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Demographic inference using spectral methods on SNP data, with an analysis of the human out-of-Africa expansion.

Lukic S, Hey J.

Genetics. 2012 Oct;192(2):619-39. doi: 10.1534/genetics.112.141846. Epub 2012 Aug 3.


Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data.

Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD.

PLoS Genet. 2009 Oct;5(10):e1000695. doi: 10.1371/journal.pgen.1000695. Epub 2009 Oct 23.


Human population dispersal "Out of Africa" estimated from linkage disequilibrium and allele frequencies of SNPs.

McEvoy BP, Powell JE, Goddard ME, Visscher PM.

Genome Res. 2011 Jun;21(6):821-9. doi: 10.1101/gr.119636.110. Epub 2011 Apr 25.


Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation.

Jouganous J, Long W, Ragsdale AP, Gravel S.

Genetics. 2017 Jul;206(3):1549-1567. doi: 10.1534/genetics.117.200493. Epub 2017 May 11.


The effect of recent admixture on inference of ancient human population history.

Lohmueller KE, Bustamante CD, Clark AG.

Genetics. 2010 Jun;185(2):611-22. doi: 10.1534/genetics.109.113761. Epub 2010 Apr 9.


Demographic inference reveals African and European admixture in the North American Drosophila melanogaster population.

Duchen P, Zivkovic D, Hutter S, Stephan W, Laurent S.

Genetics. 2013 Jan;193(1):291-301. doi: 10.1534/genetics.112.145912. Epub 2012 Nov 12.


Accuracy of Demographic Inferences from the Site Frequency Spectrum: The Case of the Yoruba Population.

Lapierre M, Lambert A, Achaz G.

Genetics. 2017 May;206(1):439-449. doi: 10.1534/genetics.116.192708. Epub 2017 Mar 24.


Early back-to-Africa migration into the Horn of Africa.

Hodgson JA, Mulligan CJ, Al-Meeri A, Raaum RL.

PLoS Genet. 2014 Jun 12;10(6):e1004393. doi: 10.1371/journal.pgen.1004393. eCollection 2014 Jun.


The Effects of Migration and Assortative Mating on Admixture Linkage Disequilibrium.

Zaitlen N, Huntsman S, Hu D, Spear M, Eng C, Oh SS, White MJ, Mak A, Davis A, Meade K, Brigino-Buenaventura E, LeNoir MA, Bibbins-Domingo K, Burchard EG, Halperin E.

Genetics. 2017 Jan;205(1):375-383. doi: 10.1534/genetics.116.192138. Epub 2016 Nov 22.


Non-equilibrium allele frequency spectra via spectral methods.

Lukić S, Hey J, Chen K.

Theor Popul Biol. 2011 Jun;79(4):203-19. doi: 10.1016/j.tpb.2011.02.003. Epub 2011 Mar 2.


The effect of single nucleotide polymorphism identification strategies on estimates of linkage disequilibrium.

Akey JM, Zhang K, Xiong M, Jin L.

Mol Biol Evol. 2003 Feb;20(2):232-42.


Human genetic data reveal contrasting demographic patterns between sedentary and nomadic populations that predate the emergence of farming.

Aimé C, Laval G, Patin E, Verdu P, Ségurel L, Chaix R, Hegay T, Quintana-Murci L, Heyer E, Austerlitz F.

Mol Biol Evol. 2013 Dec;30(12):2629-44. doi: 10.1093/molbev/mst156. Epub 2013 Sep 24.


Robust demographic inference from genomic and SNP data.

Excoffier L, Dupanloup I, Huerta-Sánchez E, Sousa VC, Foll M.

PLoS Genet. 2013 Oct;9(10):e1003905. doi: 10.1371/journal.pgen.1003905. Epub 2013 Oct 24.


Ancient west Eurasian ancestry in southern and eastern Africa.

Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, Stoneking M, Pakendorf B, Reich D.

Proc Natl Acad Sci U S A. 2014 Feb 18;111(7):2632-7. doi: 10.1073/pnas.1313787111. Epub 2014 Feb 3.


Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.

Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF.

Genome Res. 2016 Mar;26(3):291-300. doi: 10.1101/gr.196634.115. Epub 2016 Feb 17. Erratum in: Genome Res. 2016 May;26(5):717.1.


The Great Migration and African-American Genomic Diversity.

Baharian S, Barakatt M, Gignoux CR, Shringarpure S, Errington J, Blot WJ, Bustamante CD, Kenny EE, Williams SM, Aldrich MC, Gravel S.

PLoS Genet. 2016 May 27;12(5):e1006059. doi: 10.1371/journal.pgen.1006059. eCollection 2016 May.


Lactase persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists.

Breton G, Schlebusch CM, Lombard M, Sjödin P, Soodyall H, Jakobsson M.

Curr Biol. 2014 Apr 14;24(8):852-8. doi: 10.1016/j.cub.2014.02.041. Epub 2014 Apr 3.


Linkage disequilibrium sharing and haplotype-tagged SNP portability between populations.

Huang W, He Y, Wang H, Wang Y, Liu Y, Wang Y, Chu X, Wang Y, Xu L, Shen Y, Xiong X, Li H, Wen B, Qian J, Yuan W, Zhang C, Wang Y, Jiang H, Zhao G, Chen Z, Jin L.

Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1418-21. Epub 2006 Jan 23.


Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels.

Frisse L, Hudson RR, Bartoszewicz A, Wall JD, Donfack J, Di Rienzo A.

Am J Hum Genet. 2001 Oct;69(4):831-43. Epub 2001 Aug 29.

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