Friday, June 15, 2007

Taxonomy: Species Identification

I haven't been blogging much lately because I've been trying to work out how best to talk about the single biggest problem in my PhD so far: species identification.

I want to measure genome sizes for a wide range of metazoans - in other words, lots of animals, across a number of Phyla (the highest taxonomic level within the 'Kingdom' Animalia1). People who study individual groups of organisms name themselves after that group - so people who work on lots of different insects call themselves "Entomologists"; people who study molluscs are "Malacologists", people who study Fungi are "Mycologists". If you know the relevant Latin and (ancient) Greek word-roots, these titles all make sense. I don't have a problem with these titles; I have a problem with the relative scarcity of some specialists and their poor publication record of monographs for non-specialists, i.e. for ME. I'm a generalist!

Identification keys for all sorts of obscure and not-so-obscure groups have been published; many get revised every decade or so as the taxonomy of those groups gets revised. For example, I have heard rumours of an upcoming revision and simultaneous new identification key for nematodes of the order Rhabditida. Sounds good, yes, please do this... RIGHT NOW. I cannot frickin' identify roundworms to save my life.

Most of the existing keys that I've been able to find have not been to species. Some work down as far as genus; many go only as far as family. While these are useful, in providing clues and keywords for further searches, they don't actually solve my problem for any given unknown 'bug' sitting in a puddle of ethanol under my dissecting microscope. Specialists, I imagine, do not have this problem, at least not as often as I do - if you work on freshwater isopods, for example, you probably have already met the most common 20 species in your area, and you know just by looking at a specimen which family to look for it in first. Myself, I have to start by working out which friggin' PHYLUM this critter belongs in (most things turn out to be arthropods; but some related things are actually in other phyla, like Tardigrada; others are obviously Mollusca, or Annelida, or...), then work my way down to Class, Order, and Family, before searching for another key for that family (if it exists) to get down to genus or species.

One obvious problem with very detailed, species-level keys is that they tend to be an order of magnitude longer and more complicated than a key for the same group to family. For example, I have two keys for Collembola2, one in an entomology textbook, the other in the excellent book Soil Biology Guide. The first goes to family, and covers a mere six steps on about half a page. The second goes to genus, and covers 140 steps over 25 pages. This comparison is a little unfair, because the first key references family descriptions on another full page, and has one accompanying figure covering a whole page; the second key includes descriptions for each genus within the key (when one reaches a particular genus endpoint through the key) and numerous full- or half-page figures.

This is turning into a psuedo-rant, possibly because I'm sitting at school at 7:00 on a Friday evening writing about something that frustrates me every day and, while I do not think I am being kept awake by this issue, I do know that my thoughts frequently turn to this unresolved problem in the interval between putting away my book and turning out the light and the actual onset of sleep. So, I should truncate this before I get too ranty.

I mostly wanted people to know that I am still planning on maintaining this blog on a semi-regular basis, to apologize for the recent lack of activity around here, and simultaneously provide some insight into some of my day-to-day activities. In this case, the hour-or-so-on-average per day process of grinding through identification keys, trying to count setae on body segments of very small animals that you may not have been aware even exist. The upside of all this is that when I do successfully3 identify something, I feel like I've accomplished some difficult task, which is a good feeling, and I'm learning tons about broad-scale biodiversity in a seriously under-studied realm. I still don't know what to call myself - "invertebrates" is a polyphyletic category. Any suggestions? I'm currently thinking of just calling myself a "Zoologist", since I'm happy to examine pretty much any animal.

1. Yes, yes, I know the whole concept of Kingdoms is basically obsolete; the fact remains that "Metazoa" is a monophyletic group, and therefore taxonimically and phylogenetically acceptable. Barring exceptions that are sure to appear soon from either novel discoveries (especially from the deep ocean) or re-categorizations of things currently known as "Protista".

2. Incidentally, the picture shown in the Wikipedia article for Collembola is of an unidentified species of genus Isotoma, which is in the same family (and the picture looks remarkably like) as the three individuals (all likely the same species) that I pulled out of a soil sample earlier this week. So I feel slightly less confident in my identification of my specimens as Proisotoma sp.

3. Even those identifications I get to without any Choose-Your-Own-Adventure style backtracking or really tentative guesses are not 100% certain to me. Which is why I need to contact a range of experts, professional taxonomists, to help me confirm my identifications and help me with the stuff that's not in the keys. Most of these people work at major museums; as such, I have never met such a person (for any taxon) in person. Just one more novel experience that forms part of my PhD. That's a good thing (the new experience, I mean), I think.

As an aside: how do I put my little footnote indicators as superscript, rather than as their current form of a number merely in the smallest text size accessible in Blogger's text editor? I like numbered footnotes better than asterixes.


Anonymous said...

how do I put my little footnote indicators as superscript, rather than as their current form of a number merely in the smallest text size accessible in Blogger's text editor?

Try this:

Anonymous said...

Google still amazes me. Your blog is already #17 on for "blogger superscript".

There is no Blogger stylesheet for superscript, so you'll have to use the HTML workaround listed above.