The Neolithic trace in mitochondrial haplogroup U8
Joana Barbosa Pereira 1,2 , Marta Daniela Costa 1,2 , Pedro Soares 2 , Luísa Pereira 2,3 , Martin Brian Richards 1,4 1 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, 2 Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal, 3 Faculdade de Medicina da Universidade do Porto, Porto, Portugal, 4 School of Applied Sciences, University of Huddersfield, Huddersfield, UK
The mitochondrial DNA (mtDNA) still remains an important marker in the study of human history, especially if considering the increasing amount of data available. Among the several questions regarding human history that are under debate, the model of expansion of agriculture into Europe from its source in the Near East is still unclear. Recent studies have indicated that clusters belonging to haplogroup K, a major clade from U8, might be related with the Neolithic expansions. Therefore, it is crucial to identify the founder lineages of the Neolithic in Europe so that we may understand the real genetic input of the first Near Eastern farmers in the current European population and comprehend how agriculture spread so quickly throughout all Europe. In order to achieve this goal, a total of 55 U8 samples from the Near East, Europe and North Africa were selected for complete characterisation of mtDNA. A maximum-parsimonious phylogenetic tree was constructed using all published sequences available so far. Coalescence ages of specific clades were estimated using ρ statistic, maximum likelihood and Bayesian methods considering a mutation rate for the complete molecule corrected for purifying selection. Our results show that U8 dates to ~37-54 thousand years ago (ka) suggesting that this haplogroup might have been carried by the first modern humans to arrive in
Europe, ~50 ka. Haplogroup K most likely originated in the Near East~23-32 ka where it might have remained during the Last Glacial Maximum, between 26-19 years ago. The majority of K subclades date to the Late Glacial and are related with the repopulation of Europefrom the southern refugia areas. Only a few lineages appear to reflect post glacial, Neolithic or post-Neolithic expansions, mostly occurring within Europe. The major part of the lineages dating to the Neolithic period seems to have an European origin with exception of haplogroup K1a4 and K1a3. Clade K1a4 appears to be originated from the Near Eastwhere it also reaches its highest peak of diversity. Despite the main clades of K1a4 arose in the Near East during the Late Glacial, its subclade K1a4a1 dates to ~9-11 ka and is most likely related with the Neolithic dispersal to Europe. Similarly, K1a3 probably originated in the Near East during the Late Glacial and its subclade K1a1a dispersed into Europe ~11-13 ka alongside with the expansion of agriculture.
Late Glacial Expansions in
Europe revealed through
the fine-resolution characterisation of mtDNA haplogroup U8
Marta Daniela Costa 1,2 , Joana Barbosa Pereira 1,2 , Pedro Soares 2 , Luisa Pereira 2,3 , Martin Brian Richards 1,4 1 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK, 2 IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal, 3 Faculdade de Medicina, Universidade do Porto, Porto, Portugal, 4 School of Applied Sciences, University of Huddersfield, Huddersfield, UK
The maternally inherited and fast evolving mitochondrial DNA (mtDNA) molecule is a highly informative tool with which to reconstruct human prehistory. This has become even more true in recent years, as mtDNA based studies are becoming more robust and powerful due to the availability of complete mtDNA genomes. These allow better mutation rate estimates and fine-resolution characterisation of the phylogeography of mtDNA haplogroups, or named clades. MtDNA haplogroup K, the major subclade of U8, occurs at low frequencies through West Eurasian populations, and is much more common in Ashkenazi Jews. However, the lack of variation on the first hypervariable segment (HVSI) has precluded any meaningful phylogeographic analysis to date. We therefore completely sequenced 50 haplogroup K and 5 non-K U8 mtDNA samples from across Europe and the Near East, and combined them with 343 genomes previously deposited in GenBank, in order to reconstruct a detailed phylogenetic tree. By combining several inference methods, including maximum parsimony, maximum likelihood and Bayesian inference it was possible to trace the timescale and geography of the main expansions and dispersals associated with this lineage. We confirmed that haplogroup K, dating to ~32 thousand years (ka) ago, descended from the U8 clade, which coalesces ~48 ka ago. The latter is close to the timing of the first arrival of modern humans in Europe and U8 could be one of the few surviving mtDNA lineages brought by the first settlers from the Near East. U8 split into the widespread U8b, at ~43 ka, and U8a, which seems to have expanded only in Europe ~24 ka ago. Considering the pattern of diversity and the geographic distribution, haplogroup K is most likely to have arisen in the Near East, ~32 ka ago. However, some subclades were evidently carried to Europe during the Last Glacial Maximum (LGM). We observed significant expansions of haplogroup K lineages in the Late Glacial period (14-19 ka), reflecting expansions out of refuge areas in southwest and possibly also southeast Europe.
Reticulated origin of domesticated tetraploid wheat
Peter Civan Centro de Ciencias do Mar, Universidade do
Algarve, Faro, Portugal
The past 15 years have witnessed a notable scientific interest in the topic of crop domestication and the emergence of agriculture in the
Near East. Multi-disciplinary approaches brought a significant amount of new data and a multitude of hypotheses and interpretations. However, some seemingly conflicting evidence, especially in the case of emmer wheat, caused certain controversy and a broad scientific consensus on the circumstances of the wheat domestication has not been reached, yet. The past phylogenetic research has translated the issue of wheat domestication into somewhat simplistic mono- /polyphyletic dilemma, where the monophyletic origin of a crop signalizes rapid and geographically localized domestication, while the polyphyletic evidence suggests independent, geographically separated domestication events. Interestingly, the genome-wide and haplotypic data analyzed in several studies did not yield consistent results and the proposed scenarios are usually in conflict with the archaeological evidence of lengthy domestication. Here I suggest that the main cause of the above mentioned inconsistencies might lie in the inadequacy of the divergent, tree-like evolutional model. The inconsistent phylogenetic results and implicit archaeological evidence indicate a reticulate (rather than divergent) origin of domesticated emmer. Reticulated genealogy cannot be properly represented on a phylogenetic tree; hence different sets of samples and genetic loci are prone to conclude different domestication scenarios. On a genome-wide super-tree, the conflicting phylogenetic signals are suppressed and the origin of domesticated crop may appear monophyletic, leading to misinterpretations of the circumstances of the Neolithic transition. The network analysis of multi-locus sequence data available for tetraploid wheat clearly supports the reticulated origin of domesticated emmer and durum wheat. The concept of reticulated genealogy of domesticated wheat sheds new light onto the emergence of Near-Eastern agriculture and is in agreement with current archaeological evidence of protracted and dispersed emmer domestication.
High-coverage population genomics of diverse African hunter-gatherers
Joseph Lachance 1 , Benjamin Vernot 2 , Clara Elbers 1 , Bart Ferwerda 1 , Alain Froment 3 , Jean-Marie Bodo 4 , Godfrey Lema 5 , Thomas Nyambo 5 , Timothy Rebbeck 1 , Kun Zhang 6 , Joshua Akey 2 , Sarah Tishkoff 1 1 University of Pennsylvania, Philadelphia, PA, USA, 2 University of Washington, Seattle, WA, USA, 3 IRD-MNHN, Musee de l'Homme, Paris, France, 4 Ministere de la Recherche Scientifique et de l’Innovation, Yaounde, Cameroon, 5 Muhimbili University College of Health Sciences, Dar es Salaam, Tanzania, 6 University of California at San Diego, San Diego, CA, USA
In addition to their distinctive subsistence patterns, African hunter-gatherers belong to some of the most genetically diverse populations on Earth. To infer demographic history and detect signatures of natural selection, we sequenced the whole genomes of five individuals in each of three geographically and linguistically diverse African hunter-gatherer populations at >60x coverage. In these 15 genomes we identify 13.4 million variants, many of which are novel, substantially increasing the set of known human variation. These variants result in allele frequency distributions that are free of SNP ascertainment bias. This genetic data is used to infer population divergence times and demographic history (including population bottlenecks and inbreeding). We find that natural selection continues to shape the genomes of hunter-gatherers, and that deleterious genetic variation is found at similar levels for hunter-gatherers and African populations with agricultural or pastoral subsistence patterns. In addition, the genomes of each hunter-gatherer population contain unique signatures of local adaptation. These highly-divergent genomic regions include genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing.
Reconstructing past Native American genetic diversity in
Puerto Ricofrom contemporary populations Marina Muzzio 1,2 , Fouad Zakharia 1 , Karla Sandoval 1 , Jake K. Byrnes 3 , Andres Moreno-Estrada 1 , Simon Gravel 1 , Eimear Kenny 1 , Juan L. Rodriguez-Flores 5 , Chris R. Gignoux 6 , Wilfried Guiblet 4 , Julie Dutil 7 , The 1000 Genomes Consortium 0 , Andres Ruiz-Linares 8 , David Reich 9,10 , Taras K. Oleksyk 4 , Juan Carlos Martinez-Cruzado 4 , Esteban Gonzalez Burchard 6 , Carlos D. Bustamante 1 1 Department of Genetics, Stanford University School of Medicine, Stanford, California, USA, 2 Facultad de Ciencias Naturales, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina, 3 Ancestry. com®, San Francisco, California, USA, 4 Department of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico, 5 Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA, 6 Institute for Human Genetics, University of California San Francisco, San Francisco, California, USA, 7 Ponce School of Medicine, Ponce, Puerto Rico, 8 Department of Genetics, Evolution and Environment. University College London, London, UK, 9 Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, 10 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
The Caribbean region has a rich cultural and biological diversity, including several countries with different languages, and important historical events like the arrival of the Europeans in the late fifteenth century affected it deeply. Although it has been said that two main Native American groups peopled the Caribbean at the time of
’s voyages—the Arawakan-speaking Tainos and the Caribs—this model has been questioned because it comes from the descriptions written by the conquerors. The archaeological record shows a richer picture of trade among the islands, cultural change and diversity than what colonial documents depict, from the early settlements around 8000 B.P. to the chiefdoms and towns at the time of contact. How this area was peopled and how its inhabitants interacted with the surrounding continent are questions that remain to be answered due to the fragmentary nature of the historical and archaeological records. Columbus
We aim to reconstruct the Native American genetic diversity from the time of the Spanish arrival at the island of Puerto Rico from its contemporary population. We seek to find out how the original peopling of Puerto Rico occurred, along with which contemporary Native American populations are the most closely related to the Native tracks found. We used PCAdmix to trace Native American segments in admixed individuals, thus enabling us to reconstruct the original native lineages previous to the European and African contact.
Inference of demographic history and natural selection in African Pygmy populations from whole-genome sequencing data
Specifically, we generated local ancestry calls for the 70 parents of the 35 complete Puerto Rican trios from the wholegenome and Illumina Omni 2.5M chip Genotype data of the 1000 Genomes Project, both to examine genome-wide admixture patterns and to infer demographic historical events from ancestry tract length distributions and an ancestryspecific PCA approach, adding 55 Native American groups as potential source populations (N=475 genotyped through Illumina’s 650K array) and 15 selected Mexican trios (genotyped on Affymetrix’s 6.0 array, including about 906,000 SNPs) to provide population context. ADMIXTURE analysis has shown that in Puerto Rico there is no single source of contribution for the Native component. Rather, this component seems to include a mixture of major Mexican and Andean components with little contributions from the Amazonian isolates. On the other hand, the ancestry-specific PCA plotted the Puerto Rican Native segments tightly clustered with the Native segments of groups from the same language family as the Tainos (Equatorial-Tucanoan), showing a clear association between linguistics and genetics instead of a geographical one.
Martin Sikora 1 , Etienne Patin 2 , Helio Costa 1 , Katherine Siddle 2 , Brenna M Henn 1 , Jeffrey M Kidd 1,3 , Ryosuke Kita 1 , Carlos D Bustamante 1 , Lluis Quintana-Murci 2 1 Department of Genetics, School of Medicine, Stanford Uni, Stanford, CA, USA, 2 Unit of Human Evolutionary Genetics, Institut Pasteur, CNRS URA3012, Paris, France, 3 Departments of Human Genetics and Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
The Pygmy populations of Central Africa are some of the last remaining hunter-gatherers among present-day human populations, and can be broadly classified into two geographically separated groups, the Western and Eastern Pygmies. Compared to their neighboring populations of predominantly Bantu origin, Pygmy populations show distinct cultural and physical characteristics, most notably short stature, often referred to as the “Pygmy phenotype”. Given their distinct physical characteristics, the questions of the demographic history and origin of the Pygmy phenotype have attracted much attention. Previous studies have shown an ancient divergence (~60,000 years ago) of the ancestors of modernday Pygmies from non-Pygmies, and a more recent split of the Eastern and Western Pygmy groups. However, these studies were generally based on a relatively small set of markers, precluding accurate estimations of demographic parameters. Furthermore, despite the considerable interest, to date there is still little known about the genetic basis of the small stature phenotype of Pygmy populations.
In order to address these questions, we sequenced the genomes of 47 individuals from three populations: 20 Baka, a Pygmy hunter-gatherer population from the Western subgroup of the African Pygmies; 20 Nzebi, a neighboring nonPygmy agriculturist population from the Bantu ethnolinguistic group; as well as 7 Mbuti, Eastern Pygmy population, from the Human Genome Diversity Project (HGDP). We performed whole-genome sequencing using Illumina Hi-Seq 2000 to a median sequencing depth of 5.5x per individual. After stringent quality control filters, we call over 17 Million SNPs across the three populations, 32% of them novel (relative to dbSNP 132). Genotype accuracy after imputation was assessed using genotype data from the Illumina OMNI1 SNP array, and error rates were found to be comparable to other low-coverage studies (< 3% for most individuals). Preliminary results show relatively low genetic differentiation between the Baka and the Nzebi (mean FST = 0.026), whereas the Mbuti show higher differentiation to both Baka and Nzebi (mean FST = 0.060 and 0.070, respectively). Furthermore, we find that alleles previously found to be associated with height in other populations are not enriched for the “small” alleles in the Pygmy populations. We find a number of highly differentiated genomic regions as candidate loci for height differentiation, which will be verified using simulations under the best-fit demographic model, inferred from multi-dimensional allele frequency spectra using DaDi. Our dataset will allow a detailed investigation of the demographic history and the genomics of adaptation in these populations.Genetic structure in North African human populations and the gene flow to
Laura R Botigué 1 , Brenna M Henn 2 , Simon Gravel 2 , Jaume Bertranpetit 1 , Carlos D Bustamante 2 , David Comas 1 1 Institut de Biologia Evolutiva (IBE, CSIC-UPF), Barcelona, Spain, 2 Stanford University, Stanford CA, USA Despite being in the African continent and at the shores of the
Mediterranean, North African populations might have experienced a different population history compared to their neighbours. However, the extent of their genetic divergence and gene flow from neighbouring populations is poorly understood. In order to establish the genetic structure of North Africans and the gene flow with the Near East, Europe and sub-Saharan Africa, a genomewide SNP genotyping array data (730,000 sites) from several North African and Spanish populations were analysed and compared to a set of African, European and Middle Eastern samples. We identify a complex pattern of autochthonous, European, Near Eastern, and sub-Saharan components in extant North African populations; where the autochthonous component diverged from the European and Near Eastern component more than 12,000 years ago, pointing to a pre-Neolithic ‘‘back-to-Africa’’ gene flow. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the frequency and length distribution of migrant tracts, which has suggested a migration of western African origin into Morocco ~1,200 years ago and a migration of individuals with Nilotic ancestry into Egypt ~ 750 years ago. We characterize broad patterns of recent gene flow between Europe and Africa, with a gradient of recent African ancestry that is highest in southwestern Europeand decreases in northern latitudes. The elevated shared African ancestry in SW Europe(up to 20% of the individuals’ genomes) can be traced to populations in the North African Maghreb. Our results, based on both allele-frequencies and shared haplotypes, demonstrate that recent migrations from North Africa substantially contribute to the higher genetic diversity in southwestern Europe
Estimating a date of mixture of ancestral South Asian populations
Priya Moorjani 1,2 , Nick Patterson 2 , Periasamy Govindaraj 3 , Danish Saleheen 4 , John Danesh 4 , Lalji Singh* 3,5 , Kumarasamy Thangaraj* 3 , David Reich* 1,2 1 Harvard University, Boston, Massachusetts, USA, 2 Broad Institute, Cambridge, Massachusetts, USA, 3 Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India, 4 Dept of Public Health and Care, University of Cambridge, Cambridge, UK, 5 Genome Foundation, Hyderabad, Andhra Pradesh, India Linguistic and genetic studies have demonstrated that almost all groups inLong IBD in Europeans and recent population history
South Asiatoday descend from a mixture of two highly divergent populations: Ancestral North Indians (ANI) related to Central Asians, Middle Easterners and Europeans, and Ancestral South Indians (ASI) not related to any populations outside the Indian subcontinent. ANI and ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago, but the date of the ANI-ASI mixture is unknown. Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago. Some mixture may also be older—beyond the time we can query using admixture linkage disequilibrium—since it is universal throughout the subcontinent: present in every group speaking Indo-European or Dravidian languages, in all caste levels, and in primitive tribes. After the ANI-ASI mixture that occurred within the last four thousand years, a cultural shift led to widespread endogamy, decreasing the rate of additional mixture.
Peter Ralph, Graham Coop UC Davis,
Davis, CA, USA
Numbers of common ancestors shared at various points in time across populations can tell us about recent demography, migration, and population movements. These rates of shared ancestry over tens of generations can be inferred from genomic data, thereby dramatically increasing our ability to infer population history much more recent than was previously possible with population genetic techniques. We have analyzed patterns of IBD in a dataset of thousands of Europeans from across the continent, which provide a window into recent European geographic structure and migration.Gene flow between human populations during the exodus from
Aylwyn Scally, Richard Durbin Wellcome Trust Sanger Institute, Hinxton,
We present a novel test for historical gene flow between populations using unphased genotypes in present-day individuals, based on the sharing of derived alleles and making a minimal set of assumptions about their demographic history. We apply this test to data for three human individuals of African, European and Asian ancestry. We find that the joint distribution of European and Asian genotypes is compatible with these populations having separated cleanly at some time in the past without subsequent genetic exchange. However the same is not true of the European-African and Asian-African distributions, which instead suggest an extended period of continued exchange between African and nonAfrican populations after their initial separation.
We discuss this in comparison with recent models and estimates of separation time between these populations. We also consider the impact of recent direct experimental studies of the human mutation rate, which suggest rates of around 0.5 × 10 -9 bp -1 y -1 , substantially lower than prior estimates of 1 × 10 -9 bp -1 y -1 obtained from calibration against the primate fossil record. We show that in several places the lower rate, implying older dates, yields better agreement between genetic and non-genetic (paleoanthropological and archaeological) evidence for events surrounding the exodus of modern humans fromLong-term presence versus recent admixture: Bayesian and approximate-Bayesian analyses of genetic diversity of human populations in Central Asia
Africaand their dispersion worldwide.
Friso Palstra, Evelyne Heyer, Frederic Austerlitz Eco-anthropologie et Ethnobiologie UMR 7206 CNRS, Equipe Genetique des Populations Humaines, Museum National d'Histoire Naturelle, Paris, France
A long-standing goal in population genetics is to unravel the relative importance of evolutionary forces that shape genetic diversity. Here we focus on human populations in Central Asia, a region that has long been known to contain the highest genetic diversity on the Eurasian continent. However, whether this variation principally reflects long-term presence, or rather the result of admixture associated with repeated migrations into this region in more recent historical times, remains unclear. Here we investigate the underlying demographic history of Central Asian populations in explicit relation to Western Europe, Eastern Asia and the Middle East. For this purpose we employ both full Bayesian and approximate-Bayesian analyses of nuclear genetic diversity in 20 unlinked non-coding resequenced DNA regions, known to be at least 200 kb apart from any known gene, mRNA or spliced EST (total length of 24 kb), and 22 unlinked microsatellite loci.
Using an approximate Bayesian framework, we find that present patterns of genetic diversity in Central Asia may be best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians) with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications that this region might have genetically influenced Western European populations, rather than vice versa. A further evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both long-term presence and admixture in more recent historical times.
Population structure and evidence of selection in the Khoe-San and Coloured populations from southern Africa
Carina Schlebusch 1 , Pontus Skoglund 1 , Per Sjödin 1 , Lucie Gattepaille 1 , Sen Li 1 , Flora Jay 2 , Dena Hernandez 3 , Andrew Singleton 3 , Michael Blum 2 , Himla Soodyall 4,5 , Mattias Jakobsson 1 1 Uppsala University, Uppsala, Sweden, 2 Université Joseph Fourier, Grenoble, France, 3 National Institute on Aging (NIH), Bethesda, USA, 4 University of the Witwatersrand, Johannesburg, South Africa, 5 National Health Laboratory Service, Johannesburg, South Africa
The San and Khoe people currently represent remnant groups of a much larger and widely distributed population of hunter-gatherers and pastoralists who had exclusive occupation of southern Africa before the arrival of Bantu-speaking groups in the past 1,200 years and sea-borne immigrants within the last 350 years. Mitochondrial DNA, Y-chromosome and autosomal studies conducted on a few San groups revealed that they harbour some of the most divergent lineages found in living peoples throughout the world.
We used autosomal data to characterize patterns of genetic variation among southern African individuals in order to understand human evolutionary history, in particular the demographic history of
Africa. To this end, we successfully genotyped ~ 2.3 million genome wide SNP markers in 220 individuals, comprising seven Khoe-San, two Coloured and two Bantu-speaking groups from southern Africa. After quality filtering, the data were combined with publicly available SNP data from other African populations to investigate stratification and demography of African populations.
We also applied a newly developed method of estimating population topology and divergence times. Genotypes and inferred haplotypes were used to assess genetic diversity, patterns of haplotype variation and linkage disequilibrium in different populations. We found that six of the seven Khoe-San populations form a common population lineage basal to all other modern human populations. The studied Khoe-San populations are genetically distinct, with diverse histories of gene flow with surrounding populations. A clear geographic structuring among Khoe-San groups was observed, the northern and southern Khoe-San groups were most distinct from each other with the central Khoe-San group being intermediate. The Khwe group contained variation that distinguished it from other Khoe-San groups. Population divergence within the Khoe-San group is approximately 1/3 as ancient as the divergence of the Khoe-San as a whole to other human populations (on the same order as the time of divergence between West Africans and Eurasians). Genetic diversity in some, but not all, Khoe-San populations is among the highest worldwide, but it is influenced by recent admixture. We furthermore find evidence of a Nilo-Saharan ancestral component in certain Khoe-San groups, possibly related to the introduction of pastoralism to southern Africa.
Impacts of life-style on human evolutionary history: A genome-wide comparison of herder and farmer populations in Central Asia
We searched for signatures of selection in the different population groups by scanning for differentiated genome-regions between populations and scanning for extended runs of haplotype homozygosity within populations. By means of the selection scans, we found evidence for diverse adaptations in groups with different demographic histories and modes of subsistence.
Michael C. Fontaine 1,2 , Laure Segurel 2,3 , Christine Lonjou 4 , Tatiana Hegay 5 , Almaz Aldashev 6 , Evelyne Heyer 2 , Frederic Austerlitz 1,2 1 Ecology, Systematics & Evolution. UMR8079 Univ. Paris Sud - CNRS - AgroParisTech, Orsay, France, 2 EcoAnthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cite, Paris, France, 3 Department of Human Genetics, University of Chicago, Chicago, USA, 4 C2BiG (Centre de Bioinformatique/Biostatistique Genomique d’Ile de France), Plateforme Post-genomique P3S, Hopital Pitie Salpetriere, Paris, France, 5 Uzbek Academy of Sciences, Institute of Immunology, Tashkent, Uzbekistan, 6 Institute of Molecular Biology and Medicine, National Center of Cardiology and Internal Medicine, Bishkek,
Bayesian inference of the demographic history of Niger-Congo speaking populations
Kyrgyzstan Human populations use a variety of subsistence strategies to exploit an exceptionally broad range of habitats and dietary components. These aspects of human environments have changed dramatically during human evolution, giving rise to new selective pressures. Here we focused on two populations in Central Asia with long-term contrasted lifestyles: Kyrgyz’s that are traditionally nomadic herders, with a traditional diet based on meat and milk products, and Tajiks that are traditionally agriculturalists, with a traditional diet based mostly on cereals. We genotyped 93 individuals for more than 600,000 SNP markers (Human-660W-Quad-V1.0 from Illumina) spread across the genome. We first analysed the population structure of these two populations in the world-wide context by combining our results with other available genome-wide data. Principal component and Bayesian clustering analyses revealed that Tajiks and Kirgiz’s are both admixed populations which differed however from each other with respect to their ancestry proportions: Tajiks display a much larger proportion of common ancestry with European populations while Kirgiz’s share a larger common ancestry with Asiatic populations. We then examined the region of the genome displaying unusual population differentiation between these two populations to detect natural selection and checked whether they were specific to Central Asia or not. We complemented these analyses with haplotype-based analyses of selection.
Isabel Alves 1,2 , Lounès Chikhi 2,3 , Laurent Excoffier 1,4 1 CMPG, Institute of Ecology and Evolution, Berne, Switzerland, 2 Population and Conservation Genetics Group, Instituto Gulbenkian de Ciência, Oeiras, Portugal, 3 CNRS, Université Paul Sabatier, ENFA, Toulouse, France, 4 Swiss Institute of Bioinformatics, Lausanne, Switzerland
The Niger-Congo phylum encompasses more than 1500 languages spread over sub-Saharan Africa. This current wide range is mostly due to the spread of Bantu-speaking people across sub-equatorial regions in the last 4000-5000 years. Although several genetic studies have focused on the evolutionary history of Bantu-speaking groups, much less effort has been put into the relationship between Bantu and non-Bantu Niger-Congo groups. Additionally, archaeological and linguistic evidence suggest that the spread of these populations occurred in distinct directions from the core region located in what is now the border between
Nigeriaand Cameroontowards West and , respectively. We have performed coalescent simulations within an approximate Bayesian computation (ABC) framework in order to statistically evaluate the relative probability of alternative models of the spread of Niger-Congo speakers and to infer demographic parameters underlying these important migration events. We have analysed 61 high-quality microsatellite markers, genotyped in 130 individuals from three Bantu and three non Bantu-speaking populations, representing a "Southern wave" or the Bantu expansion, and a "Western wave", respectively. Preliminary results suggest that models inspired by a spatial spread of the populations are better supported than classical isolation with migration (IM) models. We also find that Niger-Congo populations currently maintain high levels of gene flow with their neighbours, and that they expanded from a single source between 200 and 600 generations, even though available genetic data do not provide enough information to accurately infer these demographic parameters. South Africa
A genetic study of skin pigmentation variation in India
Mircea Iliescu1 , Chandana Basu Mallick 2,3 , Niraj Rai 4 , Anshuman Mishra 4 , Gyaneshwer Chaubey 2 , Rakesh Tamang 4 , Märt Möls 3 , Rie Goto 1 , Georgi Hudjashov 2,3 , Srilakshmi Raj 1 , Ramasamy Pitchappan 5 , CG Nicholas Mascie-Taylor 1 , Lalji Singh 4,6 , Marta Mirazon-Lahr 7 , Mait Metspalu 2,3 , Kumarasamy Thangaraj 4 , Toomas Kivisild 1,3 1 Division of Biological Anthropology, University of Cambridge, Cambridge, UK, 2 Evolutionary Biology Group, Estonian Biocentre, Tartu, Estonia, 3 Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, 4 Centre for Cellular and Molecular Biology, Hyderabad, India, 5 Chettinad Academy of Research and Education, Chettinad Health City, Chennai, India, 6 Banaras Hindu University, Varanasi, India, 7 Leverhulme Centre for Human Evolutionary Studies, Division of Biological Anthropology, University of Cambridge, Cambridge, UK
Human skin colour is a polygenic trait that is primarily determined by the amount and type of melanin produced in the skin. The pigmentation variation between human populations across the world is highly correlated with geographic latitude and the amount of UV radiation. Association studies together with research involving different model organisms and coat colour variation have largely contributed to the identification of more than 378 pigmentation candidate genes. These include TYR OCA2, that are known to cause albinism, MC1R responsible for the red hair phenotype, and genes such as MATP, SLC24A5 and ASIP that are involved in normal pigmentation variation. In particular, SLC24A5 has been shown to explain one third of the pigmentation difference between Europeans and Africans. However, the same gene cannot explain the lighter East Asian phenotype; therefore, light pigmentation could be the result of convergent evolution. A study on UK residents of Pakistani, Indian and Bangladeshi descent found significant association of SLC24A5, SLC45A2 and TYR genes with skin colour. While these genes may explain a significant proportion of interethnic differences in skin colour, it is not clear how much variation such genes explain within Indian populations who are known for their high level of diversity of pigmentation. We have tested 15 candidate SNPs for association with melanin index in a large sample of 1300 individuals, from three related castes native to South India. Using logistic regression model we found that SLC24A5 functional SNP, rs1426654, is strongly associated with pigmentation in our sample and explains alone more than half of the skin colour difference between the light and the dark group of individuals. Conversely, the other tested SNPs fail to show any significance; this strongly argues in favour of one gene having a major effect on skin pigmentation within ethnic groups of South India, with other genes having small additional effects on this trait. We genotyped the SLC24A5 variant in over 40 populations across India and found that latitudinal differences alone cannot explain its frequency patterns in the subcontinent. Key questions arising from this research are when and where did the light skin variant enter South Asia and the manner and reason for it spreading across the Indian sub-continent. Hence, a comprehensive view of skin colour evolution requires that in depth sequence information be corroborated with population (genetic) history and with ancient DNA data of past populations of