21.4; 40.5) kya and 33.0 (13.3; 52.8) with our synonymous rate. [...] The closest link in the tree with the Near East is the root of haplogroup U, placing any early migration into Europe involving U5 or its ancestors between ~55 kya and ~30 kya.

The new chronology of human mtDNA. As you can see, about 2/3 of the age of mtDNA represents within-Africa variation. L3 Africans and Eurasians are much closer related (matrilineally) than they are with any other Africans. The next closest relation is with L2 Africans, separated by L3's by ~43ky.



American Journal of Human Genetics doi:10.1016/j.ajhg.2009.05.001

Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

Pedro Soares et al.

Abstract

There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at 15 kya that - unlike the uncorrected clock - matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 5570 kya, 520 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses.

Link

Y chromosome haplogroup G phylogeny updated (Sims et al. 2009)

Figure 1 has the updated phylogeny with the new SNPs.

PLoS ONE doi:10.1371/journal.pone.0005792.g001

Improved Resolution Haplogroup G Phylogeny in the Y Chromosome, Revealed by a Set of Newly Characterized SNPs

Lynn M. Sims et al.

Abstract

Background

Y-SNP haplogroup G (hgG), defined by Y-SNP marker M201, is relatively uncommon in the United States general population, with only 8 additional sub-markers characterized. Many of the previously described eight sub-markers are either very rare (2–4%) or do not distinguish between major populations within this hg. In fact, prior to the current study, only 2% of our reference Caucasian population belonged to hgG and all of these individuals were in sub-haplogroup G2a, defined by P15. Additional Y-SNPs are needed in order to differentiate between individuals within this haplogroup.

Principal Findings

In this work we have investigated whether we could differentiate between a population of 63 hgG individuals using previously uncharacterized Y-SNPs. We have designed assays to test these individuals using all known hgG SNPs (n = 9) and an additional 16 unreported/undefined Y-SNPS. Using a combination of DNA sequence and genetic genealogy databases, we have uncovered a total of 15 new hgG SNPs that had been previously reported but not phylogenetically characterized. Ten of the new Y-SNPs are phylogenetically equivalent to M201, one is equivalent to P15 and, interestingly, four create new, separate haplogroups. Three of the latter are more common than many of the previously defined Y-SNPs. Y-STR data from these individuals show that DYS385*12 is present in (70%) of G2a3b1-U13 individuals while only 4% of non-G2a3b1-U13 individuals posses the DYS385*12 allele.

Conclusions

This study uncovered several previously undefined Y-SNPs by using data from several database sources. The new Y-SNPs revealed in this paper will be of importance to those with research interests in population biology and human evolution.

Link

Birth size and IQ in Asian children

2.19 IQ points for an extra kg of birth weight seems quite meager.

Pediatrics. 2009 Jun;123(6):e1011-e1016.

The Influence of Birth Size on Intelligence in Healthy Children.

Broekman BF, Chan YH, Chong YS, Quek SC, Fung D, Low YL, Ooi YP, Gluckman PD, Meaney MJ, Wong TY, Saw SM.

OBJECTIVE. Birth parameters have been hypothesized to have an influence on IQ. However, studies within the range of normal birth size have been sparse. With this study we examined the associations between birth length, birth weight, head circumference, and gestational age within the normal birth size range in relation to childhood IQ in Asian children. METHODS. A cohort of 1979 of 2913 Asian children aged 7 to 9 years, recruited from 3 schools in Singapore, were followed yearly from 1999 onward. Birth parameters were recorded by health personnel. Childhood IQ was measured with the Raven's Standard Progressive Matrices at ages 8 to 12. RESULTS. The mean IQ score across the sample (n = 1645) was 114.2. After controlling for multiple confounders for every 1-cm increment in birth length, 1 kg in birth weight, or 1 cm in head circumference, there was a corresponding increase in IQ of 0.49 points (P for trend less than .001), 2.19 points (P for trend = .007) and .62 points (P for trend = .003), respectively. These associations persisted even after exclusion of premature children and children with extreme weights and head circumferences. CONCLUSIONS. Longer birth length, higher birth weight, or larger head circumferences within the normal birth size range are associated with higher IQ scores in Asian children. Our results suggest that antenatal factors reflected in altered rates of growth but within the normative range of pregnancy experiences play a role in generating cognitive potential. This has implications for targeting early intervention and preventative programs.

Link

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

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