a tree reconstructed using just the coding region sequences (Fig. 2). Although the topologies of the two trees were essentially the same, the tree of sequences with the D-loop removed showed generally higher bootstrap values. For this reason, in studying the phylogenetic relationships among the mitochondrial lineages, we focused solely on the coding region (1601).
Since they weren't using the usual D-loop markers, they decided against the usual mtDNA haplogroup nomenclature, based on L, M, N, etc. Their results are essentially equivalent, however:
Branch 1 and branch 2 are delineated by the nucleotide positions 8701, 9540, 10398, 10400, 10873, 14783, 15043, and 15301 relative to the Cambridge reference sequence (CRS; Anderson et al. 1981), consistent with what are sometimes referred to as haplogroups N (branch 1) and M (branch 2) (1601).
Our analysis shows a striking difference between the genetic history of females and the reported history of males in the Australian Aboriginal population. As noted previously, the mitochondrial diversity in Australia is relatively high. The pattern seen in the Y-chromosome is different in that an Australia-specific haplotype (DYS390.1del/RPS4Y711T) is found in about 50% of males in Australia (Kayser et al. 2001; Redd et al. 2002). . . Kayser et al. (2001) proposed that the high frequency of a unique haplotype in Australia is the result of a population expansion that started from a few hundred individuals. In this case, the predominance of a unique Y-chromosome haplotype in Australia would be the result of a founder effect. However, there does not appear to be a corresponding loss of genetic diversity resulting from a bottleneck seen among mitochondrial lineages (1604 -- my emphasis).
Archaeological evidence indicates that humans were present in New Guinea at least 40,000 years ago (Groube et al. 1986), at which time it was still joined with Australia. Our data show that some Australian sequences do share a closer ancestry with some New Guinean sequences than they do with other sequences on branch 1. In addition, . . . New Guinean and Australian sequences are more closely related to each other than either are to the Asian sequences. This may suggest that Australia and New Guinea were colonized jointly or that, if not, these populations have admixed since colonization. . . Our mitochondrial data imply that some lineages from the populations of Australia and New Guinea have shared a common history since the initial colonization of Sahul. . . .The lack of a common Y-chromosome haplotype found both in Australia and in theNew Guinea highlands (or in any other Melanesian population) argues against the concept that the New Guinean and Australian populations are derived from the same migration event (Kayser et al. 2001). However, the Australia-specific Y chromosome haplotype could have arisen after the colonization of Sahul and therefore is absent in other populations.Our mitochondrial data show no clear similarity between Australian Aborigines and the three southern Indian sequences examined, although a detailed examination of this hypothesis would require the analysis of additional individuals from the Indian Subcontinent. Nevertheless, mitochondrial DNA only provides information on the genetic history of females, and given the contrast between the mitochondrial DNA and the Y chromosome patterns, it appears that additional studies of autosomal loci are also necessary to obtain a balanced view of the evolutionary history of the peoples in this region.
I'll be discussing some of the themes raised above in my next post, when I finally try to put all the various bits and pieces of evidence together into some kind of theory.