Phylogenetic Star Contraction Applied to Asian and Papuan mtDNA Evolution

Abstract

In the past decade, mitochondrial DNA (mtDNA) of 826 representative East Asians and Papuans has been typed by high-resolution (14-enzyme) restriction fragment length polymorphism (RFLP) analysis. Compared with mtDNA control region sequencing, RFLP typing of the complete human mitochondrial DNA generally yields a cleaner phylogeny, the nodes of which can be dated assuming a molecular clock. We present here a novel star contraction algorithm which rigorously identifies starlike nodes (clusters) diagnostic of prehistoric demographic expansions. Applied to the Asian and Papuan data, we date the out-of-Africa migration of the ancestral mtDNA types that founded all Eurasian (including Papuan) lineages at 54,000 years. While the proto-Papuan mtDNA continued expanding at this time along a southern route to Papua New Guinea, the proto-Eurasian mtDNA appears to have drifted genetically and does not show any comparable demographic expansion until 30,000 years ago. By this time, the East Asian, Indian, and European mtDNA pools seem to have separated from each other, as postulated by the weak Garden of Eden model. The east Asian expansion entered America about 25,000 years ago, but was then restricted on both sides of the Pacific to more southerly latitudes during the Last Glacial Maximum around 20,000 years ago, coinciding with a chronological gap in our expansion dates. Repopulation of northern Asian latitudes occurred after the Last Glacial Maximum, obscuring the ancestral Asian gene pool of Amerinds.

Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes

“…Median-joining networks were constructed by use of the Network 4.1 program 35,36 (http://www.fluxus-engineering.com), based on Y-chromosomal haplotype data and on nucleotide variation in the HVRI region (positions from 16048 to 16383) and in the coding region of the mtDNA. The repeat sizes of the Y-chromosomal microsatellite markers were weighted according to the mutation rates of the different loci 37 and the e value was set to 0.…”

Mitochondrial DNA analysis reveals diverse histories of tribal populations from India

“…An alternative hypothesis is that southern tribes have a specific mtDNA gene pool as compared to other Indian populations, indicating a long period of isolation and/or different history from other tribal groups. An example of the latter is PNG, 41,49 in which most sequences are found in two clusters (within clusters III and XI, Figure 5) characterized by long branches (not shown). However, southern Indian sequences are intermingled throughout the tree, clustering with sequences from multiple populations.…”

“…This result is consistent with the suggestion that the east Asian and Indian mtDNA pools have been separated from each other for about 30 000 years. 49 It has been hypothesized that the peopling of Sahul (PNG and Australia) may have been the result of an early migration from east Africa through the Indian subcontinent following the 'southern route'. 1,3,56 Australian populations exhibited an average Fst distance of 0.067 with east Eurasians and of 0.089 with Indians (but only 0.062 if South tribes excluded), whereas the average Fst values separating Australians from PNG or African (!Kung excluded) populations were 0.194 and 0.145, respectively.…”

“…In addition, Forster et al 49 have proposed an mtDNA control region motif (16223C and 16357C) which could represent a signature of an early migration from Africa to Sahul through the southern route. This motif was not found in any Indian tribal mtDNA; 16357C had a frequency of only 2.1% and was always associated with 16223T, while 16223C had a frequency of 27.9%.…”

Mitochondrial DNA variability in populations from East Timor (Timor Leste)

“…This haplogroup is considered to be widely spread in East Asia and its presence in Southeast Asia is interpreted as Austronesian genetic influence from East Asia [9]. Two of those sequences (12%) displayed the so-called bPolynesian motifQ, a specific B4a haplotype associated with the Austronesian expansion into the Pacific [10].…”