Molecular evolution of extinct lineages

This is cool, Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes:

We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth (Mammuthus primigenius), sequenced with up to 73-fold coverage from DNA extracted from hair shaft material. Three of the sequences present the first complete mtDNA genomes of mammoth clade II. Analysis of these and 13 recently published mtDNA genomes demonstrates the existence of two apparently sympatric mtDNA clades that exhibit high interclade divergence. The analytical power afforded by the analysis of the complete mtDNA genomes reveals a surprisingly ancient coalescence age of the two clades,~1-2 million years, depending on the calibration technique. Furthermore, statistical analysis of the temporal distribution of the 14C ages of these and previously identified members of the two mammoth clades suggests that clade II went extinct before clade I. Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep.

Sympatric just means there was a spatial overlap between the lineages (see Figure 1 in the paper). I don't particular care much about the specific inferences being made here; I just think it's really cool that this sort of work can be performed on an extinct lineage of organisms. Of course, mammoth and mtDNA are optimal targets for this sort of research. Mammoth are big, widespread and were extant across a region where there is a high likelihood of preservation (low temperatures and permafrost), while mtDNA is relatively copious and so a greater likelihood exists of usable quantities remaining even after eons of degradation. But ultimately time is probably the biggest factor, mammoth were around relatively recently in terms of natural historical scales.

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In the sake of fairness, it's worth reporting that mitochondrial DNA (mtDNA) may not be as flawed as previously thought (see the original paper here).
From here: "Cronin et al.
Mitochondrial DNA (mtDNA) is one of the most used markers in molecular ecology1. A good molecular marker for population level studies should be neutral, so that researchers can use it to infer things like:
Dr. Rob weighs in on the lack of a relationship between mitochondrial DNA (mtDNA) polymorphism and population size.

Read about it at Science Daily. They talk of the two clades as separate "species" (1 million year genetic distance may justify that I guess) and they also say that their mtDNA is much more complex than that of both species of elephants and that hey had very low mtDNA diversity.

In any case, it's certainly interesting that whole mtDNA reconstruction is possible when hairs are available.