Leveraging known Pacific colonisation times to test models for the ancestry of Southeast Asians

The most widely accepted model for the colonization of Remote Oceania by Austronesian-speaking bearers of the Lapita complex ~ 3 ka (3000 years ago) links it to a broader Neolithic expansion from China, via Taiwan, ~ 4.5–6 ka. However, analyses of mitochondrial DNA haplogroup B4a1a1a, prevalent among Remote Oceanians today, have both supported and challenged this scenario. Here, we analyze 1364 B4a1a1 mitogenomes (234 novel) from 68 islands and compare age estimates with radiocarbon dates for colonization. We estimate the settlement of Remote Oceania ~ 3.2 [2.7; 3.75] ka, matching radiocarbon ages, and then extrapolate the age in Near Oceania. B4a1a1a arose around the northern coasts of New Guinea at least 6 ka, following Early Holocene dispersals from Asia. Technological advances (e.g., in sailing), fueled by interaction networks alongside the arrival of Late Holocene migrants from Taiwan or ISEA and putative environmental changes, likely triggered the expansion of Lapita colonists carrying B4a1a1a from New Guinea into Remote Oceania.