Ancient Human Migrations Research Articles

Genomic articulations of indigeneity

Indigenous peoples’ and genome scientists’ respective definitions and practices of making ‘indigeneity’ illustrate their competing notions of identity, origins, and futures. This article explores these genomic and indigenous ‘articulations’ of indigeneity, both their similarities and profound differences. Scientists who study ancient global human migrations and human genome diversity draw on an understanding of ‘indigeneity’ that appears to overlap with, but fundamentally contradicts, the use of this concept by the global indigenous movement. Genomic articulations privilege genetic ancestry as defining indigenous ‘populations’. In contrast, indigenous articulations of indigeneity emphasize political status and biological and cultural kinship constituted in dynamic, long-standing relations with each other and with living landscapes. To demonstrate how differences in definitions matter, I draw examples from several scientific and indigenous projects that entangle DNA knowledge with judgments about indigenous identities, and I note resulting policy implications. I first examine two key narratives of indigeneity and race that underlie the genomic articulation of indigeneity: ‘indigenous peoples are vanishing’ and ‘we are all related/all African’. I then explore two cases where genomic and indigenous articulations clash and overlap – the ‘Kennewick Man’ case and the use of DNA testing for tribal enrollment. Yet genomic articulations, with their greater truth-governing power, may inadvertently reconfigure indigeneity in ways that can undermine tribal and First Nations’ self-determination and the global indigenous anticolonial movement. Indeed, some indigenous peoples have recently adopted genomic articulations of identity, perhaps to their own detriment.

Impact of Human Migrations on Diversity of Helicobacter pylori in Cambodia and New Caledonia

Helicobacter pylori is a major gastric bacterial pathogen, presumed to have established itself in the human stomach approximately 100,000years ago. Helicobacter pylori co-evolved with its host, and human migrations shaped the expansion and the diversity of strains around the world. Here, we investigated the population structure and the genomic diversity of H.pylori in New Caledonia and Cambodia, where humans of different origins are living. Both multilocus sequence typing (MLST) and macro-array experiments were performed to assess polymorphism of housekeeping genes and to compare differences in gene contents among strains of H.pylori. The macro-array analysis based on variations of the flexible gene pools was consistent with the contribution of ancestral H.pylori populations to modern strains. Most of the CDS variably present encode proteins of unknown function, selfish DNA, and transposases. In New Caledonia-where humans are of several ethnic origins-strains belonged to four different genetic populations, reflecting the diversity of human populations. Melanesians and Polynesians were infected mainly by strains assigned to hspMaori, whereas Caucasians were infected by hspWAfrica, hpEurope, and hpNEAfrica strains. In contrast, strains from Khmer patients belonged to only two subpopulations: hspEAsia and hpEurope. In the two countries, both ancient and recent human migrations may have influenced the diversity of H.pylori. Our present results are consistent with the possibility of admixture of strains in multiethnic communities. This increases the global polymorphism of H.pylori without evidence of functional change or impact on fitness and virulence.

The Pottery Trail From Southeast Asia to Remote Oceania

ABSTRACT A set of unique circumstances created a durable archaeological record of ancient human migration from Southeast Asia to Remote Oceania, useful as a global model of population dispersals. Finely made pottery with a very specific decorative signature is found in multiple locations in the Philippines and western Oceania, constituting a shared cultural trait that can be traced, both geographically and chronologically, to a specific homeland. Especially important for human migration models, this decorated pottery is linked to a system of cultural origin, so the spread as a diagnostic tradition can be related to the spread of a cultural group. Even more important, this decorated pottery appeared with the first peopling of the remote Pacific Islands, thus providing a clear and datable chronicle of where and when people spread from one location to another. The pottery trail points to a homeland in the Philippine Neolithic about 2000–1800 BC, followed by expansion into the remote Mariana Islands 1500 BC, and then slightly later into the Lapita world of Melanesia and Polynesia.

Assessment of patrilineal gene pool of the Iranian Azeris.

The Iranian Azeris are the largest ethno-linguistic minority in Iran who live mainly in the north-west part of the country. Located in the crossroad of ancient human migrations the Iranian Azeris bear the complicated historical influence of the region in their gene pool. Despite the importance of Iranian Azeris in reconstructing the historical event of the Middle-East, their (genetic) origin still remains heavily disputed. In this study we tried to evaluate the rates of genetic contribution of possible source populations (namely, indigenous Iranian, Caucasian, and Central Asian) in the gene pool of modern Iranian Azeris through paternally inherited Y-chromosomal 6 STR markers. The assessment of genetic distances reveals that the Iranian Azeris are mixed population with substantial North Caucasian genetic contribution being genetically much closer to their immediate neighboring ethnic groups. Based on the results of admixture analysis we can conclude that there are significant Caucasian and no visible Central Asian contribution to the gene pool of modern Iranian Azeris.

Mitochondrial Haplogroups and Polymorphisms Reveal No Association with Sporadic Prostate Cancer in a Southern European Population

BackgroundIt is known that mitochondria play an important role in certain cancers (prostate, renal, breast, or colorectal) and coronary disease. These organelles play an essential role in apoptosis and the production of reactive oxygen species; in addition, mtDNA also reveals the history of populations and ancient human migration. All these events and variations in the mitochondrial genome are thought to cause some cancers, including prostate cancer, and also help us to group individuals into common origin groups. The aim of the present study is to analyze the different haplogroups and variations in the sequence in the mitochondrial genome of a southern European population consisting of subjects affected (n = 239) and non-affected (n = 150) by sporadic prostate cancer.Methodology and Principal FindingsUsing primer extension analysis and DNA sequencing, we identified the nine major European haplogroups and CR polymorphisms. The frequencies of the haplogroups did not differ between patients and control cohorts, whereas the CR polymorphism T16356C was significantly higher in patients with PC compared to the controls (p = 0.029). PSA, staging, and Gleason score were associated with none of the nine major European haplogroups. The CR polymorphisms G16129A (p = 0.007) and T16224C (p = 0.022) were significantly associated with Gleason score, whereas T16311C (p = 0.046) was linked with T-stage.Conclusions and SignificanceOur results do not suggest that mtDNA haplogroups could be involved in sporadic prostate cancer etiology and pathogenesis as previous studies performed in middle Europe population. Although some significant associations have been obtained in studying CR polymorphisms, further studies should be performed to validate these results.

The Caucasus as an Asymmetric Semipermeable Barrier to Ancient Human Migrations

The Caucasus as an Asymmetric Semipermeable Barrier to Ancient Human Migrations

Molecular evidence of host influences on the evolution and spread of human tapeworms

The taeniasis/cysticercosis complex is included in the list of neglected zoonotic diseases by the World Health Organization due to its significant impact on public health in tropical areas. Cysticercosis is still endemic in many regions of Asia, Africa and Latin America. Long absent in Europe and in other developed countries, cysticercosis has recently re-emerged in the United States and Canada, due to immigration, travel and local transmission. This has encouraged the use of molecular data to understand better the influence of animal and human hosts on the emergence and spread of Taenia species. The increasing number of mitochondrial sequences now available from human tapeworms and recent advances in computational tools has enabled reconstruction of the biogeography and evolutionary history of these organisms. New molecular data have provided insights into the biogeography of T. solium, T. asiatica and T. saginata. A Bayesian statistical framework using variable evolutionary rates from lineage to lineage has allowed an improved timescale analysis of human tapeworms. The dates of divergence obtained were compared to the timing of evolutionary events in the history of their hosts, based on the hypothesis that Taenia spp. and their hosts share a common history. Herein, we review changes in the definitive and secondary hosts and human interactions that underlie the differentiation and evolution of tapeworms. Species diversification of Taenia seems to be closely linked with the evolution of intermediate hosts in response to climatic events during the Pleistocene. Different genotypes of T. solium emerged when European and Asian wild boar Sus spp. populations diverged. Taenia saginata emerged when wild cattle Bos primigenius evolved and when zebu Bos indicus and taurine Bos taurus ancestors separated. Humans through migrations and later with the development of farming and animal husbandry may have had a significant impact on the spread and diversification of tapeworms. Migrations of Homo erectus from Africa to Asia and later of Homo sapiens facilitated the diversification and dispersal of T. solium and T. saginata populations. The development of animal husbandry, making Sus scrofa and Bos taurus preferential intermediate hosts, led to the worldwide distribution of parasites. New molecular data combined with an innovative dating method allow us to explain the ways in which ancient human migrations promoted the emergence and spread of taeniasis and cysticercosis around the world. Another intriguing phenomenon explained better by our approach is the influence of human settlement on the spread of these parasites in recently inhabited areas. The diverse nature of T. solium currently observed in Madagascar may correspond to multiple imports of the parasite during Austronesian migrations, while in Mexico a recent influence of humans during the colonial period is more likely. Human activities, especially food preparation and husbandry methods, remain responsible for the transmission and persistence of these parasites.

The Caucasus as an Asymmetric Semipermeable Barrier to Ancient Human Migrations

The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.

Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia

The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i) a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii) a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii) a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv) the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v) migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.

The peopling history of continental East Asia revealed by the HLA system

The origin of modern humans in East Asia is a hot issue in molecular anthropology. Based on results from Y chromosome, mtDNA and SNP etc, some scholars proposed that modern humans first entered East Asia by a southern route and expanded northward. However, concerning to the very diverse genetic markers of the HLA system, few analyses have been performed for East Asia. For this reason, we collected and analyzed HLA data from 76 distinct Continental East Asian populations tested for five HLA loci (HLA-A, -B, -C, -DPB1, and/or -DRB1). We observed that some HLA alleles distribute unevenly in the North and in the South, and that the genetic diversity (heterozygosity of the populations) decreased from north to south. While our results support the existence of a southern route, we also conclude that genetic contribution of ancient human migrations through a northern route has probably also been ancient and substantial.

Challenging views on the peopling history of East Asia: The story according to HLA markers

The peopling of East Asia by the first modern humans is strongly debated from a genetic point of view. A north-south genetic differentiation observed in this geographic area suggests different hypotheses on the origin of Northern East Asian (NEA) and Southern East Asian (SEA) populations. In this study, the highly polymorphic HLA markers were used to investigate East Asian genetic diversity. Our database covers a total of about 127,000 individuals belonging to 84 distinct Asian populations tested for HLA-A, -B, -C, -DPB1, and/or -DRB1 alleles. Many Chinese populations are represented, which have been sampled in the last 30 years but rarely taken into account in international research due to their data published in Chinese. By using different statistical methods, we found a significant correlation between genetics and geography and relevant genetic clines in East Asia. Additionally, HLA alleles appear to be unevenly distributed: some alleles observed in NEA populations are widespread at the global level, while some alleles observed in SEA populations are virtually unique in Asia. The HLA genetic variation in East Asia is also characterized by a decrease of diversity from north to south, although a reverse pattern appears when one only focuses on alleles restricted to Asia. These results reflect a more complex migration history than that illustrated by the "southern-origin" hypothesis, as genetic contribution of ancient human migrations through a northern route has probably been quite substantial. We thus suggest a new overlapping model where northward and southward opposite migrations occurring at different periods overlapped.

Book Reviews: Ancient Human Migrations: A Multidisciplinary Approach edited by Peter N. Peregrine, Ilia Peiros, and Marcus Feldman

Book Reviews: Ancient Human Migrations: A Multidisciplinary Approach edited by Peter N. Peregrine, Ilia Peiros, and Marcus Feldman

Ethnic and Geographic Differentiation of Helicobacter pylori within Iran

The bacterium Helicobacter pylori colonizes the human stomach, with individual infections persisting for decades. The spread of the bacterium has been shown to reflect both ancient and recent human migrations. We have sequenced housekeeping genes from H. pylori isolated from 147 Iranians with well-characterized geographical and ethnic origins sampled throughout Iran and compared them with sequences from strains from other locations. H. pylori from Iran are similar to others isolated from Western Eurasia and can be placed in the previously described HpEurope population. Despite the location of Iran at the crossroads of Eurasia, we found no evidence that the region been a major source of ancestry for strains across the continent. On a smaller scale, we found genetic affinities between the H. pylori isolated from particular Iranian populations and strains from Turks, Uzbeks, Palestinians and Israelis, reflecting documented historical contacts over the past two thousand years.

“Anti-colonial Genomic Practice?” Learning from the Genographic Project and the Chacmool Conference

I want to commend the organizers of the Chacmool Conference panel. All too often attempts to discuss the broader social and cultural dimensions of genetic studies of ancient human migrations devolve into simplistic celebrations or condemnations. It is heartening to find here an example of a conference session that managed to avoid these dangerous poles, and to grapple instead with the hard task of discerning the issues raised and not raised by genomic studies of human migrations and history. I would like to devote my commentary to exploring what might be learned from the discussions at Chacmool.

Comparison of the distribution patterns of BK polyomavirus lineages among China, Korea and Japan: Implications for human migrations in northeast Asia

BKV is widespread among humans, infecting children asymptomatically and then persisting in renal tissue. Based on the serological or phylogenetic method, BKV isolates worldwide are classified into four subtypes (I-IV), with subtypes I and IV further divided into several genetically-distinct subgroups. Since, similarly to JCV, a close relationship exists between BKV lineages and human populations, BKV should be useful as a marker to trace human migrations. To elucidate ancient human migrations in northeast Asia, urine samples were collected from immunocompetent elderly patients in Shanghai, China; Anyang, South Korea; and various locations in Japan. Partial and complete BKV genomes from these samples were amplified and sequenced using PCR, and the determined sequences were classified into subtypes and subgroups by phylogenetic and SNP analyses. In addition, based on an SNP analysis, the major subtype I subgroup (I/c) was classified into two subdivisions, I/c/Ch and I/c/KJ. The distribution patterns of BKV subgroups and subdivisions among the three regions were compared. Some aspects of the subgroup and subdivision distribution were more similar between Korea and Japan, but others were more similar between China and Korea or between China and Japan. Based on these findings, we inferred various northeast Asian migrations. Most of the JCV-based inferences of northeastern Asian migrations were consistent with those based on BKV, but the previously suggested migration route from the Asian continent to the Japanese archipelago seemed to need revision.

Ancestral European roots of Helicobacter pylori in India

BackgroundThe human gastric pathogen Helicobacter pylori is co-evolved with its host and therefore, origins and expansion of multiple populations and sub populations of H. pylori mirror ancient human migrations. Ancestral origins of H. pylori in the vast Indian subcontinent are debatable. It is not clear how different waves of human migrations in South Asia shaped the population structure of H. pylori. We tried to address these issues through mapping genetic origins of present day H. pylori in India and their genomic comparison with hundreds of isolates from different geographic regions.ResultsWe attempted to dissect genetic identity of strains by multilocus sequence typing (MLST) of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC) and phylogeographic analysis of haplotypes using MEGA and NETWORK software while incorporating DNA sequences and genotyping data of whole cag pathogenicity-islands (cagPAI). The distribution of cagPAI genes within these strains was analyzed by using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. All the isolates analyzed revealed European ancestry and belonged to H. pylori sub-population, hpEurope. The cagPAI harbored by Indian strains revealed European features upon PCR based analysis and whole PAI sequencing.ConclusionThese observations suggest that H. pylori strains in India share ancestral origins with their European counterparts. Further, non-existence of other sub-populations such as hpAfrica and hpEastAsia, at least in our collection of isolates, suggest that the hpEurope strains enjoyed a special fitness advantage in Indian stomachs to out-compete any endogenous strains. These results also might support hypotheses related to gene flow in India through Indo-Aryans and arrival of Neolithic practices and languages from the Fertile Crescent.

The Genographic Project Public Participation Mitochondrial DNA Database

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.

Tiny travel companions

Since the first modern humans left their birthplace in Eastern Africa and slowly spread to populate every inhabitable place on the planet, Homo sapiens has been a migratory animal. Over thousands of years, these travellers unknowingly carried excess baggage on their journeys: countless microbes in and on their bodies, which evolved along with their host. By applying the tools of modern genomics to reconstruct the phylogenetic trees of these viruses, bacteria, fungi and protozoa, scientists hope to provide new insights into how our ancestors ventured throughout the world. Answering the questions of when and how humans started moving out of Africa or when the first settlers populated the Americas has so far relied on genetic markers from mitochondrial DNA (mtDNA) or the Y chromosome. As mitochondria are inherited from the mother, analysis of mtDNA identifies ancestors through the maternal line, whereas Y‐DNA can trace origins using the paternal line. These studies, together with archaeological, anthropological and linguistic evidence, have generated a now widely accepted “standard model for evolution of modern humans” (Cavalli‐Sforza & Feldman, 2003). According to this model, our species moved from its original homeland in Africa to the Near East approximately 60,000–70,000 years ago, later spreading to southern Asia and Australasia, then to Europe and Central Asia, and finally entered the Americas through the Bering Strait about 14,000–20,000 years ago (Fig 1). Figure 1. Map of early human migration patterns. Credit: National Geographic Maps, Washington, DC, USA. mtDNA, mitochondrial DNA. In addition to these human markers, scientists have begun to study the evolution of viruses along with their human hosts to refine the migration patterns of H. sapiens . “The geographical distribution of viruses can reveal patterns of ancient human migrations, especially in the cases in which they are transmitted vertically and move in narrow, ethnically restricted streams of …

Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines.

Helicobacter pylori infection of humans is so old that its population genetic structure reflects that of ancient human migrations. A closely related species, Helicobacter acinonychis, is specific for large felines, including cheetahs, lions, and tigers, whereas hosts more closely related to humans harbor more distantly related Helicobacter species. This observation suggests a jump between host species. But who ate whom and when did it happen? In order to resolve this question, we determined the genomic sequence of H. acinonychis strain Sheeba and compared it to genomes from H. pylori. The conserved core genes between the genomes are so similar that the host jump probably occurred within the last 200,000 (range 50,000–400,000) years. However, the Sheeba genome also possesses unique features that indicate the direction of the host jump, namely from early humans to cats. Sheeba possesses an unusually large number of highly fragmented genes, many encoding outer membrane proteins, which may have been destroyed in order to bypass deleterious responses from the feline host immune system. In addition, the few Sheeba-specific genes that were found include a cluster of genes encoding sialylation of the bacterial cell surface carbohydrates, which were imported by horizontal genetic exchange and might also help to evade host immune defenses. These results provide a genomic basis for elucidating molecular events that allow bacteria to adapt to novel animal hosts.

Variable host-pathogen compatibility in Mycobacterium tuberculosis.

Mycobacterium tuberculosis remains a major cause of morbidity and mortality worldwide. Studies have reported human pathogens to have geographically structured population genetics, some of which have been linked to ancient human migrations. However, no study has addressed the potential evolutionary consequences of such longstanding human-pathogen associations. Here, we demonstrate that the global population structure of M. tuberculosis is defined by six phylogeographical lineages, each associated with specific, sympatric human populations. In an urban cosmopolitan environment, mycobacterial lineages were much more likely to spread in sympatric than in allopatric patient populations. Tuberculosis cases that did occur in allopatric hosts disproportionately involved high-risk individuals with impaired host resistance. These observations suggest that mycobacterial lineages are adapted to particular human populations. If confirmed, our findings have important implications for tuberculosis control and vaccine development.