Thursday, April 7, 2011

Molecular techniques and species discovery.

I received a link to this poll in my e-mail through the Entomological Collections Network listserv. While I appreciate being able to give my imput, most of the important questions, (e.g. "do you think molecular techniques help in species discovery" were yes/no questions with no space for comments. The most interesting of these was "Do you think molecular techniques can accelerate species description?" To which I answered no, emphatically.

Despite complaints to the contrary, species description is not a particularly difficult process. While Botanical and Zoological Nomenclature differ in that the botanical code requires the primary description to be written in Latin, they otherwise have all the same features. There is a brief introduction and materials and methods, followed by the diagnosis (short description meant to separate the new species from other known members of that group) and description (longer statement of all aspects of the morphology). Typically there are illustrations, which can be achieved with a microscope that has a grid eyepiece (or a camera, if you're lucky enough to work with larger organisms). Then the material examined, remarks on biology, systematics and distribution, and works cited. I have already discussed techniques to accelerate the activities that go into species description before the actual writing part. Notice that none of those include any molecular techniques.

The simple truth is, while molecular techniques may speed up the process of resolving cryptic species complexes, they seldom (if ever?) increase the speed at which species are described. Current estimates are that there are millions of undescribed species on Earth, most of those being arthropods. And I propose that many of these are sitting in museums and unsorted trap samples. The ICZN still requires a formal description for a name to be recognized, and without a name it's very difficult to talk about something. If you look at what characters people are using in their descriptions and diagnoses, 99% of the time these are gross morphology. And, for the vast majority of all the species yet to be described, this is all that is necessary. To make things easier, there are journals such as Zootaxa which specialize in publishing descriptions of new species, and have accelerated peer review and publication time within a month.

Accelerated species description will not occur when everyone has a lab equipped with a pyrosequencer. Accelerated species description will occur when biologists as morphologists spend more time contemplating Evenhuis' Steps to Enlightenment and Taxonomic Nirvanna. The only way species get described is by writing a paper, and the only way diagnoses and descriptions get written is by looking at the organisms. Collecting from poorly sampled regions, sorting old trap samples, building taxonomic libraries, photographing and illustrating type specimens, and many many hours at the microscope examining morphology, these are how species description will accelerate. Not by molecular techniques.

Friday, April 1, 2011

We just lost a giant.

Thomas Eisner died last friday.

If you have not read For Love of Insects, I highly suggest it. E.O Wilson called him a modern Jean Henri Fabre for good reason.

One note about the NY Times article: check out the black and white photo of Eisner at his scope. My advisor pointed out that it's a Wild M5, what many still consider is the ultimate stereo microscope for it's simplicity, durability and clarity of optics. I have one (not my own) at my lab bench, and I plan on purchasing one eventually. Production of these scopes ceased in the 1980s and Leica scopes (the company Wild Herrburg merged with) are just not the same quality. It's telling that great biologists such as Eisner used this very scope.

Book Review: Foundations of Systematics and Biogeography.

Ebach and Williams "new" book has been out for several years now, and while Platnick, Brower, and Amorim previously weighed in, none of these are as critical and scathing as Ferris's recent review in Cladistics.

The book does, though, contain things we did not know—indeed, there are things here that no one has ever known. Among these revelations are that cephalaspids are placoderms; that Haeckel was responsible for grouping by overall similarity whereas Cuvier and Huxley had nothing to do with it; that Sokal and Sneath (1963) were primarily interested in phylogeny; that Nelson never accepted transformation; that Hennig used only congruent characters, because Sokal and Sneath said so; that paraphyly has no connection with symplesiomorphy; that DNA sequences have no hierarchic structure—unless used by Patterson; that parsimony is limited to binary characters, is closely linked to grouping by overall similarity, and does not draw conclusions of homoplasy; that reversals do not really happen and would be plesiomorphies if they did; that all un3ts data are phenetic—unless used by Patterson; that 3ta and ppa are not methods, being inspection of the data instead; that transformation is a myth; and that transformation is nonetheless distortion. A reader would have to be rather poorly informed to fall for this nonsense, which is to say that the book has obviously been designed to victimize just such readers. Ignorance is strength. This brings us back to Platnick's (2009, p. 281) central comment:

It should be especially useful for students.

Like Williams and Ebach, he has realized that tricking the least experienced students is the only chance that 3ta has left. No doubt publishers relish such recommendations. If Platnick’s endorsement were believed, Springer would get their $90 a head regardless of the damage done to students.


I haven't yet had time to purchase a copy and read it, so I can't really weigh in from my perspective. Generally, I trust the evidence Ferris presents in his review. The main conflict centers around the use of three taxa analysis (3ta), and whether or not it is a useful method for phylogenetic inference. This old method takes three taxa from a set to be analyzed, decides which two are more closely related to each other than to the third, and puts them back into the mix, rinse, repeat, until all relationships are resolved. This seems to me to be a wholly inefficient way of parsimoniously finding a summary of relationships, and according to Ferris's review, may be more likely to create paraphyletic groupings than path finding the shortest trees by heuristics (approximation) and collapsing to a consensus. Consider if you had 30 species to search, which is millions of combinations. This is not the same as simply trying to resolve the relationship between three taxa alone. The simplicity of such an arangement means there are only three hypotheses (topologies), of which one is correct. An example would be simply trying to find the relationship of Ephemeroptera, Odonata and Neoptera. Relationships within each of those groups or outside are irrelevant to the question: are Ephemeroptera and Odonata more closely related to each other than either is to the Neoptera? Another issue I find is the emphasis that a so called "reversal" of a character could never be considered a synapomorphy. To which I ask, at what level?

Farris's comments makes the whole of Foundations seem to be a strange reactionary piece against traditional pattern cladistics, whereas traditional pattern cladistics is seen as reactionary by many molecular biologists today. I am not saying I'm going to remove Urhomology from my blogroll; I still value many of the statements Ebach and Williams have made there. It was while reading through the backposts I was inspired to write the statement "Homology is the key to the heart of biology", which continues to be a motto for me in regards to the importance of homology (synapomorphy) in figuring out the history of life and the pattern of evolution. I appreciate their rejection of paraphyly and their use of the term phylophenetics when discussing molecular phylogenetics as it is done currently. Even if the authors dwell on false or bad premises it does not carry that those ideas could not be instrumentally true in regards to the right premises.

When I finally purchase and read Foundations of Systematics and Biogeography, I'll let you know if my opinions change.