The transition from the Last Glacial Maximum (LGM, ~26,000–21,000 years ago) to the mid-Holocene (~6000 years ago) involved a significant global mean sea level (GMSL) rise of ~135 m. This rise, punctuated by rapid increases termed meltwater pulses (MWPs), dramatically altered coastal landscapes, particularly in Southeast Asia's Sundaland continental shelf. Sundaland, encompassing present-day Malay Peninsula, Sumatra, Borneo, and the Philippines, was a vast landmass inhabited by modern humans since ~70,000–50,000 years ago. The descendants of these early inhabitants include the Andamanese, Malaysian, and Philippine Negritos. Archaeological data confirm continuous inhabitation of the Malay Peninsula, but the impact of post-LGM climate changes on these populations remains unclear, with previous studies relying on limited genetic data. This research addresses this gap by integrating high-resolution paleogeographic reconstruction of sea-level rise with comprehensive human demographic history inferred from high-depth whole-genome sequence data from the GenomeAsia 100K consortium. Southeast Asia, uniquely experiencing major land area reduction during this period while maintaining continuous human occupation, provides an ideal setting for this study. The high-resolution approach allows for a detailed investigation of the paleoclimate's impact on past and present human demography.

Previous research on the impact of climate change on Sundaland populations has primarily relied on mitochondrial DNA, Y chromosome data, genotyping data, offering limited resolution. Studies suggested climate changes influenced these populations, but the full extent of this influence, particularly the impact of sea-level rise on migration patterns, remained unclear. Existing paleogeographic maps lacked the temporal and spatial resolution needed to accurately assess the impact of specific meltwater pulses on human populations. This study improves upon previous research by utilizing high-coverage whole-genome sequencing data, allowing for a more comprehensive and unbiased assessment of population history and migration patterns. The integration of highly resolved paleogeographic maps further enhances the accuracy of the analysis, by directly linking specific sea-level changes to population dynamics.

This study employed a two-pronged approach: 1) reconstructing sea-level rise since the LGM to generate high-resolution paleogeographic maps of Southeast and South Asia and 2) inferring human demographic history using high-depth whole-genome sequence data from the GenomeAsia 100K Consortium. For the paleogeographic reconstruction, the ICE-6G_C global ice history model and the HetM-LHL140 3D Earth model were used to infer sea-level rise at 500-year increments from 26,000 years ago to the present. These models incorporated data from various far-field sites, including sediment cores from the Sundaland Shelf and Singapore, to constrain GMSL change and accurately represent the timing and magnitude of MWPs 1A and 1B. Paleotopographic maps were generated every 500 years to assess land cover change. For the genomic analysis, 763 high-coverage whole-genome datasets from 59 ethnic groups native to Southeast and South Asia (with European populations as reference groups) were analyzed. Population structure and admixture were assessed using principal component analysis (PCA) and ADMIXTURE. Admixture history was reconstructed using Treemix and qpGraph. Multiple Sequentially Markovian Coalescent (MSMC) analysis was used to estimate effective population size changes over time, and MSMC-IM was used to estimate migration rates. The study incorporated analyses of X chromosomes and autosomes to detect potential gender biases in migration. By integrating paleogeographic and genomic data, this study provides a comprehensive analysis of how sea-level rise and land area reduction influenced prehistoric human migration.

The study found that meltwater pulses 1A and 1B caused significant land area reduction in Southeast Asia, particularly in Sundaland. The PCA and ADMIXTURE analyses revealed a substantial Malaysian Negrito ancestry in Mainland Southeast Asians and South Asian Austroasiatic groups. Five key findings support this observation: 1) South Asian Austroasiatic groups clustered closer to Malaysian Negritos in PCA than to other South Asian groups; 2) ADMIXTURE identified significant Malaysian Negrito ancestry in Mainland Southeast Asians and South Asian Austroasiatic groups; 3) qpGraph modeling showed that admixture between Dravidian and Malaysian Negrito groups best explained the South Asian Austroasiatic groups; 4) MSMC analysis indicated a dramatic increase in population size for South Asian Austroasiatic groups, suggesting gene flow from Malaysian Negritos; 5) MSMC-IM analysis estimated the timing of admixture between Malaysian Negritos and South Asian Austroasiatic groups at ~12,000–9,000 years ago. The analysis of X chromosome data indicated a male bias in this migration. Further analysis revealed multiple population splits in Southeast Asia coinciding with MWPs, indicating that the rising sea levels and subsequent land reduction were likely major drivers of the population structure and genetic diversity observed today. The study also estimated population size and density, finding that population density in Island Southeast Asia increased significantly after MWP1B, likely driving the migration of Malaysian Negritos to Mainland Southeast Asia and South Asia.

The findings demonstrate that sea-level rise during the LGM to mid-Holocene transition had a profound impact on prehistoric human populations in Southeast and South Asia. The significant Malaysian Negrito ancestry in South Asian Austroasiatic groups provides strong evidence of forced migration driven by population pressure caused by significant land loss. This migration represents the earliest documented case of large-scale human migration driven by sea-level rise, offering crucial insights into the adaptability and resilience of prehistoric human populations facing significant environmental challenges. The study's integration of paleogeographic and genomic data allows for a more nuanced understanding of the complex interplay between environmental change and human migration. The results challenge previous hypotheses regarding the origin of admixture in South Asian Austroasiatic groups and provide strong evidence for direct migration from Malaysian Negritos.

This study provides the first comprehensive evidence linking sea-level rise to large-scale human migration in prehistoric times. The findings show that meltwater pulses 1A and 1B caused significant land area loss in Sundaland, leading to population pressure and subsequent migration of Malaysian Negritos into South Asia. This interdisciplinary approach highlights the importance of considering environmental changes when investigating human demographic history. Future research could focus on expanding the genomic dataset to include more diverse populations and investigating the environmental and cultural factors that facilitated the successful adaptation and integration of migrating groups.

The study relies on the accuracy of the ICE-6G_C and HetM-LHL140 models for sea-level reconstruction, which involve inherent uncertainties. The selection of representative populations for MSMC analysis might not fully capture the diversity within each group. Additional research could focus on refining the models and expanding the dataset to increase the accuracy and robustness of the results. The interpretation of the genetic data depends on the assumptions of the various statistical methods used for analysis. Future research could test and compare the use of alternative models and methods to further validate the study's conclusions.