Thanks for sharing. Here is how I saw this paper/video. I thought it was a very cool, labour intensive project especially for an MSc. There's a ton of theoretically heavy concepts most notably: what is a species. I would be cautious to say this rocks the world of of C. viridis taxonomy but would say it is a welcome addition to a contentious discussion of split or lump.
What she did that was the most novel about this is add neutral nuclear gene trees. To date mitochondrial DNA (mtDNA) has been only method used to tease these groups apart (see below). mtDNA is helpful and interesting especially for recent divergences as it has a smaller effective population size (inherited only through the mother so 50% of the pop) in which the frequency of a gene shifts more quickly than in nuclear DNA (nDNA; inherited from both parents). For each gene/loci you can make a tree similar to a species tree (but don't necessarily line up to a species trees; see incomplete linage sorting) which gives insight into the evolutionary history of that species/population/individual. mtDNA is inherited more or less as a single unit so each gene tells a similar story so adding nDNA allows her to tell a more complete story. I thought she did a good job but next time someone will do 20 loci or even resequence the whole genome so I would not say this is the final statement in this debate.
http://www.sciencedirect.com/science/ar ... 039990756X
http://clweb02.chrislands.com/clshops/S ... ouglas.pdf
Her methods were also novel to the this study system (C. viridis). The Bayesian method she used uses many repetitions of a model(s) to give a probability that said model is close to the "real" value. Neat stuff but very jargony and many people can likely speak to the intricacies of these methods better than I can (
http://en.wikipedia.org/wiki/Bayes_factor).
I'll wait for these to make it through peer review process before I start changing the species on my photos but that does not mean that I necessarily I disagree with her findings but I think she may need to do some further sampling in some areas. That she separates C. o. oreganus with the southern species a sister species to C. o. helleri is interesting but her lack of sampling in the presumed contact zone between the two C. o. oreganus does not rule out that they freely interbreed and may in fact interbreed with C. o. helleri as well which would explain the divergence and similarities using isolation by distance. This might be an argument against elevating these clades.
She uses the evolutionary species concept which is interesting as it does not really address issues of reproductive isolation which is the focus of the more widely used biological species concept. Hybrids are well known in snakes including between well defined species of Crotalus (let alone subspecies) so elevating these may be difficult (see Diadophis).
http://www.jstor.org/stable/3892206?seq ... b_contents
http://www.bioone.org/doi/full/10.1894/ ... 2.0.CO%3B2
I thought it was a cool thesis and I await the peer-reviewed paper(s) it spawns.
All the best,
Nick