Here at AMNH, I am surrounded by drawers and drawers, bottles and bottles, and cabinets and cabinets of specimens. A fair number of these are type specimens and my colleagues have spent their careers carefully describing and depositing these and other specimens into collections. They publish these species descriptions in journals according to the rules of the International Code of Zoological Nomenclature. Bacterial taxonomists are an even stricter lot - they insist that all papers that name a new species are published in a single journal, the International Journal for Systematic and Evolutionary Bacteriology. (I have bucked that rule.) In my work on malaria parasites, I have often been met with harsh reviews when I have tried to publish anything that has a sequence, but not a matching bloodsmear. Working on parasites with multiple life stages can be particularly challenging for species descriptions - ideally one would have specimens, images, measurements, etc from each step of the life cycle..but those can be hard to obtain for many - or even most - parasites. In a recent paper, Chris Austin and I argued that incorporating DNA sequences into species descriptions can help bridge that gap.
The use of these sequences, however, should not come at the expense of traditional morphological analyses. Two recent papers "describe" new species of malaria parasites without really describing them. One was published in a the high impact journal PLoS Pathogens, and names a new species of Plasmodium in chimpanzees. Even though the authors say they examined slides of the new species under a microscope, there are no images, measurements, or discussions of morphological features that might allow a reader to visually differentiate the new species. To the contrary, they remark that the samples look a lot like P. falciparum. There is no type specimen. A subsequent paper with other samples from chimpanzees definitely hints that it may not be a new species, but may instead be another species known to infect chimps: P. reichenowi. Similarly, another paper recently reported a new species of Plasmodium in capybara. This discovery was particularly surprising given that no New World mammal malaria parasites are known, save for some in primates that are genetically indistinguishable from a human parasite. In this paper, again, there is no traditional description, there is no type specimen, there is a single image of the parasite's smallest and most challenging to identify stage, and the genetic results are of a paralogous gene represented by an unrooted cladogram.
I know that there has been a lot of discussion about electronic journals and ePubs ahead of print either work with or violate the "code", but I have to ask, has traditional taxonomy gone extinct? Is this happening in other fields, too?
Archiving the genomes of all species
16 hours ago