Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise

ARTICLE https://doi.org/10.1038/s42003-023-04510-0 OPEN Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise 1234567890():,; Hie Lim Kim 1,2,3 ✉, Tanghua Li 4, Namrata Kalsi2,3, Hung Tran The Nguyen1,3, Timothy A. Shaw Khai C. Ang3,5,6, Keith C. Cheng3,5,6, Aakrosh Ratan 3,7, W. Richard Peltier8, Dhrubajyoti Samanta Mahesh Pratapneni3,9, Stephan C. Schuster 2,3,10 & Benjamin P. Horton 1,4 4, 4, Rapid sea-level rise between the Last Glacial Maximum (LGM) and the mid-Holocene transformed the Southeast Asian coastal landscape, but the impact on human demography remains unclear. Here, we create a paleogeographic map, focusing on sea-level changes during the period spanning the LGM to the present-day and infer the human population history in Southeast and South Asia using 763 high-coverage whole-genome sequencing datasets from 59 ethnic groups. We show that sea-level rise, in particular meltwater pulses 1 A (MWP1A, ~14,500–14,000 years ago) and 1B (MWP1B, ~11,500–11,000 years ago), reduced land area by over 50% since the LGM, resulting in segregation of local human populations. Following periods of rapid sea-level rises, population pressure drove the migration of Malaysian Negritos into South Asia. Integrated paleogeographic and population genomic analysis demonstrates the earliest documented instance of forced human migration driven by sea-level rise. 1 Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, N2-01c-63, 639798 Singapore, Singapore. 2 Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01n-27, 637551 Singapore, Singapore. 3 GenomeAsia 100K Consortium, 8 Eu Tong Sen Street #14-94, 059818 Singapore, Singapore. 4 Earth Observatory of Singapore, Nanyang Technological University, 50 Nanyang Avenue, N2-01a-15, 639798 Singapore, Singapore. 5 The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA. 6 Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA. 7 Center for Public Health Genomics, University of Virginia, 1335 Lee Street, West Complex 3rd Floor, MSB 3235, Charlottesville, VA 22903, USA. 8 Department of Physics, University of Toronto, 60 St George Street, Toronto, Ontario M5S 1A7, Canada. 9 Emerge Ventures Pte. Ltd., 8 Eu Tong Sen Street #14-94, 059818 Singapore, Singapore. 10 School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore, Singapore. ✉email: COMMUNICATIONS BIOLOGY | (2023)6:150 | https://doi.org/10.1038/s42003-023-04510-0 | www.nature.com/commsbio 1 ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-023-04510-0 T he transition from the Last Glacial Maximum (LGM; ~26,000–21,000 years ago) to the mid-Holocene (~6000 years ago) was the last major period of global warming in Earth’s history. During this period, the Global Mean Sea Level (GMSL) rose ~135 m1–3. This rise in GMSL was characterised by rapid increases over short (decadal and centennial) timescales, termed meltwater pulses (MWPs)4, superimposed on a longerterm secular rise1,2,5,6. Both short and long-term GMSL rise changed coastal landscapes, not only in northern and southern hemispheres but also in equatorial regions of Southeast Asia. The Sundaland continental shelf, which was exposed as a large landmass including the present-day Malay Peninsula, Sumatra, Borneo and the Philippines, for over 50,000 years before the transition from the LGM7–10, was impacted by flooding and submerging of large areas. Modern humans have inhabited the exposed Sundaland continental shelf since ~70,000–50,000 years ago11. The present-day descendants of these early inhabitants are the indigenous tribes of the Andaman Islands, Malay Peninsula, Thailand, and Philippines, referred to as Andamanese, Malaysian and Philippine Negritos, respectively12,13. Locally, these tribes are referred to as Orang Semang in Malaysia, whereas Aeta and Ati groups are part of indigenous groups living in the Philippines14–19. Archaeological data indicates that these indigenous tribes have continuously inhabited the Malay Peninsula20–22. Previous studies suggest that climate changes since the LGM have influenced populations living in the Sundaland by inferring population history mostly based on mitochondrial DNA23–25 or Y chromosome data26,27, and genotyping data28. However, only the level of resolution provided by whole-genome sequence datasets allows the study of the unbiased demographic history of indigenous populations inhabiting Sundaland before and during the postLGM sea-level rise. Here, we combine the reconstruction of 1) sea-level rise since the LGM to produce highly resolved spatial and temporal paleogeographic maps of Southeast and South Asia; and 2) the human demographic history inferred using high-depth, human whole-genome sequence datasets generated from an extensive set of ethnicities of Southeast and South Asia by the GenomeAsia 100 K consortium29. The natural history of the Sundaland region demonstrates the impact of rising sea levels on pre-historic, equatorial human populations. Southeast and South Asian regions are particularly suited for understanding the impact due to the long-standing modern human occupation. Importantly, Southeast Asia is the only region globally that experienced major reductions in the land area during the transition from the LGM, and at the same time, has continuously been occupied by today’s indigenous human populations. Hence, our high-resolution paleogeographic/population genomic study outlines the impact of paleoclimate changes on past and present human demography. Results Rapid sea-level rise in Southeast Asia. Using the ICE-6G_C global ice history model2,30 and HetM-LHL140 3D Earth model31,32 we infer the rate of sea-level rise in Southeast and South Asia at 500-year increments. The resulting paleotopographic maps cover a timespan of 26,000 years ago to the present (Fig. 1, Supplementary Movie). GMSL is shown to have risen from ~−122 m to −1 m between 22,000 years ago to 6000 years ago, which was punctuated by two periods of rapid sea-level rise (MWP1A and 1B, Fig. 1b). Between 22,000 and 16,000 years ago, the rate of GMSL rose ≤5 mm/year, subsequently accelerating to a maximum of ~46 mm/year between 14,500–14,000 years ago (MWP1A). GMSL continued to rise at a rate of ~10 mm/year for 3000 years before another rapid increase occurred with a rate of 2 ~22 mm/year between 11,500–11,000 years ago (MWP1B) at the beginning of the Holocene (Fig. 1b). According to our model, during the early Holocene, the rate of GMSL rise decreased from ~10 to ~3 mm/year. In Southeast and South Asia, the midHolocene is characterised by a highstand varying in timing and magnitude8. In Singapore, the highstand reached a magnitude of ~4 m 5200 years ago, relative (...truncated)