Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers

Abstract

Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain–related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.

Exploring archaeogenetic studies of dental calculus to shed light on past human migrations in Oceania

“…Missing data for some islands was obtained from alternative sources 58,59 . Preservation of microbial DNA in calculus and of human DNA in bone samples was compared in the Pacific and in Europe using previously published datasets 1,5,15,24,60,61 . For details see Supplemental Methods.…”

“…Total DNA was extracted from 0.5-7 mg of dental calculus per individual, using a silica column-based extraction protocol optimized for the recovery of short DNA fragments, adapted for dental calculus 1–3 . The extracts were prepared into double-stranded libraries with partial uracil-DNA-glycosylase (UDG) treatment 4,5 and dual indexing 6–8 . The libraries were sequenced to a depth of 10.5 ± 2.3 million reads (mean ± standard deviation) on an Illumina Nextseq with 75-bp paired-end sequencing chemistry.…”

“…Archaeogenetics studies of ancient human migrations are conventionally conducted by analyzing human DNA from skeletal elements, such as teeth and the petrous portion of the temporal bone. Human population movements across the Pacific have been reconstructed in this manner, revealing successive waves of migration during the Pleistocene and Holocene 1–5 . However, ancient DNA work in the Pacific is challenging as the studied populations are closely related and migrations take place over short periods of time.…”

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

“…Duplicate reads were marked using picard-tools MarkDuplicates (broadinstitute.github.io/picard). We further downloaded 2, 359 individuals sequenced with 1240k target enrichment capture sequencing (Fer-nandes et al, 2020; Fowler et al, 2022; Fu et al, 2016; Harney et al, 2021, 2022; Kennett et al, 2022; Lazaridis et al, 2022, 2016, 2017; Lipson et al, 2017, 2022; Liu et al, 2022b; Mathieson et al, 2015, 2018; Narasimhan et al, 2019; Novak et al, 2021; Olalde et al, 2018, 2019; Patterson et al, 2022; Prendergast et al, 2019; Reitsema et al, 2022; Rivollat et al, 2020; Sirak et al, 2021; Tiesler et al, 2022; Villalba-Mouco et al, 2021) directly in BAM-format. For both data sets, we used the task in (Link et al, 2017) to count the number of reads that aligned to each chromosome, ignoring duplicates and reads with a mapping quality below 30.…”

Genomic perspectives on human dispersals during the Holocene

“…Long-Distance Sea Voyages into Oceania. Austronesian movement through ISEA and into Near Oceania (New Guinea and nearby islands) was likely achieved by island-hopping and intervisible water crossings, which would not have required sophisticated boating technology (although ancient DNA evidence from the Mariana Islands supports a direct migration ~3.5 kya from the Philippines across more than 2,000 km of open ocean (111,112). Austronesians probably continued from eastern Indonesia along the New Guinea coast, eventually reaching the Bismarck Archipelago ~3.4 kya (113).…”