Friday Fish: Pegasus volitans

A seamoth, family Pegasidae, order Pegasiformes. This is a very small and very strange family; my Fishes of the World, 2nd Edition (Nelson, 1984) describes a single genus, with five species, and only this family in the order. It also describes the family as

"Body oddly shaped (broad and depressed), encased in bony plates; mouth small and toothless, beneath a long flattened rostrum (formed by fused nasals), with an unusual mechanism for protrusion of the jaws...

Image from WildSingapore's flickr page, here.

Friday Fish: Gymnothorax funebris

The Green Moray, a member of the species-rich family Muraenidae, order Anguiliformes (the true eels). This photo was sent to me by Necator - thank you very much!

Friday Fish: Calamoichthys calabaricus

This is one of the world's only surviving bichirs, an order of fishes (Polypteriformes) lumped in with some other weirdos (such as last week's coelocanth) that are not the ray-finned fishes that most people are more familiar with. In ichthyology and evolutionary-history classes, they always seem to get listed with the other oddballs next to or after the "main event" fishes, which in practice always seems to be composed primarily of the Perciformes. That's a rant for another day, if ever. There appears to have been some recent systematic work on the bichirs, as the alternate genus name Erpetoichthys also shows up.

Picture from here.

Friday Fish: Latimeria chalumnae

The Coelocanth. The most famous "living fossil", the lobe-finned fish that lives in the sea (rather than muddy and prone to dehydration tropical fresh waters), and has accidentally been associated with South Africa's former racist government. They give birth to live young, which should provide a stumble for any wishing to apply the term "primitive" to these famous-but-poorly studied fish.

Photo from here: http://marinebio.org/species.asp?id=54

Dr. Rob E. Roughley

I received an email today, informing me that a man I was proud to call a colleague and fellow traveller in this business of science has died. Professor R. E. Roughley was not someone I knew well, but I did benefit from knowing him as much as I did, and I am saddened by his death.

Rob was an expert on water beetles, particularly of the family Dytscidae, which is a group I worked on for the time I was based in Guelph. Rob provided excellent advice on methods of capturing, identifying, and generally working on these beetles and other small animals commonly found in the numerous small lakes, ponds, streams, and rivers of North America. His advice was always useful, and I can think of many instances where his help turned my fieldwork, collecting aquatic animals, from hopeless to bountiful.

We shared a glass or two of whiskey while we were both in Churchill in the summer of 2007. I raise my glass now to his fond memory. Goodbye Professor Roughley, you will be missed.

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.

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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.

The Localness of Taxonomy

Yesterday was Linneaus' 300th birthday, apparently, so I'm a day late on this post. But I only really thought of it today, though the idea has been bouncing around my head for about a week.

By "localness" I mean the non-universality of taxonomic terms, particularly mid-level terms like "Order" and "Family". What I mean is that it's quite nonsensical to compare families, for example, across much higher levels like phyla. It's a non-sequitor to describe an order of Arachnid arthropods, such as Araneida (spiders) in terms of an order of Mammalian chordates such as Carnivora.

What the hell is Martin talking about?

This is an idea that's been oozing around my skull, formless and labile, for about a week. I've been reading way too much of Soil Biology Guide (edited by D.L. Dindall) recently, a book I highly recommend, so my mind has become clogged with obscure words for obscure taxa. Like Opiliones. What the hell are Opiliones? That question is actually more than one - what are these beasts? What taxonomic level does it describe? Why is it a chapter title in a book about things that live in dirt?

The beasts in question are somewhat-commonly referred to as "harvestmen" or "daddy-long-legs". They're arachnids, part of the same class of animals that includes spiders, mites, termites and a lots of other, much less well-known critters. Apparently, there are lots of soil-dwelling forms (with short legs) (to answer the third question) and even the long-legged, surface-striding species typically lay their eggs below ground, and often prey on unfortunate soil-dwellers that venture onto the surface.

Fig. 1. A scan of page 542 of Soil Biology Guide. Are these not the scariest-looking creatures you've ever seen? Imagine that coming at you, striding along on eight long, spindly, many-jointed legs, picking up things and sucking out their precious bodily fluids. Being a small invert would be very scary.
The figure legend reads: Fig. 19.20. Zuma acuta, lateral view. [From Briggs (1971b).] Fig. 19.21. Sclerobunus robustus robustus, lateral view. [From Briggs (1971b).] Fig. 19.22. Sclerobunus nondimorphicus, lateral view. [From Briggs (1971b).] Fig. 19.23. Claw of leg IV of Metanonychus nigricans oregonus: (A) dorsal view; (B) lateral view. [From Briggs (1971b).] Fig. 19.24. Paranonychus brunneus, lateral view. [From Briggs (1971b).]

The taxonomic level for "Opiliones" is an Order. At this point my weird exclamations at the top of this post come in to play. More familiar orders might be things like Primata (Primates: monkeys, apes, etc.) or Passerines (Song birds, including everything from LBFs galore to robins, sparrows, crows, etc.). But how can I compare Harvestmen to Primates? The term "order" doesn't make sense divorced from higher taxonomic levels. I don't think it's at all valid to think of the diversity of Opilione forms in terms of the diversity of songbirds. Perhaps if we stay within the same phylum (Arthropoda).... does it make sense to compare the spiders to a single order of insects, like Coleoptera? Besides the obvious (ridiculous) raw-diversity difference (to a first approximation, most animals are beetles, Coleoptera, though there are an awful lot of spiders), everyday experience suggests comparing spiders (an order) to all insects (a class). At least, in my everday experience...

This becomes an issue of explaining what I do to a non-scientist. An ecologist, or evolutionary biologist of almost any specialization should be able to grok pretty quickly the idea that "I'm looking for a maximum diversity of animals to study, at the highest taxonomic levels" means "I collect inverts, including insects, spiders, crustaceans, snails, worms, and other, more obscure things" (a statement that spans taxonomic levels from order up to superphyla). But how many "normal" people, non-scientists, ever think about the (enormous) differences between, say, earthworms and sea cucumbers?

Moving on with another weird non-sequitor (are any non-sequitors not weird?)... in the science fiction novel Moving Mars, by Greg Bear, which I read more than ten years ago, one of the main characters gets a brain implant that is essentially a computer memory chip that provides her with intuititive understanding of basic physics. Without getting into a discussion of what constitutes "basic" physics, I'd like such chips to be invented, preferably at the earliest possible opportunity. Rather than a chip for physics (which would, admittedly, be highly kick-ass), I'd like one for taxonomy. I want to know intuitively what Tricladida, Solifugae, Mesostigmata, and Pauropoda are. I want to know without thinking about it which groups of invertebrates would be most useful to study, from the perspective of broadening our understanding of fundamental evolutionary processes like selection. And why the hell are so many things named "Psuedo-X"?

Literature Cited:
Briggs, TS. 1971. The harvestmen of family Triaenonychidae in North America (Opiliones). Occas Pap Calif Acad Sci 90: 1-43.
Dindal, DL. (ed.) 1990. Soil Biology Guide. John Wiley & Sons, New York
Edgar, AL. 1990. Opiliones (Phalangida). In: Soil Biology Guide, ed. Dindal, DL. John Wiley & Sons, New York, pp 529-581.