Induse jõe oru inimeste, parside, India juutide ja Tharu hõimu geneetilise põlvnemise piiritlemine

Väitekirja elektrooniline versioon ei sisalda publikatsiooneKäesolev on viies Tartu Ülikoolis valminud väitekiri Lõuna-Aasia rahvaste geneetilisest ajaloost. Asustatud kaasaegse inimese poolt märksa enne viimase jääaja maksimumi, elab tänapäeval selles regioonis üle 1.8 miljardi inimese – pea veerand inimkonnast. Seega ei ole võimalik süvitsi mõista kaasaegse inimese geneetise varieeruvuse kujunemist, sh eriti väljapool Sahara-alust Aafrikat, omamata detailsemat teadmist Lõuna-Aasia rahvaste geneetikast Väitekiri põhineb neljal ilmunud artiklil. Neist esimeses uurisime Kirde-Indiat asustavaid rahvaid seoses võimaliku pärinevusega Induse oru kultuurist ja järgnenud vedade ajastust. Teine ja kolmas artikkel on pühendatud migratsioonidele, mis tõid Indiasse religioosses mõttes uusi rahvagruppe: parsid Iraanist alates 7. sajandi lõpupoolelt ja juudid, kelle saabumine Indiasse on toimunud mitme lainena. Neljandas artiklis on vaatluse all Nepaalis, kuid ka India põhjapoolsetes osariikides elutsev rahvarohke tharu hõim. Esimes artikli huvitavamaks leiuks on usutavasti juba vedade ajastust tuntud Rori populatsiooni genoomis väljenduv suurem geneetiline afiinsus põhjapoolse stepivööndi rahvastega, samuti ka lääne-eurooplastega, mis räägib põhja-lõunasuunalistest migratsiooni(de)st eelajaloolisel ajal. Parside saabumist Lõuna-Aasiasse seostatakse Iraani islamiseerumisega 7. sajandil. Võrreldes parside genoome nende ajaloolises kontekstis leidsime ulatusliku segunemise Lõuna-Aasia rahvastega, sealjuures asümeetriliselt isa ja emaliinides. Sama saab väita ka Indias judaistliku traditsiooni elemente säilitanud erinevate kogukondade kohta, kelle genoomis on siiski selgelt säilunud Lähis- ja Kesk-Ida pärandit. Puudutavalt aga geneetiliselt ulatuslikult varieeruvat tharu hõimu, kelle hulgas on selgesti eristatav ka Ida-Aasia komponent, segunenuna Lõuna-Aasia pärandiga, paistab õigustatud olevat neid vaadelda esmajoones mitte sedavõrd deemilise, kuivõrd just kultuurilise konstruktsioonina.Presented hereby is the 5th in a series of PhD theses prepared in Tartu University, addressing genetics of population history of the South Asian peoples. Inhabited considerably before the Last Glacial Maximum, the region harbors by now about 1.8 billion humans – almost a quarter of the global population. Therefore, understanding of present-day variation of the latter, in particular outside sub-Saharan Africa, is not possible without deeper knowledge about genetics of South Asian populations. This thesis is based on four published papers. The first one is focused on selected populations inhabiting northeastern Indus Valley, bearing, in particular, in mind ancient Indus Valley civilization and following it Vedic period. The second and the third paper address historically somewhat better known migrations, bringing to India religiously distinct Parsi and Jewish peoples. The fourth paper analyses the genetic variation of a populous Tharu tribe, living predominantly in Nepal, but also in northern provinces of India. Perhaps the most interesting finding of the first paper is that the presumably identified already in Vedic texts, Ror population exhibits significant genetic affinity with northern Steppe and West European peoples, testifying about prehistoric north to south migration(s). The arrival of Parsis to South Asia in 7th century was a consequence of the Islamization of Iran. Comparing Parsi genomes in their historic contexts, we observed their extensive admixture with South Asians, in particular, asymmetrically in paternal and maternal lineages. Nearly the same can be said about different Indian communities that preserved Judaist traditions: their genomes show affinities to peoples living in the Near and Middle East. As far as the genetically highly diverse Tharu tribe is concerned, a clearly distinct East Asian contribution can be seen, admixed with South Asian genetic heritage. It seems justified to identify the Tharu as cultural, rather than demic phenomenon.https://www.ester.ee/record=b542949

"Like sugar in milk": reconstructing the genetic history of the Parsi population.

BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India. RESULTS: Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East. CONCLUSIONS: Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest

Origin and spread of human mitochondrial DNA haplogroup U7

Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region

Recombinant Newcastle Disease Virus (NDV) Expressing Sigma C Protein of Avian Reovirus (ARV) Protects against Both ARV and NDV in Chickens

Newcastle disease (ND) and avian reovirus (ARV) infections are a serious threat to the poultry industry, which causes heavy economic losses. The mesogenic NDV strain R2B is commonly used as a booster vaccine in many Asian countries to control the disease. In this seminal work, a recombinant NDV strain R2B expressing the sigma C (σC) gene of ARV (rNDV-R2B-σC) was generated by reverse genetics, characterized in vitro and tested as a bivalent vaccine candidate in chickens. The recombinant rNDV-R2B-σC virus was attenuated as compared to the parent rNDV-R2B virus as revealed by standard pathogenicity assays. The generated vaccine candidate, rNDV-R2B-σC, could induce both humoral and cell mediated immune responses in birds and gave complete protection against virulent NDV and ARV challenges. Post-challenge virus shedding analysis revealed a drastic reduction in NDV shed, as compared to unvaccinated birds

The Genetic Ancestry of Modern Indus Valley Populations from Northwest India

The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years.status: publishe

The Genetic Ancestry of Modern Indus Valley Populations from Northwest India

The Indus Valley has been the backdrop for several historic and prehistoric population movements between South Asia and West Eurasia. However, the genetic structure of present-day populations from Northwest India is poorly characterized. Here we report new genome-wide genotype data for 45 modern individuals from four Northwest Indian populations, including the Ror, whose long-term occupation of the region can be traced back to the early Vedic scriptures. Our results suggest that although the genetic architecture of most Northwest Indian populations fits well on the broader North-South Indian genetic cline, culturally distinct groups such as the Ror stand out by being genetically more akin to populations living west of India; such populations include prehistorical and early historical ancient individuals from the Swat Valley near the Indus Valley. We argue that this affinity is more likely a result of genetic continuity since the Bronze Age migrations from the Steppe Belt than a result of recent admixture. The observed patterns of genetic relationships both with modern and ancient West Eurasians suggest that the Ror can be used as a proxy for a population descended from the Ancestral North Indian (ANI) population. Collectively, our results show that the Indus Valley populations are characterized by considerable genetic heterogeneity that has persisted over thousands of years

The phylogeography of Y-chromosome haplogroup H1a1a-M82 reveals the likely Indian origin of the European Romani populations

<div><p>Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indian-specific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India.</p> </div

The Phylogeography of Y-Chromosome Haplogroup H1a1a-M82 Reveals the Likely Indian Origin of the European Romani Populations

Linguistic and genetic studies on Roma populations inhabited in Europe have unequivocally traced these populations to the Indian subcontinent. However, the exact parental population group and time of the out-of-India dispersal have remained disputed. In the absence of archaeological records and with only scanty historical documentation of the Roma, comparative linguistic studies were the first to identify their Indian origin. Recently, molecular studies on the basis of disease-causing mutations and haploid DNA markers (i.e. mtDNA and Y-chromosome) supported the linguistic view. The presence of Indianspecific Y-chromosome haplogroup H1a1a-M82 and mtDNA haplogroups M5a1, M18 and M35b among Roma has corroborated that their South Asian origins and later admixture with Near Eastern and European populations. However, previous studies have left unanswered questions about the exact parental population groups in South Asia. Here we present a detailed phylogeographical study of Y-chromosomal haplogroup H1a1a-M82 in a data set of more than 10,000 global samples to discern a more precise ancestral source of European Romani populations. The phylogeographical patterns and diversity estimates indicate an early origin of this haplogroup in the Indian subcontinent and its further expansion to other regions. Tellingly, the short tandem repeat (STR) based network of H1a1a-M82 lineages displayed the closest connection of Romani haplotypes with the traditional scheduled caste and scheduled tribe population groups of northwestern India

Genetic Structure of Tibeto-Burman Populations of Bangladesh: Evaluating the Gene Flow along the Sides of Bay-of-Bengal

<div><p>Human settlement and migrations along sides of Bay-of-Bengal have played a vital role in shaping the genetic landscape of Bangladesh, Eastern India and Southeast Asia. Bangladesh and Northeast India form the vital land bridge between the South and Southeast Asia. To reconstruct the population history of this region and to see whether this diverse region geographically acted as a corridor or barrier for human interaction between South Asia and Southeast Asia, we, for the first time analyzed high resolution uniparental (mtDNA and Y chromosome) and biparental autosomal genetic markers among aboriginal Bangladesh tribes currently speaking Tibeto-Burman language. All the three studied populations; Chakma, Marma and Tripura from Bangladesh showed strikingly high homogeneity among themselves and strong affinities to Northeast Indian Tibeto-Burman groups. However, they show substantially higher molecular diversity than Northeast Indian populations. Unlike Austroasiatic (Munda) speakers of India, we observed equal role of both males and females in shaping the Tibeto-Burman expansion in Southern Asia. Moreover, it is noteworthy that in admixture proportion, TB populations of Bangladesh carry substantially higher mainland Indian ancestry component than Northeast Indian Tibeto-Burmans. Largely similar expansion ages of two major paternal haplogroups (O2a and O3a3c), suggested that they arose before the differentiation of any language group and approximately at the same time. Contrary to the scenario proposed for colonization of Northeast India as male founder effect that occurred within the past 4,000 years, we suggest a significantly deep colonization of this region. Overall, our extensive analysis revealed that the population history of South Asian Tibeto-Burman speakers is more complex than it was suggested before.</p></div