The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
The genomic formation of First American ancestors in East and Northeast Asia
Abstract
Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000–18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia. One Sentence Summary: Ancient Beringians do not form the deepest American lineage, but harbor admixture from Amur River Basin populations.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
This East Asian lineage is the primary ancestor (60-70%) of the Indigenous peoples of the Americas (arctic and non-arctic peoples).
“It reflects early admixture with the Denisovans and is the primary ancestor (60–70%) of the Indigenous peoples of the Americas (arctic and non-arctic peoples) [61,71,72].”
From Beringia and the peopling of the Western Hemisphere (2023) · cites this paper as [71]
This East Asian lineage reflects early admixture with the Denisovans.
“It reflects early admixture with the Denisovans and is the primary ancestor (60–70%) of the Indigenous peoples of the Americas (arctic and non-arctic peoples) [61,71,72].”
From Beringia and the peopling of the Western Hemisphere (2023) · cites this paper as [71]
The 'Ancient Beringians' were a later offshoot of the North American ANA population.
“It now appears, however, that the ‘Ancient Beringians’ were a later offshoot of the North American ANA population [71].”
From Beringia and the peopling of the Western Hemisphere (2023) · cites this paper as [71]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
ANGSD: Analysis of Next Generation Sequencing Data
Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014) · BMC Bioinformatics · doi:10.1186/s12859-014-0356-4 · Cited by 2,982
Massive migration from the steppe was a source for Indo-European languages in Europe
Haak, W., Lazaridis, I., Patterson, N., Rohland, N., Mallick, S., Llamas, B., Brandt, G., Nordenfelt, S., Harney, E., Stewardson, K., et al. (2015) · Nature · doi:10.1038/nature14317 · Cited by 1,940
Self-citationReconstructing Indian population history
Reich, D., Thangaraj, K., Patterson, N., Price, A. L., & Singh, L. (2009) · Nature · doi:10.1038/nature08365 · Cited by 1,674
Self-citationmapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters
Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P. L. F., & Orlando, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt193 · Cited by 1,669
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584
Self-citationPopulation genomics of Bronze Age Eurasia
Allentoft, M. E., Sikora, M., Sjögren, K.-G., Rasmussen, S., Rasmussen, M., Stenderup, J., Damgaard, P. B., Schroeder, H., Ahlström, T., Vinner, L., et al. (2015) · Nature · doi:10.1038/nature14507 · Cited by 1,550
Genome-wide patterns of selection in 230 ancient Eurasians
Mathieson, I., Lazaridis, I., Rohland, N., Mallick, S., Patterson, N., Roodenberg, S. A., Harney, E., Stewardson, K., Fernandes, D., Novak, M., et al. (2015) · Nature · doi:10.1038/nature16152 · Cited by 1,515
Self-citationAncient human genomes suggest three ancestral populations for present-day Europeans
Lazaridis, I., Patterson, N., Mittnik, A., Renaud, G., Mallick, S., Kirsanow, K., Sudmant, P. H., Schraiber, J. G., Castellano, S., Lipson, M., et al. (2014) · Nature · doi:10.1038/nature13673 · Cited by 1,357
Self-citationGenome sequence of a 45,000-year-old modern human from western Siberia
Fu, Q., Li, H., Moorjani, P., Jay, F., Slepchenko, S. M., Bondarev, A. A., Johnson, P. L. F., Aximu-Petri, A., Prüfer, K., de Filippo, C., et al. (2014) · Nature · doi:10.1038/nature13810 · Cited by 1,023
Self-citationInsights into human genetic variation and population history from 929 diverse genomes
Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science · doi:10.1126/science.aay5012 · Cited by 1,020
Self-citationUpper Palaeolithic Siberian genome reveals dual ancestry of Native Americans
Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford Jr, T. W., Orlando, L., Metspalu, E., et al. (2014) · Nature · doi:10.1038/nature12736 · Cited by 963
Genomic insights into the origin of farming in the ancient Near East
Lazaridis, I., Nadel, D., Rollefson, G., Merrett, D. C., Rohland, N., Mallick, S., Fernandes, D., Novak, M., Gamarra, B., Sirak, K., et al. (2016) · Nature · doi:10.1038/nature19310 · Cited by 955
Self-citationAncient human genome sequence of an extinct Palaeo-Eskimo
Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., et al. (2010) · Nature · doi:10.1038/nature08835 · Cited by 849
An early modern human from Romania with a recent Neanderthal ancestor
Fu, Q., Hajdinjak, M., Moldovan, O. T., Constantin, S., Mallick, S., Skoglund, P., Patterson, N., Rohland, N., Lazaridis, I., Nickel, B., et al. (2015) · Nature · doi:10.1038/nature14558 · Cited by 802
Self-citationRevising the human mutation rate: implications for understanding human evolution
Scally, A., & Durbin, R. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3295 · Cited by 610
The genome of a Late Pleistocene human from a Clovis burial site in western Montana
Rasmussen, M., Anzick, S. L., Waters, M. R., Skoglund, P., DeGiorgio, M., Stafford, T. W., Rasmussen, S., Moltke, I., Albrechtsen, A., Doyle, S. M., et al. (2014) · Nature · doi:10.1038/nature13025 · Cited by 562
Self-citationThe genomic history of the Iberian Peninsula over the past 8000 years
Olalde, I., Mallick, S., Patterson, N., Rohland, N., Villalba-Mouco, V., Silva, M., Dulias, K., Edwards, C. J., Gandini, F., Pala, M., et al. (2019) · Science · doi:10.1126/science.aav4040 · Cited by 552
Self-citationGenomic evidence for the Pleistocene and recent population history of Native Americans
Raghavan, M., Steinrücken, M., Harris, K., Schiffels, S., Rasmussen, S., DeGiorgio, M., Albrechtsen, A., Valdiosera, C., Ávila-Arcos, M. C., Malaspinas, A.-S., et al. (2015) · Science · doi:10.1126/science.aab3884 · Cited by 540
Self-citationThe prehistoric peopling of Southeast Asia
McColl, H., Racimo, F., Vinner, L., Demeter, F., Gakuhari, T., Moreno-Mayar, J. V., van Driem, G., Gram Wilken, U., Seguin-Orlando, A., de la Fuente Castro, C., et al. (2018) · Science · doi:10.1126/science.aat3628 · Cited by 517
Fenner, J. N. (2005) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20188 · Cited by 508
Archaeogenomic evidence reveals prehistoric matrilineal dynasty
Kennett, D. J., Plog, S., George, R. J., Culleton, B. J., Watson, A. S., Skoglund, P., Rohland, N., Mallick, S., Stewardson, K., Kistler, L., et al. (2017) · Nature Communications · doi:10.1038/ncomms14115 · Cited by 301
Self-citationLate Pleistocene exploration and settlement of the Americas by modern humans
Waters, M. R. (2019) · Science · doi:10.1126/science.aat5447 · Cited by 176
Pouyet, F., Aeschbacher, S., Thiéry, A., & Excoffier, L. (2018) · eLife · doi:10.7554/elife.36317 · Cited by 153
Harney, É., May, H., Shalem, D., Rohland, N., Mallick, S., Lazaridis, I., Sarig, R., Stewardson, K., Nordenfelt, S., Patterson, N., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05649-9 · Cited by 136
Self-citationAncient DNA sheds light on the genetic origins of early Iron Age Philistines
Feldman, M., Master, D. M., Bianco, R. A., Burri, M., Stockhammer, P. W., Mittnik, A., Aja, A. J., Jeong, C., & Krause, J. (2019) · Science Advances · doi:10.1126/sciadv.aax0061 · Cited by 120
Self-citation
Flagged first, then by citations
Research works printed but not linked: 105
- 10.1016/j.gde.2016.06.016 · DOI
- 10.1086/693388 · DOI
- 10.1038/nature25173 · DOI · Paper page
- B. A. Potter , J. D. Reuther , V. T. Holliday , C. E. Holmes , D. S. Miller , N. Schmuck , Early colonization of Beringia and Northern North America: Chronology, routes, and adaptive strategies. Quat. Int. 444, 36-55 (2017). · DOI · Paper page
- 10.1371/journal.pone.0000829 · DOI · Paper page
- 10.1126/science.aao5473 · DOI · Paper page
- 10.1126/sciadv.aat5473 · DOI · Paper page
- 2020, The timing and effect of the earliest human arrivals in North America, Nature, 584, 93, 10.1038/s41586-020-2491-6 · DOI
- 2019, The population history of northeastern Siberia since the Pleistocene, Nature, 570, 182, 10.1038/s41586-019-1279-z · DOI · Paper page
- 2019, Palaeo-Eskimo genetic ancestry and the peopling of Chukotka and North America, Nature, 570, 236, 10.1038/s41586-019-1251-y · DOI
- 10.1073/pnas.1413131111 · DOI
- 10.1126/science.aav2621 · DOI
- 10.1016/j.cell.2018.10.027 · DOI
- 10.1038/nature11258 · DOI · Paper page
- 10.1126/science.aar6851 · DOI · Paper page
- 10.1371/journal.pgen.1004530 · DOI
- 2020, Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and across Eurasia, Cell, 181, 1232, 10.1016/j.cell.2020.04.037 · DOI
- 10.1126/sciadv.1601877 · DOI
- 2020, Ancient genomes from northern China suggest links between subsistence changes and human migration, Nat. Commun, 11, 2700, 10.1038/s41467-020-16557-2 · DOI
- C.-C. Wang et al., https://www.biorxiv.org/content/10.1101/2020.03.25.004606v1 2020). · DOI
- 10.1371/journal.pcbi.1004842 · DOI
- 2019, The genetic history of admixture across inner Eurasia, Nat. Ecol. Evol, 3, 966, 10.1038/s41559-019-0878-2 · DOI
- 2020, Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations, Commun. Biol, 3, 437, 10.1038/s42003-020-01162-2 · DOI
- 2019, The formation of human populations in South and Central Asia, Science, 365, aat7487, 10.1126/science.aat7487 · DOI
- 10.1126/science.1255832 · DOI · Paper page
- 10.1038/nature14895 · DOI · Paper page
- 10.1016/j.cub.2017.09.030 · DOI
- 2011, The relationship of Nivkh to Chukotko-Kamchatkan revisited, Lingua, 121, 1359, 10.1016/j.lingua.2011.03.001 · DOI
- 10.1093/molbev/msr048 · DOI · Paper page
- 10.1126/sciadv.1501385 · DOI · Paper page
- 10.1073/pnas.1905060116 · DOI
- 2018, The first horse herders and the impact of early Bronze Age steppe expansions into Asia, Science, 360, aar7711, 10.1126/science.aar7711 · DOI
- 10.1371/journal.pgen.0020190 · DOI · Paper page
- 10.1126/science.1188021 · DOI · Paper page
- 10.1534/genetics.112.145037 · DOI · Paper page
- 2019, General theory for stochastic admixture graphs and F-statistics, Theor. Popul. Biol, 125, 56, 10.1016/j.tpb.2018.12.002 · DOI
- 10.1101/gr.094052.109 · DOI · Paper page
- É. Harney et al., https://www.biorxiv.org/content/10.1101/2020.04.09.032664v1 (2020). · DOI
- 10.1038/nature23310 · DOI
- 10.1016/j.cub.2016.12.060 · DOI
- 10.1038/s41586-018-0094-2 · DOI
- 10.1038/nature25778 · DOI
- 10.1038/s41467-018-02825-9 · DOI
- 10.1038/nature25738 · DOI · Paper page
- 2019, Late Pleistocene human genome suggests a local origin for the first farmers of central Anatolia, Nat. Commun, 10, 1218, 10.1038/s41467-019-09209-7 · DOI
- 2019, Ancient genomes reveal Yamnaya-related ancestry and a potential source of Indo-European speakers in Iron Age Tianshan, Curr. Biol, 29, 2526, 10.1016/j.cub.2019.06.044 · DOI
- 2019, Survival of Late Pleistocene hunter-gatherer ancestry in the Iberian peninsula, Curr. Biol, 29, 1169, 10.1016/j.cub.2019.02.006 · DOI
- 10.1038/s41467-018-08220-8 · DOI
- 2020, The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean, Nat. Ecol. Evol, 4, 334, 10.1038/s41559-020-1102-0 · DOI
- 2020, Ancient genomes reveal social and genetic structure of Late Neolithic Switzerland, Nat. Commun, 11, 1915, 10.1038/s41467-020-15560-x · DOI
- 2020, Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia, Nat. Commun, 11, 939, 10.1038/s41467-020-14523-6 · DOI
- 2020, Efficiently inferring the demographic history of many populations with allele count data, J. Am. Stat. Assoc, 115, 1472, 10.1080/01621459.2019.1635482 · DOI
- 10.1038/ncomms10408 · DOI
- 10.1371/journal.pgen.1003905 · DOI
- M. Lipson , Applying f4-statistics and admixture graphs: Theory and examples. Mol. Ecol. Resour. 10.1111/1755-0998.13230 (2020). · DOI
- 10.1073/pnas.1813608115 · DOI · Paper page
- 2016, Genomic analyses inform on migration events during the peopling of Eurasia, Nature, 538, 238, 10.1038/nature19792 · DOI
- 2020, Ancient West African foragers in the context of African population history, Nature, 577, 665, 10.1038/s41586-020-1929-1 · DOI
- 10.1101/001347 · DOI
- E. Frichot , S. Schoville , G. Bouchard , O. François , Correcting principal component maps for effects of spatial autocorrelation in population genetic data. Front. Genet. 10.3389/fgene.2012.00254 (2012). · DOI
- 2009, A genealogical interpretation of principal components analysis, PLoS Genet, 5, 1000686, 10.1371/journal.pgen.1000686 · DOI · Paper page
- 10.1038/ng0508-491 · DOI
- 10.1038/ng.139 · DOI
- 10.1371/journal.pone.0170940 · DOI
- 10.1016/j.tree.2005.07.005 · DOI · Paper page
- E. Willerslev , A. Cooper , Ancient DNA. Proc. Biol. Sci. 272, 3-16 (2005). · DOI · Paper page
- 10.2144/000114558 · DOI · Paper page
- M. Meyer , M. Kircher , Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb. Protoc. 2010, pdb.prot5448 (2010). · DOI
- 10.1186/s13104-016-1900-2 · DOI
- 10.1093/bioinformatics/btp324 · DOI · Paper page
- 10.1186/s13059-016-0918-z · DOI · Paper page
- 10.1093/bioinformatics/btp352 · DOI · Paper page
- 2017, A working model of the deep relationships of diverse modern human genetic lineages outside of Africa, Mol. Biol. Evol, 34, 889
- 10.1126/science.aat3188 · DOI
- 10.1073/pnas.1520844113 · DOI
- 10.1126/science.aba0909 · DOI
- J. Kari , “Some linguistic insights into Dena’ina prehistory” in Athapaskan linguistics: current perspectives on a language family (Trends in Linguistics. State-of-the-Art Reports), E.-D. Cook , K. D. Rice , Eds. (Mouton de Gruyter, 1989), pp. 533–574. · DOI
- J. Kari , “Linguistic traces of Dena’ina strategy at the archaic periphery” in Adventures through time: readings in the anthropology of Cook Inlet, Alaska: proceedings of a symposium, N. Yaw Davis , W. E. Davis , Eds. (Cook Inlet Historical Society, Anchorage, AK, 1996), pp. 51–63.
- 1958, [Voprosy yazykoznaniya], 1, 21
- 2003, Diachronic typology and the genealogical unity of Chukotko-Kamchatkan, Linguist. Typology, 7, 51
- M. Fortescue , Comparative Chukotko-Kamchatkan dictionary (De Gruyter, Berlin, 2005). · DOI
- T. Kurebito , M. Kurebito , Y. Nagayama , C. Ono , M. Yazu , Comparative basic vocabulary of the Chukchee-Kamchatkan language family (Endangered Languages of the Pacific Rim, Faculty of Informatics, Osaka Gakuin University, Suita, 2001), vol. 1.
- 1962, La place du kamtchadal parmi les langues soi-disant paleosiberiennes, Orbis, 11, 579
- A. P. Volodin , [Chukotko-Kamchatkan languages]” in [Languages of the World: Paleoasiatic languages], A. P. Volodin , Ed. (Indrik, Moscow, 1997), pp. 12–22.
- S. Georg , A. P. Volodin , Die itelmenische Sprache: Grammatik und Texte (Tunguso-Sibirica, Harrassowitz, Wiesbaden, 1999), vol. 5.
- S. G. Thomason , T. Kaufman , Language contact, creolization, and genetic linguistics (University of California Press, Berkeley, 1988). · DOI
- A. S. Kassian et al. http://www.academia.edu/39903804/ (2019).
- 2015, Proto-Indo-European-Uralic comparison from the probabilistic point of view, J. Indo-Eur. Stud, 43, 301
- M. Fortescue , Comparative Nivkh dictionary (Languages of the World. Dictionaries, LINCOM GmbH, München, 2016), vol. 62.
- D. Anthony , The Horse, the Wheel, and Language: How Bronze-Age Riders from the Eurasian Steppes Shaped the Modern World (Princeton University Press, Princeton, NJ, 2007). · DOI
- J. Nichols , Linguistic diversity in space and time (University of Chicago Press, Chicago, 1992). · DOI
- M. Fortescue , E. Vajda , Mid-Holocene Language Connections Across Bering Strait (Brill, Leiden, in press).
- O. Mudrak , S. Nikolaev , Gilyak and Chukchi-Kamchatkan as Almosan-Keresiouan languages: Lexical evidence (Preliminary report) (Explorations in Language Macrofamilies, Universitätsverlag Dr. Norbert Brockmeyer, Bochum, 1989), pp. 67–87.
- 2015, Toward the reconstruction of Proto-Algonquian-Wakashan. Part 1: Proof of the Algonquian-Wakashan relationship, J. Language Relationship, 13, 23, 10.31826/jlr-2015-131-206 · DOI
- 2015, Toward the reconstruction of Proto-Algonquian-Wakashan. Part 2: Algonquian-Wakashan sound correspondences, J. Language Relationship, 13, 289
- L. R. Morgan , Kootenay-Salishan linguistic comparison. A preliminary study (M.A. thesis, University of British Columbia, Vancouver, 1982).
- M. Dryer , “Kutenai, Algonquian and the Pacific Northwest from an areal perspective” in Papers of the 38th Algonquian Conference, H. C. Wolfart , Ed. (University of Manitoba, Winnipeg, 2007), pp. 155–206.
- J. H. Greenberg , Language in the Americas (Stanford University Press, Stanford, CA, 1987).
- I. Goddard , “Comparative Algonquian” in The languages of Native America: Historical and comparative assessment. L. Campbell , M. Mithun , Eds. (University of Texas Press, Austin, TX, 1979), pp. 70–132. · DOI
- L. Campbell , W. J. Poser , Language Classification: History and Method (Cambridge University Press, Cambridge, 2008). · DOI
- H. Matsumae et al., http://www.biorxiv.org/content/10.1101/513929v1 (2019). · DOI
- E. Vajda , “Patterns of innovation and retention in templatic polysynthesis” in Handbook of Polysynthesis, M. Fortescue , M. Mithun , N. Evans , Eds. (Oxford University Press, Oxford, 2017), pp. 363–391. · DOI
- P. Bakker , “Algonquian-Ritwan (Kutenai) and Salish: Proving a distant genetic relationship” in Papers for the 41st International Conference on Salish and neighbouring languages (University of British Columbia Press, Vancouver, 2006), pp. 1–32.
- 2000, Grammatical convergence and the genesis of diversity in the Northwest Coast Sprachbund, Anthropol. Linguistics, 42, 1
- 1929, in Encyclopedia Britannica (A &, 5, 128
Cited by
Sorted by citations
Beringia and the peopling of the Western Hemisphere
Hoffecker, J. F., Elias, S. A., Scott, G. R., O'Rourke, D. H., Hlusko, L. J., Potapova, O., Pitulko, V., Pavlova, E., Bourgeon, L., & Vachula, R. S. (2023) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2022.2246 · Cited by 17
Metadata
- Authors
- Ning, C., Fernandes, D., Changmai, P., Flegontova, O., Yüncü, E., Maier, R., Altınışık, N. E., Kassian, A. S., Krause, J., Lalueza-Fox, C., Manica, A., Potter, B. A., Robbeets, M., Sirak, K., Siska, V., Vajda, E. J., Vyazov, L. A., Wang, K., Wang, L., Wu, X., Xiao, X., Zhang, F., Reich, D., Schiffels, S., Pinhasi, R., Cui, Y., & Flegontov, P.
- Publisher
- openRxiv
- Published
- 2020-10-12
- Cited by
- 19
- References
- 25
- Type
- Preprint
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review