Melanesian mtDNA Complexity

Abstract

Melanesian populations are known for their diversity, but it has been hard to grasp the pattern of the variation or its underlying dynamic. Using 1,223 mitochondrial DNA (mtDNA) sequences from hypervariable regions 1 and 2 (HVR1 and HVR2) from 32 populations, we found the among-group variation is structured by island, island size, and also by language affiliation. The more isolated inland Papuan-speaking groups on the largest islands have the greatest distinctions, while shore dwelling populations are considerably less diverse (at the same time, within-group haplotype diversity is less in the most isolated groups). Persistent differences between shore and inland groups in effective population sizes and marital migration rates probably cause these differences. We also add 16 whole sequences to the Melanesian mtDNA phylogenies. We identify the likely origins of a number of the haplogroups and ancient branches in specific islands, point to some ancient mtDNA connections between Near Oceania and Australia, and show additional Holocene connections between Island Southeast Asia/Taiwan and Island Melanesia with branches of haplogroup E. Coalescence estimates based on synonymous transitions in the coding region suggest an initial settlement and expansion in the region at ∼30–50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval ∼3,500–8,000 YBP. However, there are some important variance components in molecular dating that have been overlooked, and the specific nature of ancestral (maternal) Austronesian influence in this region remains unresolved.

Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea

“…Concerning NRY, the Solomon Islanders harbor more diverse NRY lineages than the Massim; for example, several C, K, M and O lineages present in the Solomon Islanders 18 are absent from our Massim sample, but are also found in the Bismarck Archipelago. 14 Similarly for mtDNA, the Northern Melanesian lineages M27 and M28 are found in the Solomons 18 and in the Bismarcks, 15 but not in our Massim sample. Thus, it is likely that there were direct links between the Bismarcks and the Solomons that bypassed the Massim region.…”

“…In reconstructing the demographic history of Oceania, our results not only fill an important gap between previous genetic studies on the mainland of New Guinea in the west, 9-13 the Bismarck Archipelago in the north [14][15][16] and the Solomon Islands in the east, 17,18 but also provide further insights into how human culture impacts on human genetics.…”

“…1,2 Previous studies have addressed human genetic variation in Oceania, particularly Polynesia, [3][4][5][6][7][8] mainland New Guinea [9][10][11][12][13] and Island Melanesia. [14][15][16][17][18] One area of Near Oceania (NO) yet understudied from a human genetic perspective is the island region off the southeastern tip of New Guinea (Figure 1). Administratively designated the Milne Bay Province of Papua New Guinea (PNG), this area encompasses the D'Entrecasteaux Islands (ie, Normanby, Fergusson, Dobu and Goodenough), the Trobriand Islands, the Woodlark group (ie, Gawa, Woodlark and the Laughlan Islands), the Louisiade Archipelago (ie, Misima, Sudest, Rossel and the islands of the Calvados chain), as well as a portion of the nearby PNG mainland.…”

Molecular population genetics of SLC4A1 and Southeast Asian Ovalocytosis

“…4,10 Because Austronesian speakers throughout the Pacific and Indian Ocean are thought to be related to aboriginal Taiwanese, [11][12][13] it is somewhat surprising that we did not find haplotypes similar to SAO in our Taiwanese sample. There are two possible explanations for this pattern.…”

“…and to examine whether the pattern of polymorphism in the surrounding genomic region reflects a history of natural selection. In addition, we compare patterns of sequence variation in Indonesia with samples from two other populations, one from Austronesian-speaking aboriginal Taiwanese individuals, who are suggested by linguistic and genetic evidence to be the source population of the Austronesian expansion, [11][12][13] and a second population from Japan, which harbors the Memphis polymorphism, but not SAO.…”