Multidisciplinary Approach to the Study of Ethnogenesis: Genogeography and Phylogeography of Tuvan Tribal Groups

Introduction. The territory of South Siberia has historically been a crossroads of ancient migration routes. So, the complex process of ethnogenesis across the region requires multidisciplinary insights of historians, ethnographers, anthropologists, linguists, and geneticists. Goals. The work aims to substantiate the possibility of a comprehensive study of Tuvan tribal groups on the basis of the latter’s gene pools and structures. Materials and methods. The most efficient tool thereto is the Y chromosome since it is inherited — like the clan/tribal name proper — paternally, has a high variety, makes it possible to reconstruct migration waves, and may yield genetic dates. These properties of the Y chromosome make it an additional historical source within comprehensive ethnographic, historical, linguistic, anthropological, and genetic studies of ancestral groups among peoples to have retained the memory of clan/tribal structures. Results. The early 21st century has witnessed an intensive research of the Tuvan Y-chromosomal gene pool — with no sufficient data on corresponding tribal groups mentioned. The analysis of Tuvan tribal structures is complicated by a number of factors, such as the administrative/territorial system of the Qing Empire in Tuva (1757–1912), introduction of a passport system in Tuva (1945–1947) when not clan/tribal names but rather personal ones were registered as surnames, and an increase in unmarried cohabitation that violates the patrilineal system. Y-chromosomal analyses of the largest Tuvan tribal groups Mongush and Oorzhak show that the bulk of their gene pool are North Eurasian haplogroups (N*, N1a2, N3a, Q) associated with the autochthonous population of the area nowadays inhabited by Tuvans. At the same time, Central Asian haplogroups (C2, O2) make up less than a fifth (17 %) of the gene pool. A targeted analysis of the most frequent branch (C2a1a2a2a2-SK1066) of the Central Asian haplogroup C2 shows it had originated about 900 years ago in the territory of Northeast Mongolia, and thus could not have reached Tuva before the 11th–12th centuries AD. Anthropological data also attest to the late admixture of the Central Asian cluster into the Tuvans and their tribal groups. The North Eurasian haplogroups completely dominate within the gene pool of tribal groups Kol, Oyun, and Khertek, which results in that the share of Central Asian lineages drops to 3%. Conclusions. In general, the paper shows the Mongolian expansion had no essential genetic impacts on the Y-chromosomal gene pool of Tuvan tribal groups, but — in contrast — did overwhelmingly influence ethnocultural, economic, and linguistic spheres

The Connection of the Genetic, Cultural and Geographic Landscapes of Transoxiana

We have analyzed Y-chromosomal variation in populations from Transoxiana, a historical region covering the southwestern part of Central Asia. We studied 780 samples from 10 regional populations of Kazakhs, Uzbeks, Turkmens, Dungans, and Karakalpaks using 35 SNP and 17 STR markers. Analysis of haplogroup frequencies using multidimensional scaling and principal component plots, supported by an analysis of molecular variance, showed that the geographic landscape of Transoxiana, despite its distinctiveness and diversity (deserts, fertile river basins, foothills and plains) had no strong influence on the genetic landscape. The main factor structuring the gene pool was the mode of subsistence: settled agriculture or nomadic pastoralism. Investigation of STR-based clusters of haplotypes and their ages revealed that cultural and demic expansions of Transoxiana were not closely connected with each other. The Arab cultural expansion introduced Islam to the region but did not leave a significant mark on the pool of paternal lineages. The Mongol expansion, in contrast, had enormous demic success, but did not impact cultural elements like language and religion. The genealogy of Muslim missionaries within the settled agricultural communities of Transoxiana was based on spiritual succession passed from teacher to disciple. However, among Transoxianan nomads, spiritual and biological succession became merged

Phylogeography of human Y-chromosome haplogroup Q3-L275 from an academic/ citizen science collaboration

Background: The Y-chromosome haplogroup Q has three major branches: Q1, Q2, and Q3. Q1 is found in both Asia and the Americas where it accounts for about 90% of indigenous Native American Y-chromosomes; Q2 is found in North and Central Asia; but little is known about the third branch, Q3, also named Q1b-L275. Here, we combined the efforts of population geneticists and genetic genealogists to use the potential of full Y-chromosome sequencing for reconstructing haplogroup Q3 phylogeography and suggest possible linkages to events in population history. Results: We analyzed 47 fully sequenced Y-chromosomes and reconstructed the haplogroup Q3 phylogenetic tree in detail. Haplogroup Q3-L275, derived from the oldest known split within Eurasian/American haplogroup Q, most likely occurred in West or Central Asia in the Upper Paleolithic period. During the Mesolithic and Neolithic epochs, Q3 remained a minor component of the West Asian Y-chromosome pool and gave rise to five branches (Q3a to Q3e), which spread across West, Central and parts of South Asia. Around 3–4 millennia ago (Bronze Age), the Q3a branch underwent a rapid expansion, splitting into seven branches, some of which entered Europe. One of these branches, Q3a1, was acquired by a population ancestral to Ashkenazi Jews and grew within this population during the 1st millennium AD, reaching up to 5% in present day Ashkenazi. Conclusions: This study dataset was generated by a massive Y-chromosome genotyping effort in the genetic genealogy community, and phylogeographic patterns were revealed by a collaboration of population geneticists and genetic genealogists. This positive experience of collaboration between academic and citizen science provides a model for further joint projects. Merging data and skills of academic and citizen science promises to combine, respectively, quality and quantity, generalization and specialization, and achieve a well-balanced and careful interpretation of the paternal-side history of human populations

The genetic prehistory of the Baltic Sea region

Correction: Nature communications 9 (2018), art. no. 1494 doi:10.1038/s41467-018-03872-yWhile the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from similar to 9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.Peer reviewe

Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities

The first farmers from Central Europe reveal a genetic affinity to modern-day populations from the Near East and Anatolia, which suggests a significant demographic input from this area during the early Neolithic

From cheek swabs to consensus sequences : an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes

Background: Next-generation DNA sequencing (NGS) technologies have made huge impacts in many fields of biological research, but especially in evolutionary biology. One area where NGS has shown potential is for high-throughput sequencing of complete mtDNA genomes (of humans and other animals). Despite the increasing use of NGS technologies and a better appreciation of their importance in answering biological questions, there remain significant obstacles to the successful implementation of NGS-based projects, especially for new users. Results: Here we present an ‘A to Z’ protocol for obtaining complete human mitochondrial (mtDNA) genomes – from DNA extraction to consensus sequence. Although designed for use on humans, this protocol could also be used to sequence small, organellar genomes from other species, and also nuclear loci. This protocol includes DNA extraction, PCR amplification, fragmentation of PCR products, barcoding of fragments, sequencing using the 454 GS FLX platform, and a complete bioinformatics pipeline (primer removal, reference-based mapping, output of coverage plots and SNP calling). Conclusions: All steps in this protocol are designed to be straightforward to implement, especially for researchers who are undertaking next-generation sequencing for the first time. The molecular steps are scalable to large numbers (hundreds) of individuals and all steps post-DNA extraction can be carried out in 96-well plate format. Also, the protocol has been assembled so that individual ‘modules’ can be swapped out to suit available resources

A társadalmak környezeti sebezhetősége, ellenálló- és alkalmazkodó képessége:a korai történelmi példáktól a sérülékenység globalizációjáig (Environmental vulnerability, resilience and adaptation capacities of societies: their historical examples and globalization)

Detailed phylogenetic tree of the haplogroup Q3-L275. 47 Q3-L275 samples and 1 Q1a-M346 outgroup. Constructed with the Phylomurka software using MP criteria, from the alignment obtained with read depth > = 2, base quality > = 15 and mapping quality > = 10, call rate = 60%. (XLSX 279 kb

Neolithic Mitochondrial Haplogroup H Genomes and the Genetic Origins of Europeans

Haplogroup H dominates present-day Western European mitochondrial DNA variability (\u3e40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria

The genetic prehistory of the Greater Caucasus

5月16日，厦门大学人类学系、德国马普所、德国考古所、俄罗斯文化遗产联合会、奥地利维也纳大学人类学系、爱尔兰都柏林大学学院考古系、罗蒙诺索夫莫斯科国立大学考古系和人类学博物馆、俄罗斯国立东方艺术博物馆、俄罗斯联邦达吉斯坦考古与民族志研究所历史系、美国韦尔斯利学院人类学系、瑞士巴塞尔大学史前与考古科学研究所、德国国家遗产博物馆等36家单位的46位共同作者组成的国际合作团队在BioRxiv上预发表论文《The genetic prehistory of the Greater Caucasus》，厦门大学人类学系王传超研究员为论文的第一作者和通讯作者，也是该国际团队中的唯一一位来自中国的合作者。【Abstract】Archaeogenetic studies have described the formation of Eurasian 'steppe ancestry' as a mixture of Eastern and Caucasus hunter-gatherers. However, it remains unclear when and where this ancestry arose and whether it was related to a horizon of cultural innovations in the 4th millennium BCE that subsequently facilitated the advance of pastoral societies likely linked to the dispersal of Indo-European languages. To address this, we generated genome-wide SNP data from 45 prehistoric individuals along a 3000-year temporal transect in the North Caucasus. We observe a genetic separation between the groups of the Caucasus and those of the adjacent steppe. The Caucasus groups are genetically similar to contemporaneous populations south of it, suggesting that - unlike today - the Caucasus acted as a bridge rather than an insurmountable barrier to human movement. The steppe groups from Yamnaya and subsequent pastoralist cultures show evidence for previously undetected Anatolian farmer-related ancestry from different contact zones, while Steppe Maykop individuals harbour additional Upper Palaeolithic Siberian and Native American related ancestry.This work was funded by the Max Planck Society and the German Archaeological Institute (DAI). C.C.W. was funded by Nanqiang Outstanding Young Talents Program of Xiamen University (X2123302) and the Fundamental Research Funds for the Central Universities. 该研究由德国马普学会、德国考古所、厦门大学南强青年拔尖人才支持计划资助

Author Correction: The genetic prehistory of the Baltic Sea region

The original version of this Article omitted references to previous work, which are detailed in the associated Author Correction. These omissions have been corrected in both the PDF and HTML versions of the Article