Thursday, September 19, 2019

The hidden trials of the taxonomic impediment.

So. I'm coming back after a long hiatus because this paper dropped not long ago and I've got feelings. Here's the press release.

A quick summary: Sarah Meierotto of the University of Kentucky and several of her colleagues collaborated with the Area de Conservacion Guanacaste project to describe 18 new species of parasitoid wasps reared in Guanacaste province, Costa Rica. The kicker is they did this entirely from sequences of Cytochrome C Oxidase subunit 1 (CO1) mitochondrial DNA sequences, sometimes known as the "barcode gene". Aside from a single habitus photograph of each species, they offer no morphological treatment of any of these species, and their only diagnostic characters are DNA nucleotides at certain positions. This has resulted in a somewhat heated conversation among taxonomists about the validity and usefulness of these new species "descriptions".

Before I go into those criticisms, I should mention that this isn't the first time a taxonomist has described species from barcodes only. Andrew Brower published
ten new species of moths from barcodes only a decade ago, but his purpose was to preemptively criticize DNA-only descriptions of new species. Quoting his abstract, "the application of names to concepts does not corroborate or endorse the biological validity of those concepts."

Meierotto and her colleagues, in contrast, say this is a "revolutionary protocol" for species description. Are these descriptions available? According to Commisioner Thomas Pape they meet all the criteria for availability. Quibbling about whether listing of base pairs are symbols or words is not really helpful.

But, are they valid? That's a much more difficult and interesting (and hair-tearing) question. How did we get to this point?

The new species are described in two different braconid genera, Zelomorpha and Hemichoma. The genus Zelomorpha has more than 50 previously described species, while Hemichoma has less than ten. Both of these genera were revised in a 2006 dissertation by University of Kentucky student Carlos Eduardo Sarmiento-Monroy. As far as I can tell, none of these manuscript names were ever published. Dissertations are not considered available under the ICZN, so Dr. Sarmiento-Monroy would have needed to publish these names in a journal, book, or other publication to become available; he never did. This year, Meierotto published a taxonomic review of Zelomorpha and Hemichoma with coauthors including Michael Sharkey, who was both the dissertation advisor for Sarmiento-Monroy and is second author on the DNA-only paper. This taxonomic review includes a large number of "new combinations", but as far as I can tell it has no new species.

What I suspected happened is that Sarmiento-Monroy completed his dissertation and never got around to publishing the species names. Maybe he disappeared, or moved on to work on some other group, or decided he hated braconid wasps so much he never wanted anything to do with them again. The names were never published. However, all the tantalizing species descriptions, photos, diagnostic information, these all still exist in dissertation form. All of that was copyright to the author, meaning, anyone couldn't come along and publish it for him. So, Michael Sharkey passed the project along to his new graduate student, Sarah Meierotto. Or maybe Sharkey continued working on the group in the intervening time. Anyway. The morphological species concepts were well known, even some genetic concepts were well known, but all the descriptions, diagnoses, and photographs would have to be redone, from scratch.

Anyone who has ever done any taxonomic work before, I can hear your groans through cyberspace.

So, they got the idea to publish some new names using the simplest description, just the barcodes. They already had some of these, but Daniel Janzen has a ton more via the ACG caterpillar rearing and barcoding project. Meierotto and Sharkey knew which species in ACG referred to new species and previously described species, because they had all of Sarmiento-Monroy's barcodes. So they took Sarmiento-Monroy's species concepts that matched with those species in ACG, eliminated everything but the barcode, gave them all new names, took habitus photographs for each species, and voila. Taxonomy published. Or so I'm guessing.

This is all my imagination. I repeat, I don't know how this happened. But it seems likely, and I don't have a problem with it. There are all sorts of reasons for the taxonomic impediment: poor 100 year old descriptions, missing type specimens, a new genus named for every new species (thank you, Townsend). These are obvious, but there are many more hidden reasons for a lack of taxonomic progress. Often times there is a taxonomic scion, the last, greatest worker in a particular family. They remember everything, all the names, the relationships, all the hypotheses. And when they pass, they take all of that knowledge with them and leave behind no heirs. Often times a group isn't difficult by way of some taxonomic mistake, but just because it is naturally so. All the distinct species groups grade together at the boundaries, all the distinct species are apparently species complexes. And sometimes, all the knowledge is there, but it's behind a copyright wall and therefore cannot be published and acknowledged.

As a taxahacker, I only really care about what is helpful, about what actually progresses our understanding. So finding some way around the dissertation impediment appeals to me. Let copyright rot if it aids our work. However, the key word is "helpful". When I plan a natural history work, I think, who is this for? Who is this helping? Most of the time I consider my fellow and future researchers. They'll probably be using a stereomicroscope, similar to what I use or with worse optics. They'll probably not have a large research laboratory with genetic tools for identification. And they'll probably be people with only incidental interest in the group. Perhaps they work in field ecology, or pest management, or evolutionary biology. They will care little for single species descriptions, and appreciate in-depth revisions the most.

In sum, the average researcher that comes to your work is not going to have access to genetic sequencing equipment. They will have eyes and a microscope. We should aim to write for this level of technology. Any species description that omits morphological characters is effectively useless. Are Meierotto et al. species valid? The above train of literature would suggest yes. At least, they aren't junior synonyms of previously described species. But they aren't helpful, not to any reasonable student of braconid wasps. From Sarmiento-Monroy's dissertation I see that color patterns are necessary but insufficient for identifying Zelomorpha species. There are other necessary components, the shape of the head, the hairing and crenulations of the cuticle, the structure of the genitalia. Many of these aren't visible in a habitus photograph. I suppose I could refer the sequences in the paper back to the dissertation to find the diagnostic characters, but what a hassle!

Natural history science isn't a filing heuristic. Our job isn't to simply give all the things names, in whatever way possible, and organize them into the prettiest tree. The authors state that we must work ever faster with the biodiversity crisis upon us. To what end? I learned very little about Zelomorpha species from this article, nothing that wasn't already available through previous works or the ACG database. I learned that there are many species and have pretty colors. Replace "species" with "postage stamps" in that sentence; "all science is physics or stamp collecting." No, taxonomy is not Pokemon. Every insect species is a hypothesis of metapopulations. Every genus is a hypothesis of species relationships. Every piece of evidence presented, morphological, genetic, behavioral, either corroborates or negates these hypotheses. As Brower said, "the application of names to concepts does not corroborate or endorse the biological validity of those concepts." The names themselves do nothing. They are often satisfying or amusing, but they don't actually increase our knowledge. They're just a filing code. The problem with the paper isn't that the names are unavailable or invalid. The problem is that the species are poorly described. If this is the answer to the biodiversity crisis, then future generations will know nothing of Zelomorpha danjohnsoni, except that it lived in Costa Rica, fed on a species of noctuid caterpillars, and had black wings and an orange body. Oh, and its mtDNA sequence had A's and T's and C's and G's at particular positions. Hardly a useful fact if the species is extinct.

Yet, I understand authors' desires. There's a deep need to put a name on things, even if naming them doesn't actually help us understand them better. It's questionable science, but it's art I guess? So I'm torn.


Christopher Taylor said...

A couple of comments, the first a point of pure pedantry. It is possible for a dissertation to count as published if it meets the general requirements (production of a sufficient number of identical copies, yada yada). Most probably don't, of course. I've just had this question on my mind a little lately because a manuscript I'm currently working on is potentially affected by an (as far as I can tell) unpublished thesis.

The main thing confusing me here, though, is why the authors couldn't incorporate the descriptive work from the thesis. If it already exists in some capacity, surely it would be more effective to include it than not? Why couldn't Sarmiento-Monroy be invited as an author? Even if they couldn't directly work on the current paper at this time, then that would at least allow the current authors to extract what they needed from the thesis. Is Sarmiento-Monroy's supervisor no longer in touch with them? Did they have a falling out with their supervisor and are refusing to communicate? Are they still insisting that yes, they will get around to publishing their dissertation work some day, just give them some time? I can't help wondering a bit about whether shenanigans should be called here.

Nick said...

This is a great post. Similar attitudes are becoming too common elsewhere in natural history. We are getting a lot of highlights papers but no monographs or thorough descriptions.