December 29, 2007

How Turkish are the Anatolians? (new Alu insertion polymorphism study)

In my 2005 blog post How Turkish are the Anatolians, I estimated, based on Y chromosome frequencies the Central Asian Turkic contribution to the modern-day Anatolians.
Using the figure of 38.5%, the paternal contribution of Turks to the Anatolian population is estimated to about 11%. In lieu of the approximation, allowing for 33% relative error in either direction for both the true frequency of Mongoloid lineages in Anatolia and in early Turks, we obtain a range of 6-22%. It would thus appear that the Turkish element is a minority one in the composition of the Anatolians, but it is by no means negligible.
In a subsequent post on Non-Caucasoid admixture in Turks I estimated that the combined (bi-parental) contribution of Mongoloids in Turks:
Based on these numbers, the non-Caucasoid admixture in Turks can be quantified as 1.87% Negroid, and 6.18% Mongoloid, total 8.05%.
Given that Central Asians, including the likely Turkic ancestors of modern-day Turkish-speaking Anatolians are partly Mongoloid, this later estimate is compatible with a genetic contribution similar to that quoted above.

So, I was pleased to see a new study based on a different set of autosomal Alu insertion polymorphisms from a group of Turkish scientists that arrived at a similar estimate of the Central Asian admixture in Anatolians. So, it appears that about 1/8 of ancestry of Anatolians (equivalent to one great grandparent) came from a Central Asian Turk.

It is very refreshing to see a paper by Turkish scientists who acknowledge what exactly that other 7/8 of the Anatolians' ancestry actually consists of:
Before Seljuks, Anatolia was under the rule of Eastern Romans but was mainly inhabited by people of Greek origin for nearly two millennia (Toynbee, 1970). The process of change of language and religion by the Seljuks that is assimilation of the residents but not the invaders in Anatolia, was one of the puzzles of history (Toynbee, 1970). As the part of puzzle, estimation of the relative size of arriving nomads was the concern of many studies.

American Journal of Physical Anthropology (online early) 10.1002/ajpa.20772

Alu insertion polymorphisms and an assessment of the genetic contribution of Central Asia to Anatolia with respect to the Balkans

Ceren Caner Berkman et al.

In the evolutionary history of modern humans, Anatolia acted as a bridge between the Caucasus, the Near East, and Europe. Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, nomadic groups from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. In the present study, insertion frequencies of 10 Alu loci (A25 = 0.07, APO = 0.96, TPA25 = 0.44, ACE = 0.37, B65 = 0.57, PV92 = 0.18, FXIIIB = 0.52, D1 = 0.40, HS4.32 = 0.66, and HS4.69 = 0.30) have been determined in the Anatolian population. Together with the data compiled from other databases, the similarity of the Anatolian population to that of the Balkans and Central Asia has been visualized by multidimensional scaling method. Analysis suggested that, genetically, Anatolia is more closely related with the Balkan populations than to the Central Asian populations. Central Asian contribution to Anatolia with respect to the Balkans was quantified with an admixture analysis. Furthermore, the association between the Central Asian contribution and the language replacement episode was examined by comparative analysis of the Central Asian contribution to Anatolia, Azerbaijan (another Turkic speaking country) and their neighbors. In the present study, the Central Asian contribution to Anatolia was estimated as 13%. This was the lowest value among the populations analyzed. This observation may be explained by Anatolia having the lowest migrant/resident ratio at the time of migrations.


December 22, 2007

South Asian chapter of human prehistory

Molecular Biology and Evolution, doi:10.1093/molbev/msm277

mtDNA Variation Predicts Population Size in Humans and Reveals a Major Southern Asian Chapter in Human Prehistory

Quentin D. Atkinson et al.

The relative timing and size of regional human population growth following our expansion from Africa remains unknown. Human mitochondrial DNA (mtDNA) diversity carries a legacy of our population history. Given a set of sequences, we can use coalescent theory to estimate past population size through time and draw inferences about human population history. However, recent work has challenged the validity of using mtDNA diversity to infer species population sizes. Here we use Bayesian coalescent inference methods, together with a global dataset of 357 human mtDNA coding region sequences, to infer human population sizes through time across eight major geographic regions. Our estimates of relative population sizes show remarkable concordance with the contemporary regional distribution of humans across Africa, Eurasia and the Americas, indicating that mtDNA diversity is a good predictor of population size in humans. Plots of population size through time show slow growth in sub-Saharan Africa beginning 143-193kya, followed by a rapid expansion into Eurasia after the emergence of the first non-African mtDNA lineages 50-70kya. Outside Africa, the earliest and fastest growth is inferred in Southern Asia ~52kya, followed by a succession of growth phases in Northern and Central Asia (~49kya), Australia (~48kya), Europe (~42kya), the Middle East and North Africa (~40kya), New Guinea (~39kya), the Americas (~18kya), and a second expansion in Europe (~10-15kya). Comparisons of relative regional population sizes through time suggest that between approximately 45kya and 20kya most of humanity lived in Southern Asia. These findings not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.


Y chromosomes and mtDNA in African farmers and hunter-gatherers

Molecular Biology and Evolution, doi:10.1093/molbev/msm279

Contrasting Signatures of Population Growth for Mitochondrial DNA and Y Chromosomes among Human Populations in Africa

Maya Metni Pilkington et al.

A history of Pleistocene population expansion has been inferred from the frequency spectrum of polymorphism in the mitochondrial DNA (mtDNA) of many human populations. Similar patterns are not typically observed for autosomal and X-linked loci. One explanation for this discrepancy is a recent population bottleneck, with different rates of recovery for haploid and autosomal loci as a result of their different effective population sizes. This hypothesis predicts that mitochondrial and Y chromosomal DNA will show a similar skew in the frequency spectrum in populations that have experienced a recent increase in effective population size. We test this hypothesis by re-sequencing 6.6 kb of non-coding Y chromosomal DNA and 780 basepairs of the mtDNA cytochrome c oxidase subunit III (COIII) gene in 172 males from five African populations. Four tests of population expansion are employed for each locus in each population: Fu's Fs statistic, the R2 statistic, coalescent simulations and the mismatch distribution. Consistent with previous results, patterns of mtDNA polymorphism better fit a model of constant population size for food-gathering populations and a model of population expansion for food-producing populations. In contrast, none of the tests reveal evidence of Y chromosome growth for either food-gatherers or food-producers. The distinct mtDNA and Y chromosome polymorphism patterns most likely reflect sex-biased demographic processes in the recent history of African populations. We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last five thousand years.


December 16, 2007

mtDNA haplogroups of indigenous Mexican populations

Hum Biol. 2007 Jun;79(3):313-20.

Characterization of mtDNA haplogroups in 14 Mexican indigenous populations.

Peñaloza-Espinosa RI, Arenas-Aranda D, Cerda-Flores RM, Buentello-Malo L, González-Valencia G, Torres J, Alvarez B, Mendoza I, Flores M, Sandoval L, Loeza F, Ramos I, Muñoz L, Salamanca F.

In this descriptive study we investigated the genetic structure of 513 Mexican indigenous subjects grouped in 14 populations (Mixteca-Alta, Mixteca-Baja, Otomi, Purépecha, Tzeltal, Tarahumara, Huichol, Nahua-Atocpan, Nahua-Xochimilco, Nahua-Zitlala, Nahua-Chilacachapa, Nahua-Ixhuatlancillo, Nahua-Necoxtla, and Nahua-Coyolillo) based on mtDNA haplogroups. These communities are geographically and culturally isolated; parents and grandparents were born in the community. Our data show that 98.6% of the mtDNA was distributed in haplogroups A1, A2, B1, B2, C1, C2, D1, and D2. Haplotype X6 was present in the Tarahumara (1/53) and Huichol (3/15), and haplotype L was present in the Nahua-Coyolillo (3/38). The first two principal components accounted for 95.9% of the total variation in the sample. The mtDNA haplogroup frequencies in the Purépecha and Zitlala were intermediate to cluster 1 (Otomi, Nahua-Ixhuatlancillo, Nahua-Xochimilco, Mixteca-Baja, and Tzeltal) and cluster 2 (Nahua-Necoxtla, Nahua-Atocpan, and Nahua-Chilacachapa). The Huichol, Tarahumara, Mixteca-Alta, and Nahua-Coyolillo were separated from the rest of the populations. According to these findings, the distribution of mtDNA haplogroups found in Mexican indigenous groups is similar to other Amerindian haplogroups, except for the African haplogroup found in one population.


December 14, 2007

Hawks et al. paper on accelerated recent human evolution

I would love to have blogged about this paper, but John explains it so clearly in this post that any additional comments are superfluous.

In any case, here are my €0.02: The paper has a simple but powerful idea: that really useful mutations are more likely to occur in large populations than in small ones: mutations are random accidents that happen in bodies; the more bodies you have, the more likely it is you'll get a really neat one.

All populations have the capacity to evolve by shifting around the frequencies of the different alleles in their gene pools. But, the kinds of alleles that evolution can work with are not the same. Large populations have a greater repertoire of alleles to work with.

But, some species with really huge numbers don't really evolve that fast. This is because they have already reached an adaptive plateau; they are already well-suited to their environments and don't face large selection pressures.

New challenging environments + growing population = accelerated human evolution.

Recent acceleration of human adaptive evolution

John Hawks, Eric T. Wang, Gregory Cochran, Henry C. Harpending, and Robert K. Moyzis

Genomic surveys in humans identify a large amount of recent positive selection. Using the 3.9-million HapMap SNP dataset, we found that selection has accelerated greatly during the last 40,000 years. We tested the null hypothesis that the observed age distribution of recent positively selected linkage blocks is consistent with a constant rate of adaptive substitution during human evolution. We show that a constant rate high enough to explain the number of recently selected variants would predict (i) site heterozygosity at least 10-fold lower than is observed in humans, (ii) a strong relationship of heterozygosity and local recombination rate, which is not observed in humans, (iii) an implausibly high number of adaptive substitutions between humans and chimpanzees, and (iv) nearly 100 times the observed number of high-frequency linkage disequilibrium blocks. Larger populations generate more new selected mutations, and we show the consistency of the observed data with the historical pattern of human population growth. We consider human demographic growth to be linked with past changes in human cultures and ecologies. Both processes have contributed to the extraordinarily rapid recent genetic evolution of our species.

Tracing Human Migrations with Y chromosomes and mtDNA (new Underhill/Kivisild paper)

This is a very important review paper which is a must-read for anyone interested in human population history. The new results allued in the abstract involve the discovery of the CF and DE clades, which the authors propose were involved in separate Out-of-Africa founder events. Previously, with the exception of the Paleoafrican Y-chromosome clades A and B, all other human Y chromosomes fell into three separate clades C, DE (also known as YAP), and F. Now, C and F are shown to be united by a common ancestory into a new clade CF.

Annu Rev Genet. 2007 Dec 1;41:539-564.

Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations.
Underhill PA, Kivisild T.

Well-resolved molecular gene trees illustrate the concept of descent with modification and exhibit the opposing processes of drift and migration, both of which influence population structure. Phylogenies of the maternally inherited mtDNA genome and the paternally inherited portion of the nonrecombining Y chromosome retain sequential records of the accumulation of genetic diversity. Although knowledge regarding the diversity of the entire human genome will be needed to completely characterize human genetic evolution, these uniparentally inherited loci are unique indicators of gender in modulating the extant population structure. We compare and contrast these loci for patterns of continuity and discreteness and discuss how their phylogenetic diversity and progression provide means to disentangle ancient colonization events by pioneering migrants from subsequent overlying migrations. We introduce new results concerning Y chromosome founder haplogroups C, DE, and F that resolve their previous trifurcation and improve the harmony with the mtDNA recapitulation of the out-of-Africa migration.


Human population sizes, divergence times and rates of gene flow

Genetics. 2007 Dec;177(4):2195-207.

Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, x and y chromosome resequencing data.

Garrigan D, Kingan SB, Pilkington MM, Wilder JA, Cox MP, Soodyall H, Strassmann B, Destro-Bisol G, de Knijff P, Novelletto A, Friedlaender J, Hammer MF.

We estimate parameters of a general isolation-with-migration model using resequence data from mitochondrial DNA (mtDNA), the Y chromosome, and two loci on the X chromosome in samples of 25-50 individuals from each of 10 human populations. Application of a coalescent-based Markov chain Monte Carlo technique allows simultaneous inference of divergence times, rates of gene flow, as well as changes in effective population size. Results from comparisons between sub-Saharan African and Eurasian populations estimate that 1500 individuals founded the ancestral Eurasian population approximately 40 thousand years ago (KYA). Furthermore, these small Eurasian founding populations appear to have grown much more dramatically than either African or Oceanian populations. Analyses of sub-Saharan African populations provide little evidence for a history of population bottlenecks and suggest that they began diverging from one another upward of 50 KYA. We surmise that ancestral African populations had already been geographically structured prior to the founding of ancestral Eurasian populations. African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow. In particular, Y chromosome gene flow appears to be asymmetric, i.e., from the Bantu-speaking population into other African populations. Conversely, mitochondrial gene flow is more extensive between non-African populations, but appears to be absent between European and Asian populations.


December 02, 2007

ASHG 2007 abstracts

You can get the 656-page volume of abstracts (pdf) of this year's American Society of Human Genetics meeting. Some titles/abstracts that caught my eye.

A. Rosa et al.

Mitochondrial haplogroup H1 is protective for stroke.

S. Sharma et al.

The Autochthonous Origin and a Tribal Link of Indian Brahmins: Evaluation Through Molecular Genetic Markers

The co-existence and associated genetic evidences for the major rival models: i) recent Central Asian introduction of Indian caste system, ii) rank related west Eurasian admixture, iii) South Asian origin for Indian caste communities, and iv) late Pleistocene heritage of tribal and caste populations, leave the question of the origin of caste system in India hazy and obscure. To resolve the issue, we screened 621 Y-chromosomes (of Brahmins, occupying upper most caste position and Dalits and Tribals with the lower most positions in the Indian caste hierarchical system) with fifty-five Y-chromosomal binary markers and Y-microsatellite markers and compiled a data set of 2809 Y-chromosomes (681 Brahmins, 2128 Tribals and Dalits) for conclusions. Overall, no consistent difference was observed in Y-haplogroups distribution between Brahmins, Dalits and Tribals, except for some differences confined to a given geographical region. A peculiar observation of highest frequency (upto 72.22%) of Y-haplogroups R1a1* in Brahmins, hinted at its presence as a founder lineage for this caste group. The widespread distribution and high frequency across Eurasia and Central Asia of R1a1* as well as scanty representation of its ancestral (R*, R1* and R1a*) and derived lineages across the region has kept the origin of this haplogroup unresolved. The analyses of a pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians, bearing R1a1* haplogroup resolved the controversy of origin of R1a1*. The conclusion was drawn on the basis of: i) presence of this haplogroup in many of the tribal populations such as, Saharia (present study) and Chenchu tribe in high frequency, ii) the highest ever reported presence of R1a* (ancestral haplogroup of R1a1*) in Kashmiri Pandits (Brahmins) and Saharia tribe, and iii) associated averaged phylogenetic ages of R1a* (~18,478 years) and R1a1* (~13,768 years) in India. The study supported the autochthonous origin of R1a1 lineage and a tribal link to Indian Brahmins.

Population structure in Sweden - A Y-chromosomal and mitochondrial DNA analysis.

T. Lappalainen et al.

A population sample representing the current Swedish population was analyzed for both maternally and paternally inherited markers with the aim of characterizing the genetic variation and structure of a modern North European population. We genotyped 12 Y-chromosomal and 27 mitochondrial DNA SNPs from DNA extracted and amplified from Guthrie cards of all the children born in Sweden during one week in 2003. The sample set consisted of 1914 samples (960 males) grouped according to place of birth. The ancient migration patterns are reflected in the clear north-south gradients in several palaeolithic and neolithic haplogroups in the mtDNA (U5, I, K, T, X) and the Y chromosome (R1b, N3). The haplogroup frequencies of the counties closest to Finland and Norway showed clear associations to the neighboring populations, resulting from the formation of the nations during the past millennium. Moreover, the recent immigration waves of the 20th century are visible both maternally and paternally, and have led to increased diversity and divergence from the main population in the major cities. Unfavorable population development in the ancient or recent past can be detected in several remote counties with low diversities and other signs of low population size and/or population crises. In conclusion, our study yielded valuable information about the various factors affecting the structure of the modern Swedish population that is vital for the use of the population in large population-based studies. Our sampling strategy, nonselective on the current population rather than stratified according to ancestry, represents the future of genetic studies in the increasingly panmictic populations of the world.

Relic Distribution of Y-Chromosome Haplogroup D Suggests Ancient Paleolithic Migration of Modern Humans in Eastern Asia.

H. Shi et al.

The Y chromosome haplogroup D is East Asian specific and prevalent in Tibetan and Japanese populations (30%-40%), but rare in other East Asian populations (<5%). We analyzed 5,174 Y chromosomes from 74 East Asian populations by typing haplogroup D related SNPs and eight Y chromosome microsatellite loci. We identified six sublineages under haplogroup D, and their distribution across East Asia suggested an ancient Paleolithic south-to-north migration, which likely predates the previously proposed northward diaspora of modern humans (reflected by the dominant occurrence of O3-M122 in East Asians) resulting in current relic distribution of haplogroup D in East Asia.

E. Marchani et al. Culture creates genetic structure in Daghestan.

M. Coelho et al. On the edge of the Bantu expansions: patterns of mtDNA and Y-chromosome variation in southwestern Angola.

J.S. Friedlaender et al. The genetic structure of Pacific Islanders.

ESHG 2007 abstracts

I had previously posted about a presentation in this year's ESHG conference about the Y chromosomes of Etruscans. At that time, there was no abstract online, but I noticed that the book of abstracts is available (pdf). The conference took place last June and there will be probably publications coming out of the presentations there.

Some interesting abstracts; you will probably find many more in the volume's 396 pages.

Related to the abstract below about ACTN in Finnish athletes.

P1206. ACTN and ACE genotypes in Greek elite athletes

I. D. Papadimitriou et al.

Only a few attempts have been made to shed light upon the influence of genes in making an Olympic champion. The aim of our study is to elucidate the genetic differences among a group of 101 elite Greek power-oriented track and field athletes and a random representative sample (181) of the Greek population by analyzing ACTN3 and ACE genotypes. Athletes were defined as elite and included to the sample if they had represented Greece at the international level. Standard molecular genetic methodologies were followed. Genotype and allele frequencies were compared between elite athletes and controls by the Chi-squared test using the statistical package GENEPOP V. 3.4. Preliminary results for ACE locus indicated that the gene frequencies in the Greek elite athletes are similar to other northern European populations. Furthermore, concerning the ACTN3 locus, it was showed that ACTN3 genotype and allele frequencies in the top power-oriented athletes were statistically significantly different from those in the random
sample of the Greek population: the frequency of the RR ACTN3 genotype in power-oriented athletes vs. the general population was 47.94% vs. 25.97%. The difference was even more prominent for comparison of the subgroup of sprinters to controls. The results suggest an overall
strong association between the presence of the RR genotype and elite power performance. Therefore, the ACTN3 gene might be used as a molecular genetic marker to at least partially predict an athlete’s ability to achieve peak power and sprinting performance.

C17. Origin of the Etruscans: novel clues from the Y chromosome lineages

A. Piazza et al.

Three hypotheses have been proposed on the origin of the distinctive Etruscan civilization and language that flourished ca. 3,000 years before present (BP) in Central Italy: 1) an external Anatolian source (Lydia and Lemnos) as claimed by Herodotus, 2) an autochthonous
process of formation from the preceding Villanovan society as firstly proposed by Dionysius of Halicarnassus and 3) an influence from Northern Europe. A synthetic geographical map summarizing 34 classical genetic markers in Italy differentiates a genetically homogeneous
Central Italian region between the Arno and Tiber rivers (ancient Etruria) from the rest of Italy. While this fact was tentatively interpreted as a genetic footprint of the Etruscans, its verification remained a challenge due to lack of data on differentiation of such markers and its calibration
with time. Here we show the genetic relationships of modern Etrurians, who mostly settled in Tuscany, with other Italian, Near Eastern and Aegean peoples by comparing the Y-chromosome DNA variation in 1,264 unrelated healthy males from: Tuscany-Italy (n=263), North Italy (n=306), South Balkans (n=359), Lemnos island (n=60), Sicily and Sardinia (n=276). The Tuscany samples were collected in Volterra (n=116), Murlo (n=86) and Casentino Valley (n=61).
We found traces of recent Near Eastern gene flow still present in Tuscany, especially in the archaeologically important village of Murlo. The samples from Tuscany show eastern haplogroups E3b1-M78, G2*-P15, J2a1b*-M67 and K2-M70 with frequencies very similar to those observed in Turkey and surrounding areas, but significantly different from those of neighbouring Italian regions. The microsatellite haplotypes associated to these haplogroups allow inference of ancestor lineages for Etruria and Near East whose time to the most recent common ancestors is relatively recent (about 3,500 years BP) and supports a possible non autochthonous post-Neolithic signal associated with the Etruscans.

P1135. Y chromosome analysis in subpopulations of Bashkirs from Russia

A. S. Lobov et al.

The Volga-Ural region which is located between Europe and Asia has been the arena of permanent genetic exchanges among Siberian, Central Asian, Eastern European populations. We have sampled seven Bashkir subpopulations from different parts of the Volga-Ural region and neighboring areas of Russia: Orenburg (N=79), Perm (N=72), Samara and Saratov (N=51), and from Bashkortostan Republic: Abzelilovskiy (N=152), Sterlibashevskiy (N=54), Baimakskiy (N=95), and Burzaynskiy area (N=82). These samples are currently being analyzed using 24 diallelic markers of Y-chromosome (M89, M9, M20, M48, M73, M130, M170, M172, M175, M201, M207, M214, M217, M231, M253, M269, M306(M173), P15, P37, P43, SRY1532, Tat, 92R7(M74), 12f2). According to our preliminary findings Turkic speaking Bashkirs are characterized by prevalence of R1b3 and R1a lineages. Among all subpopulations, Perm and Baimakskiy area represent with hight frequency (0.748 0.769,).It indicate there closeness with West European populations. Haplogroup R1a have frequency value 0.486 in Samara and Saratov’s Bashkirs and frequency value 0.370 Bashkirs from Sterlibashevskiy area. The N3 characterize for subpopulation Bashkirs from Sterlibashevskiy area (0.537), Orenburg (0.342). Bashkirs from Abzelilovskiy area have main frequency (0.474). These differences possibly indicate that different subpopulations of Bashkirs have different origin. We found that Bashkirs from Perm district were characterized by relatively low genetic diversity, which could be explained by founder effect. Bashkirs from Orenburg region which are anthropologically closer to Ugro-Finnic populations are characterized by high frequency of N3 haplogroup. We will try to compare our results with archeologycal, historycal and anthropological data in discussed about of origin of different groups Bashkir

P1191. Analysis of mitochondrial DNA polymorphism in four Siberian ethnic groups

M. V. Golubenko et al.

Mitochondrial DNA polymorphism was studied in 1130 individuals from 12 populations of the most numerous Siberian peoples - Altaians (4 populations), Tivinians (3 populations), Yakuts (2 populations) and Buryats (3 populations). 308 different HVS1 haplotypes were revealed
in total which belong to 34 different mtDNA haplogroups, mainly of East-Eurasian origin. Portion of “West-Eurasian” mtDNA haplogroups was the highest in Altaians (up to 46%) and Buryats (up to 20%). AMOVA analysis has shown that 95,78% of HVSI variation was within populations, 2.09% could be explained by inter-population differentiation and 2.09% was variability between ethnic groups. Test on differentiation of polymorphism in population pairs has shown that in all cases except the pair of Yakut samples the differentiation was significant. AMOVA analysis for separate ethnic groups revealed the highest degree of intraethnic differentiation for Altaians (3.78%), followed by Tuvinians (2.61%) and then Buryats (0.43%). Comparison of spectrum of
haplogroups and individual haplotypes in the populations under investigation also shows significant differentiation of native Siberian populations. Only two haplotypes from haplogroup C and one haplotype from D could be considered as common for all four ethnicities. One more
haplotype from C was abundant in Tuvinians, Yakuts and Buryats but rare in Altaians. Substantial number of haplotypes was population-specific. Analysis of migrations and interethnic marriages revealed various effects of these factors depending both on ethnicity and particular
population. The results suggest considerable ethnic differentiation in the studied Siberian peoples, as well as geographic differentiation.

P1192. Paleomolecular genetic analyses (mitochondrial and nuclear DNA polymorphisms) on some Thracian populations from Romania, dating from the Bronze and Iron Age

G. M. Cardos et al.

We have performed this study on the skeletal remains of some old Thracian populations from Romania, dating from the Bronze and Iron Age. Therefore, within our research we analysed mtDNA (HVR I and HVR II regions) and nuclear DNA (vWA31A Microsatellite) polymorphisms
in order to show the degree of their genetic kinship with other old and modern European populations, especially with nowadays Romanian population. We also amplified the Amelogenin gene to identify the genetic sex of old individuals. We have used three methods for DNA-extraction from human fossils and adapted them on the degradation
state of the biological material: the phenol-chloroform DNA extraction method, the DNA extraction method with guanidine-tiocianate and silica-particles, and the DNA-extraction method with Invisorb Forensic After amplifying by PCR, the mtDNA sequences were sequenced
by the Sanger method. The nuclear vWA31A Microsatellite polymorphisms and the Amelogenin gene sequences were demonstrated on PAA gel, Ag-stained.
We have compared the mtDNA sequences of 50 old Thracian individuals with mtDNA sequences of the present-day Romanian population and other European, Asian and African modern and old populations. The frequencies of vWA31A Microsatellite were compared with similar genetic data of other modern populations from all over the world. Our results suggest that the old Thracian populations might have made an important contribution to the foundation of the modern genetic Romanian pool and also reflect an evident genetic similarity between the old Thracian populations and other modern populations from South-East Europe.

P1193. Analyses of mitochondrial and Y-chromosomal lineages in modern Hungarian, Szekler and ancient Hungarian populations

B. Csányi et al.

Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic language family. High-resolution mtDNA analysis of 27 ancient samples (10th-11th centuries), 101 modern Hungarian, and 76 modern Hungarian-speaking Szekler samples was performed. Only two of 27 ancient Hungarian samples are unambiguously Asian: the rest belong to one of the western Eurasian haplogroups. Statistical analyses, including 57 European and Asian populations, revealed that some Asian affinities and the genetic effect of populations who came into contact with ancient Hungarians during their migrations are seen. Though strong differences appear when the ancient Hungarian samples are analyzed according to apparent social status, as judged by grave goods. mtDNA results demonstrate that significant genetic differences exist between the ancient and recent Hungarian-speaking populations. The Y-chromosomal base substitution ”Tat”, proved to be a valuable marker in the Finno-Ugric context. The Tat C allele is widespread in many Uralic-speaking populations, while it is virtually absent in recent Hungarians. To further elucidate this finding we studied this polymorphism on 100 modern Hungarian, 97 Szekler and 4 ancient Hungarian samples. Our data revealed that only one Szekler men carries the C allele among the modern individuals, whereas out of the four skeletal remains two possess the mutation. Furthermore we examined 22 Y-chromosomal binary markers to analyze the paternal genetic diversity of the two recent populations.
Our results show that Hungarians and Szeklers share basically the same genetic components found in other European populations, genetically closely related and close to other populations from Central Europe and the Balkan.

P1219. Possible common origin for the Tibeto-Burman and Austro-Asiatic speaking populations of India: a Y-chromosome study

Gospel of Judas revisited

April D. Deconick in the New York Times:
AMID much publicity last year, the National Geographic Society announced that a lost 3rd-century religious text had been found, the Gospel of Judas Iscariot. The shocker: Judas didn’t betray Jesus. Instead, Jesus asked Judas, his most trusted and beloved disciple, to hand him over to be killed. Judas’s reward? Ascent to heaven and exaltation above the other disciples.

It was a great story. Unfortunately, after re-translating the society’s transcription of the Coptic text, I have found that the actual meaning is vastly different. While National Geographic’s translation supported the provocative interpretation of Judas as a hero, a more careful reading makes clear that Judas is not only no hero, he is a demon.


So what does the Gospel of Judas really say? It says that Judas is a specific demon called the “Thirteenth.” In certain Gnostic traditions, this is the given name of the king of demons — an entity known as Ialdabaoth who lives in the 13th realm above the earth. Judas is his human alter ego, his undercover agent in the world. These Gnostics equated Ialdabaoth with the Hebrew Yahweh, whom they saw as a jealous and wrathful deity and an opponent of the supreme God whom Jesus came to earth to reveal.


I have wondered why so many scholars and writers have been inspired by the National Geographic version of the Gospel of Judas. I think it may stem from an understandable desire to reform the relationship between Jews and Christians. Judas is a frightening character. For Christians, he is the one who had it all and yet betrayed God to his death for a few coins. For Jews, he is the man whose story was used by Christians to persecute them for centuries. Although we should continue to work toward a reconciliation of this ancient schism, manufacturing a hero Judas is not the answer.

December 01, 2007

Ancient mtDNA from Iron Age Denmark

Am J Phys Anthropol. 2007 Nov 28 [Epub ahead of print]

Rare mtDNA haplogroups and genetic differences in rich and poor Danish Iron-Age villages.

Melchior L, Gilbert MT, Kivisild T, Lynnerup N, Dissing J.

The Roman Iron-Age (0-400 AD) in Southern Scandinavia was a formative period, where the society changed from archaic chiefdoms to a true state formation, and the population composition has likely changed in this period due to immigrants from Middle Scandinavia. We have analyzed mtDNA from 22 individuals from two different types of settlements, Bøgebjerggård and Skovgaarde, in Southern Denmark. Bøgebjerggård (ca. 0 AD) represents the lowest level of free, but poor farmers, whereas Skovgaarde 8 km to the east (ca. 200-270 AD) represents the highest level of the society. Reproducible results were obtained for 18 subjects harboring 17 different haplotypes all compatible (in their character states) with the phylogenetic tree drawn from present day populations of Europe. This indicates that the South Scandinavian Roman Iron-Age population was as diverse as Europeans are today. Several of the haplogroups (R0a, U2, I) observed in Bøgebjerggård are rare in present day Scandinavians. Most significantly, R0a, harbored by a male, is a haplogroup frequent in East Africa and Arabia but virtually absent among modern Northern Europeans. We suggest that this subject was a soldier or a slave, or a descendant of a female slave, from Roman Legions stationed a few hundred kilometers to the south. In contrast, the haplotype distribution in the rich Skovgaarde shows similarity to that observed for modern Scandinavians, and the Bøgebjerggård and Skovgaarde population samples differ significantly (P approximately 0.01). Skovgaarde may represent a new upper-class formed by migrants from Middle Scandinavia bringing with them Scandinavian haplogroups.


November 30, 2007

Objective beauty in the classical canon

From the paper:
The main question we addressed in the present study was whether there is an objective beauty, i.e., if objective parameters intrinsic to works of art are able to elicit a specific neural pattern underlying the sense of beauty in the observer. Our results gave a positive answer to this question. The presence of a specific parameter (the golden ratio) in the stimuli we presented determined brain activations different to those where this parameter was violated. The spark that changed the perception of a sculpture from “ugly” to beautiful appears to be the joint activation of specific populations of cortical neurons responding to the physical properties of the stimuli and of neurons located in the anterior insula.
PLoS One

The Golden Beauty: Brain Response to Classical and Renaissance Sculptures

Cinzia Di Dio et al.


Is there an objective, biological basis for the experience of beauty in art? Or is aesthetic experience entirely subjective? Using fMRI technique, we addressed this question by presenting viewers, naïve to art criticism, with images of masterpieces of Classical and Renaissance sculpture. Employing proportion as the independent variable, we produced two sets of stimuli: one composed of images of original sculptures; the other of a modified version of the same images. The stimuli were presented in three conditions: observation, aesthetic judgment, and proportion judgment. In the observation condition, the viewers were required to observe the images with the same mind-set as if they were in a museum. In the other two conditions they were required to give an aesthetic or proportion judgment on the same images. Two types of analyses were carried out: one which contrasted brain response to the canonical and the modified sculptures, and one which contrasted beautiful vs. ugly sculptures as judged by each volunteer. The most striking result was that the observation of original sculptures, relative to the modified ones, produced activation of the right insula as well as of some lateral and medial cortical areas (lateral occipital gyrus, precuneus and prefrontal areas). The activation of the insula was particularly strong during the observation condition. Most interestingly, when volunteers were required to give an overt aesthetic judgment, the images judged as beautiful selectively activated the right amygdala, relative to those judged as ugly. We conclude that, in observers naïve to art criticism, the sense of beauty is mediated by two non-mutually exclusive processes: one based on a joint activation of sets of cortical neurons, triggered by parameters intrinsic to the stimuli, and the insula (objective beauty); the other based on the activation of the amygdala, driven by one's own emotional experiences (subjective beauty).


November 27, 2007

Genetic variation in Native Americans

See Figure 7 for evidence of the substructure within the Native American race.

PLoS Genetics Vol. 3, No. 11, e185 doi:10.1371/journal.pgen.0030185

Genetic Variation and Population Structure in Native Americans

Sijia Wang et al.

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.


November 21, 2007

Genetic structure of European Americans

NOTE: I inadvertetdly posted a draft of this post. Here is the final post; I will leave the draft online since some people already commented on it, before I noticed it.

A previous study on Europeans discovered that Caucasoid Europeans, who form a genetic cluster on a global scale can be further distinguished into subclusters that are correlated with ancestry and geography. Now, a new study on European Americans (hat tip gnxp) appearing in the free online journal PLoS Genetics has carried out a similar analysis of the genetic structure of American "Caucasians".

What I find fascinating about this new study is that an ethnic subgroup within American Caucasoids, namely Ashkenazi Jewish Americans can be distinguished at this point from other Caucasoids. Here is the clustering based on the validated set of markers from the paper:

The distinctiveness of Jewish Americans is probably due to their having a portion of Middle Eastern ancestry. We can only say that Jewish Americans are clearly genetically distinct from the other ethnic groups presented in the study, although it is unclear whether they are distinct from other groups of Middle Eastern background.

As biologically-averse intellectuals continue to question the very existence of race, pragmatic scientists are moving into an era when not only race, but ethnicity may become genetically identifiable.

Unlike race which by definition refers to an identifiable biological cluster, ethnicity may (or may not) refer to such a cluster.

Ethnic distinctiveness is due to both culture and biology, and the relative proportions of the two factors are specific to a particular ethnic group.

When ethnic groups have split recently, co-inhabit a geographical space, frequently intermarry, etc., then it is likely that they will have small biological differences, whereas other ethnic groups may be biologically as well as culturally distinct.

We should be careful to note that there are two levels of ethnic biological distinctiveness: group distinctiveness and individual distinctiveness:

Group distinctiveness means: if you are given the photographs of ten Englishmen on one side and ten Russians on the other, you would be able to decide with a very high level of success which group represented the Russians and which one the Englishmen.

Individual distinctiveness means: if you are given the photographs of ten Englishmen and ten Russians in random order, you would still be able to sort out the Russians from the Englishmen; whether this is possible, and with what level of success is less obvious than in the previous case.

We must wait for more studies with larger samples and more markers to study the biological component of human ethnicity. At present, some groups do seem to have individual distinctiveness in a particular societal context and with a particular set of markers (e.g., Jewish vs. non-Jewish Americans), while others are less distinct (e.g., Greek vs. Italian Americans).

November 20, 2007

Genetic structure of European Americans

UPDATE (Nov 21)See also some discussion here.

PLoS Genetics (early release)

Discerning the ancestry of European Americans in genetic association studies

Alkes Price et al.

European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false positive or negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries. Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European and Ashkenazi Jewish ancestry are the main sources of European American population structure. Building on this insight, we constructed a panel of 300 validated markers that are highly informative for distinguishing these ancestries. We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data.


November 19, 2007

Sea level rise and the beginning of the Neolithic

From a EurekAlert release about this paper:
The researchers created reconstructions of the Mediterranean and Black Sea shoreline before and after the rise in sea levels. They estimated that nearly 73,000 square km of land was lost to the sea over a period of 34 years. Based on our knowledge of historical population levels, this could have led to the displacement of 145,000 people. Archaeological evidence shows that communities in southeast Europe were already practising early farming techniques and pottery production before the Flood. With the catastrophic rise in water levels it appears they moved west, taking their culture into areas inhabited by hunter-gatherer communities.

Catastrophic early Holocene sea level rise, human migration and the Neolithic transition in Europe

Chris S.M. Turney et al.


The collapse of the Laurentidenext term Ice Sheet and release of freshwater 8740–8160 years ago abruptly raised global sea levels by up to 1.4 m. The effect on human populations is largely unknown. Here we constrain the time of the main sea level rise and investigate its effect on the onset of the Neolithic across Europe. An analysis of radiocarbon ages and palaeoshoreline reconstruction supports the hypothesis that flooding of coastal areas led to the sudden loss of land favoured by early farmers and initiated an abrupt expansion of activity across Europe, driven by migrating Neolithic peoples.


November 11, 2007

Anthropological Research Page status

Just a quick note to readers of the Anthropological Research Page (ARP), which used to be hosted at Due to a problem with the host (supposed hacker attack), the ARP will no longer to be hosted in Angeltowns.

All the content of the ARP can be found in the Internet Archive, with the latest version being here. The formatting is a bit off, but otherwise all the content is preserved. I will re-upload the ARP to a suitable server once I find the time.

Waist-hip-ratio of mothers and children's intelligence

There is a related story in the New Scientist about the following article.

Evolution and Human Behavior (in press)

Waist-hip ratio and cognitive ability: is gluteofemoral fat a privileged store of neurodevelopmental resources?

William D. Lassek, Steven J.C. Gaulin


Upper-body fat has negative effects and lower-body fat has positive effects on the supply of long-chain polyunsaturated fatty acids that are essential for neurodevelopment. Thus, waist-hip ratio (WHR), a useful proxy for the ratio of upper-body fat to lower-body fat, should predict cognitive ability in women and their offspring. Moreover, because teenage mothers and their children compete for these resources, their cognitive development should be compromised, but less so for mothers with lower WHRs. These predictions are supported by data from the Third National Health and Nutrition Examination Survey. Controlling for other correlates of cognitive ability, women with lower WHRs and their children have significantly higher cognitive test scores, and teenage mothers with lower WHRs and their children are protected from cognitive decrements associated with teen births. These findings support the idea that WHR reflects the availability of neurodevelopmental resources and thus offer a new explanation for men's preference for low WHR.

October 28, 2007

Overweight and obesity in young Greek men

Obes Rev. 2007 Oct 24; [Epub ahead of print]

Prevalence of overweight and obesity in young Greek men.

Papadimitriou A, Fytanidis G, Papadimitriou DT, Priftis KN, Nicolaidou P, Fretzayas A.

We determined the prevalence of overweight and obesity in young Greek men in 2006 and examined variations related to their place of residence and educational level. Body height and weight were measured in 2568 conscripts of the Greek army, aged 19-26 years. The calculated body mass index (BMI, kg m(-2)) was correlated to their socio-demographic characteristics, i.e. level of education and place of residence (urban or rural). Overweight and obesity were defined according to the World Health Organization classification. Mean BMI (standard deviation) of the conscripts was 24.7 (4.2). The prevalence of overweight (30 > BMI >/= 25 kg m(-2)) was 28.5% and correlated positively with a higher educational level, whereas the prevalence of obesity (BMI >/= 30 kg m(-2)) was 10.4% and correlated positively with a lower educational level. Our data were compared with those of similar studies performed in the years 1969: BMI 23.8 (1.4) (P < 0.0001) and 1990: BMI 23.8 (2.9) (P < 0.0001), showing a positive secular trend for BMI in Greek conscripts in the last 16 years. In conclusion, we documented an alarmingly high prevalence of overweight and obesity among young Greek men.


Long Live the 28th October 1940

How humans became warlike altruists

Via Yann, I am alerted to a new Science report on the evolution of parochial altruism. The authors describe how hypothetical genes for parochialism (P) and altruism (A) could have co-evolved. Parochial altruists (PA) risk death in combat with other groups. How could the PA combination evolve? 

The authors suggest that PA fighters do risk death, but in conflicts between groups, it is the groups with more PAs that have a higher chance of winning. Thus, while parochial altruists are selected against (because they risk their lives for their group), they are also selected for (because they kill off more members of less-PA groups in violent conflicts). Moreover, the losing side's numbers are replenished by conquerors' genes (thus becoming more PA).

The authors contend that archeologically-derived estimates of group warfare are consistent with their scenario for the evolution parochial altruism. One would think that other, more recent, historical examples could also be used, e.g., between city-state warfare in classical Greece. 

The paper's innovation is that a seemingly "irrational" behavior from selfish genes' point of view could nonetheless evolve. The genes that cause their bearers to die in patriotic battles may die, but their competing alleles on the losing side may suffer more.

Science 26 October 2007:
Vol. 318. no. 5850, pp. 636 - 640
DOI: 10.1126/science.1144237

The Coevolution of Parochial Altruism and War

Jung-Kyoo Choi1 and Samuel Bowles2*

Altruism—benefiting fellow group members at a cost to oneself—and parochialism—hostility toward individuals not of one's own ethnic, racial, or other group—are common human behaviors. The intersection of the two—which we term "parochial altruism"—is puzzling from an evolutionary perspective because altruistic or parochial behavior reduces one's payoffs by comparison to what one would gain by eschewing these behaviors. But parochial altruism could have evolved if parochialism promoted intergroup hostilities and the combination of altruism and parochialism contributed to success in these conflicts. Our game-theoretic analysis and agent-based simulations show that under conditions likely to have been experienced by late Pleistocene and early Holocene humans, neither parochialism nor altruism would have been viable singly, but by promoting group conflict, they could have evolved jointly.

October 20, 2007

Domestication of barley

Genetics. 2007 Oct 18; [Epub ahead of print]

Molecular phylogeography of domesticated barley traces expansion of agriculture in the Old World.

Saisho D, Purugganan M.

Okayama University.

Barley (Hordeum vulgare ssp. vulgare) was first cultivated 10,500 years ago in the Fertile Crescent and is one of the founder crops of Eurasian agriculture. Phylogeographic analysis of five nuclear loci and morphological assessment of two traits in >250 domesticated barley accessions reveals that landraces found in South and East Asia are genetically distinct from those in Europe and North Africa. A Bayesian population structure assessment method indicates that barley accessions are subdivided into 6 clusters, and that barley landraces from 10 different geographical regions of Eurasia and North Africa show distinct patterns of distribution across these clusters. Using haplotype frequency data, it appears that the Europe/North Africa landraces are most similar to the Near East population (FST = 0.15) as well as wild barley (FST = 0.11) and are strongly differentiated from all other Asian populations (FST = 0.34 to 0.74). A neighbor-joining analysis using these FST estimates also supports a division between Europe, North African and Near East barley types from more easterly Asian accessions. There is also differentiation in the presence of a naked caryopsis and spikelet row number between eastern and western barley accessions. The data support the differential migration of barley from two domestication events that led to the origin of barley - one in the Fertile Crescent and another further east, possibly at the eastern edge of the Iranian Plateau - with European and North African barley largely originating from the former while much of Asian barley arising from the latter. This suggests that cultural diffusion or independent innovation are responsible for the expansion of agriculture to areas of South and East Asia during the Neolithic Revolution.


On the James Watson Black IQ controversy

There are two issues regarding the recent controversy started by James Watson's comments about the intelligence of Africans.
The scientist, who won the Nobel prize for his part in discovering the structure of DNA, was quoted in an interview in The Sunday Times saying he was “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours - whereas all the testing says not really.”
The first issue is that Watson's statements, whether one agrees with them or not should not be punished, and represent a valid stance to the problem of population differences in intelligence. Of course institutions (such as the Cold Spring Harbor lab) have the right to choose who works for them, but they also have the responsibility to foster free speech.

One would be sympathetic to CSH's condemnation of Watson if it was done on scientific grounds. For example, a scientist denying the fact of evolution could not reasonably expect to have no reprecussions in his career. Institutions are expected to make sure they don't promote bad science, which is not necessarily unorthodox science (which should be encouraged), but rather unargued or anti-empirical science.

However, CSH's stance has been motivated by political or social considerations. How could it be otherwise, since the identification of intelligence-fostering genes differentiating populations has not come about yet. The prudent stance is to be agnostic about this issue, until such genes are discovered, or their continued non-discovery makes one doubtful of their existence.

The second issue is that Watson's factual comments are entirely accurate! Sub-Saharan Africans do indeed have lower intelligence than people in western societies. That is an observable fact (fact F). What is not certain is whether or not this fact is due to inherent genetic deficiencies (position A) or due to environmental or socio-cultural problems (position B). Social policies should take into account F while the scientists figure out whether A or B explains F.

As an analogy, a cook has to take into account that his knife is blunt before he figures out whether it is blunt because it was made poorly or from repeated use.

According to Watson:
A priori, there is no firm reason to anticipate that the intellectual abilities of people geographically separated during their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of mankind will not be enough to make it so.
Once again, Watson's comments are reasonable. Notably they do not identify which populations may have inherent (evolutionary) differences in intelligence, nor do they attempt to quantify the importance of such differences. They simply state the -a priori sensible- stance of a scientist that a phenomenon (e.g., the evolution of cognitive ability) would not have proceeded in the same way under different circumstances.

UPDATE: A post-controversy article by James Watson in the Independent. Excerpt:
We do not yet adequately understand the way in which the different environments in the world have selected over time the genes which determine our capacity to do different things. The overwhelming desire of society today is to assume that equal powers of reason are a universal heritage of humanity. It may well be. But simply wanting this to be the case is not enough. This is not science.

October 18, 2007

Limitations of genetic ancestry testing

From the EurekAlert release about an upcoming Science article:
Some of the tests’ limitations identified by Bolnick and her co-authors include:
  • Most tests trace only a few of your ancestors and a small portion of your DNA,
  • Tests are unlikely to identify all of the groups or locations around the world where a test-taker’s relatives are found,
  • Tests may report false negatives or false positives,
  • Limited sample databases mean test results are subject to misinterpretation,
  • There is no clear connection between DNA and racial/ethnic identity,
  • Tests cannot determine exactly where ancestors lived or what ethnic identity they held.

Neanderthals had same version of FOXP2 "language gene" as modern humans

Via National Geographic:
A team of European researchers tested Neandertal bones recovered from a Spanish cave for a certain gene, called FOXP2, that has been dubbed "the speech and language gene."

It's the only gene known so far that plays a key role in language. When mutated, the gene primarily affects language without affecting other abilities.

The new study suggests that Neandertals (often spelled Neanderthals) had the same version of this gene that modern humans share—a different version than is found in chimpanzees and other apes.

"From the point of this gene, there is no reason to think that Neandertals did not have language as we do," said the study's lead author, Johannes Krause of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

"Of course many genes are involved in language, so we can't say from this result alone that Neandertals spoke just as modern humans do," Krause added.

Genome-wide detection of positive selection

Nature 449, 913-918 (18 October 2007) | doi:10.1038/nature06250; Received 8 August 2007; Accepted 13 September 2007

Genome-wide detection and characterization of positive selection in human populations

Pardis C. Sabeti et al.

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2)1. We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection2, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus3, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation4, 5, in Europe; and EDAR and EDA2R, both involved in development of hair follicles6, in Asia.


October 14, 2007

Conservation of frequently used words in Indo-European languages

I wonder what implications -if any- this finding has on attempts to date the PIE language before the dispersal of its speakers. After all, PIE is constructed based on words found in several (at least two) daughter languages, and thus will tend to use words that are conserved more (since they have survived in more than one language). The implication of this article is that conserved words are replaced at a slower rate. Hence, it is important to take into account the rates of evolution of different terms when trying to figure out how long ago two languages shared a common ancestor.

Nature 449, 717-720 (11 October 2007) | doi:10.1038/nature06176; Received 30 April 2007; Accepted 17 August 2007

Frequency of word-use predicts rates of lexical evolution throughout Indo-European history

Mark Pagel et al.

Greek speakers say "ουρα", Germans "schwanz" and the French "queue" to describe what English speakers call a 'tail', but all of these languages use a related form of 'two' to describe the number after one. Among more than 100 Indo-European languages and dialects, the words for some meanings (such as 'tail') evolve rapidly, being expressed across languages by dozens of unrelated words, while others evolve much more slowly—such as the number 'two', for which all Indo-European language speakers use the same related word-form1. No general linguistic mechanism has been advanced to explain this striking variation in rates of lexical replacement among meanings. Here we use four large and divergent language corpora (English2, Spanish3, Russian4 and Greek5) and a comparative database of 200 fundamental vocabulary meanings in 87 Indo-European languages6 to show that the frequency with which these words are used in modern language predicts their rate of replacement over thousands of years of Indo-European language evolution. Across all 200 meanings, frequently used words evolve at slower rates and infrequently used words evolve more rapidly. This relationship holds separately and identically across parts of speech for each of the four language corpora, and accounts for approximately 50% of the variation in historical rates of lexical replacement. We propose that the frequency with which specific words are used in everyday language exerts a general and law-like influence on their rates of evolution. Our findings are consistent with social models of word change that emphasize the role of selection, and suggest that owing to the ways that humans use language, some words will evolve slowly and others rapidly across all languages.


October 10, 2007

Y chromosomes from the Gulf of Oman

European Journal of Human Genetics advance online publication 10 October 2007; doi: 10.1038/sj.ejhg.5201934

Y-chromosome diversity characterizes the Gulf of Oman

Alicia M Cadenas


Arabia has served as a strategic crossroads for human disseminations, providing a natural connection between the distant populations of China and India in the east to the western civilizations along the Mediterranean. To explore this region's critical role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analysis of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) was performed. The role of the Levant in the Neolithic dispersal of the E3b1-M35 sublineages is supported by the data, and the distribution and STR-based analyses of J1-M267 representatives points to their spread from the north, most likely during the Neolithic. With the exception of Yemen, southern Arabia, South Iran and South Pakistan display high diversity in their Y-haplogroup substructure possibly a result of gene flow along the coastal crescent-shaped corridor of the Gulf of Oman facilitating human dispersals. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience significant heterozygote deficiencies at various hypervariable autosomal STR loci.


October 04, 2007

TEDtalk by Zeresenay Alemseged

An interesting talk (video) by a paleoanthropologist working in Ethiopia:
About this Talk

Paleoanthropologist Zeresenay Alemseged is looking for the roots of humanity in Ethiopia's badlands. Here he talks about what he has found -- including the oldest skeleton yet discovered of a hominid child -- and how Africa holds the clues to what makes us human.

About Zeresenay Alemseged

Zeresenay "Zeray" Alemseged digs in the Ethiopian desert, looking for the earliest signs of humanity. His most exciting find: the 3.3-million-year-old bones of Selam, a 3-year-old hominid child, from the species Australopithecus afarensis.
Lots more TEDtalks if you love science.

October 01, 2007

Neanderthals of the East

A new paper from Svante Paabo's team that shows that Neanderthals may have lived further to the east that can be assumed based on paleoanthropological evidence. Roughly speaking, to identify some remains as Neanderthals, anthropologists have to detect features belonging to the "constellation of features" typical of that species. However, when the material is limited in quantity, one cannot do this: most of the Neanderthal-identifying features are missing! Obviously, this is not a problem with DNA methods, since DNA can be extracted from small bone and tooth fragments.

Nature advance online publication 30 September 2007 | doi:10.1038/nature06193

Neanderthals in central Asia and Siberia

Johannes Krause et al.

Morphological traits typical of Neanderthals began to appear in European hominids at least 400,000 years ago1 and about 150,000 years ago2 in western Asia. After their initial appearance, such traits increased in frequency and the extent to which they are expressed until they disappeared shortly after 30,000 years ago. However, because most fossil hominid remains are fragmentary, it can be difficult or impossible to determine unambiguously whether a fossil is of Neanderthal origin. This limits the ability to determine when and where Neanderthals lived. To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation. Thus, the geographic range of Neanderthals is likely to have extended at least 2,000 km further to the east than commonly assumed.


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.


August 19, 2007

Dispersal of haplogroup N from Siberia into Eastern Europe

J Hum Genet. 2007 Aug 17; [Epub ahead of print]

Y-chromosome haplogroup N dispersals from south Siberia to Europe.

Derenko M, Malyarchuk B, Denisova G, Wozniak M, Grzybowski T, Dambueva I, Zakharov I.

In order to reconstruct the history of Y-chromosome haplogroup (hg) N dispersals in north Eurasia, we have analyzed the diversity of microsatellite (STR) loci within two major hg N clades, N2 and N3, in a total sample of 1,438 males from 17 ethnic groups, mainly of Siberian and Eastern European origin. Based on STR variance analysis we observed that hg N3a is more diverse in Eastern Europe than in south Siberia. However, analysis of median networks showed that there are two STR subclusters of hg N3a, N3a1 and N3a2, that are characterized by different genetic histories. Age calculation of STR variation within subcluster N3a1 indicated that its first expansion occurred in south Siberia [approximately 10,000 years (ky)] and then this subcluster spread into Eastern Europe where its age is around 8 ky ago. Meanwhile, younger subcluster N3a2 originated in south Siberia (probably in the Baikal region) approximately 4 ky ago. Median network and variance analyses of STR haplotypes suggest that south Siberian N3a2 haplotypes spread further into Volga-Ural region undergoing serial bottlenecks. In addition, median network analysis of STR data demonstrates that haplogroup N2-A is represented by two subclusters, showing recent expansion times. The data obtained allow us to suggest Siberian origin of haplogroups N3 and N2 that are currently widespread in some populations of Eastern Europe.


August 15, 2007

The new Ming the Merciless

I haven't watched the new incarnation of Flash Gordon on SCI-FI Channel, but can anyone spot a difference between the Ming character from the 1930s serial and last FG movie and the newest one?

Hypothesis about the origins of hemochromatosis

Med Hypotheses. 2007 Aug 7; [Epub ahead of print]

Hemochromatosis: A Neolithic adaptation to cereal grain diets.

Naugler C.

The Neolithic period in Europe marked the transition from a hunter-gatherer diet rich in red meat to an iron-reduced cereal grain diet. This dietary shift likely resulted in an increased incidence of iron deficiency anemia, especially in women of reproductive age. I propose that hereditary hemochromatosis and in particular the common HFE C282Y mutation may represent an adaptation to decreased dietary iron in cereal grain-based Neolithic diets. Both homozygous and heterozygous carriers of the HFE C282Y mutation have increased iron stores and therefore possessed an adaptive advantage under Neolithic conditions. An allele age estimate places the origin of the HFE C282Y mutation in the early Neolithic period in Northern Europe and is thus consistent with this hypothesis. The lower incidence of this mutation in other agrarian regions (the Mediterranean and Near East) may be due to higher dietary intakes of the iron uptake cofactor vitamin C in those regions. The HFE C282Y mutation likely only became maladaptive in the past several centuries as dietary sources of iron and vitamin C improved in Northern Europe.