Abstract
Uniparental genetic systems are unique sex indicators and complement the study of autosomal diversity by providing landmarks of human migrations that repeatedly shaped the structure of extant populations. Our knowledge of the variation of the male-specific region of the Y chromosome in Native Americans is still rather scarce and scattered, but by merging sequence information from modern and ancient individuals, we here provide a comprehensive and updated phylogeny of the distinctive Native American branches of haplogroups C and Q. Our analyses confirm C-MPB373, C-P39, Q-Z780, Q-M848, and Q-Y4276 as the main founding haplogroups and identify traces of unsuccessful (pre-Q-F1096) or extinct (C-L1373*, Q-YP4010*) Y-chromosome lineages, indicating that haplogroup diversity of the founder populations that first entered the Americas was greater than that observed in the Indigenous component of modern populations. In addition, through a diachronic and phylogeographic dissection of newly identified Q-M848 branches, we provide the first Y-chromosome insights into the early peopling of the South American hinterland (Q-BY104773 and Q-BY15730) and on overlying inland migrations (Q-BY139813).
Highlights
The Americas were the last continents to be colonised by modern humans
TAhemNeroirctah A[1m7,e6r8ic–a7n3]Y. cThhroemNosoormthes America were characteriscehdrobmyotshoemmesarwkeerreP3ch9a[r6a9c]t,ewrisheedrebays tthhoesemfarrokmerSPo3u9th[6A9m], ewrihcear,eiansittihalolsye from S indicated as C3*,Awmeererirceac,einntiltyiaclllyassinifideicdaatesdC-aMs PCB33*7, 3w[e3r8e], raescuenbt-llyinecalagsesiofifeCd-La1s3C73-M, wPhBi3c7h3 [38], a is mainly presenltinineaNgeorotfhCE-Lu1ra3s7i3a,.which is mainly present in North Eurasia
We significantly increase the resolution of Q-M1107 and confirm haplogroups C-MPB373, Q-Z780, Q-M848, and Q-Y4276, together with C-P39, as the main Native American founding lineages
Summary
The Americas were the last continents to be colonised by modern humans. For decades, scientists of different disciplines have debated the modes and times of their peopling [1,2,3,4,5] reaching a consensus on the Asian origin of the first settlers, their entrance from Siberia across Beringia before 16 thousand years ago (kya) or even earlier [6,7], and a rapid southward migration to the Southern Cone as attested by Monte Verde in Chile (~14.5 kya) and other archaeological sites [8,9]. Genomic analyses of modern and ancient individuals have identified at least two ancestral Pleistocene components that, once entered into North America, underwent splits and admixture while moving southward [10,11,12]. To explain these results, different models have been proposed [13]. Additional Pleistocene Indigenous components carried by still unsampled ancient populations (UPopA, UPopI) were identified in Central and South America [11,14,15], adding further complexity to the peopling scenarios. Due to the uneven male/female native population decline and the high historical rate of European male-mediated admixture into Native American communities, the Y chromosome gene pool was the most affected [16,17,18,19]
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