Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia.

François Vallée,Aurélien Luciani,Murray P Cox

doi:10.1534/genetics.116.191379

Abstract

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.

Highlights

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
Key questions include (i) whether incoming individuals with Asian ancestry had greater fecundity and/or propensity to migrate than local individuals with Papuan ancestry; (ii) whether a widely proposed bias favoring marriages between Asian women and Papuan men is required to explain increased rates of Asian variants on the X chromosome relative to the autosomes (Hage and Marck 2003; Cox et al 2010); and (iii) how far individuals with Asian ancestry had encroached into western Island Southeast Asia prior to the Neolithic expansion (Spriggs 2012; Lipson et al 2014)
We describe a new computer model that can be used to explore human movements and interactions in Island Southeast Asia from the Neolithic to the present

Summary

Introduction

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. Our choice of model framework reflects the complexity of regional history, including a challenging geography (a complex arrangement of islands and sea), migration at variable scales (both short and long distance mobility), and the action of social behaviors (such as sex-biased Asian– Papuan marriage preferences), all while requiring patterns of genetic diversity to be tracked simultaneously across a full gamut of marker types [autosomes, X chromosome, mitochondrial DNA (mtDNA), and Y chromosome] This model is not intended as an end in itself, but is instead integrated with Bayesian statistical inference to explicitly estimate demographic and social parameters that may have led to the Asian ancestry proportions observed in nuclear genetic markers across Island Southeast Asia today (Cox et al 2010; Wilder, et al 2011; Tumonggor, et al 2014). Key questions include (i) whether incoming individuals with Asian ancestry had greater fecundity and/or propensity to migrate than local individuals with Papuan ancestry (perhaps due to improved farming and maritime technologies); (ii) whether a widely proposed bias favoring marriages between Asian women and Papuan men is required to explain increased rates of Asian variants on the X chromosome relative to the autosomes (Hage and Marck 2003; Cox et al 2010); and (iii) how far individuals with Asian ancestry had encroached into western Island Southeast Asia prior to the Neolithic expansion (Spriggs 2012; Lipson et al 2014)

Methods

Results

Discussion

Conclusion