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Re: Tuataras are the roadrunners of molecular evolution.

I've now read the paper. I expected a tetrapod phylogeny or something, where *Sphenodon* has a longer branch than *Alligator*... nope. It just takes subfossil tuatara DNA (8800 to 500 years old), compares it to modern tuatara DNA, and calculates a rate of evolution assuming all samples represent a single population through time. Also, the DNA in question is the mitochondrial control region, not a gene.

I was wondering if the rate estimate might be inflated by assuming that the
early Holocene bones were ancestral to modern samples, whereas common sense
would suggest they might well be distinct species, or in any case that their
mitochondrial lineages had split much earlier.

I agree. The subfossils come from all over North and South Island.

though there is mention there of sequences
clustering by geographic region regardless of date.
Is the analysis OK, do you think?

As explained in the supplementary information, that analysis has two steps. First, a neighbor-joining analysis that was used to get a topology. This topology was then fed into a maximum-likelihood analysis to get branch lengths. The reasons for this bizarre approach aren't explained anywhere. It's bizarre because:
1) neighbor-joining is phenetics, not phylogenetics;
2) neighbor-joining alone produces both a topology and branch lengths;
3) maximum-likelihood alone, too, produces both a topology and branch lengths.
The logical approach would have been to use maximum-likelihood alone. Unless I've missed something -- but given the complete lack of explanations, I can't figure out what that could be.

On the other hand, what would hyper-variable mitochondrial control regions
have to do with rate of morphological (or indeed physiological) evolution?

As far as I can tell, nothing whatsoever...