Maternal history of Oceania from complete mtDNA genomes: contrasting ancient diversity with recent homogenization due to the Austronesian expansion

Abstract

sample sizes and number of populations analyzed (e.g., see Soares et al.,42 Benton et al.43). Our data set is, to our knowledge, the most comprehensive to date, and consists of 1,331 whole mitochondrial genome sequences from 34 populations spread from the Bismarck Archipelago to Polynesia (Figure 1). To facilitate comprehension and visualization of the patterns of variation, these 34 populations have been amalgamated into six groups on the basis of geographic proximity and/or shared cultural features (Figure 1). The first group consists of populations from New Britain in the Bismarck Archipelago (Anem, Ata, Nakanai) and the second group consists of populations from Bougainville and Buka (Buin, Buka, Nagovisi, Nasioi, Siwai, Torau), two islands at the northern tip of the Solomons Archipelago that politically are part of Papua New Guinea, and the easternmost site of known settlement in Pleistocene Oceania.5 The only other confirmed pre-Austronesian settlements in the Solomons Archipelago are sites from Guadalcanal with indications of human occupation approximately 6 ka ago.44,45 The third group consists of populations found in the islands of the rest of the Solomons Archipelago (Choiseul, Gela, Guadalcanal, Isabel, Kolombangara, Makira, Malaita, Ranongga, Russell, Savo, Shortlands, Simbo, Vella Lavella). Santa Cruz is the only population to be grouped alone; it is treated separately because it has been shown to be a genetic outlier in previous studies of mtDNA and Y chromosome variation41,46 as well as being linguistically distinct. Originally classified as a Papuan language, currently the Santa Cruz language and closely related languages of the Temotu group are thought to represent a very deep branch of the Oceanic family of Austronesian languages.47 The final two groupings concern populations believed to be predominantly of Austronesian heritage: these include