Kotatsu
Phthirapterist
I'm not sure where I said they were synonyms - phylogeny is a description of relatedness (a family tree, as such) while taxonomy is the system of nomenclature describing the groups. Not synonyms, but the fields are related.
Maybe you didn't, but I sort of got the impression you were at least treating them as more or less synonymous. Also, it was late and I'd just come home from boardgaming (which I sort of lost), and may not have been paying as much attention as I should have.
Morphology is slowly giving way to genetics in understanding phylogeny, and in some fields taxonomic reform has occured as a result. Admittedly, my main field was pathological microbiology, where molecular genetics was causing massive changes in how bacteria were classified.
In phylogeny, yes. I can't think of more than a handful of pure morphologically based phylogenies on the groups that interest me from the 2000s. However, once you've produced your phylogenetic tree and discovered that there is a need for taxonomic change, you would still need to use morphology to describe these new species. As I recall, even Hebert --- the main proponent of DNA barcoding --- even supported his contention (based on a COI phylogeny) that there were more butterflies of a certain group in Costa Rica on morphological differences in the caterpillars.
Also, when giving name to clades of higher ranks (which is also a common result in phylogenetic research), these are usually named after morphological or other non-genetic characters. I don't even know how a taxonomy that isn't based on morphology would look like in this case, but then again, I don't work with microorganisms.
Seriously? I've known of reclassification of wallaby sub-species in north Queensland which was done on genetic analysis alone. That was a few years ago now, admittedly, and it wasn't my field of work but rather a colleague I had worked with.
And this work was both taxonomic and entirely without morphology? Or was it phylogenetic and had implications for taxonomy?
Naturally, there are thousands of examples of molecular work which change the taxonomy in fundamental ways, like moving around genera between families or species among genera. However, these works cannot stand alone. If you find that a certain species previously placed in a certain genus should instead properly be placed in another one based on genetic sequencing, you would still have to --- if you wanted to do it properly --- study the morphology of this new set of species and come up with a new definition of what this genus consists of.
I'd find it odd that a species could be classified as distinct from other morphologically identical populations. However we're not talking about distinctions of species, but rather populations within a species.
Yeah, cryptic species are really bothersome. I have been (and am still) working with them a bit, in annelids, but a recurring theme is that even if we know that a certain complex consists of three genetically different species, we'd still have a thorough look at the morphology and see if they really are identical or not. Often, we can find differences in morphology which we'd never have looked for if we hadn't had the genetic data first. As an example, there is in press now a paper working on a common Tubificid, which is known to contain as many as six or seven genetically distinct cryptic species. This paper divided the genotypes into their respective groups and studied some aspects of the sperm ultrastructure and (I think) the glandularisation of the spermatheca, and found consistent morphological differences which corresponded to genetic groups. In a paper of my own (which is now undergoing some revision prior to resubmitting), we found three cryptic species within a common annelid, and while we have made no attempt to do a morphological study in that paper (and as I've moved on to other groups, I personally most likely never will), we have made some preliminary morpological observations sufficient to have a basis to separate the species on morphology alone. The same goes for all the recent studies of cryptic annelids (me and my former supervisor recently finished a review of this): if not morphological differences, then at least environmental, physiological or developmental ones. But the morphology is at least addressed, if only to say that they are morphologically identical concerning the established characters.
I will have to admit my field is no longer in pathology, but rather in science communication and education. So I'm always happy to defer to expertise from those in the field. However, unless there has been a large counter revolution to work I was familiar with last decade, genetic comparison can indeed be enough to bring into question whether taxonomic descriptions based solely on morphology (and significantly for bacteria, biochemistry) were accurate.
I don't dispute that. I just wouldn't call that a taxonomical work, but a phylogenetic one, which would have to be supplemented by a taxonomical work (a revision or so), and in that work, you'd either have to address morphology, or see your work being dismissed as largely useless. The people on the receiving end of taxonomic work will always want to be able to tell the creatures apart...