Poor Taxonomic Practice takes some F****ing Liberties!

Bortolus, A. 2008. Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology. Ambio 37 (2): 114-118.

As you may have guessed from the title of this post, I'm kind of pissed. I got forwarded a copy of this paper earlier today, and was horrified by the results presented in it. Bortolus presents the results of a paper survey of 80 ecological papers published from 2005 to 2007 in ten top-ranked peer-reviewed ecology journals. The subjects of this survey were community ecology studies dealing with more than one species of organism, and for each study Bortolus took note of the sources for the identifications of the taxa surveyed. I hardly need point out how significant such identifications would be for the papers in question - after all, if the subjects of an ecological study are not reliably identified then the usefulness and significance of the entire study comes into question. So you would think that it would be pretty important for the authors to demonstrate the firmness of their identifications, no? Well, let me show you the graph of the results:



Note that the numbers do not necessarily add up to 100%. A single paper might haved used more than one form of identification. I also disagree slightly with Bortolus' treatment of "grey" (not or not significantly peer-reviewed) literature - lumping the citation of field guides in with unpublished theses does somewhat overlook that excellent field guides do exist for some taxa (most notably birds), and even amateurs without formal taxonomic experience may through these field guides hold a significant amount of expertise in identifying the taxa covered (also, of course, field guides are widely available and consultable while theses are not). Nevertheless, let me point out the part of the results that has incensed me the most. It's the second bar from the left. Fully a third of the papers surveyed gave no authority whatsoever for the identity of the species surveyed! It's not as if the bar was set particularly high for citing an authority, either. Acknowledging the input of a taxonomist who identified specimens (or having a taxonomist as one of the authors) counted. Noting that one of the authors of the paper had personally identified the taxa counted, or the use of a cited identification key, counted. All it would have taken in most cases would have been a couple of sentences. And yet, it seems that this is a couple of sentences too many in a lot of cases.

Of course, the availability of voucher specimens would do a lot to alleviate these concerns. I've written before about the importance of voucher specimens that allow other researchers to check specimen identifications. so how many of the papers surveyed noted the availability of voucher specimens?

2.5%.

Yes, you read right. Two point fricking five percent. What is more, those papers that did record voucher specimens were invariably among those that acknowledged the input of a professional taxonomist in some way, and so were probably not among the more suspect class in the first place.

As is de rigeur in this kind of discussion, Bortolus gives us examples of the kind of errors that can result from poor taxonomic practice. Some errors are fairly innocuous, but others can have fairly serious consequences. There's the case of a restoration programme in San Francisco that included the propagation and replanting of the native littoral grass Spartina foliosa. Unfortunately, the actual specimens propagated were not S. foliosa, but the non-native S. densiflora, and as a result of the programme S. densiflora was transformed from a minor adventive to a significant invasive. There's the case of three morphologically similar but ecologically distinct Mytilus mussel species, the decline of one of which due to the invasive spread of another went unnoticed for many years. There's the case of a failure to distinguish Anopheles mosquito species in Burma resulting in the long-term targeting of a non-malaria-carrying species by control programmes instead of the actual malaria vector. Bad taxonomy does matter.

Some of my readers may protest that it seems a little harsh to expect identification sources from authors who may be very familiar with the species involved and hence might be trusted to identify them reliably. To which I reply, bullshit. One of the main principles of science is that it is not enough to simply assert that one "just knows". And besides, is it really asking that much? Biomolecular studies, for instance, are expected to include full details of methods used, and it would not be considered unusual for an author to cite Saiki et al. (1988), no matter how many thousands of PCR reactions that author might have conducted during their career. Also, there are significant ethical considerations involved. In failing to cite or acknowledge their identification sources, authors are doing a significant disservice to the taxonomists on whose work their own relies. It is exactly this assumption that the reliability of taxon identifications can be taken for granted that has resulted in the undervaluing and loss of taxonomic expertise in many parts of the world. Is a passing mention in the acknowledgements really that much to ask?

8 comments:

  1. Don't get me started!

    Vials of mixed species with two different frakkin' 'data' labels that both have a code number and no locality ...

    Quadrat-chuckers who think that systematics is 'technicians' work. (That one's a whole kaleidoscope of offensive. It not only takes a swipe at taxonomists but also at techies.)

    And ... oh, that's right ... I wasn't going to get started.

    I'm with you.

    ReplyDelete
  2. Excellent points. As an evolutionary biologist / ecologist working on a PhD project containing a serious species-identification issue, I've done a bit of thinking on this and related problems.

    Foremost, though, is: What is it, exactly, that taxonomists do? I would love to work with a taxonomist, an expert who can identify the odd and obscure things I find... but I am certain the majority of taxonomists do not spend their time eagerly awaiting the next alcohol-soaked batch of haphazardously-gathered critters. I assume you, and other taxonomists, spend your time doing science, and not only identifying hordes of specimens.

    Because I do not know what taxonomists do, what they want to do, I find it difficult to approach taxonomists for help with my project. The handful of taxonomists I have approached have been almost-universally enthusiastic and friendly, but whenever I write to them I always worry that I will bother and annoy them with yet-another request to identify some bugs.

    I try to offer co-authorship, too, as it seems only fair. My data (genome sizes) cannot be presented without confident, accurate species identifications; I consider that level of critical input worth at least co-authorship. But I have nothing else to offer, and I am accutely aware of how busy with many projects most (all?) working scientists are. And I don't want to appear the ass by stating something like "I'll make you a co-author if you tell me what my bugs are".

    In summary, I wish to avoid the poor taxonomic practice you describe here, but I'm not sure how best to do so.

    ReplyDelete
  3. On a related note...

    Milner AM. 1994. Colonization and succession of invertebrate communities in a new stream in Glacier Bay National Park, Alaska. Freshwater Biology 32: 387-400.

    Milner reviews about 12 years worth of field work on a stream formed by a retreating glacier in Alaska, looking at colonization and succession among stream-dwelling invertebrates. In the discussion, there are some interesting points about the usefulness of tracking species, rather than higher taxa such as genera, as apparently many other ecology studies may be prone to do.

    ReplyDelete
  4. What is it, exactly, that taxonomists do?

    Writes learned treatises, of course ;-). Yes, most taxonomists will have their own projects they are working on. But this does not mean they necessarily won't be interested in helping with yours.

    The handful of taxonomists I have approached have been almost-universally enthusiastic and friendly, but whenever I write to them I always worry that I will bother and annoy them with yet-another request to identify some bugs.

    Well, as the saying goes, you'll never know until you ask. Of course, what a given taxonomist wants in return for their input probably depends entirely on the person. They may be quite happy to work with you. Or they may not have the time to do the work themselves but be quite happy to help train you so you can do the IDs yourself. Or, admittedly, they may want to be paid. And yes, co-authorship would often be a nice carrot - the "publish or perish" dictum currently holds as much in taxonomy as any other field :-).

    It is becoming more common these days for ecologists to do their own taxonomic work, due to the shortage of available taxonomists. I suppose just treat it like any other part of your methods - cite what tools you used, and include your justifications for any uncertainties. And, most importantly, deposit voucher specimens!

    In the discussion, there are some interesting points about the usefulness of tracking species, rather than higher taxa such as genera, as apparently many other ecology studies may be prone to do.

    This isn't surprising. After all, a 'genus' is ultimately just a construct of convenience (or, more accurately, which level of diveregence between two taxa you want to call a 'genus' is). The genus Drosophila for instance, contains about 2000 species. The genus Pan contains two or three. I wouldn't expect the two to be directly ecologically comparable.

    ReplyDelete
  5. I wouldn't expect the two to be directly ecologically comparable.

    I whined about this some time ago.

    http://brummellblog.blogspot.com/2007/05/localness-of-taxonomy.html

    It's nice to see someone explicitly agree with me that taxonomic categories higher than species are artificial (which is not to say they're not useful).

    ReplyDelete
  6. It's nice to see someone explicitly agree with me that taxonomic categories higher than species are artificial (which is not to say they're not useful).

    Not artificial, as such, but certainly arbitrary. To explain what I mean - imagine if you have three species forming a distinct evolutionary group, and you know two of the species also form a group of their own to the exclusion of the third. There is no objective guide on whether you should recognise one genus of three species or two genera with two species in one and one in the other. The evolutionary groups are real, but which one you chose to recognise as a "genus" is fairly arbitrary.

    Nice work on using Opiliones as your example in your post, by the way! (says Christopher the Opiliones researcher ;-) ).

    ReplyDelete
  7. David Marjanović9 June 2008 at 03:10

    Pet-peeve alert:

    (which is not to say they're not useful)

    They are not just not useful, they are actively misleading, because people commonly count them and believe they have quantified biodiversity, when in fact they have quantified various people's opinions instead. If you want to quantify biodiversity, you have to do it. Counting genera, families or orders is self-deception.

    ReplyDelete
  8. David, I think you've misunderstood what Brummel meant a little. I took his meaning as that higher categories might still be useful in other contexts (such as communication) while not useful in biodiversity quantification.

    ReplyDelete

Markup Key:
- <b>bold</b> = bold
- <i>italic</i> = italic
- <a href="http://www.fieldofscience.com/">FoS</a> = FoS