Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences

Abstract

The expansion of modern humans to the American continent after the Last Glacial Maximum led the way to the present-day distribution of American aborigines. Recent advances in autosomal DNA research and expanded testing of mtDNA lineages has provided a clearer picture of the number and timing of founding lineages. However, both autosomal DNA and mtDNA research have provided unresolved competing theories between the short-term and the long-term models of the Beringian standstill hypothesis. Further, the source of founding paternal lineages of American aborigines and their relationship with ancient Siberia populations remains ambiguous. In this study, we reanalyzed a 7.0 Mbp region of 132 paternal Y-chromosome sequences, including 39 newly reported ones, of male samples from American aborigines and Eurasian populations. Among Eurasian samples, we identified Y-chromosome branches that are most closely related to known American aborigine founding lineages, that is, Q1-L804 links to Q1-M3, Q1-L330 links to Q1-Z780, Q1-M120 links to Q1-B143, and C2-F1756 links to C2-P39. The revised phylogenetic tree and age estimates indicate a narrow timeframe (~15.3-14.3 kya) for the upper time limit of human entry to the American continent. Our analysis suggests that the in situ differentiation of Q-M242 in Central Eurasia and South Siberia region gave rise to numerous sub-lineages older than 15.3 kya, and the founding of Paleo-Indian paternal lineages is part of the great Q1-L53 diffusion throughout the Eurasia after the Last Glacial Maximum. The results of our study will assist in future studies of the history of modern populations in Eurasia and the Americas.

Post‐last glacial maximum expansion of Y‐chromosome haplogroup C2a‐L1373 in northern Asia and its implications for the origin of Native Americans

“…As discussed in the section above, most samples of rare C2a‐L1373 sublineages were found in populations from low latitude regions of northern Asia, such as the Amur River region, the Mongolian Plateau, the northern boundary of China, and adjacent areas. Previous studies have also demonstrated that the Amur River region is the urheimat of F1756, M504, and M86, before their expansion in the last several thousand years (Derenko et al, 2006; Duggan et al, 2013; Malyarchuk et al, 2010; Malyarchuk et al, 2013; Wei et al, 2017; Wei, Wang, et al, 2018; Wei, Yan, et al, 2018; Zhang et al, 2018; Zhong et al, 2010). Based on these findings and available ancient DNA (like NEO239 individual of haplogroup C2a2‐MPB373 and the UKY001 individual of C2a1a1a1*‐B473, see Figure 1), we propose that the initial differentiation of C2a‐L1373 began in the low latitude region of northern Asia (likely the Amur River region), and the continuous splitting pattern of C2a‐L1373 between 18 and 14 kya may correspond to the repeopling of northern Asia, from south to north and west, after the LGM.…”

“…Due to the high frequencies of F1756, M504, and M86 among modern populations, most previous studies have focused on the expansion process of these three major subbranches of C2a‐L1373 and their role during the formation of proto‐Mongols, modern Mongolic‐speaking populations, and Tungusic‐speaking populations (Derenko et al, 2006; Duggan et al, 2013; Malyarchuk et al, 2010; Malyarchuk et al, 2013; Wei et al, 2017; Wei, Wang, et al, 2018; Wei, Yan, et al, 2018; Zhang et al, 2018; Zhong et al, 2010). In this study, we focused on the early differentiation history of rare subbranches of C2a‐L1373.…”

“…According to previous investigations, the paternal gene pool of populations in northern Asia is composed of four Y‐chromosome haplogroups and numerous rare lineages; for example, haplogroup N‐M78, the only founding paternal lineage of Uralic‐speaking populations, reached high frequencies in numerous Tungus‐, Mongolic‐, and Turkic‐speaking populations (Rootsi et al, 2007), while haplogroup C2a‐M504 is one of the founding paternal lineages of Mongolic‐speaking populations (Wei, Wang, et al, 2018; Wei, Yan, et al, 2018). Studies of both ancient DNA and modern populations have demonstrated that haplogroup C2a‐F1756 was the dominant lineage in ancient Donghu, Xianbei, Shiwei, and Rouran populations (Li et al, 2018; Wang et al, 2012; Wei et al, 2017; Zhang et al, 2018).…”

“…Haplogroup C2a‐M86 is the only founding paternal lineage of Tungusic‐speaking people (Derenko et al, 2006; Duggan et al, 2013; Lell et al, 2002; Liu et al, 2020). Most sublineages of these four paternal haplogroups emerged in the last 5,000 years (Liu et al, 2020; Wei et al, 2017; Wei, Wang, et al, 2018; Wei, Yan, et al, 2018).…”

“…Two recent ancient DNA studies provided more details about demographic history in Northeast Asia, Chukotka and North America since the late Pleistocene (Flegontov et al, 2019; Yu et al, 2020). In general, ancient DNA evidence generated by modern techniques are inconsistent with the basal arguments for the “Long‐term Beringia standstill hypothesis.” In our previous study, we identified the most closely related haplogroup to founding lineages of indigenous peoples of the Americas among Eurasian samples and proposed that the appearance of the ancestor group of indigenous peoples of the Americas was part of the great Q1‐L53 diffusion throughout Eurasia after the LGM (Wei, Wang, et al, 2018; Wei, Yan, et al, 2018).…”