June 24, 2012

SMBE 2012 abstracts (Part II)

Some more abstracts from SMBE 2012.


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 Europe from 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 East where 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 Rico from 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 Columbus’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.   
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.   

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.
 Inference of demographic history and natural selection in African Pygmy populations from whole-genome  sequencing data
 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 Southern Europe
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 Europe and 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 in South Asia today 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.   
Long IBD in Europeans and recent population history 
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 Africa, and the timeline of recent human  evolution  
Aylwyn Scally, Richard Durbin  Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK 
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 from Africa and their dispersion worldwide.
Long-term presence versus recent admixture: Bayesian and approximate-Bayesian analyses of genetic  diversity of human populations in Central Asia 
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.   

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. 
Impacts of life-style on human evolutionary history: A genome-wide comparison of herder and farmer  populations in Central Asia 
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,  

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. 
Bayesian inference of the demographic history of Niger-Congo speaking populations 
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 Nigeria and Cameroon towards West and South Africa, 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.

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 Eurasia



15 comments:

princenuadha said...

"Here we analyze data from about 60 South Asian groups to estimate that major ANI-ASI mixture occurred 1,200-4,000 years ago."

How come you didn't highlight this?

"The major part of the lineages dating to the Neolithic period seems to have an European origin with exception of haplogroup K1a4 and K1a3."

So much of the neolithic spread in European was done by meso Europeans, maybe.

"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."

Funny. That DNA tribes said that some of the southern royalty in ancient Egypt were south African like. I think I'm calling shenanigans.

Dienekes said...

How come you didn't highlight this?

Because it's based on ROLLOFF, and until the creators of ROLLOFF release the software (1+ year overdue) and explain why HAPMIX built by many of the same people produces 2x older dates, I don't take its dates seriously.

apostateimpressions said...

<< We characterize broad patterns of recent gene flow between Europe and Africa, with a gradient of recent African ancestry that is highest in southwestern Europe and 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. >>

20% 'African' admixture in southern Spain seems rather high?

Presumably most of that would be caucasian?

Raúl said...

""We characterize broad patterns of recent gene flow between Europe and Africa, with a gradient of recent African ancestry that is highest in southwestern Europe and 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.""

Does the "based on both allele-frequencies and shared haplotypes" affirmation mean that this is the same as talking about autosomal contribution?

Annie Mouse said...

"20% 'African' admixture in southern Spain seems rather high?

Presumably most of that would be caucasian?"

North African, so yes, what is called European (in an Asian/African/European split), and whatyou might call caucasian. Actual sub-saharan african is surprisingly low in Spain.

Nirjhar007 said...

There is a clear archaeologic record and explaination also for the start of the 4 to1.2 kya(if correct) major ANI ASI admixture and i'm not talking about the Indo-aryan theory or rather story.

terryt said...

"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".

And I very much suspect that the same could be said of human development. It seems most are committed to seeing a single origin for all humans whereas the evidence could easily be interpreted as indicating a reticulate origin for humans. Perhaps this desire to see human origins as originating in a single region at a specific time is a survival of creationist beliefs.

"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".

That recent, to reach what look like comparatively easy islands to reach. Yet people still insist that 50,000 years before then these people's ancestors had moved by boat along the far more dangerous South Eurasian coastline.

eurologist said...

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.

This is a very good study, demonstrating yet again that we need whole genome (mt-DNA) or high-resolution (y-DNA) analysis to make any kind of headway in understanding origins and migrations, given the old ages of many of these haplogroups. However - why mention Near East in this context? It makes it sound like the majority of people entering Europe came from the Near East.

ANI and ASI have been estimated to have diverged from a common ancestor as much as 60,000 years ago

I have mentioned multiple times that after Toba (~70,000 ya), for most of the time, much of the subcontinent was so dry (no Monsoon) as to completely separate NW Indian/ Pakistani inhabitants from S/ SE Indians (hence the close relation between people in the NW and Caucasians/ Europeans, today). Diffusion should have resumed after the Younger Dryas and again in the Holocene Optimum.

Onur said...

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.

This admixture date of Egypt is testable on modern-day Egyptians. ~750 years ago means it is well after the Islamization of Egypt, and due to the nature of Islamic society and slavery it is expected to have affected only the Muslims of Egypt. So if it is found that Christian Egyptians (=Copts) don't carry that admixture, this will confirm the findings of this paper.

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).

By "Indo-Iranians" and "Turco-Mongols" are they referring to the modern-day Indo-Iranians and Turco-Mongols (not a valid term if they excluded Mongols, as Turkic speakers are called Turkic, not Turco-Mongol, and Mongolic speakers are called Mongol or Mongolic, thus the term Turco-Mongol can be used only when Turkic speakers and Mongolic speakers are grouped together) of Central Asia, or to the Indo-Iranians and Turco-Mongols prior to their contact?

sykes.1 said...

Would you care to comment on:

Anatole A. Klyosov*, Igor L. Rozhanskii, Advances in Anthropology
2012. Vol.2, No.2, 80-86.

Based on Y haplogroups, they seem to be suggesting that the Eurasian/African split occurred very much early than normally believed (say, 160,000 years ago) and that it might have occurred in Eurasia rather than Africa.

Is this a legitimate journal, and are these guys real scientists? I am dubious.

Aren Allahverdian said...

Is this a legitimate journal, and are these guys real scientists? I am dubious.

Your're right. Klyosev's methods and conclusions are so questionable that they render his work basically unscientific.

Michael Boblett said...

Regarding the mitochondrial subclades of U8 and their entry into Europe, the authors state: 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." Is there any way of getting a look at this tree, and specifically at the coalescence ages? As a K1a10, I am curious to know when our sister-clade K1a9 parted company from us. The former is rooted quite far back in Ireland, the latter appears in Ashkenazic Jews. There's a story I'd like to unravel!

bmdriver said...

Researchers led by Mait Metspalu of Evolutionary Biology Group of Estonia studied 600,000 Single Nucleotide Polymorphism (SNP) markers among 30 ethnic groups in India. The human genomes consists of chromosomes, represented by the double helix and specific locations on the chromosome can be identified using markers with the common ones being micro-satellite markers and SNP markers. Among the two, SNP markers are popular for gene fine mapping. The study takes data from existing genetic studies and combines it with new data from North Indian and South Indian population to trace the external influences from Europe.

One of the ancestral components—the ANI—is common not just in South Asia, but also in West Asia and Caucasus while the ASI is limited to South Asia. While this may seem to clearly demarcate the natives and the foreign migrants, it does not. Except for some Astroasiatic tribes and two small Dravidian tribes in Tamil Nadu and Kerala, all other South Indians have more than 40% of the ANI component. This means that everyone except these few groups are not purely native.

The important question then is this: When did the ANI mix with the ASI?. If that period is between 1900 BCE and 1500 BCE, then it would confirm the many versions of Aryan theory in existence right now. When these researchers modeled the data, they could not find any evidence of a dramatic Central Asian migration for this period.

So they went back and till about 12500 Years Before Present (YBP) they could not find any evidence. Thus the mixing of the ANI and ASI did not happen 140 generations before as was believed, but probably more than 500 generations back (Each generation is 25 year, Making it at least 12,000years old).

The paper explicitly mentions Max Muller’s theory and says that it is hard to find evidence for such a migration following the collapse of the Harappan civilization.

German Dziebel said...

I combed through the SMBE 2012 abstracts, too, and found a couple more interesting research reports.
See here http://anthropogenesis.kinshipstudies.org/2012/06/howler-monkeys-neandertals-pygmies-khoisans-and-more-society-for-molecular-biology-and-evolution-2012/

Nirjhar007 said...

Climate was the reason: http://m.yahoo.com/w/legobpengine/news/huge-ancient-civilization-collapse-explained-123449804.html?orig_host_hdr=news.yahoo.com&.intl=US&.lang=en-US
The other theory is a drunken story:-D.