Ancient Genomic Evidence for Multiple Migration Waves and Denisovan Admixture in Prehistoric Southeast Asian Island Populations, 3000-500 BP

This study investigates palaeogenomic evidence for migration wave timing, Austronesian expansion routes, and Denisovan introgression signals in prehistoric Southeast Asian island populations from ancient DNA within the context of palaeogenomics and prehistoric population genetics, an area of growing scientific importance given its implications for Austronesian expansion reconstruction, prehistoric Pacific population movement modeling, and Southeast Asian prehistory synthesis. Using shotgun and target-enrichment ancient DNA sequencing with ADMIXTURE, TreeMix, D-statistics, and qpAdm population structure and admixture analysis, we examine multiple Austronesian migration pulses from Taiwan displacing Papuan-related hunter-gatherer populations with variable admixture, retaining Denisovan introgression signatures in proportion to Papuan ancestry in 84 ancient individuals from 24 archaeological sites across Philippines, Sulawesi, Maluku, and Timor-Leste (4-38x coverage, mean 12.4x) drawn from 24 cave and midden archaeological sites across island Southeast Asia with skeletal remains dated 500-3000 BP by AMS radiocarbon. Results indicate that D-statistics confirm Denisovan introgression in 68.4% of individuals with >30% Papuan ancestry (mean D-stat 0.024), with a third pre-Austronesian migration wave identified by qpAdm in 12 Wallacean individuals dated 1800-2400 BP (p < 0.001), with Denisovan signal in 68.4% of high-Papuan-ancestry individuals; third migration wave in 12 Wallacean individuals as the primary quantitative benchmark. Concordance between primary and confirmatory measurement approaches exceeded 93%, validating the analytical framework. These findings contribute empirically to palaeogenomics and prehistoric population genetics and carry actionable implications for the design of programs and policies targeting Austronesian expansion reconstruction, prehistoric Pacific population movement modeling, and Southeast Asian prehistory synthesis.