Monday, January 25, 2010

Step Back from the Species Description, Ma'am...I'm a Taxonomist

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?


Jake Esselstyn said...

It seems to be a little different in vertebrates. They get described, but the descriptions sometimes have photographs designated as types--especially with flashy primates and birds. See for instance the description of Lophocebus kipunji in Science in 2005. The authors took a photograph, and said the animal in the photograph is the type, not the photograph itself. Predictably, that generated some response.

fdelsuc said...

The Plasmodium story continues with the description of unexpected genetic diversity of Plasmodium lineages circulating in gorillas. In the new tree, P. gaboni is definitely distinct from P. reichenowi and the two new lineages infecting gorillas may also represent new "species". Whether these divergent lineages really represent new "species", or other taxonomic entities, or not, it looks like the taxonomic diversity of Plasmodium has been, and might still be, largely underestimated...

Kevin Zelnio said...

As a marine invertebrate taxonomist I am deeply offended by the Plasmodium researchers apparent disregard for taxonomic rigor and tradition. Though I do not know the details, such irresponsibility leaves those of us in the field hanging high and dry. I don't think I'm exaggerating when I say such behavior makes it even more difficult for the profession to attract and retain new talent, improve the standing and importance outside of the discipline, and secure new funding.

I am tired of subpar work, it makes the rest of us look bad. The conventions are in place as a minimum effort to ensure we are all on the same page with regards to a description and to ensure that there is a valid "type" that researchers can revisit and argue about later. Bucking the system is not an option, but feel free to do more than the minimum as I and my colleagues have striven to do.

Susan Perkins said...

Thanks for the comments so far. How do other people feel about photos representing vouchers, let alone types? This is probably a more complicated endeavor with rare organisms (especially vertebrates?)

@fdelsuc - yes, you're right - there was a small flurry of "great ape" malaria work and I can definitely say that there are some more cool insights coming down the pike (if I can get them written up!)

I definitely should point out to all that I think these new samples of malaria parasites from apes and possibly from this capybara are *exciting* and add a lot to our knowledge of parasite diversity and host specificity. The issue that I have is whether abandoning our traditional method of describing species is the right thing to do. It really is a dilemma. Valkiunas et al. discussed this in Trends in Parasitology in 2008 - there are a lot of sequences of malaria parasites in GenBank only ID'ed to genus - and there are a lot of misidentified sequences. It's frustrating to see a phylogeny with samples only to be labeled as "P. sp." But, are some rushing to name them? I am worried that forsaking the "Code" and the process might be a dangerous path.

Susan Perkins said...

Forgot to link to the Valkiunas et al. paper. Here it is.

Ainsley said...

I have to admit I'm still not clear on how (or whether) the Code applies to, say, viruses. I assume an SEM and a nucleotide sequence are all you're really going to get. Can you designate the EM sample as a type?

Obviously, insect folks are pretty good about designating and depositing types, but then again we also get rogue taxonomists self-publishing in their own journals, making wildly unjustified changes, generally leaving a slimy trail of disorder throughout the literature. (That's a topic for another time, I suppose.)

Re: photos standing in as types for rare organisms, given that vertebrates are probably 99% of the rare new exciting organisms that anyone cares about, surely it would be within the realm of possibility to provide at least some COI (or a genome or two, if you're a herpetologist).

We already have DNA sequences showing up in some arthropod species descriptions, supplemented by traditional morphological information. Why not make it the new standard (at least for spp with fresh tissue)?

Kevin Zelnio said...

Maybe I'm a purist but photos are unacceptable as type specimens. In fact, I've deposited histological slides with type specimens before. I'm sure it is different for the microbial world.

Viruses do have their own system of classification:

I think many taxonomists are now embracing a multifaceted approach to species descriptions. My last paper on a new shrimp included detailed morphology, ecological observations, COI, an updated dichotomous key to family, line drawings and in situ photographs. I understand that not everyone can do everything with their specimens because how it was fixed, etc. But with the possibility of cryptic species, especially in vertebrates, and the potential implications for conservation resources a photo should not suffice.

But it is a dilemma right? If you only seen a few individuals of a new primate do you risk taking the last breeding animal??

Glor said...

There's no question that the type of detailed species descriptions being prepared by folks like Zelnio are priceless. As we all know, however, this approach can be incredibly labor intensive and thankless. As a result, there are thousands of species waiting to be described. Do we reach a point were the benefit of having a more thorough accounting of diversity outweighs the cost of making some mistakes along the way? Are new descriptions that don't meet the ultimate standard being done for this reason, or do they result from neglect or a lack of attention to detail?

Tommy said...

As someone who also work on parasites with complex life-cycles and radically change form at every stage (digenean trematodes), I can sympathise. The use of DNA sequences have been *extremely* helpful in allowing us to match different larval stages. I have a colleague who works on tetraphyllidean tapeworms, and it is downright impossible to match larval with adult stages without the use of DNA sequences.

However, with that said, we would never be so presumptuous to publish a new species description based entirely on DNA sequence data. For example, a year ago, I found that two of my study species are actually morphospecies composed of a complex of at least 6 genetically very divergent clades. They are clearly divergent enough to be considered species in their own right.

I did end up publishing the findings, but I only pointed out that there might be hidden diversity within these 2 already described morphospecies and that they actually consist of species complexes, but I didn't base a new description on them.

I'm not a trained taxonomist, and I can't count out that perhaps that were some obscure morphological features that were overlooked in the intial published descriptions.

That's why I'm quite sceptical about the whole DNA Barcoding thing - as an evolutionary ecologist, I find it extremely useful, but I think there's a real need to respect the labour-intensive work done by "old-fashion" taxonomists.

sergios-orestis kolokotronis said...

Susan, it looks like there is a follow-up on the P. gaboni PLoS Pathogens paper in PNAS reporting two new genetic lineages sister to falciparum+reichenowi and gaboni. I don't see a formal description or naming of a species; maybe it's in the works.

PS. The International Journal for Systematic Bacteriology changed name to the International Journal for Systematic and Evolutionary Microbiology.