Admixture and natural selection shaped genomes of an Austronesian-speaking population in the Solomon Islands

"Feeling at home in Vanuatu": Integration of newcomers from the East during the last millennium

Several localities across the Vanuatu archipelago (Melanesia), so-called 'Polynesian Outliers', are inhabited by communities that display Polynesian linguistic and cultural features although being located outside the Polynesian Triangle. Several introductions of Polynesian genetic components to Central and Southern Vanuatu during the last millenium have resulted in the cultural distinctiveness observed among the Polynesian Outliers in Vanuatu. However, social, political or economic process surrounding the exchange of genes between Polynesian and local individuals remain unidentified. Recent bioanthropological studies suggest the existence of female mobilities from neighboring regions to Vanuatu but also to the Polynesian Outliers of Taumako (Solomon Islands) within patrilocal societies. We aim to examine the hypothesis that Polynesian biological affinities observed in ancient individuals from Vanuatu are gendered or sex-specific, and that some of the Polynesian migrations during the last millennium may have involved practices of exogamy. By reconstructing phenotypes and biological identities from 13 archaeologically-recovered human skulls (400-300 years ago) from "Polynesian-related" regions of Vanuatu, we provide new insights to better contextualize the settlement patterns of Polynesian individuals. Eastern-Pacific associated phenotype are observable in 4 women from the Eretok burial complex (Efate region) and the Polynesian Outlier of Futuna, who were buried in close proximity to individuals with Western-Pacific associated phenotype. We suggest that close integration of individuals from the East into the local Vanuatu society, as well as the practice of exogamy, might have been key processes contributing to the preservation of Polynesian cultural features in Vanuatu over the past millennium. Our finding are cross-referenced with oral records from these two areas, as well as the known genetic makeup of the Vanuatu Polynesian Outliers.

Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations

Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.

Admixture with indigenous people helps local adaptation: admixture-enabled selection in Polynesians

Background

Homo sapiens have experienced admixture many times in the last few thousand years. To examine how admixture affects local adaptation, we investigated genomes of modern Polynesians, who are shaped through admixture between Austronesian-speaking people from Southeast Asia (Asian-related ancestors) and indigenous people in Near Oceania (Papuan-related ancestors).

Methods

In this study local ancestry was estimated across the genome in Polynesians (23 Tongan subjects) to find the candidate regions of admixture-enabled selection contributed by Papuan-related ancestors.

Results

The mean proportion of Papuan-related ancestry across the Polynesian genome was estimated as 24.6% (SD = 8.63%), and two genomic regions, the extended major histocompatibility complex (xMHC) region on chromosome 6 and the ATP-binding cassette transporter sub-family C member 11 (ABCC11) gene on chromosome 16, showed proportions of Papuan-related ancestry more than 5 SD greater than the mean (> 67.8%). The coalescent simulation under the assumption of selective neutrality suggested that such signals of Papuan-related ancestry enrichment were caused by positive selection after admixture (false discovery rate = 0.045). The ABCC11 harbors a nonsynonymous SNP, rs17822931, which affects apocrine secretory cell function. The approximate Bayesian computation indicated that, in Polynesian ancestors, a strong positive selection (s = 0.0217) acted on the ancestral allele of rs17822931 derived from Papuan-related ancestors.

Conclusions

Our results suggest that admixture with Papuan-related ancestors contributed to the rapid local adaptation of Polynesian ancestors. Considering frequent admixture events in human evolution history, the acceleration of local adaptation through admixture should be a common event in humans.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01900-y.

New insights into human immunity from ancient genomics

Population genetic studies have clearly indicated that immunity and host defense are among the functions most frequently subject to natural selection, and increased our understanding of the biological relevance of the corresponding genes and their contribution to variable immune traits and diseases. Herein, we will focus on some recently studied forms of human adaptation to infectious agents, including hybridization with now-extinct hominins, such as Neanderthals and Denisovans, and admixture between modern human populations. These studies, which are partly enabled by the technological advances in the sequencing of DNA from ancient remains, provide new insight into the sources of immune response variation in contemporary humans, such as the recently reported link between Neanderthal heritage and susceptibility to severe COVID-19 disease. Furthermore, ancient DNA analyses, in both humans and pathogens, allow to measure the action of natural selection on immune genes across time and to reconstruct the impact of past epidemics on the evolution of human immunity.