abstract: "Genetic studies have revealed a cline between Asian and Papuan genetic\
  \ ancestry across Island Southeast Asia, with most change occurring abruptly in\
  \ eastern Indonesia. Evidence suggests that this pattern is the joint outcome of\
  \ geographic, demographic and social features. This agent-based model simulates\
  \ social behavior, technological advantages and demography within an explicit geographical\
  \ framework to determine how these factors influenced prehistoric human movements,\
  \ and hence, modern patterns of genetic diversity.\r\n\r\nIn brief, a network of\
  \ populations is laid across Southeast Asia, with connections only allowed within\
  \ a defined radius.  All humans within a population are initially assigned to one\
  \ of two ancestries: Asian or Papuan. The model allows different Asian starting\
  \ distributions, ranging from Asian groups being restricted to mainland Asia, or\
  \ instead distributed across parts of western Island Southeast Asia (such as Taiwan,\
  \ Sumatra and Borneo). The remaining populations are initiated as Papuan. Individuals\
  \ then migrate and mix during a simulated Neolithic farming expansion, beginning\
  \ 4500 years ago. Agents can be unmarried (allowing them to migrate and/or marry),\
  \ and once married, family agents can have children, but can no longer move.\r\n\
  \r\nSix parameters are explored: the fecundity of Asian agents, the fecundity of\
  \ Papuan agents, the migration probability of Asian agents, the migration probability\
  \ of Papuan agents, preferential marriage between Asian women and Papuan men, and\
  \ the initial distribution of Asian populations. The patterns of Asian-Papuan mixture\
  \ created by these processes are compared with those found in  real genomic data\
  \ using standard statistical inference methods.\r\n\r\nVall\xE9e, F., A. Luciani\
  \ and M.P. Cox. 2016. [Reconstructing demography and social behavior during the\
  \ Neolithic expansion from genomic diversity across Island Southeast Asia](http://doi.org/10.1534/genetics.116.191379).\
  \ *Genetics* 204:1495\u20131506."
authors:
- family-names: "Vall\xE9e"
  given-names: "Fran\xE7ois"
- affiliation: Massey University
  email: murray.p.cox@gmail.com
  family-names: Cox
  given-names: Murray
cff-version: 1.2.0
date-released: '2016-12-09'
identifiers:
- type: url
  value: https://www.comses.net/codebases/5014/releases/1.0.0/
keywords:
- asian
- demographic expansion
- island southeast asia
- neolithic
- papuan
- population genetics
license: GPL-3.0
message: If you use this software, please cite it using the metadata from this file.
title: Modeling Asian-Papuan Admixture during the Neolithic Expansion across Island
  Southeast Asia
type: software
url: https://www.comses.net/codebases/5014/releases/1.0.0/
version: 1.0.0
