Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Sikora, Martin; Seguin-Orlando, Andaine; Sousa, Vítor C.; Albrechtsen, Anders; Korneliussen, Thorfinn Sand; Ko, Amy J.; Rasmussen, Simon; Dupanloup, Isabelle; Nigst, Philip R.; Bosch, Delphine; Renaud, Gabriel; Allentoft, Morten E.; Margaryan, Ashot; Vasilyev, Sergey; Veselovskaya, Elizaveta; Borutskaya, S.B.; Devièse, Thibaut; Comeskey, Dan; Higham, Thomas; Manica, Andrea; Foley, Robert; Meltzer, David J.; Nielsen, Rasmus; Excoffier, Laurent; Lahr, Marta Mirazón; Orlando, Ludovic; Willerslev, Eske

doi:10.1126/science.aao1807

Cited by 290 publications

(224 citation statements)

References 137 publications

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“…To make inferences on the genetic relationship of IK002 with geographically diverse human populations, we merged the IK002 genomic data with a diverse panel of previously published ancient genomes [22][23][24][25][26][27][28] , as well as 300 high-coverage present-day genomes from the Simons Genome Diversity Project (SGDP) [29] . We extracted genotypes for a set of 2,043,687 SNP sites included in the "2240K" capture panel [30] .…”

Section: Testing Whether Ik002 Is the Direct Descendant Of The Upper mentioning

confidence: 99%

Jomon genome sheds light on East Asian population history

Gakuhari

Nakagome

Rasmussen

et al. 2019

Preprint

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Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

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Section: Testing Whether Ik002 Is the Direct Descendant Of The Upper mentioning

confidence: 99%

Jomon genome sheds light on East Asian population history

Gakuhari

Nakagome

Rasmussen

et al. 2019

Preprint

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“…Ancient DNA studies are beginning to show some of the complexity of human genetic history, including providing evidence for large-scale intercontinental movements in the last 30,000 years or so 3,[21][22][23][24][25][26] . The out-of-Africa model requires major intercontinental movements 40,000-60,000 years ago, as well as later expansion into the Americas.…”

Section: Mainmentioning

confidence: 99%

Early replacement of West Eurasian male Y chromosomes from the east

Agdzhoyan

Balanovsky

Xue

et al. 2019

Preprint

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The genomes of humans outside Africa originated almost entirely from a single migration out ~50,000-60,000 years ago 1,2 , followed closely by mixture with Neanderthals contributing ~2% to all non-Africans 3,4 . However, the details of this initial migration remain poorlyunderstood because no ancient DNA analyses are available from this key time period, and present-day autosomal data are uninformative due to subsequent population movements/reshaping 5 . One locus, however, does retain extensive information from this early period: the Y-chromosome, where a detailed calibrated phylogeny has been constructed 6 . Three present-day Y lineages were carried by the initial migration: the rare haplogroup D, the moderately rare C, and the very common FT lineage which now dominates most non-African populations 6,7 . We show that phylogenetic analyses of haplogroup C, D and FT sequences, including very rare deep-rooting lineages, together with phylogeographic analyses of ancient and present-day non-African Y-chromosomes, all point to East/South-east Asia as the origin 50,000-55,000 years ago of all known non-African male lineages (apart from recent migrants). This implies that the initial Y lineages in populations between Africa and eastern Asia have been entirely replaced by lineages from the east, contrasting with the expectations of the serial-founder model 8,9 , and thus informing and constraining models of the initial expansion.3 MainA consensus view has emerged that the genomes of present-day human populations outside Africa originate almost entirely from a single major migration out around 50,000-70,000 years ago, accompanied or followed soon after by mixture with Neanderthals contributing ~2% to the genome of all non-Africans 4,10 . This mixture event is reliably dated from the length of the Neanderthal segments to 7,000-13,000 years before the time when the ancient-DNA-yielding fossil Ust'-Ishim lived (45,000 years ago) 3 . Thus Neanderthal mixture took place 52,000-58,000 years ago, and the migration out of Africa was probably within this time interval or shortly before, so most likely 52,000-60,000 years ago. The admixed population then expanded rapidly over most of Eurasia and Australia 1,2 . As a result, people were present over much of this vast region by 50,000 years ago. The details of this initial expansion, however, remain poorly characterised. Did it follow a coastal route, an inland route, or multiple routes? Where and when did the ancestors of present-day populations begin to diverge? To what extent do present-day populations retain the genetic imprint of these early patterns? Ancient DNA studies using samples 50,000-60,000 years old could potentially provide definitive answers to these questions, but have not so far been reported because of the absence of suitable samples. Genome-wide analyses of present-day populations show a steady decrease in genetic variation with travelling distance from Africa, and have been interpreted in terms of a 'serial founder' model which predicts such a decrease 8,9 . Whil...

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“…Mitochondrial DNA sequences were reconstructed using endoCaller from schmutzi 63 , and haplogroups assigned with HaploGrep 65 . Y chromosome haplogroups were assigned from reads overlapping SNPs included in the Y-DNA haplogroup tree from the International Society of Genetic Genealogy (ISOGG; http://www.isogg.org, version 13.37), as previously described 39 . Phylogenetic analysis was carried out on haploid SNP calls from high coverage individuals obtained with samtools/bcftools 66 , using RAxML 67 with the ASC_GTRGAMMA model 44 .…”

Section: Authentication Mitochondrial Dna and Chromosome Y Analysesmentioning

confidence: 99%

“…Panel 3 ("CGG WGS") includes all genome-wide SNPs genotyped across high coverage modern and ancient individuals with shotgun sequencing data. Genotyping was carried separately for each diploid individual using samtools/bcftools 66 , and filtered as previously described 39 (Supplementary Information section 5). Pseudo-haploid genotypes for low-coverage ancient individuals were obtained by sampling a random high-quality read at each covered SNP position of the respective panels.…”

Section: Analysis Panelsmentioning

confidence: 99%

The population history of northeastern Siberia since the Pleistocene

Sikora

Pitulko

Sousa

et al. 2018

Preprint

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Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we analyze 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-yearold (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of "Ancient North Siberians" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and "Ancient Paleosiberians" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the "Neosiberians" from which many contemporary Siberians derive. We detect gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic throughout the Late Pleistocene and Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia. Northeastern Siberia (the modern Russian Far East) is one of the most remote and extreme environments colonized by humans. Extending from the Taimyr Peninsula in the west to the Pacific Ocean in the east, and from the China/Russia border north to the Arctic Ocean, the region is home to dozens of diverse ethnolinguistic groups. Recent genetic studies of the

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Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Cited by 290 publications

References 137 publications

Jomon genome sheds light on East Asian population history

Jomon genome sheds light on East Asian population history

Early replacement of West Eurasian male Y chromosomes from the east

The population history of northeastern Siberia since the Pleistocene

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