March 31, 2010

Lactose intolerant prehistoric northern European hunter-gatherers (Malmstrom et al. 2010)

BMC Evolutionary Biology 2010, 10:89 doi:10.1186/1471-2148-10-89

High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe

Helena Malmstrom et al.

Abstract (provisional)

Genes and culture are believed to interact, but it has been difficult to find direct evidence for the process. One candidate example that has been put forward is lactase persistence in adulthood, i.e. the ability to continue digesting the milk sugar lactose after childhood, facilitating the consumption of raw milk. This genetic trait is believed to have evolved within a short time period and to be related with the emergence of sedentary agriculture.

Here we investigate the frequency of an allele (-13910*T) associated with lactase persistence in a Neolithic Scandinavian population. From the 14 individuals originally examined, 10 yielded reliable results. We find that the T allele frequency was very low (5%) in this Middle Neolithic hunter-gatherer population, and that the frequency is dramatically different from the extant Swedish population (74%).

We conclude that this difference in frequency could not have arisen by genetic drift and is either due to selection or, more likely, replacement of hunter-gatherer populations by sedentary agriculturalists.


March 28, 2010

World's oldest technical project in Kalambaka

My translation of parts of the article in the Vima which appears to be the most informative source for the new discoveries:
In Kalambaka, the most ancient technical project

The most ancient technical project of Greece, probably in the world, is found in the Theopetra cave of Kalambaka and is 23,000 years old. It is a stone wall that had been constructed in the entrance of the cave, blocking its entrance by 2/3. This construction -stone pile to be precise- was studied and dated by the "Democritus" center, which presented yesterday the results. The age coincides precisely with the coldest period of the last glacial age, suggesting that the Paleolithic inhabitants of the cave had constructed this wall at its entrance to protect themselves from the harsh cold of the times.

Remnants of fire, tools made of pyritolithus (?) and quartz, early jewellery from deerteeth, stone implements and ceramics have come to light in the prehistoric cave of Theopetra during the excavations conducted by Dr. Nina Kyparissi-Apostolika for 25 years, ephor of Palaeoanthropology and Speleology of southern Greece of the Ministry of Culture. Human skeletons have been rarely discovered. On the contrary, there are many animal bones from all periods during which the cave was in use. Of interest are finds from the Mesolithic age related to ceramic production and cultivation. There is barley, wheat, and lentil in wild (Paleolithic age) form, but also as cultivars, which suggests that these people had discovered cultivation as the result of millennia-long efforts and not as the result of population movements from the Near East.

March 27, 2010

Natural selection behind population differentiation

A very important finding of the paper is that the correlation between recombination rate and genetic differentiation (as measured by Fst) is stronger between Africans and non-Africans, and weaker between Europeans and Chinese. To simplify, we can say that Eurasians and Africans have diverged from each other to a great part because of selection (in either Eurasians, or Africans, or both) that took them away (genetically) from their common ancestor. On the other hand, differentiation between Europeans and Chinese is to a greater extent neutral, i.e., the result of demographic separation, rather than independent processes of selection.

PLoS Genetics doi:10.1371/journal.pgen.1000886

Human Population Differentiation Is Strongly Correlated with Local Recombination Rate

Alon Keinan et al.


Allele frequency differences across populations can provide valuable information both for studying population structure and for identifying loci that have been targets of natural selection. Here, we examine the relationship between recombination rate and population differentiation in humans by analyzing two uniformly-ascertained, whole-genome data sets. We find that population differentiation as assessed by inter-continental FSTshows negative correlation with recombination rate, with FST reduced by 10% in the tenth of the genome with the highest recombination rate compared with the tenth of the genome with the lowest recombination rate (P≪10−12). This pattern cannot be explained by the mutagenic properties of recombination and instead must reflect the impact of selection in the last 100,000 years since human continental populations split. The correlation between recombination rate andFST has a qualitatively different relationship for FST between African and non-African populations and for FST between European and East Asian populations, suggesting varying levels or types of selection in different epochs of human history.


March 26, 2010

Ancient DNA from Korean mummies

Mol Biol Rep. 2010 Mar 21. [Epub ahead of print]

A genetic investigation of Korean mummies from the Joseon Dynasty.

Kim NY, Lee HY, Park MJ, Yang WI, Shin KJ.

Two Korean mummies (Danwoong-mirra and Yoon-mirra) found in medieval tombs in the central region of the Korean peninsula were genetically investigated by analysis of mitochondrial DNA (mtDNA), Y-chromosomal short tandem repeat (Y-STR) and the ABO gene. Danwoong-mirra is a male child mummy and Yoon-mirra is a pregnant female mummy, dating back about 550 and 450 years, respectively. DNA was extracted from soft tissues or bones. mtDNA, Y-STR and the ABO gene were amplified using a small size amplicon strategy and were analyzed according to the criteria of ancient DNA analysis to ensure that authentic DNA typing results were obtained from these ancient samples. Analysis of mtDNA hypervariable region sequence and coding region single nucleotide polymorphism (SNP) information revealed that Danwoong-mirra and Yoon-mirra belong to the East Asian mtDNA haplogroups D4 and M7c, respectively. The Y-STRs were analyzed in the male child mummy (Danwoong-mirra) using the AmpFlSTR((R)) Yfiler(TM) PCR Amplification Kit and an in-house Y-miniplex plus system, and could be characterized in 4 loci with small amplicon size. The analysis of ABO gene SNPs using multiplex single base extension methods revealed that the ABO blood types of Danwoong-mirra and Yoon-mirra are AO01 and AB, respectively. The small size amplicon strategy and the authentication process in the present study will be effectively applicable to future genetic analyses of various forensic and ancient samples.


March 24, 2010

Ancient mtDNA from Denisova Cave

Nicholas Wade writes in the NY Times:
But they say the genetic material extracted from the bone, an element called mitochondrial DNA, belonged to a distinct human lineage that migrated out of Africa at a different time from the two known archaic human species. Homo erectus, found in East Asia, left Africa two million years ago, and the ancestor of Neanderthals emigrated some 500,000 years ago. The number of differences found in the child’s DNA indicate that its ancestors left Africa about one million years ago, the researchers say. Their report is published online in the journal Nature.


The finger bone was found in a layer laid down on the cave floor between 48,000 and 30,000 years ago, according to radiocarbon dating. At that time, toward the end of the Pleistocene Ice Age, which ended 10,000 years ago, the climate was probably much colder. The people of the new lineage presumably wore clothes, Dr. Krause said, because chimpanzees and gorillas cannot withstand much cold, suggesting that fur alone is inadequate protection.
Nature doi:10.1038/nature08976

The complete mitochondrial DNA genome of an unknown hominin from southern Siberia

Johannes Krause et al.


With the exception of Neanderthals, from which DNA sequences of numerous individuals have now been determined1, the number and genetic relationships of other hominin lineages are largely unknown. Here we report a complete mitochondrial (mt) DNA sequence retrieved from a bone excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago. This indicates that it derives from a hominin migration out of Africa distinct from that of the ancestors of Neanderthals and of modern humans. The stratigraphy of the cave where the bone was found suggests that the Denisova hominin lived close in time and space with Neanderthals as well as with modern humans2, 3, 4.


March 21, 2010

Y-chromosomes of Albanian populations (Ferri et al. 2010)

This is a very important study as it shows (for the first time) some detail on Albanian populations. From a first reading of the evidence, we can say that:
  • the Ghegs resemble Kosovar Albanians in having a higher frequency of E1b1b1.
  • Tosks on the other hand have a higher frequency of I.
  • The high J2 frequency resembles Greeks, with the expected 10 to 1 or so ratio between J2 and J1, and is dissimilar from northwestern Balkan populations. Past studies have shown however, that J2b is dominant in Albanian, rather than J2a which is dominant in most Greek populations tested so far (although J2b is also represented).
  • Similar frequencies to Greeks are also found in R1.
  • There is also a relative paucity of G compared to Greeks, and limited introgression of Gypsy chromosomes (H1) in the main Albanian groups (Gheg and Tosk).

International Journal of Legal Medicine DOI: 10.1007/s00414-010-0432-x

Y-STR variation in Albanian populations: implications on the match probabilities and the genetic legacy of the minority claiming an Egyptian descent

Gianmarco Ferri et al.

Y chromosome variation at 12 STR (the Powerplex® Y system core set) and 18 binary markers was investigated in two major (the Ghegs and the Tosks) and two minor (the Gabels and the Jevgs) populations from Albania (Southern Balkans). The large proportion of haplotypes shared within and between groups makes the Powerplex 12-locus set inadequate to ensure a suitable power of discrimination for the forensic practice. At least 85% of Y lineages in the Jevgs, the cultural minority claiming an Egyptian descent, turned out to be of either Roma or Balkan ancestry. They also showed unequivocal signs of a common genetic history with the Gabels, the other Albanian minority practising social and cultural Roma traditions.


March 18, 2010

Preference for masculine/feminine-looking men and national health

Supplementary Table 1 has the relevant data. I have sorted the data on national health index, and average masculinity preference.

Note that country scores were limited only to those judges who identified themselves as White.

Some observations:
  • As the authors note health index is related inversely with preference for masculinity. However, there are some interesting cases:
  • Canada and the USA have similar (high) masculinity preferences, even though they differ substantially in the health index.
  • Iceland and Norway (small sample sizes, but we can combine the two) have a good health index as does Sweden, but a much stronger preference than masculinity than Sweden.
  • The vast majority of EU nations are around ~0.4 in the masculinity preference index.
An untested factor is variation in the levels of facial masculinity across different nations. Differences in preference may not reflect differences in health, but rather differences in average facially-expressed masculinity. It would be interesting to use anthropometric data to test this possible influence, as "White" populations from different nations are not anthropometrically equivalent.

Another untested factor is the racial makeup of different nations. It is fairly striking that the top nations in masculinity preference (we can exclude Bulgaria with its small sample) are all the ones with the longest histories of racial co-existence. This may have altered attractiveness standards in these countries, as the Caucasoids within each country may have altered perceptions of attractiveness due either to familiarization with other races or (conversely) due to a desire to distance themselves from them phenotypically.

PS: You can download the paper and other face-related research at the Facelab.

Proceedings of the Royal Society B doi:10.1098/rspb.2009.2184

The health of a nation predicts their mate preferences: cross-cultural variation in women's preferences for masculinized male faces

Lisa M. DeBruine et al.


Recent formulations of sexual selection theory emphasize how mate choice can be affected by environmental factors, such as predation risk and resource quality. Women vary greatly in the extent to which they prefer male masculinity and this variation is hypothesized to reflect differences in how women resolve the trade-off between the costs (e.g. low investment) and benefits (e.g. healthy offspring) associated with choosing a masculine partner. A strong prediction of this trade-off theory is that women's masculinity preferences will be stronger in cultures where poor health is particularly harmful to survival. We investigated the relationship between women's preferences for male facial masculinity and a health index derived from World Health Organization statistics for mortality rates, life expectancies and the impact of communicable disease. Across 30 countries, masculinity preference increased as health decreased. This relationship was independent of cross-cultural differences in wealth or women's mating strategies. These findings show non-arbitrary cross-cultural differences in facial attractiveness judgements and demonstrate the use of trade-off theory for investigating cross-cultural variation in women's mate preferences.


Dogs were probably domesticated in the Near East rather than East Asia

Nicholas Wade writes in the NY Times:
Borrowing methods developed to probe the genetics of human disease, researchers have concluded that dogs were probably first domesticated from wolves somewhere in the Middle East, in contrast to an earlier survey suggesting dogs originated in East Asia.

This finding puts the first known domestication — that of dogs — in the same place as the domestication of plants and other animals, and strengthens the link between the first animal to enter human society and the subsequent invention of agriculture about 10,000 years ago.
From a methodological standpoint, this study shows how we shouldn't infer population history and dispersals from the study of uniparental markers. It is quite possible that the most recent common ancestor (MRCA) at a locus may have lived at a different location than the ancestral population, prior to its dispersal.

With dogs, mtDNA seemingly coalesces to an East Asian ancestor, a finding that has recently been both challenged and re-affirmed. However, this new Nature paper shows that in terms of overall genomic diversity the Middle East rather than East Asia is the region where grey wolves were first domesticated, becoming the earliest dog populations.

Any locus (in this case mtDNA) may have its MRCA in a location somewhere across its geographical range. In fact it is expected that due to either luck or advantage, successful mutations at every locus may arise throughout a species' range, and indeed should be more likely to arise in more populous areas (more bodies = more new mutations).

It is by looking at multiple genetic loci that the true history of a species may be inferred. But this, too, requires caution, as great genetic diversity may arise from either great antiquity or substantial admixture (being at the crossroads).

Indeed, "central" regions of a species have the tendency to accumulate a greater level of variation, since genetic mutations must travel a shorter distance to get there, from their point of origin.

All in all, I am a priori skeptical of attempts to reconstruct population history (in either dogs or humans) from modern population data. Nonetheless, this study casts serious doubt on the East Asian origin of dogs, and adds support for the Near Eastern hypothesis.

From the press release:
"That research made extrapolations about how the domestic dog has evolved from examination of one region in the mitochondrial genome," Wayne said. "This new Nature paper is a much more comprehensive analysis because we have analyzed 48,000 markers distributed throughout the nuclear genome to try to conclude where the most likely ancestral population is.

"What we found is much more consistent with the archaeological record," he said. "We found strong kinship to Middle Eastern gray wolves and, to some extent, European gray wolves — but much less so to any wolves from East Asia. Our findings strongly contradict the conclusions based on earlier mitochondrial DNA sequence data."

Eighty percent of dog breeds are modern breeds that evolved in the last few hundred years, Wayne said. But some dog breeds have ancient histories that go back thousands of years.

"We sampled both groups, the modern explosion of dog breeds and some of the ancient lineages," he said. "Our data were aimed at resolving questions about the origin of domestic dogs, the evolution of dog breeds, and the history of dog breeds and relationships to their closest wild progenitor, the gray wolf."

The first dogs that appeared in the Middle Eastern archaeological record date back some 12,000 to 13,000 years, Wayne said. Wolves have been in the Old World for hundreds of thousands of years. The oldest dogs from the archaeological record come from Europe and Western Russia. A dog from Belgium dates back 31,000 years, and a group of dogs from Western Russia is approximately 15,000 years old, Wayne said.

"We know that dogs from the Middle East were closely associated with humans because they were found in ancient human burial sites," Wayne said. "In one case, a puppy is curled up in the arms of a buried human."

Some very old strains of dogs, with a history dating back more than several thousand years, may be mixed with modern breeds, enhancing their diversity in certain areas such as East Asia, Wayne said, interpreting the higher mitochondrial DNA diversity in that area of the globe.

There is one small set of East Asian breeds that does not indicate a strong Middle East origin, showing instead a high level of genetic sharing with Chinese wolves. This finding suggests there was some intermixing between East Asian dog breeds and East Asian wolves; the data do not make clear how long ago this occurred.

"However, the vast majority of dogs that we studied show significant levels of sharing with Middle Eastern wolves," said Novembre, a population geneticist who studies genetic diversity and the lessons that can be learned from it.

Nature doi:10.1038/nature08837

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Bridgett M. vonHoldt et al.


Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication1, 2. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data3. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.


March 17, 2010

Abstracts from AAPA 2010

Some abstracts from the upcoming (April 14-17) meeting of the American Association of Physical Anthropologists.

Why are pygmies small? An anthropometrical and anthropogenetical question
Pygmy populations from central Africa have the shortest stature worldwide. The name “pygmy” indeed comes from the Greek “pugmaios” that is a measure of length. This reduced stature has been the subject of numerous endocrinological studies and many evolutionary hypotheses have suggested that this phenotype was an adaptation to the rainforest (hot, humid and dense environment), to alimentation or due to life history trade-offs (high mortality). We have anthropometrical data for a sample of more than 1000 individuals from 7 pygmy populations and 3 neighbouring farmer populations from Gabon, Cameroon and Central African Republic. DNA samples are also available for a large number of individuals. The analysis of anthropometrical data shows that all pygmy groups have a male mean stature under 160 cm (this was used in the definition settled by Cavalli-Sforza in1986) and that a high variability exists between various pygmy populations. Verdu et al. (2009) published a genetic analysis based on neutral microsatellites on the same populations and found that pygmies present a variable admixture proportion with nonpygmies. Comparing this data with our anthropometrical data at the individual level we find a strong correlation between level of admixture and stature, thus strongly supporting the existence of a genetic component in pygmy short stature. We developed a candidate-gene approach to search for such genetic factor and will present current results on various genes located in the GH-IGF1 axis.
New evidence on headshaping from the Early Byzantine Maroneia in Thrace, Greece.

The first case of headshaping from Early Byzantine Greece was identified in 2006 at the cemetery of Maroneia (5th-6th c. A.D.). Biocultural evidence suggested the presence of a female individual culturally linked to Hunic traditions. This paper analyzes the second case of headshaping on a female skeleton uncovered in 2009 and allows for the wider discussion of the presence of a larger group related to the Huns in the city of Maroneia. The skull was examined by combining macroscopic observation and x-ray. Points of pressure are recorded in the frontal, post-coronal and occipital regions resulting in an undulation of diploic bone. Possible bilateral pressure on the frontal bone has produced an artificially narrowed frontal. The skull extends posterosuperiorly. These features suggest the application of bandaging producing circular modification. Both headshaped skulls exhibit the same type of modification. Similarly, both women were buried in a supine position, without offerings, just like the remaining 36 deceased individuals in the cemetery of Maroneia. Headshaping was unknown among Byzantine customs. On the contrary, the Huns who attacked the Balkans twice and who unsuccessfully threatened Maroneia in 411 practiced a pronounced form of circular headshaping. Consequently, biocultural evidence strongly supports the hypothesis that a group linked to the Huns was installed at the city and was assimilated into this Early Byzantine society. Future biogeochemical analysis needs to be undertaken in order to investigate migration patterns. However, headshaping reflects the cosmopolitan character of Maroneia, an important urban center in a province of the Byzantine Empire.

The genetic legacy of indigenous Caribbean peoples: Evidence from autosomal and mitochondrial data.

Archeological evidence suggests that autochthonous peoples began to migrate into the eastern island chain in the Caribbean, known as the Lesser Antilles, as early as 7200 years BP. Upon the arrival of Europeans, an estimated 2-4 million people lived on these islands. Within 32 years of contact, the native populations had virtually disappeared from the region due to European-introduced disease, abuse, and genocide. This lead many scholars to conclude that indigenous Caribbean people had become extinct. However, small pockets of indigenous communities have survived and are present today on several Lesser Antillean islands. Furthermore, ethnohistoric data suggests that gene flow occurred between autochthonous peoples and enslaved Africans beginning in the colonial period. In this study, we examine the genetic legacy of autochthonous Caribbean peoples from the Lesser Antilles in contemporary African- Caribbean populations as evidenced from mitochondrial data and novel autosomal data. A total of 516 individuals from eight Caribbean islands were typed for 109 ancestry informative markers and a subset of individuals were also typed for their mitochondrial haplogroup. Mitochondrial haplogroups indicate that 5% of the sample has indigenous ancestry while admixture estimates from autosomal markers show 4% indigenous ancestry. Both lines of data suggest that despite the dramatic postcontact decline in population size, indigenous Caribbean people have made notable genetic contributions to contemporary African-Caribbean populations. Furthermore, these genetic contributions vary according to the genetic system typed and across the islands.
Chuvash origins: Evidence frommtDNA Markers.
ORION M. GRAF et al.

A sample of 96 unrelated individuals from Chuvashia, Russia was sequenced for hypervariable region-I (HVR-I) of the mtDNA molecule. The Chuvash speak a Turkic language that is not mutually intelligible to other extant Turkish groups, and their genetics are distinct from Turkic-speaking Altaic groups. Some scholars have suggested that they are remnants of the Golden Horde, while others have advocated that they are the products of admixture between Turkic and Finno-Ugric speakers who came into contact during the 13th century. Earlier genetic research using autosomal DNA markers suggested a Finno-Ugric origin for the Chuvash. This study examines non-recombining DNA markers to better elucidate their origins. The majority of individuals in this sample exhibit haplogroups H (31%), U (22%), and K (11%), all representative of western and northern Europeans, but absent in Altaic or Mongolian populations. Multidimensional scaling (MDS) was used to examine distances between the Chuvash and 8 reference populations compiled from the literature. Mismatch analysis showed a unimodal distribution. Along with neutrality tests (Tajima’s D (-1.43365) p less than 0.05, Fu’s FS (-25.50518) p less than 0.001), the mismatch distribution is suggestive of an expanding population. These tests suggest that the Chuvash are not related to the Altai and Mongolia along their maternal line but supports the “Elite” hypothesis that their language was imposed by a conquering group-- leaving Chuvash mtDNA largely of Eurasian origin with a small amount of Central Asian gene flow. Their maternal markers appear to most closely resemble Finno-Ugric speakers rather than fellow Turkic speakers.
Population history and substructure of Anatolia and Turkey as evidenced by craniofacial diversity.

Anatolia, the Asian segment of Turkey, is an area of evolutionary importance for human groups who used this corridor as a bridge for migration between the Caucasus, Western Asia and Europe since Lower Paleolithic times. Historically, Anatolia has been occupied by diverse civilizations, including the Byzantine and Ottoman Empires. This study is an attempt to understand Turkish population substructure and history by examining craniofacial diversity through several temporal periods framed within a population genetic model. If the region of Anatolia has been used as a migratory corridor for peoples spanning disparate geographic areas (Balkans, Central Asia, and East Asia), then gradual craniofacial change is expected due to these migrations coupled with extensive admixture. Studies using mtDNA indicate a pre-Neolithic expansion resulting in extensive migration, while Y chromosome studies reveal haplogroup clustering and gene flow from the Caucus with less admixture from Central and East Asia. Overall, our results indicate minimal Turkish population substructure. When crania were separated into sex, our results are consistent with uniparental marker population history. Female crania show a distinctness with modern groups and are actually more similar to Neolithic European and Near Eastern populations. This would indicate a relatively stable female population in Anatolia since Neolithic times. Male crania are more heterogeneous and cluster within a larger geographic zone of Eurasia and the Near East consistent with greater male migration. There is little support for admixture from Central or East Asian groups. These results support the hypothesis for a Turkic language displacement with insignificant genetic exchange.
Genetic analyses reveal a history of serial founder effects, admixture between longseparated founding populations in Oceania, and interbreeding with archaic humans.

Genetic anthropologists continue to debate whether human neutral genetic variation primarily reflects a continuum of demes connected by local gene flow or colonization and serial founder effects. A second unresolved issue concerns the genetic contribution of archaic species to the modern human gene pool. Some studies suggest that this contribution was substantial and that it played an important role in human adaptation. These issues remain unresolved because of inadequacies and biases in datasets, problems in statistical methodology, and the failure to recognize that different evolutionary processes may produce similar outcomes. This study redresses these limitations by analyzing gene identity within and between populations in a dataset comprised of 614 STRs assayed in 1,983 people from 99 widespread populations. Our strategy is to fit hierarchical models to these data and examine residual deviations from the models. Each model involves nesting smaller units such as populations into larger units such as continental regions. It is possible to restate many of these models as either expansions or reductions of each other and thereby identify aspects of population structure that have had a major impact on the overall pattern of diversity. The strong fit of a model estimated using the Neighbor Joining algorithm indicates that human genetic diversity primarily reflects a history of successive founder effects associated with our exodus from Africa, not a continuum of demes connected by gene flow. Residual deviations from the model suggest: 1) the genomes of Oceanic peoples are the product of two independent waves of migration to the region and admixture, and 2) genetic exchange occurred between archaic and modern humans after their initial divergence.
Correlations between genetic ancestry and superficial traits indicate substantial admixture stratification in Brazil.

Brazil is one of the most admixed countries in the world. How this admixture affected the distribution of genetic ancestry across Brazilian ethnic (“Color”) groups is a fundamental question which to date has only received minimal attention. In an effort to systematically study variation in genetic ancestry in Brazil, we collected DNA and various phenotypic measures from 596 volunteers in Brasilia, Brazil. Participants were asked to provide their self-described “Color” as defined by the Brazilian census (Preta/Black, Parda/Brown, Branca/White, Indigena/Indigenous, Amarela/Yellow). Phenotype data was collected from each subject including hair texture, highresolution eye photographs, skin and hair color by reflectometry, and three-dimensional facial photographs. To estimate genomic ancestry, DNA from each participant was genotyped using 176 ancestry informative markers (AIMs), autosomal SNPs with large frequency differences between parental populations known to contribute to Brazilian admixture (West African, East Asian, European and Indigenous American). Although genomic ancestry shows significant overlap across “Color” groups, there are highly significant differences in average proportional ancestry. Additionally, analyses comparing trait values and genetic ancestry show significant correlations consistent with expectations of populations stratified with respect to genetic ancestry. Ethnographic research indicates that designations of “Color” are fluid and largely based on physical traits as opposed to known ancestry. This likely contributes to the observed ancestry overlap between ethnic groups and the strong association between phenotype and group. This study emphasizes the importance of genetic marker based estimates of ancestry as well as objective assessment of superficial traits in understanding the admixture process.
Geographic structure of genetic variation in North America: Population fissions and European admixture.

A satisfactory understanding of how modern Native North America populations are biologically related to each other requires increased sampling of populations and/or genetic markers and testing of the fit of different models of population structure. To this end, we combine new autosomal microsatellite data from Native North American populations with previously published data. Using J.C. Long’s Generalized Hierarchical Modeling software, we evaluate the fit of different trees to the data. Although we observe a correlation between population pairwise genetic and geographic distances, as expected with a long-term process of isolation by distance, we show that this correlation likely results from geographically-structured population fissions. This pattern could result from the initial peopling of North America or from a later process. The magnitude of European ancestry in the sampled populations, as estimated with the software structure, varies drastically among geographic regions, and may limit our ability to use modern genetic variation to investigate Native North American prehistory.This study was funded by the Wenner-Gren Foundation for Anthropological Research, grant number 7580 to K.B. Schroeder and D.G. Smith, and by the National Science Foundation, grant BCS- 0422144 to R.S. Malhi, B.M. Kemp, and D.G. Smith.
Coalescent modeling of Yakut origins points to small founding population based on mtDNA variation.

Based on archaeological and ethnohistorical evidence, the Yakut people of northeastern Siberia are considered to be descendants of ancient Turkic-speaking populations once living in the distant Altai- Sayan region on the Russian- Mongolian border. The results of phylogeographic studies on Siberian mtDNA variation have been generally concordant with a southern Yakut origin, although the timing of the northern migration, the size of the founder group and the degree of genetic admixture with non-Turkic Siberian populations are less apparent. In an effort to better understand Yakut origins, we modeled 25 demographic scenarios, including parameters such as effective population size, growth rate and gene flow, and tested by coalescent simulation whether any are consistent with the patterns of mtDNA diversity observed in present-day Yakuts. The models consist of either two simulated demes that represent Yakuts and a South Siberian ancestral population, or three demes that also include a regional Northeast Siberian population that served as a source of localized gene flow into the Yakut deme. The model that produced the best fit to the observed data defined a founder group with an effective female population size of only 150 individuals, migrating northwards approximately 1,000 years BP and undergoing significant admixture with neighboring populations in Northeastern Siberia. These simulation results indicate a pronounced founder effect that was primarily kin-structured and reconcile reported discrepancies between Yakut mtDNA and Y chromosome diversity levels.
The role of selection-nominated candidate genes in determining Indigenous American skin pigmentation.
World-wide variability in skin pigmentation has been a subject of anthropological inquiry from the beginning of our discipline. Recent genomic studies indicate that skin pigmentation is one of the most rapidly evolving phenotypes in many human populations and that genes underlying skin pigmentation have been subject to some of the most extreme selective pressures of any genes in the human genome. Unlike previous research, this study both identifies pigmentation genes that have undergone selection in Indigenous American populations and tests the influences of these genes on skin color in admixed individuals. 906,600 single nucleotide polymorphisms (SNPs) were surveyed for signatures of selection in indigenous populations from Central and South America. Evidence of selection was identified by comparison to HapMap Phase I populations using reduction in heterozygosity (lnRH), Locus- Specific Branch Length (LSBL), Tajima’s D, and haplotype block structure. In the 12 pigmentation candidate genes that show the strongest evidence of selection (ADAM17, POMC, AP3B1, OPRM1, SILV, OCA2/HERC, PLDN, MYO5A, RAB27A, CYP1A2, ATRN, and ASIP), 48 SNPs selected to represent the overall variation in the selection nominated candidate genes were genotyped in individuals of admixed Indigenous American and European ancestry. These SNPs show substantial allele frequency differences between the parental populations. Using admixture based regression model analyses, genes contributing to darker skin pigmentation in Indigenous Americans were found. This study not only identified skin pigmentation genes contributing to skin color variation in previously understudied Indigenous American populations, it validated the usefulness of using population genetic tests of selection to identify functional genes. This study was generously funded by the National Science Foundation Dissertation Improvement Grant 0925976

March 10, 2010

Digging deeper into East African human Y chromosome lineages

Hum Genet. 2010 Mar 6. [Epub ahead of print]

Digging deeper into East African human Y chromosome lineages.

Gomes V, Sánchez-Diz P, Amorim A, Carracedo A, Gusmão L.

The most significant and widely studied remodeling of the African genetic landscape is the Bantu expansion, which led to an almost total replacement of the previous populations from the sub-Saharan region. However, a poor knowledge exists about other population movements, namely, the Nilotic migration, which is a pastoralist dispersal that, contrary to the Bantu expansion, impacted only East African populations. Here, samples from a Ugandan Nilotic-speaking population were studied for 37 Y chromosome-specific SNPs, and the obtained data were compared with those already available for other sub-Saharan population groups. Although Uganda lies on the fringe of both Bantu and Nilotic expansions, a low admixture with Bantu populations was detected, with haplogroups carrying M13, M182 and M75 mutations prevailing in Nilotes together with a low frequency of the main Bantu haplogroups from clade E1b1a-M2. The results of a comparative analysis with data from other population groups allowed a deeper characterization of some lineages in our sample, clarifying some doubts about the origin of some particular Y-SNPs in different ethnic groups, such as M150, M112 and M75. Moreover, it was also possible to identify a new Y-SNP apparently specific to Nilotic groups, as well as the presence of particular haplogroups that characterize Nilotic populations. The detection of a new haplogroup B2a1b defined by G1, could be, therefore, important to differentiate Nilotes from other groups, helping to trace migration and admixture events that occurred in eastern Africa.


March 08, 2010

Genome-Wide Genotyping of Pooled Samples to assess genetic ancestry (Chiang et al. 2010)

On the left: genetic differentiation between Chinese and Japanese using 420 Ancestry Informative Markers vs. 420 random SNPs. Note that the "fuzzy" picture on B would be better resolved if a larger number of SNPs had been used.

Clean genetic separation of Japanese from other East Asians was achieved here (using 350K SNPs) and here (using 200K SNPs), with Koreans forming a bridge between the Japanese and other Mongoloids.

PLoS Genetics doi:10.1371/journal.pgen.1000866

Rapid Assessment of Genetic Ancestry in Populations of Unknown Origin by Genome-Wide Genotyping of Pooled Samples

Charleston W. K. Chiang et al.


As we move forward from the current generation of genome-wide association (GWA) studies, additional cohorts of different ancestries will be studied to increase power, fine map association signals, and generalize association results to additional populations. Knowledge of genetic ancestry as well as population substructure will become increasingly important for GWA studies in populations of unknown ancestry. Here we propose genotyping pooled DNA samples using genome-wide SNP arrays as a viable option to efficiently and inexpensively estimate admixture proportion and identify ancestry informative markers (AIMs) in populations of unknown origin. We constructed DNA pools from African American, Native Hawaiian, Latina, and Jamaican samples and genotyped them using the Affymetrix 6.0 array. Aided by individual genotype data from the African American cohort, we established quality control filters to remove poorly performing SNPs and estimated allele frequencies for the remaining SNPs in each panel. We then applied a regression-based method to estimate the proportion of admixture in each cohort using the allele frequencies estimated from pooling and populations from the International HapMap Consortium as reference panels, and identified AIMs unique to each population. In this study, we demonstrated that genotyping pooled DNA samples yields estimates of admixture proportion that are both consistent with our knowledge of population history and similar to those obtained by genotyping known AIMs. Furthermore, through validation by individual genotyping, we demonstrated that pooling is quite effective for identifying SNPs with large allele frequency differences (i.e., AIMs) and that these AIMs are able to differentiate two closely related populations (HapMap JPT and CHB).


March 07, 2010

Major East-West divide in Indonesian Y chromosomes

As usual I have my reservations about the time estimates in this paper, but it is very useful as a guide to genetic variation in Indonesia, an island nation of composite origins where the indigenous population forms part of the S/SE Asia/Oceania zone of "Australoids", probably reflecting early out-of-Africa humans taking the southern route, while this population has been influenced by movements from the north: Caucasoids into India, and Mongoloids or Mongoloid-influenced people into Indonesia.

Getting back to the ever-present time issue; the inferences on this paper are, of course, based on assumption about Y-STR diversity accumulation that I have criticized elsewhere and I will not repeat.

But, isn't it strange that the authors claim a Paleolithic gene pool, while, at the same time, discovering a sharp divide? Common sense dictates that genetic distinctions across a long time span would be blurred, and there would be no sharp divide.

Sharp divides are created by recent population movements and are maintained by insurmountable geographical barriers (e.g., the Sahara or the Pacific) that persist for a long-time.

Molecular Biology and Evolution, doi:10.1093/molbev/msq063

Major East-West Division Underlies Y Chromosome Stratification Across Indonesia

Tatiana M. Karafet et al.


The early history of Island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul 45 thousand years ago and the much later Neolithic expansion of Austronesian-speaking farmers 4,000 years ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 SNPs/indels and 12 Y-STRs, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., ?ST = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M and S subclades) and likely reflect the initial wave of colonization of the region, while the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201, P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122, O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion.


March 04, 2010

Ancient mtDNA from the US Southwest

Journal of Archaeological Science doi:10.1016/j.jas.2010.01.024

Ancestral Puebloan mtDNA in context of the greater southwest

Meradeth H. Snowa et al.


Ancient DNA (aDNA) was extracted from the human remains of seventy-three individuals from the Tommy and Mine Canyon sites (dated to PI-II and PIII, respectively), located on the B-Square Ranch in the Middle San Juan region of New Mexico. The mitochondrial DNA (mtDNA) haplogroups of 48 (65.7%) of these samples were identified, and their frequency distributions were compared with those of other prehistoric and modern populations from the Greater Southwest and Mexico. The haplogroup frequency distributions for the two sites were statistically significantly different from each other, with the Mine Canyon site exhibiting an unusually high frequency of haplogroup A for a Southwestern population, indicating the possible influence of migration or other evolutionary forces. However, both sites exhibited a relatively high frequency of haplogroup B, typical of Southwestern populations, suggesting continuity in the Southwest, as has been hypothesized by others ([Carlyle, 2003], [Carlyle et al., 2000], [Kemp, 2006], [Malhi et al., 2003] and [Smith et al., 2000]). The first hypervariable region of twenty-three individuals (31.5%) was also sequenced to confirm haplogroup assignments and compared with other sequences from the region. This comparison further strengthens the argument for population continuity in the Southwest without a detectable influence from Mesoamerica.


March 02, 2010

Female-to-Male Breeding Ratio in Modern Humans (Labuda et al. 2010)

Related: Gender differences in reproductive success (Brown et al. 2009)

The American Journal of Human Genetics, 25 February 2010

Female-to-Male Breeding Ratio in Modern Humans—an Analysis Based on Historical Recombinations

Damian Labuda et al.


Was the past genetic contribution of women and men to the current human population equal? Was polygyny (excess of breeding women) present among hominid lineages? We addressed these questions by measuring the ratio of population recombination rates between the X chromosome and the autosomes, ρX/ρA. The X chromosome recombines only in female meiosis, whereas autosomes undergo crossovers in both sexes; thus, ρX/ρA reflects the female-to-male breeding ratio, β. We estimated β from ρX/ρA inferred from genomic diversity data and calibrated with recombination rates derived from pedigree data. For the HapMap populations, we obtained β of 1.4 in the Yoruba from West Africa, 1.3 in Europeans, and 1.1 in East Asian samples. These values are consistent with a high prevalence of monogamy and limited polygyny in human populations. More mutations occur during male meiosis as compared to female meiosis at the rate ratio referred to as α. We show that at α ≠ 1, the divergence rates and genetic diversities of the X chromosome relative to the autosomes are complex functions of both α and β, making their independent estimation difficult. Because our estimator of β does not require any knowledge of the mutation rates, our approach should allow us to dissociate the effects of α and β on the genetic diversity and divergence rate ratios of the sex chromosomes to the autosomes.


March 01, 2010

Predicting Phenotype from Genotype: Normal Pigmentation (Valenzuela et al. 2010)

Yann Klimentidis points me to this new paper on predicting human pigmentation phenotype from genotype. The paper is interesting in view of the recent finding that lactose intolerance phenotype is not very well captured by the known genetic variation.

The current paper looks at how well normal pigmentation (skin, hair, and eye color) is predicted from known genotypes. The sample consists of individuals from the University of Arizona.

From the paper:
The three most frequent SNPs found in the range from the highest R2 model to the first inflection of the graph were used to construct an MLR model for each trait. These models accounted for significant variation in each of the four measured traits: scalp-hair total melanin (76.3%), natural log of the ratio of eumelanin-to-pheomelanin (43.2%), skin reflectance (45.7%), and eye color (74.8%) (Table 3).
Obviously two caveats should be raised:

(i) that the associations are dependent on the sample. It is not clear how the percentage of variation explained would be altered in a population of different ethnic origins -not represented in the UoA.
(ii) that the associations may be mediated by other genetic factors, not yet discovered.

With respect to (ii), pigmentation appears to be a "success story" of genome-wide association studies, as a relatively small number of SNPs accounts for such a high level of variation (about 3/4 for the best traits). However, the missing 1/4 should also make us cautious when we attempt to infer the pigmentation of a sample, in either a forensic or an archaeological context.

Journal of Forensic Science doi:10.1111/j.1556-4029.2009.01317.x

Predicting Phenotype from Genotype: Normal Pigmentation

Robert K. Valenzuela et al.


Genetic information in forensic studies is largely limited to CODIS data and the ability to match samples and assign them to an individual. However, there are circumstances, in which a given DNA sample does not match anyone in the CODIS database, and no other information about the donor is available. In this study, we determined 75 SNPs in 24 genes (previously implicated in human or animal pigmentation studies) for the analysis of single- and multi-locus associations with hair, skin, and eye color in 789 individuals of various ethnic backgrounds. Using multiple linear regression modeling, five SNPs in five genes were found to account for large proportions of pigmentation variation in hair, skin, and eyes in our across-population analyses. Thus, these models may be of predictive value to determine an individual’s pigmentation type from a forensic sample, independent of ethnic origin.