RPM and Kambiz comment on a paper which argues for the utility of mtDNA in phylogeography.
Remember,
- there is lots of mtDNA that is easy to extract because there are so many mitochondria within eukaryotic cells
- it mutates fast, building up a lot of genetic variation, in a neutral matter (i.e., perfect "clock")
- it is uniparental, passed from mother to daughter, making the coalescent model congenially tractable
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It's not so much the phylogentic utility of mtDNA that's in question, it's whether mtDNA polymorphism adequately captures population size changes.
it mutates fast, building up a lot of genetic variation, in a neutral matter
But that's what's being called into question! Any selection at any site in the molecule will affect polymorphism everywhere else on the molecule.
It's not that mtDNA is a poor locus for popgen analysis. mtDNA is like any other locus. We need to sample multiple independent loci to understand demographic history.