Evidence for Post-Settlement Contact and Adaptation within the Pacific Using Ancient Microbes

Bastien Llamas1*, Laura S. Weyrich2, Sterling Wright2, Christine K. Ta2, Nicole Moore2, Raphael Eisenhofer3, Atholl Anderson4, Greg Nelson5, Jessica Stone5, Scott M. Fitzpatrick5, Sunny O. Ngirmang6, Calvin Emesiochel6, Keith Dobney7, Sebastian Duchene8, Ashleigh Porter8, Eric Conte8, and Guillaume Molle8

Human migration into the Pacific represents one of the most rapid and far-reaching dispersals in human history. Although archaeological and genomic research has clarified many aspects of these movements, less is known about how people biologically adapted to the diverse environments encountered across Pacific archipelagos. Ancient microbial DNA preserved in dental calculus provides an opportunity to investigate both human mobility and biological adaptation through time. Here we analyse ancient oral microbiomes from 77 individuals from Palau (3000-2000 BP), French Polynesia (700-100 BP), and Aotearoa New Zealand, and compare them with previously published datasets from ancient Japan and Great Britain. After authentication and contamination filtering, 68 individuals yielded well-preserved oral microbiomes suitable for analysis. Ancient Pacific oral microbiomes were predominantly characterised by Methanobrevibacter-associated anaerobic communities that are now rare in industrialised populations, and their core taxa differed from those observed in contemporaneous Europeans. Phylogenomic analysis of Anaerolineaceae bacterium oral taxon 439 recapitulates known human migration patterns into the Pacific and reveals mixed microbial clusters across Eastern Polynesian archipelagos, consistent with continued interactions following initial settlement. Oral microbiome composition also differed significantly between archipelagos and island ecotypes, indicating that local environmental conditions shaped microbial communities. In particular, individuals from atoll environments show increased abundance of taxa associated with periodontal disease, including Filifactor alocis, suggesting that ecological adaptation may have influenced long-term oral health. These findings demonstrate that ancient oral microbiomes can reveal both patterns of human mobility and biological responses to new environments during the settlement of the Pacific.