Friday, January 20, 2012

An Addendum to 'Misconceptions About Taxonomy'.

Original post is here.

I have been reading Steven Jay Gould's Wonderful Life: The Burgess Shale and the Nature of History. The work in entirety is a controversial illustration of a quiet yet revolutionary change in biology, which was later disputed by the researchers who made the discoveries. A section from page 80 is most relevant to my post, where Gould discusses how the romanticism of field work and the "technocratic myths about machine-based novelty" have very little to do with the new discovery of disparity of forms in the Burgess Shale.

The myth of field work, for example, proclaims that the great alteration in ideas arise from new, pristine discoveries. At the end of the trail, after weeks of blood, sweat, toil and tears, the intrepid scientist splits a rock from the most inaccessible place on the map, and cries Eureka! as he spies the fossil that will shake the world. Since the Burgess [ed.: taxonomic] revision was preceded by two full seasons of field work, in 1966 and 1967, most people assume that discoveries of this expedition prompted the reinterpretation. Well, [Harry] Whittington and company did find some wonderful specimens, and a few new species, but old [Charles] Walcott, a maniacal collector, had been there first, and had worked for five full seasons. He therefore got most of the goodies. The expeditions[...] did spur Whittington into action, but the greatest discoveries were made in museum drawers in Washington [at the Smithsonian]-- by restudying Walcott's well-trimmed specimens. The greatest bit of "field work", as we shall see, occurred in Washington during the spring of 1973, when Whittington's brilliant and eclectic student Simon Conway Morris made a systematic search through all the drawers of Walcott's specimens, consciously looking for oddities because he had grasped the germ of the key insight about Burgess disparity.
The Burgess revision did require a definite set of highly specialized methods, but the tools of this particular technology do not extend beyond ordinary light microscopes, cameras, and dental drills. Walcott missed some crucial observations because he didn't use these methods--but he could have employed all Whittington's techniques, had he ever found the time to ponder, and to recognize their importance. Everything that Whittington did to see farther and better could have been done in Walcott's day.
For the most part, taxonomy does not employ any fancy new methods. In fossils, the methods are much the same as they were 100 years ago. In insects, this is similar; we have devised some new tools to find characters in molecules, but the old visual microscope and hand drawing methods are tried and true. Most universities with a physics department have had a scanning electron microscope since the 1970s, and many biology departments have their own.

Likewise, most taxonomic work, be it on fossils, insects, soil invertebrates, or ocean plankton, does not take place in the field. Most collecting is in bulk samples, which are later sorted through, and all the items of interest are taken out by the investigator. The rest of the sample (if not tossed) is stored for future research. For example, the Field Museum of Natural History in Chicago, IL, has an extensive alcohol-stored collection of insect bulk samples from around the world. Over decades these are picked through, and discoveries are made. In addition, all museums have orphaned specimens, or specimens the collector thought were interesting but didn't have enough time to investigate. Given the diversity of life in insects, it is not surprising that any single researcher, specializing in a particular group, will overlook new species or genera in his or her picking. Just like the Burgess Shale fossils, many future discoveries are already waiting on a museum shelf.

Drawing is a reconstruction of Marella, the most common Burgess Shale arthropod fossil. © Marianne Collins, from Gould's Wonderful Life (1989).

Tuesday, January 3, 2012

The hollow curve, lumpers versus splitters, and arbitrary (yet useful) ranks.

Yesterday, science journalist Ed Yong asked "which genus has the largest number of living species" as a Google+ thread. He admitted that it was a trivial question of curiosity, and he's right. While the wood boring genus Agrilus (Coleoptera: Buprestidae) may have the most described number of species (~3000), this is not a particularly important or interesting question when it comes to taxonomy or systematics in general. However, the question spawned an energetic argument over the arbitrariness of taxonomic groups in terms of size and content, and I wanted to speak my piece about it.

[If you graph] the number of genera contained in any group [of organisms] against the number of species contained in those genera, using one axis for genera and the other for species, we get, apparently regardless of the group we are dealing and the quality of the systematic work done upon the group, a curve of a characteristic form. This has been called the "hollow curve of distribution". (from Ferris (1928) The Principles of Systematic Entomology)

In modern ecology the hollow curve describes the relative species abundance within a community, but it also describes the distribution of species within genera. A small number of genera will have a large number of species relative to the whole, and a greater number of genera will each have a relatively small number of species. Unlike ecology, this was an probably an artifact of human taxonomy and the continuous disagreement between "lumpers" and "splitters".
An exaggerated "hollow curve of distribution" for visualization, with numbers of species on the Y axis and number of genera on the X axis.

The general consensus in systematics is that species are real groups of organisms, and for the purposes of this post I would not like to argue over that point, or about genetics or species concepts. Likewise, monophyletic groups, that is, groups of species which share a single common ancestor, are also real. After the modern evolutionary synthesis and the description of classification as the depiction of evolutionary relationships and not overall similarity (regardless of relationship), monophyletic groups became the standard for describing taxa.

A simplified version of the Linnean Hierarchy (© Tutor-Vista)

However, taxonomic ranks (e.g. family, genus, tribe) above species and the decision to place a particular group as a genus or a tribe, for example, is completely subjective and somewhat arbitrary. The hollow curve of distribution was due to the choice of some taxonomists to make large genera ("lumpers"), and of others to whittle those large genera down to smaller genera over time, or to raise a genus to tribe and the subgenera within to genera ("splitters"). This is sometimes called "taxonomic inflation" by those who see this tactic as an attempt by the taxonomist to raise the public importance of his or her group of interest. These split up genera are all monophyletic groups, just much smaller, more manageable monophyletic groups. (ETA: other hypotheses in the comments)

Still, the Linnean ranking system remains useful in relating hierarchy. It is unambiguous that a tribe belongs to a family, that a subgenus belongs to a genus (ETA: though not necessarily to the genus you /think/ it belongs to, or including the members you would expect: see comment by Christopher Taylor below). If I tell you a species is of the Tribe Hydropsychini, it is taken for granted that the tribe contains genera, and is contained by a family (in this case Hydropsychidae). This makes it easy to organize the general reference system. Ranks also make it easier for taxonomist to communicate their phylogenies. (ETA: Again, see comment by Taylor below)

Unfortunately there are some taxonomists who are uncomfortable with the Linnean system of ranks. Among these are the people responsible for the Phylocode. The Phylocode eliminates the Linnean ranking system and replaces it with a hierarchy of unranked "clades", while species names are still described under the rules of the already established codes of nomenclature. This to me seems like hierarchical obfuscation. While it is very easy to communicate a hierarchy using ranks, it is very difficult to do so without them. Anti-ranking advocates complain there are not enough ranks to properly describe all the monophyletic groups, but the code doesn't prohibit the creation of new ranks above and within family level ranks, they just are not covered under the rules. If you want to talk about a semi-infra-tribe, or a super-kingdom, that's perfectly acceptable. Any other criticisms, like the issue of hybridism, are best addressed within the individual codes. To collapse and remake the entire general reference system just to eliminate rankings (which are useful in their own right) is preposterous. Enough people were upset over the Drosophila case that there may be rioting in the universities if Phylocode is ever successful.

So, while the arguments that taxonomic groupings are arbitrary is false, ranks are somewhat arbitrary and yet useful. The important notion is to not rely on them as indicators of importance. And that questions like "what's the largest genus" comes down to a trivial contest of lumpers versus splitters. In this case the winners are probably beetles (is anyone surprised?).
Agrilus derasofaciatus (CC Encyclopedia of Life)