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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.

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