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

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.

Kinship structures create persistent channels for language transmission

“…However, we also saw genetic evidence of ongoing contact between social communities that practice exogamous matrilocal or patrilocal marriage (as in ref. 21 ). In the past, contact between social communities like these would often have been synonymous with contact between speech communities.…”

Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales

“…Sex-biased migration rates were retrieved from previous model fitting on similar data, and coupled with the observed number and sizes of villages [38]. We note that the founder simulation runs for around 60 generations before terminating, which corresponds well with genetic estimates of Austronesian influx into the region and subsequent establishment [2,32]. Both the founder model and dominance effect parameters were chosen such that parameter values are consistent with observations reported in the anthropological literature.…”

“…Despite these advances, discussion of social processes impacting genetic diversity commonly focuses on the proximate genetic cause—sex-biased migration—with little emphasis on the sociocultural processes ultimately driving this behaviour. A growing body of the literature shows that sociocultural actions, extending beyond sex-biased migration to the formation of patrilineal kin groups and competition among individuals for status, can create differential patterns of sex-linked diversity at global [29,30] and regional scales [31,32]. What is less clear is how these patterns arise at very small geographical scales, and how the details of local social behaviour cascade up to more easily observed global genetic patterns.…”

Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles

“…This sex bias holds across Polynesia and is observed as far back as Island Southeast Asia 49 , and may have resulted from the practice of exogamy and matrilocal post-marital residence among early Austronesian speaking groups 50 . A sex bias is also reflected in the nuclear genomes of Austronesian speakers and appears to be a characteristic of the Pacific region as a whole 25 , 51 .…”