Human genetic diversity of coastal Papua New Guinea over the past 2500 years

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Abstract: The inhabitants of New Guinea and its outlying islands have played a significant role in the human history of the Pacific region. Nevertheless, the genetic diversity, particularly of pre-colonial communities, is still understudied. We present the first ancient genomes (aDNA) of 42 individuals from Papua New Guinea (PNG). The aDNA results of individuals from Watom Island (Bismarck Archipelago), and the south and northeastern coasts of PNG are contextualized with new (bio-) archaeological data. The individuals’ AMS dates span 2500 years of human habitation and our results demonstrate the influences of different dispersal events on the genetic makeup of ancient PNG communities. The oldest individuals show an unadmixed Papuan-related genetic signature, while individuals dating from 2100 BP carry varying degrees of an East Asian-related contribution. These results and the inferred admixture dates suggest centuries-long delay in genetic mixture with local communities after the arrival of populations with Asian ancestry. Two geographically close communities on the South Coast, AMS dated to within the last 540 years, diverge in their genetic profiles, suggesting differences in their interaction spheres involving groups with distinct ancestries. The inferred split time of these communities around 650 BP coincides with intensified settlement activity and the emergence of regional trade networks. Ethical considerations for the analysis of the ancient genomes Today, Papua New Guinea’s communities are highly structured by a huge linguistic and cultural diversity. The patterns observed today likely have roots in the distant past, but are also influenced by dynamics rooted in colonial interactions and imperialistic efforts in the present day. The combination of a high abundance of natural resources and the increased interest of WEIRD (Western, Educated, Industrialized, Rich, Democratic) countries has led to political tensions between various groups, lamentably often culminating in violence (Forsyth, Kipong et al. 2024). In such a political climate, one must consider the potential impacts of certain results when linking the past to the present. This study uses ancient genomes to investigate the genetic diversity in the past, and discusses underlying dynamics by integrating other types of data such as isotopes and AMS-dating, and contextualizing with archaeological and linguistic evidence. The majority of individual genomes produced for this study is of high quality, allowing imputation of missing sites and fine scale analyses within and between groups with the potential to link the ancient individuals to present-day individuals who have donated their genomes to science. For this study, we have purposefully chosen to not attempt to directly link the ancient individuals to their potential descendants in the region today. While the data in this study adds significantly to our understanding of the past genetic diversity, only two sites with n=22 (Nebira) and n=8 (Eriama) individuals qualify for an analysis of direct links from the past to the present. The low number of individuals, and the small geographic area they cover will certainly not be representative of the past genetic diversity for the entire South Coast where the population history before and after colonial invasion is much more complex. Additionally, the linguistic data recorded for the present-day comparative datasets suggests that among the sampled present-day individuals, only Motu speakers donated samples. Additionally, the ethnographic records rely on the statements of the participants, which could be unprecise or even wrong. Linking the few ancient individuals directly to present day groups, i.e. through IBD analysis, could potentially lead to historical misinterpretations about land in a present day context. These factors were considered when discussing whether data should be made publicly available, as is the case in almost 100% of ancient DNA studies (Anagnostou, Capocasa et al. 2015), and expected from other researchers in the field (Alpaslan-Roodenberg, Anthony et al. 2021, Bergström 2023). We have decided to make the data publicly available, but purposefully not conducted an analysis potentially able to directly link the ancient and modern individuals from the region. These comparisons could be undertaken in future with a community-driven research project. We strongly recommend other researchers interested in such analyses to carefully consider the control they have over the dissemination and communication of the results, how they can be interpreted or mis-interpreted, and how they will affect the lives of people part of the communities on the South Coast of Papua New Guinea.