Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia.
Archaeology, linguistics, and increasingly genetics are clarifying how populations moved from mainland Asia, through Island Southeast Asia, and out into the Pacific during the farming revolution. Yet key features of this process remain poorly understood, particularly how social behaviors intersected with demographic drivers to create the patterns of genomic diversity observed across Island Southeast Asia today. Such questions are ripe for computer modeling. Here, we construct an agent-based model to simulate human mobility across Island Southeast Asia from the Neolithic period to the present, with a special focus on interactions between individuals with Asian, Papuan, and mixed Asian-Papuan ancestry. Incorporating key features of the region, including its complex geography (islands and sea), demographic drivers (fecundity and migration), and social behaviors (marriage preferences), the model simultaneously tracks a full suite of genomic markers (autosomes, X chromosome, mitochondrial DNA, and Y chromosome). Using Bayesian inference, model parameters were determined that produce simulations that closely resemble the admixture profiles of 2299 individuals from 84 populations across Island Southeast Asia. The results highlight that greater propensity to migrate and elevated birth rates are related drivers behind the expansion of individuals with Asian ancestry relative to individuals with Papuan ancestry, that offspring preferentially resulted from marriages between Asian women and Papuan men, and that in contrast to current thinking, individuals with Asian ancestry were likely distributed across large parts of western Island Southeast Asia before the Neolithic expansion.
Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.
François
F
Vallée
Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand.
Aurélien
A
Luciani
Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand m.p.cox@massey.ac.nz.
Murray P
http://orcid.org/0000-0003-1936-0236
MP
Cox
D005260:Female; D006801:Humans; D008297:Male; D019143:Evolution, Molecular; D014644:Genetic Variation; D015894:Genome, Human; D063426:Human Migration; D062312:Islands; D008393:Marriage; D010219:Papua New Guinea; D010375:Pedigree; D012919:Social Behavior; D000095188:Pacific Island People / Q000235:genetics
Asian; Island Southeast Asia; Neolithic; Papuan; demographic expansion
Science. 2009 Jun 5;324(5932):1298-301
19498164
Trends Ecol Evol. 2008 Jul;23(7):347-51
18502536
Genetics. 2015 Jun;200(2):469-81
25852078
Genetics. 2011 Dec;189(4):1413-26
21968194
PLoS Genet. 2005 Oct;1(4):e54
16254603
Am J Phys Anthropol. 1976 Nov;45(3 pt. 2):641-9
998759
Trends Ecol Evol. 2010 Jul;25(7):410-8
20488578
Genetics. 2002 Dec;162(4):2025-35
12524368
Nat Commun. 2014 Aug 19;5:4689
25137359
BMC Bioinformatics. 2014 Jun 09;15:175
24913447
Science. 2009 Jan 23;323(5913):479-83
19164742
Mol Biol Evol. 2013 Apr;30(4):918-37
23300254
Genome Res. 2015 Apr;25(4):459-66
25770088
Nature. 2004 Sep 30;431(7008):562-6
15457259
Nat Commun. 2013;4:2486
24084891
Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11645-50
18703660
Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):8982-6
26150499
Genet Res (Camb). 2012 Jun;94(3):121-31
22647505
Bioinformatics. 2010 Dec 1;26(23):2993-4
20956243
Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):33-7
19104042
Mol Biol Evol. 2015 Sep;32(9):2254-62
25968961
Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4574-9
22396590
Sci Am. 2005 Jul;293(1):76-82, 84
16008305
Am J Hum Genet. 2006 Aug;79(2):230-7
16826514
J Hum Genet. 2013 Mar;58(3):165-73
23344321
BMC Genet. 2011 Nov 18;12:100
22098696
Am J Phys Anthropol. 2005 Oct;128(2):415-23
15795887
Hum Biol. 2013 Feb-Jun;85(1-3):135-52
24297223
Genome Res. 2009 Sep;19(9):1655-64
19648217
Proc Biol Sci. 2009 Jun 7;276(1664):1957-64
19324748
Proc Biol Sci. 2010 May 22;277(1687):1589-96
20106848
J Hum Genet. 2014 Sep;59(9):494-503
25078354
Nature. 2003 Dec 18;426(6968):789-96
14685227
Mol Biol Evol. 2010 Aug;27(8):1833-44
20207712
Nature. 2001 Feb 15;409(6822):860-921
11237011