Towards a new history and geography of human genes informed by ancient DNA

Towards a new history and geography of human genes informed by ancient DNA

Joseph Pickrell, David Reich

Genetic information contains a record of the history of our species, and technological advances have transformed our ability to access this record. Many studies have used genome-wide data from populations today to learn about the peopling of the globe and subsequent adaptation to local conditions. Implicit in this research is the assumption that the geographic locations of people today are informative about the geographic locations of their ancestors in the distant past. However, it is now clear that long-range migration, admixture and population replacement have been the rule rather than the exception in human history. In light of this, we argue that it is time to critically re-evaluate current views of the peopling of the globe and the importance of natural selection in determining the geographic distribution of phenotypes. We specifically highlight the transformative potential of ancient DNA. By accessing the genetic make-up of populations living at archaeologically-known times and places, ancient DNA makes it possible to directly track migrations and responses to natural selection.

A Tale of Two Hypotheses: Genetics and the Ethnogenesis of Ashkenazi Jewry

A Tale of Two Hypotheses: Genetics and the Ethnogenesis of Ashkenazi Jewry
Aram Yardumian

The debate over the ethnogenesis of Ashkenazi Jewry is longstanding, and has been hampered by a lack of Jewish historiographical work between the Biblical and the early Modern eras. Most historians, as well as geneticists, situate them as the descendants of Israelite tribes whose presence in Europe is owed to deportations during the Roman conquest of Palestine, as well as migration from Babylonia, and eventual settlement along the Rhine. By contrast, a few historians and other writers, most famously Arthur Koestler, have looked to migrations following the decline of the little-understood Medieval Jewish kingdom of Khazaria as the main source for Ashkenazi Jewry. A recent study of genetic variation in southeastern European populations (Elhaik 2012) also proposed a Khazarian origin for Ashkenazi Jews, eliciting considerable criticism from other scholars investigating Jewish ancestry who favor a Near Eastern origin of Ashkenazi populations. This paper re-examines the genetic data and analytical approaches used in these studies of Jewish ancestry, and situates them in the context of historical, linguistic, and archaeological evidence from the Caucasus, Europe and the Near East. Based on this reanalysis, it appears not only that the Khazar Hypothesis per se is without serious merit, but also the veracity of the ‘Rhineland Hypothesis’ may also be questionable.

Agriculture driving male expansion in Neolithic Time

Agriculture driving male expansion in Neolithic Time
Chuan-Chao Wang, Yunzhi Huang, Shao-Qing Wen, Chun Chen, Li Jin, Hui Li
(Submitted on 27 Nov 2013)

The emergence of agriculture is suggested to have driven extensive human population growths. However, genetic evidence from maternal mitochondrial genomes suggests major population expansions began before the emergence of agriculture. Therefore, role of agriculture that played in initial population expansions still remains controversial. Here, we analyzed a set of globally distributed whole Y chromosome and mitochondrial genomes of 526 male samples from 1000 Genome Project. We found that most major paternal lineage expansions coalesced in Neolithic Time. The estimated effective population sizes through time revealed strong evidence for 10- to 100-fold increase in population growth of males with the advent of agriculture. This sex-biased Neolithic expansion might result from the reduction in hunting-related mortality of males.

Present Y chromosomes support the Persian ancestry of Sayyid Ajjal Shams al-Din Omar and Eminent Navigator Zheng He

Present Y chromosomes support the Persian ancestry of Sayyid Ajjal Shams al-Din Omar and Eminent Navigator Zheng He
Chuan-Chao Wang, Ling-Xiang Wang, Manfei Zhang, Dali Yao, Li Jin, Hui Li
(Submitted on 21 Oct 2013)

Sayyid Ajjal is the ancestor of many Muslims in areas all across China. And one of his descendants is the famous Navigator of Ming Dynasty, Zheng He, who led the largest armada in the world of 15th century. The origin of Sayyid Ajjal’s family remains unclear although many studies have been done on this topic of Muslim history. In this paper, we studied the Y chromosomes of his present descendants, and found they all have haplogroup L1a-M76, proving a southern Persian origin.

Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers

Y Chromosomes of 40% Chinese Are Descendants of Three Neolithic Super-grandfathers
Shi Yan, Chuan-Chao Wang, Hong-Xiang Zheng, Wei Wang, Zhen-Dong Qin, Lan-Hai Wei, Yi Wang, Xue-Dong Pan, Wen-Qing Fu, Yun-Gang He, Li-Jun Xiong, Wen-Fei Jin, Shi-Lin Li, Yu An, Hui Li, Li Jin
(Submitted on 15 Oct 2013)

Demographic change of human populations is one of the central questions for delving into the past of human beings. To identify major population expansions related to male lineages, we sequenced 78 East Asian Y chromosomes at 3.9 Mbp of the non-recombining region (NRY), discovered >4,000 new SNPs, and identified many new clades. The relative divergence dates can be estimated much more precisely using molecular clock. We found that all the Paleolithic divergences were binary; however, three strong star-like Neolithic expansions at ~6 kya (thousand years ago) (assuming a constant substitution rate of 1e-9/bp/year) indicates that ~40% of modern Chinese are patrilineal descendants of only three super-grandfathers at that time. This observation suggests that the main patrilineal expansion in China occurred in the Neolithic Era and might be related to the development of agriculture.

Let my people go (home) to Spain: a genealogical model of Jewish identities since 1492

Let my people go (home) to Spain: a genealogical model of Jewish identities since 1492
Joshua S. Weitz
(Submitted on 7 Oct 2013)

The Spanish government recently announced an official fast-track path to citizenship for any individual who is Jewish and whose ancestors were expelled from Spain during the inquisition-related dislocation of Spanish Jews in 1492. It would seem that this policy targets a small subset of the global Jewish population, i.e., restricted to individuals who retain cultural practices associated with ancestral origins in Spain. However, the central contribution of this manuscript is to demonstrate how and why the policy is far more likely to apply to a very large fraction (i.e., the vast majority) of Jews. This claim is supported using a series of genealogical models that include transmissable “identities” and preferential intra-group mating. Model analysis reveals that even when intra-group mating is strong and even if only a small subset of a present-day population retains cultural practices typically associated with that of an ancestral group, it is highly likely that nearly all members of that population have direct geneaological links to that ancestral group, given sufficient number of generations have elapsed. The basis for this conclusion is that not having a link to an ancestral group must be a property of all of an individual’s ancestors, the probability of which declines (nearly) superexponentially with each successive generation. These findings highlight unexpected incongruities induced by genealogical dynamics between present-day and ancestral identities.

Ancient west Eurasian ancestry in southern and eastern Africa

Ancient west Eurasian ancestry in southern and eastern Africa
Joseph K. Pickrell, Nick Patterson, Po-Ru Loh, Mark Lipson, Bonnie Berger, Mark Stoneking, Brigitte Pakendorf, David Reich
(Submitted on 30 Jul 2013)

The history of southern Africa involved interactions between indigenous hunter-gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter-gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger-Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to approximately 900-1,800 years ago, and show that it had the largest demographic impact in Khoisan populations that speak Khoe-Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to approximately 2,700 – 3,300 years ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa, and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.

Identifiability of a Coalescent-based Population Tree Model

Identifiability of a Coalescent-based Population Tree Model
Arindam RoyChoudhury
(Submitted on 12 Apr 2013)

Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be non-identifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. 1998 [2], has been used by many authors in the last few years and is a simple tool to accurately model the changes in allele frequencies in the tree. However, the identifiability of this model has never been proven. Here we prove this model to be identifiable by showing that the model parameters can be expressed as functions of the probability distributions of subsamples. This a step toward proving the consistency of the maximum likelihood estimator of the population tree based on this model.

Efficient moment-based inference of admixture parameters and sources of gene flow

Efficient moment-based inference of admixture parameters and sources of gene flow
Mark Lipson, Po-Ru Loh, Alex Levin, David Reich, Nick Patterson, Bonnie Berger
(Submitted on 11 Dec 2012)

The recent explosion in available genetic data has led to significant advances in understanding the demographic histories of and relationships among human populations. It is still a challenge, however, to infer reliable parameter values for complicated models involving many populations. Here we present MixMapper, an efficient, interactive method for constructing phylogenetic trees including admixture events using single nucleotide polymorphism (SNP) genotype data. MixMapper implements a novel two-phase approach to admixture inference using moment statistics, first building an unadmixed scaffold tree and then adding admixed populations by solving systems of equations that express allele frequency divergences in terms of mixture parameters. Importantly, all features of the tree, including topology, sources of gene flow, branch lengths, and mixture proportions, are optimized automatically from the data and include estimates of statistical uncertainty. MixMapper also uses a new method to express branch lengths in easily interpretable drift units. We apply MixMapper to recently published data for HGDP individuals genotyped on a SNP array designed especially for use in population genetics studies, obtaining confident results for 30 populations, 20 of them admixed. Notably, we confirm a signal of ancient admixture in European populations—including previously undetected admixture in Sardinians and Basques—involving a proportion of 20-40% ancient northern Eurasian ancestry.

Reconstructing Roma history from genome-wide data

Reconstructing Roma history from genome-wide data

Priya Moorjani, Nick Patterson, Po-Ru Loh, Mark Lipson, Péter Kisfali, Bela I Melegh, Michael Bonin, Ľudevít Kádaši, Olaf Rieß, Bonnie Berger, David Reich, Béla Melegh
(Submitted on 7 Dec 2012)

The Roma people, living throughout Europe, are a diverse population linked by the Romani language and culture. Previous linguistic and genetic studies have suggested that the Roma migrated into Europe from South Asia about 1000-1500 years ago. Genetic inferences about Roma history have mostly focused on the Y chromosome and mitochondrial DNA. To explore what additional information can be learned from genome-wide data, we analyzed data from six Roma groups that we genotyped at hundreds of thousands of single nucleotide polymorphisms (SNPs). We estimate that the Roma harbor about 80% West Eurasian ancestry-deriving from a combination of European and South Asian sources- and that the date of admixture of South Asian and European ancestry was about 850 years ago. We provide evidence for Eastern Europe being a major source of European ancestry, and North-west India being a major source of the South Asian ancestry in the Roma. By computing allele sharing as a measure of linkage disequilibrium, we estimate that the migration of Roma out of the Indian subcontinent was accompanied by a severe founder event, which we hypothesize was followed by a major demographic expansion once the population arrived in Europe.