[Taxacom] Phylogenetic Classification?

[Bob Mesibov]

Winston Edwards wrote:

"Would it be possible for you to include a reference to a paper that names the molecular variants as different species using the molecular phylogeny only?"

I've seen so many papers with something like this in the title: Molecular evidence for cryptic species/speciation in blahblah, but I haven't bothered to follow any of these up to see if the authors actually *named* their new species on molecular data alone. I'm not sure the authors would have bothered, either, since they typically weren't funded to do taxonomy. The multitude of unpublished cryptic species is one of the real-world problems that make Richard Zander's comments worth noting. 

The only paper in my little specialty that comes to mind for molecular-only diagnosis is this one:

http://www3.interscience.wiley.com/journal/119111642/abstract

It appeared in the Biol J Linn Soc in 1998 and the species diagnoses derive not from a phylogeny but from allozyme differences.

A not quite so bold example is this one:

http://www.publish.csiro.au/?paper=IS07036

which diagnoses a new species based on a single-base polymorphism in 18s rRNA, a single indel in 28S rRNA and some mainly quantitative morphological differences - the kind which if found in a single widely distributed species might be regarded by a morphotaxonomist as geographical variation. One of the two species is paraphyletic in the COI tree published in that paper. At a conference last year I heard that this problem had been 'fixed' by additional exemplar sampling, and reanalysis.
-- 
Dr Robert Mesibov
Honorary Research Associate
Queen Victoria Museum and Art Gallery, and
School of Zoology, University of Tasmania
Home contact: PO Box 101, Penguin, Tasmania, Australia 7316
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Website: http://www.qvmag.tas.gov.au/mesibov.html