Human Y Chromosome Haplogroup N: A Non-trivial Time-Resolved Phylogeography that Cuts across Language Families

Abstract

The paternal haplogroup (hg) N is distributed from southeast Asia to eastern Europe. The demographic processes that have shaped the vast extent of this major Y chromosome lineage across numerous linguistically and autosomally divergent populations have previously been unresolved. On the basis of 94 high-coverage re-sequenced Y chromosomes, we establish and date a detailed hg N phylogeny. We evaluate geographic structure by using 16 distinguishing binary markers in 1,631 hg N Y chromosomes from a collection of 6,521 samples from 56 populations. The more southerly distributed sub-clade N4 emerged before N2a1 and N3, found mostly in the north, but the latter two display more elaborate branching patterns, indicative of regional contrasts in recent expansions. In particular, a number of prominent and well-defined clades with common N3a3'6 ancestry occur in regionally dissimilar northern Eurasian populations, indicating almost simultaneous regional diversification and expansion within the last 5,000 years. This patrilineal genetic affinity is decoupled from the associated higher degree of language diversity.

Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia

“…As indicated by the Y-STR network (Fig 3), there may be several particular sub-clades of O3a2b2-N6 in in Austronesian populations from Island Southeast Asia and Oceania. Additionally, whole Y-chromosome sequences of O3a2b2-N6 samples will enable accurate estimates of the timing of the origin and internal differentiation of O3a2b2a2b-B451, as well as other possible special sub-clades, in Austronesian populations, similar to previous analyses of haplogroup N-M231 in Uralic populations [48]. Additional genotyping and sequencing results will help clarify the demographic history of Austronesian populations, especially those from the Remote Oceania region.…”

Human Y-chromosome variation in the genome-sequencing era

“…Currently, studies are emerging in which novel variants discovered by resequencing are applied in large population samples 60 , but NGS approaches have already had a direct impact in some areas, as described in the following sections. …”

Estimating the impact of the Mongol expansion upon the gene pool of Tuvans

“…59 SNP-markers were genotyped: M130, M217, F2613, F2386, F1788, F3918, F3830, M86, F5485, SK1066, F3791, F11899, F5481, F11791, F14768, F3960, P53.1, CTS4021, M407, Z12266, M174, M69, M170, M253, M223, P37, M304, M267, M172, M47, M67, M92, M12, M9, M20, M231, LLY22g, M178, L708, L666, В211, М2118, VL29, Z236, F4205, P31, M122, M242, M120, M378, M207, M198, M458, M343, M73, M269, M124, M70, and chrY:15310670 T>C. The nomenclature of haplogroups (hg) in the table of hg frequencies (see the Table) is given as defined by ISOGG Y-DNA Haplogroup Tree 2018 (https://isogg.org/tree/ISOGG_ YDNATreeTrunk.html), names of new-discovered markers subdividing hg N3 into sub-clades N3a1, N3a2, N3a3, N3a4, and N3a5 being in accordance to proposed by Ilumäe and his colleagues (Ilumäe et al, 2016). …”

“…In Khori-Buryats from the Transbaikal region, a high frequency is observed -82 % (Kharkov et al, 2014), while in Mongols, N3a5 occurs rather rarely (6 %). Hg N3a* was detected in populations of South Siberia only, and was widely spread in Khakas-Sagays and Shors (up to 40 %) (Ilumäe et al, 2016) …”

“…The study on whole Y-chromosome sequencing conducted with participation of our group (Ilumäe et al, 2016) subdivided this haplogroup into several branches with their regional distribution. In gene pools of the Tuvans involved, hg N was represented by two sub-clades, namely N1a2 and N3a.…”