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.
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