Ok I'm sucked in. This has become a fun thread.

"True phylogeny" from mtDNA? Not possible. That would just be a gene tree. "True phylogeny" is currently not possible. Best we can do is make phylogenetic hypotheses based on multiple loci and various algorithms.

What we're getting at here is phylogeography and mitochondrial DNA is quite good for that for several boring reasons (effective population size 1/4 that of nuclear DNA, no recombination blah blah etc..). But it does have shortcomings as well. For example, mtDNA only gives you the maternal relationships. If there's "hybridization" from mainland males dispersing to islands, mtDNA will not tell that story. Also, if the populations have diverged recently enough, the genes will not have had time to coalesce and form reciprocally monophyletic clades.

"But how can you recognise a subspecies in molecular genetics?"

Woah. This is such a dodgy area I'm very surprised to see it come up in a captive forum. As much as I do love stirring sh*t for the sake of stirring sh*t, I’m not looking to get into an argument on molecular phylogenetics and taxonomy here. There are about a billion different opinions out there about subspecies, what they are, and what defines them (genetically distinct, geographically/reproductively isolated, and morphologically distinct, some combination thereof...). Best thing to do is dig around in the literature and form your own opinion.

There is, however, a boa phylogeography study out there. Check out Hynková et al 2009. I’m attaching a couple figures from it for your interest. It’s not perfect, but it’s a start.


Fig. 1. Map showing the major clades detected in the MP analysis from across
Central and South America.


Fig. 3. Consensus Bayesian tree of cytochrome b with outgroups.

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