Admixture, population structure, and f-statistics

Genetics

Volumn 202, Issue 4, 2016, Pages 1485-1501

  Peter, Benjamin M ^a  

^a UNIVERSITY OF CHICAGO   (United States)

Author keywords

Admixture; Gene flow; Phylogenetic network; Phylogenetics; Population genetics

Indexed keywords

ARTICLE; F STATISTICS; GENE FREQUENCY; GENETIC DRIFT; GENETIC VARIATION; MATING; PHYLOGENETIC TREE; POPULATION SIZE; POPULATION STRUCTURE; PRIORITY JOURNAL; SIMULATION; STATISTICS; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE FLOW; HUMAN; PHYLOGENY; POPULATION GENETICS; STATISTICAL MODEL;

ALGORITHMS; COMPUTER SIMULATION; GENE FLOW; GENETIC DRIFT; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY;

EID: 84978827983     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.183913     Document Type: Article

References (46)

1. Allentoft, M. E., M. Sikora, K. -G. Sjögren, S. Rasmussen, M. Rasmussen et al., 2015 Population genomics of Bronze Age Eurasia. Nature 522: 167–172.
2. Bryant, D., and V. Moulton, 2004 Neighbor-Net: an agglomera-tive method for the construction of phylogenetic networks. Mol. Biol. Evol. 21: 255–265.
3. Buneman, P., 1971 The recovery of trees from measures of dissimilarity, Mathematics in the Archaeological and Historical Sciences.
4. Buneman, P., 1974 A note on the metric properties of trees. J. Comb. Theory Ser. B 17: 48–50.
5. Cavalli-Sforza, L. L. and A. W. F. Edwards, 1967 Phylogenetic analysis: models and estimation procedures. Evolution 21: 550–570.
6. Cavalli-Sforza, L. L., and A. Piazza, 1975 Analysis of evolution: evolutionary rates, independence and treeness. Theor. Popul. Biol. 8: 127–165.
7. Durand, E., N. Patterson, D. Reich, and M. Slatkin, 2011 Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28: 2239–2252.
8. Excoffier, L., P. E. Smouse, and J. M. Quattro, 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479–491.
9. Felsenstein, J., 1973 Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25: 471–492.
10. Felsenstein, J., 1981 Evolutionary trees from gene frequencies and quantitative characters: finding maximum likelihood estimates. Evolution 35: 1229–1242.
11. Felsenstein, J., 2004 Inferring Phylogenies. Sinauer Associates, Sunderland, MA.
12. Fitch, W. M., and E. Margoliash, 1967 Construction of phylogenetic trees. Science 155: 279–284.
13. Green, R., J. Krause, A. Briggs, T. Maricic, U. Stenzel et al., 2010 A draft sequence of the Neandertal genome. Science 328: 710– 722.
14. Haak, W., I. Lazaridis, N. Patterson, N. Rohland, S. Mallick et al., 2015 Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522: 207–211.
15. Hellenthal, G., G. B. J. Busby, G. Band, J. F. Wilson, C. Capelli et al., 2014 A genetic atlas of human admixture history. Science 343: 747–751.
16. Hudson, R. R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337–338.
17. Huson, D. H., and D. Bryant, 2006 Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23: 254–267.
18. Huson, D. H., R. Rupp, and C. Scornavacca, 2010 Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, Cambridge/London/New York.
19. Lazaridis, I., N. Patterson, A. Mittnik, G. Renaud, S. Mallick et al., 2014 Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513: 409–413.
20. Lipson, M., P.-R. Loh, A. Levin, D. Reich, N. Patterson et al., 2013 Efficient moment-based inference of admixture parameters and sources of gene flow. Mol. Biol. Evol. 30: 1788–1802.
21. McCullagh, P., 2009 Marginal likelihood for distance matrices. Stat. Sin. 19: 631.
22. Patterson, N. J., P. Moorjani, Y. Luo, S. Mallick, N. Rohland et al., 2012 Ancient admixture in human history. Genetics 192: 1065–1093.
23. Pease, J. B., and M. W. Hahn, 2015 Detection and polarization of introgression in a five-taxon phylogeny. Syst. Biol. 64: 651–662.
24. Peter, B. M., and M. Slatkin, 2015 The effective founder effect in a spatially expanding population. Evolution 69: 721–734.
25. Petkova, D., J. Novembre, and M. Stephens, 2014 Visualizing spatial population structure with estimated effective migration surfaces. Nat. Genet. 48: 94–100.
26. Pickrell, J. K., and J. K. Pritchard, 2012 Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8: e1002967.
27. Pickrell, J. K., and D. Reich, 2014 Toward a new history and geography of human genes informed by ancient DNA. Trends Genet. 30: 377–389.
28. Pritchard, J. K., M. Stephens, and P. Donnelly, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
29. Raghavan, M., P. Skoglund, K. E. Graf, M. Metspalu, A. Albrechtsen et al., 2014 Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature 505: 87–91.
30. Ralph, P., and G. Coop, 2013 The geography of recent genetic ancestry across Europe. PLoS Biol. 11: e1001555.
31. Reich, D., K. Thangaraj, N. Patterson, A. L. Price, and L. Singh, 2009 Reconstructing Indian population history. Nature 461: 489–494.
32. Reich, D., N. Patterson, D. Campbell, A. Tandon, S. Mazieres et al., 2012 Reconstructing Native American population history. Nature 488: 370–374.
33. Saitou, N., and M. Nei, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406–425.
34. Schraiber, J. G., and J. M. Akey, 2015 Methods and models for unravelling human evolutionary history. Nat. Rev. Genet. 16: 727–740.
35. Semple, C., and M. A. Steel, 2003 Phylogenetics. Oxford University Press, London/New York/Oxford.
36. Slatkin, M., 1991 Inbreeding coefficients and coalescence times. Genet. Res. 58: 167–175.
37. Slatkin, M., and L. Voelm, 1991 FST in a hierarchical island model. Genetics 127: 627–629.
38. Strobeck, C., 1987 Average number of nucleotide differences in a sample from a single subpopulation: a test for population subdivision. Genetics 117: 149–153.
39. Tajima, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437–460.
40. Tavaré, S., 1984 Line-of-descent and genealogical processes, and their applications in population genetics models. Theor. Popul. Biol. 26: 119–164.
41. Wahlund, S., 1928 Zusammensetzung von populationen und kor-relationserscheinungen vom standpunkt der vererbungslehre aus betrachtet. Hereditas 11: 65–106.
42. Wakeley, J., 2009 Coalescent Theory: An Introduction. Roberts & Co. Greenwood Village, CO.
43. Weir, B. S., and C. C. Cockerham, 1984 Estimating F-statistics for the analysis of population structure. Evolution 38: 1358–1370.
44. Wright, S., 1921 Systems of mating. Genetics 6: 111–178.
45. Wright, S., 1931 Evolution in Mendelian populations. Genetics 16: 97–159.
46. Yunusbayev, B., M. Metspalu, E. Metspalu, A. Valeev, S. Litvinov et al., 2015 The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia. PLoS Genet. 11: e1005068.