Ancient genomes from the last three millennia support multiple human dispersals into Wallacea

Abstract

Previous research indicates that human genetic diversity in Wallacea—islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves—has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter–gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region’s demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600–250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.

Chronology of natural selection in Oceanian genomes

“…Several absolute dating methodologies were recently developed ( Albers and McVean, 2020 ; Speidel et al., 2019 ; Wohns et al., 2022 ), all limited by data quality (e.g., sequencing, variant calling, phasing) and by the difficulty to integrate demographic processes such as admixture events (e.g., archaic hominin introgression). Future ancient DNA data will be important to calibrate absolute genetic dating approaches ( Wohns et al., 2022 ), but it still represents a major technical challenge in tropical areas such as in most of Oceania ( Carlhoff et al., 2021 ; Oliveira et al., 2021 ). Our relative dating approach is limited by demographic movements between Wallacea and New Guinea, following the initial settlement of Sahul, which we previously described ( Brucato et al., 2021 ; Purnomo et al., 2021 ).…”

“…Our relative dating approach is limited by demographic movements between Wallacea and New Guinea, following the initial settlement of Sahul, which we previously described ( Brucato et al., 2021 ; Purnomo et al., 2021 ). Population migrations out of New Guinea led to extensive gene flows, especially in Wallacea ( Oliveira et al., 2021 ), which could influence our results, because we assigned our Wallacean data as the ancestral group. To mitigate these limitations, we focused on signals of selection present in both New Guinean and Bismarck Islander groups, less likely to be strongly biased by these secondary migratory waves in Wallacea.…”

“…Since human genetic diversity west of the Wallace line is largely dominated by Asian ancestry ( Hudjashov et al., 2017 ; Lipson et al., 2014 ), the Wallacean population on Flores Island is the best proxy in our dataset of modern genomes for a genetic signature prior to the initial settlement of north Sahul. Previous reports showed that secondary gene flows from New Guinea to Wallacea occurred during the last 20,000 years ( Brucato et al., 2021 ; Carlhoff et al., 2021 ; Oliveira et al., 2021 ; Purnomo et al., 2021 ) but they do not affect the ability to detect signals related to earlier phases of human history ( Brucato et al., 2021 ; Jacobs et al., 2019 ). Results of these selection scans were normalized with the norm function of Selscan v.1.3.0 ( Szpiech and Hernandez, 2014 ).…”

Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects

“…A more recent study of 16 paleogenomes from multiple sites in Sulawesi, Moluccas, and Lesser Sundas, which range from several hundred to ~2300 years old, also found no evidence for genetic continuity between these 16 individuals and the Leang Panninge specimen [ 54 ], indicating that this genetic discontinuity was present within 1000 years of the initial Austronesian contact. All ancient individuals also had substantial Austronesian- and Papuan-related ancestries, and most also carried a distinct MSEA-related component, with ancient Moluccans being the exception.…”

Tara bandu: On the hybridization of a sign

“…3500 years ago and the influx of Austronesian settlers into the Wallacean archipelago (O'Connor et al, 2017). Yet, quite recent research focused in Wallacea, points out that ancestry in the southern islands also reveals contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians, suggesting that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries (Oliveira et al, 2022).…”