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I too noticed quite a few taxonomic changes that had an influence on my impact assessment work (have a look at what she has done to the Mormopterus) and asked Ray Williams about it. He said (and please correct me if I am wrong Ray) that Sue has used a lot of new taxonomy that is on the verge of being published but has not yet been published and so tmany of he names are not yet valid but known to the bat world from conference presentations etc.
Until they are valid names, we are in a difficult area with the TSC Act and the authorities are not quick to pick up on bat taxonomy - it is only recently that the Wildlife Atlas has stopped telling me there is Macropus adversus near my site for example.
Obviously, if a taxon has been shifted in its entirety to a new name, then its conservation status should be carried along with it and I think our reports should note the dual names and point out the nomenclatural conflict so that in the future the report will still make sense to somebody who has only ever known the new name.
However, if only part of a taxon has been reassigned, then it is much trickier, but the logic from above should also apply as best we can. If the changes have a clear geographic basis, then that is much easier (e.g. all southern forms of species X have become species Y and the site is within the range of the southern form) but if it has been split or moved on features that occur in overlapping populations, then we have a big mess and have to very carefully identify our critters (not so easy with bats) and read the taxonomic literature (yuk).
Unfortunately, the natural world is not neat! This is an ever-present problem for unstable plant groups (e.g. Persoonia, Grevillea) and unfortunately these are full of listed threatened "species". For example, I worked on a population of a plant species listed under both TSC and EPBC Acts, and the plants we found had important distinguishing characteristics of both the common and the threatened species. A swag of specimens were sent to the scientist who published the names for adjudication and they were equally as confused as we were. They told me that when describing this group, they had very few specimens from the northern part of its range and none from the area we were working. Therefore, the characters they had relied on that were distinct in their sample were blurred by those in my sample, and would probably not have been relied on to distinguish the taxa if they had been able to work with a more geographically complete sample. But the names have been published and have a life in the conservation legislation and every time I am working in its habitat I worry it will turn up and make me spin on the spot.
My reading of the your issue Deryk is that Nyctophilus timoriensis may still be the valid name (I don't follow the taxonomic literature very closely - see above) and, as it is the legal entity that is listed on the TSC Act, anything that may be regarded as this taxonomic entity should be assessed as being listed. Eventually, if the proposed taxonomic change is accepted and published in the scientific literature, then it looks like all of the bats in Australia known as Nyctophilus timoriensis should be called the new name and so its TSC conservation status should also apply and it should be shown in a new schedule of the Act (eventually). This looks like a neat example of the first example I gave above. So another 7 part test please Deryk!
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