title: Inferring the Dynamics of Effective Population Size Using Autosomal Genomes.
abstract: Next-generation sequencing technology has provided a great opportunity for inferring human demographic history by investigating changes in the effective population size (Ne). In this report, we introduce a strategy for estimating Ne dynamics, allowing the exploration of large multi-locus SNP datasets. We applied this strategy to the Phase 1 Han Chinese samples from the 1000 Genomes Project. The Han Chinese population has undergone a continuous expansion since 25,000 years ago, at first slowly from about 7,300 to 9,800 (at the end of the last glacial maximum about 15,000 YBP), then more quickly to about 46,000 (at the beginning of the Neolithic about 8,000 YBP), and then even more quickly to reach a population size of about 140,000 (recently).
authors.affiliation: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Hou
authors.affiliation: State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), and Department of Physics, Fudan University, Shanghai, China.
authors.forename: Yin
authors.initials: Y
authors.lastname: Luo
authors.affiliation: School of Information Science and Technology, SunYat-sen University, Guangzhou, China.
authors.forename: Zhisheng
authors.initials: Z
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Hong-Xiang
authors.initials: HX
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Wang
authors.affiliation: CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Hang
authors.initials: H
authors.lastname: Zhou
authors.affiliation: Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA.
authors.forename: Leqin
authors.initials: L
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.|CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Li
authors.initials: L
authors.lastname: Jin
mesh_terms: D002681:China; D030561:Databases, Nucleic Acid; D005260:Female; D015894:Genome, Human; D006801:Humans; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011157:Population Dynamics
references.citation: Genetics. 2000 Sep;156(1):297-304
references.pmid: 10978293
references.citation: Science. 2002 Jun 21;296(5576):2225-9
references.pmid: 12029063
references.citation: Genetics. 2002 Jul;161(3):1209-18
references.pmid: 12136023
references.citation: Genetics. 2002 Jul;161(3):1307-20
references.pmid: 12136032
references.citation: Annu Rev Genet. 2002;36:721-50
references.pmid: 12359738
references.citation: Am J Hum Genet. 2002 Nov;71(5):1227-34
references.pmid: 12384857
references.citation: Bioinformatics. 2005 Jan 15;21(2):263-5
references.pmid: 15297300
references.citation: Mol Biol Evol. 2005 May;22(5):1185-92
references.pmid: 15703244
references.citation: Genetics. 2006 Apr;172(4):2431-9
references.pmid: 16489223
references.citation: Philos Trans R Soc Lond B Biol Sci. 2007 Jun 29;362(1482):987-95
references.pmid: 17317646
references.citation: Mol Biol Evol. 2008 Feb;25(2):468-74
references.pmid: 18093996
references.citation: Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5523-8
references.pmid: 19307567
references.citation: PLoS Genet. 2009 Oct;5(10):e1000695
references.pmid: 19851460
references.citation: Mol Biol Evol. 2010 Mar;27(3):570-80
references.pmid: 19906793
references.citation: Am J Hum Genet. 2009 Dec;85(6):762-74
references.pmid: 19944404
references.citation: Science. 2010 Feb 12;327(5967):883-6
references.pmid: 20056855
references.citation: Mol Ecol Resour. 2011 May;11(3):423-34
references.pmid: 21481200
references.citation: Nature. 2011 Jul 13;475(7357):493-6
references.pmid: 21753753
references.citation: Nat Genet. 2011 Sep 18;43(10):1031-4
references.pmid: 21926973
references.citation: PLoS One. 2011;6(10):e25835
references.pmid: 21998705
references.citation: Mol Biol Evol. 2012 Aug;29(8):1969-73
references.pmid: 22367748
references.citation: Nat Rev Genet. 2012 Oct;13(10):745-53
references.pmid: 22965354
references.citation: Nature. 2012 Nov 1;491(7422):56-65
references.pmid: 23128226
references.citation: Cell. 2013 Feb 14;152(4):703-13
references.pmid: 23415221
references.citation: Mol Biol Evol. 2013 Dec;30(12):2629-44
references.pmid: 24063884
references.citation: PLoS Genet. 2013 Oct;9(10):e1003905
references.pmid: 24204310
references.citation: PLoS One. 2014 Aug 29;9(8):e105691
references.pmid: 25170956
references.citation: Evolution. 1984 Nov;38(6):1358-1370
references.pmid: 28563791
references.citation: Proc Natl Acad Sci U S A. 1998 Sep 29;95(20):11763-8
references.pmid: 9751739