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 approximately 30-50,000 years before present (YBP), and a second important expansion from Island Southeast Asia/Taiwan during the interval approximately 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.

Figure 1

Haplogroup P phylogeny for Near Oceania (branches shared with Australian Aborigines also shown). The branches of P found only in Australian Aborigines, and details of the P1 branches, are available in , supplementary materials. Control region mutations are in bold, those that recur in this phylogeny are underlined, those in blue are synonymous transitions, and transversions are noted with a base suffix. Asterisks denote substitutions that can be both synonymous and nonsynomous because of gene overlap (nts 8563 and 8572). These were regarded as nonsynomous. The dotted line in the tree denotes a missing control region sequence. The poly C regions in HVS1 and 2 as well as 16519 are excluded. Proveniences are listed at the top, abbreviated as follows: NG–New Guinea, TR–Trobriands, AUS–Australian Aborigine, NB-New Britain. Sample numbers, GenBank accession numbers, and sources are listed underneath. Source abbreviations are: SV–; TK–; MI–; MP–.

Figure 2

Upper Pleistocene macrohaplogroup M phylogeny for Near Oceania (haplogroup E is excluded). Abbreviations follow figure 1. Additional sample abbreviations are BGV–Bougainville, and NI-New Ireland. Additional source abbreviation is DAM–. Boxes on M27a and b indicate inferred additional branches defined by control region sequences. The complete Q tree is presented in figure 4.

Figure 3

Haplogroup Q phylogeny. Abbreviations follow figure 1. Additional source abbreviation is JSF–.

Figure 4

Spatial frequency distribution of haplogroup B4a* and B4a1a1 in Island Southeast Asia and the western Pacific, created using the Kriging algorithm of the Surfer package of haplogroups. Figure 4b presents the detailed distribution for Northern Island Melanesia. Data details are provided in table S3.

Figure 5

Haplogroup E phylogeny. Abbreviations follow figure 1. Additional source abbreviations are CH– and JT-.

Figure 6

Spatial frequency distribution of haplogroup E1a in Island Southeast Asia and the western Pacific (6a), and details for Northern Island Melanesia (6b) created using the Kriging algorithm of the Surfer package of haplogroups. Data details and references are provided in table S3.

Figure 7

Spatial frequency distribution of haplogroup E1b in Island Southeast Asia and the western Pacific (7a), and details for Northern Island Melanesia (7b). Data details and references are provided in table S3.

Figure 8

Northern Island Melanesian Southwest mtDNA haplogroup frequency distribution taken from our series (table S2).

Figure 9

Two-dimensional multidimensional scaling plot, generated from pairwise Fst values of mtDNA variation in Northern Island Melanesian populations. First axis is horizontal, second is vertical. Papuan speaking populations are underlined.