September 26, 2007

Greater genetic drift in East Asians than in Europeans

Nature Genetics 39, 1251 - 1255 (2007)
Published online: 9 September 2007 | doi:10.1038/ng2116

Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans

Alon Keinan et al.

Large data sets on human genetic variation have been collected recently, but their usefulness for learning about history and natural selection has been limited by biases in the ways polymorphisms were chosen. We report large subsets of SNPs from the International HapMap Project1, 2 that allow us to overcome these biases and to provide accurate measurement of a quantity of crucial importance for understanding genetic variation: the allele frequency spectrum. Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians.


Anthropometric correlates of IQ

A reader alerted me to this study which re-examined Hooton's data on anthropometric correlates of IQ. Interestingly, sitting height correlates with IQ almost as strongly as (full) height, indicating that a long torso rather than long limbs is associated with statistically higher IQ.

Personality and Individual Differences

Head size correlates with IQ in a sample of Hooton’s criminal data

Jeremy E.C. Genovese


Data collected by Hooton (1939) on 676 inmates held at the Concord Reformatory in Massachusetts include both anthropometric measures and IQ scores. In this study a sample (N = 238) was drawn to assess the nonparametric correlation between measures of head size and IQ. Head length (r = .13), breadth (r = .15), height (r = .14), circumference (r = .15) and calculated volume (r = .20) correlated with IQ. Two measures of body size also correlated with IQ; height (r = .22) and sitting height (r = .19).


September 25, 2007

Deep voiced-men have more children

You might want to read the blog post on What is your voice pitch after reading this article.

Biology Letters

Voice pitch predicts reproductive success in male hunter-gatherers

C.L. Apicella et al.

The validity of evolutionary explanations of vocal sexual dimorphism hinges upon whether or not individuals with more sexually dimorphic voices have higher reproductive success than individuals with less dimorphic voices. However, due to modern birth control methods, these data are rarely described, and mating success is often used as a second-rate proxy. Here, we test whether voice pitch predicts reproductive success, number of children born and child mortality in an evolutionarily relevant population of hunter-gatherers. While we find that voice pitch is not related to reproductive outcomes in women, we find that men with low voice pitch have higher reproductive success and more children born to them. However, voice pitch in men does not predict child mortality. These findings suggest that the association between voice pitch and reproductive success in men is mediated by differential access to fecund women. Furthermore, they show that there is currently selection pressure for low-pitch voices in men.


September 06, 2007

YAP+ in South Asia

YAP+ defines haplogroup DE in the human Y chromosome phylogeny. Haplogroup D seems confined to a few Asian populations whereas haplogroup E is found in Africans and West Eurasians. Previous studies had determined that D is found at high frequencies among the short-statured isolated populations from the Andaman and Nicobar islands, and this new study indicates that D is also found in mainland South Asia among tribal Indians, albeit at lower frequencies.

Ann Hum Biol. 2007 Sep-Oct;34(5):582-6

YAP insertion signature in South Asia.

Chandrasekar A et al.

A total of 2169 samples from 21 tribal populations from different regions of India were scanned for the Y-chromosome Alu polymorphism. This study reports, for the first time, high frequencies (8-65%) of Y Alu polymorphic (YAP) insertion in northeast Indian tribes. All seven Jarawa samples from the Andaman and Nicobar islands had the YAP insertion, in conformity with an earlier study of Andaman Islanders. One isolated case with haplotype E* was found in Dungri Bhill, a western Indian population, while YAP insertion in northeast India and Andaman tribes was found in association with haplotype D* (M168, M174). YAP insertion frequencies reported in the mainland Indian populations are negligible, according to previous studies. Genetic drift may be the causative factor for the variable frequency of the YAP insertion in the mainland populations, while the founder effect may have resulted in the highest incidence of haplotype D among the Andaman Islanders. The results of YAP insertion and the evidence of previous mtDNA studies indicate an early out of Africa migration to the Andaman and Nicobar Islands. The findings of YAP insertion in northeast Indian tribes are very significant for understanding the evolutionary history of the region.

September 04, 2007

Middle Eastern origin of Neolithic pigs

Via the BBC Pig DNA reveals farming history:
Between 6,800-4,000 BC, farming methods spread across Europe, but the question of how these methods spread has not been fully established.

The two competing theories are that farming spread through cultural exchange, possibly during trading or that people migrated to Europe bringing their expertise with them.

A previous study, in 2005, analysed modern pig DNA and showed that all modern pigs are descended from European wild boar. This led researchers to conclude that early Europeans domesticated pigs independently of other farming methods.

This new study, however, has discovered that the first domesticated pigs in Europe did have Near Eastern ancestry, indicating that farmers migrated to Europe, bringing their "package" of livestock and farming methods with them.

Domestic pigs of European wild boar ancestry appear soon afterwards.

September 01, 2007

Structure of genetic variation in US populations

A new AJHG preprint looks at the genetic variation in different groups of the US population.

From the paper:
A frequent claim about human population structure is that most common variation
is shared among all populations11-13. This, of course, depends on how population
boundaries are defined, but often cited to support such comments are the comparisons of SNP frequencies in pairs of populations in the HapMap data and the Perlegen data. Analyses of these data indicated that common SNPs were frequently both shared and common among populations of predominately African, Asian, and European ancestry. However, population genetic analysis was not the intended goal of either the HapMap or the Perlegen projects, and common, shared SNPs were over sampled by the ascertainment strategies used for each project.
Also an interesting view of the genetic structure of the main US population groups.
C. Stacked bar chart inferred from results of model-based cluster analysis using STRUCTURE 2.0. Each bar represents an individual, and each bar is divided according to the fraction of cluster membership. D. Triangle plot illustrating the proportion of African, Asian, and European American ancestry of each individual (dots) estimated from STRUCTURE 2.0. (PC=principal component; AfA=African American; AsA=Asian American; EA=European Americans; HA=Latino/Hispanic Americans; MAF=minor allele frequency.)

The structure of common genetic variation in U.S. populations

Stephen L. Guthery et al.


The common variant/common disease model predicts that most risk alleles underlying complex health-related traits are common and therefore old and found in multiple populations, rather than rare or population-specific. Accordingly, there is widespread interest in assessing the population structure of common alleles. However, such assessments have been confounded by analysis of datasets with bias toward ascertainment of common alleles (e.g., HapMap, Perlegen) or in which a relatively small number of genes and/or populations were sampled. The aim of this study was to examine the structure of common variation ascertained in major U.S. populations by resequencing the exons and flanking regions of 3,873 genes in 154 chromosomes from European, Latino/Hispanic, Asian, and African Americans generated by the Genaissance Resequencing Project. The frequency distributions of private and
common single nucleotide polymorphisms (SNPs) were measured, and the extent to which common SNPs were shared across populations was analyzed using several different estimators of population structure. Most SNPs that were common in one population were present in multiple populations, but SNPs common in one population were frequently not common in other populations. Moreover, SNPs that were common in two or more populations often differed significantly in frequency from one another, particularly in comparisons of African Americans versus other U.S. populations. These findings indicate that even if the bulk of alleles underlying complex health-related traits are common SNPs, geographic ancestry might well be an important predictor of whether a person carries a risk allele.


Problems with Neanderthal genomic sequences

A new study freely available online throws into doubt the genomic sequences extracted from Neanderthal remains in two previous articles.

PLoS Genetics

Inconsistencies in Neanderthal genomic DNA sequences

Jeffrey D. Wall, Sung K. Kim

Two recently published papers describe nuclear DNA sequences that were obtained from the same Neanderthal fossil. Our reanalyses of the data from these studies show that they are not consistent with each other and point to serious problems with the data quality in one of the studies, possibly due to modern human DNA contaminants and/or a high rate of sequencing errors.