Detecting archaic introgression using an unadmixed outgroup

PLoS Genetics

Volumn 14, Issue 9, 2018, Pages

  Skov, Laurits ^a   Hui, Ruoyun ^b   Shchur, Vladimir ^c   Hobolth, Asger ^a   Scally, Aylwyn ^b   Schierup, Mikkel Heide ^a   Durbin, Richard ^b,c  

^a AARHUS UNIVERSITY   (Denmark)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EAST ASIAN; GENOME; HIDDEN MARKOV MODEL; HUMAN; INTROGRESSION; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH ASIAN; ANIMAL; ASIAN CONTINENTAL ANCESTRY GROUP; BLACK PERSON; CAUCASIAN; FOSSIL; GENETICS; HOMINID; HOMO NEANDERTHALENSIS; HUMAN GENOME; HYBRIDIZATION; OCEANIC ANCESTRY GROUP; PHYLOGENY;

AFRICAN CONTINENTAL ANCESTRY GROUP; ANIMALS; ASIAN CONTINENTAL ANCESTRY GROUP; EUROPEAN CONTINENTAL ANCESTRY GROUP; FOSSILS; GENOME, HUMAN; HOMINIDAE; HUMANS; HYBRIDIZATION, GENETIC; NEANDERTHALS; OCEANIC ANCESTRY GROUP; PHYLOGENY;

EID: 85054592756     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1007641     Document Type: Article

References (29)

1. Prufer K, Racimo F, Patterson N, Jay F, Sankararaman S, et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature505: 43–49. doi: 10.1038/nature12886 pmid: 24352235
2. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, et al. (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science338: 222–226. doi: 10.1126/science.1224344 pmid: 22936568
3. Huerta-Sanchez E, Jin X, Asan Bianba Z, Peter BM, et al. (2014) Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature512: 194–197. doi: 10.1038/nature13408 pmid: 25043035
4. Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, et al. (2017) Archaic Adaptive Introgression in TBX15/WARS2. Mol Biol Evol34: 509–524. doi: 10.1093/molbev/msw283 pmid: 28007980
5. Dannemann M, Prufer K, Kelso J, (2017) Functional implications of Neandertal introgression in modern humans. Genome Biol18: 61. doi: 10.1186/s13059-017-1181-7 pmid: 28366169
6. Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A, et al. (2014) Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years. Science346: 1113–1118. doi: 10.1126/science.aaa0114 pmid: 25378462
7. Sankararaman S, Mallick S, Patterson N, Reich D, (2016) The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans. Curr Biol26: 1241–1247. doi: 10.1016/j.cub.2016.03.037 pmid: 27032491
8. Plagnol V, Wall JD, (2006) Possible ancestral structure in human populations. PLoS Genet2: e105. doi: 10.1371/journal.pgen.0020105 pmid: 16895447
9. Vernot B, Tucci S, Kelso J, Schraiber JG, Wolf AB, et al. (2016) Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals. Science352: 235–239. doi: 10.1126/science.aad9416 pmid: 26989198
10. Prufer K, de Filippo C, Grote S, Mafessoni F, Korlevic P, et al. (2017) A high-coverage Neandertal genome from Vindija Cave in Croatia. Science.
11. Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, et al. (2016) Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies. Genome Res26: 291–300. doi: 10.1101/gr.196634.115 pmid: 26888264
12. Mondal M, Casals F, Xu T, Dall'Olio GM, Pybus M, et al. (2016) Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat Genet48: 1066–1070. doi: 10.1038/ng.3621 pmid: 27455350
13. Browning SR, Browning BL, Zhou Y, Tucci S, Akey JM, (2018) Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture. Cell173: 53–61 e59. doi: 10.1016/j.cell.2018.02.031 pmid: 29551270
14. Durvasula A, Sankararaman S, (2018) Recovering signals of ghost archaic admixture in the genomes of present-day Africans. bioRxiv.
15. Smit AFA, Hubley R, Green P (2013) RepeatMasker Open 4.0. RepeatMasker Open 40.
16. International HapMap C, Frazer KA, Ballinger DG, Cox DR, Hinds DA, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature449: 851–861. doi: 10.1038/nature06258 pmid: 17943122
17. Vernot B, Akey JM, (2014) Resurrecting surviving Neandertal lineages from modern human genomes. Science343: 1017–1021. doi: 10.1126/science.1245938 pmid: 24476670
18. Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, et al. (2016) The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature538: 201–206. doi: 10.1038/nature18964 pmid: 27654912
19. Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, et al. (2016) A genomic history of Aboriginal Australia. Nature538: 207–214. doi: 10.1038/nature18299 pmid: 27654914
20. Skoglund P, Jakobsson M, (2011) Archaic human ancestry in East Asia. Proc Natl Acad Sci U S A108: 18301–18306. doi: 10.1073/pnas.1108181108 pmid: 22042846
21. Qin P, Stoneking M, (2015) Denisovan Ancestry in East Eurasian and Native American Populations. Mol Biol Evol32: 2665–2674. doi: 10.1093/molbev/msv141 pmid: 26104010
22. Fu Q, Li H, Moorjani P, Jay F, Slepchenko SM, et al. (2014) Genome sequence of a 45,000-year-old modern human from western Siberia. Nature514: 445–449. doi: 10.1038/nature13810 pmid: 25341783
23. de Manuel M, Kuhlwilm M, Frandsen P, Sousa VC, Desai T, et al. (2016) Chimpanzee genomic diversity reveals ancient admixture with bonobos. Science354: 477–481. doi: 10.1126/science.aag2602 pmid: 27789843
24. Liu SP, Lorenzen ED, Fumagalli M, Li B, Harris K, et al. (2014) Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears. Cell157: 785–794. doi: 10.1016/j.cell.2014.03.054 pmid: 24813606
25. Palkopoulou E, Lipson M, Mallick S, Nielsen S, Rohland N, et al. (2018) A comprehensive genomic history of extinct and living elephants. Proc Natl Acad Sci U S A115: E2566–E2574. doi: 10.1073/pnas.1720554115 pmid: 29483247
26. Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, et al. (2014) Gibbon genome and the fast karyotype evolution of small apes. Nature513: 195–201. doi: 10.1038/nature13679 pmid: 25209798
27. Kelleher J, Etheridge AM, McVean G, (2016) Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes. PLoS Comput Biol12: e1004842. doi: 10.1371/journal.pcbi.1004842 pmid: 27145223
28. Smith TCA, Arndt PF, Eyre-Walker A, (2018) Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans. PLoS Genet14: e1007254. doi: 10.1371/journal.pgen.1007254 pmid: 29590096
29. Genomes Project C, Auton A, Brooks LD, Durbin RM, Garrison EP, et al. (2015) A global reference for human genetic variation. Nature526: 68–74. doi: 10.1038/nature15393 pmid: 26432245