So what do systematists do for spring break?

Thanks to a post on Darren Naish’s blog Tetrapod Zoology about plastic pelicans the taxon of interest was pelicans. For people who actually care how I got the tree hear are the methods. Otherwise just skip it and go check out the tree. I only did a parsimony analysis, but if I get bored I’ll do a Bayesian analysis also. As I’m not a pelican taxonomist I’ll leave the result interpretation to someone who actually knows something about these birds.

Methodology

Sequence data

Due to my inability to get morphological data and the fact I was on spring break so didn’t want to spend the entire time tracking down original descriptions etc to code a morph matrix my analysis is only of molecular data mined off of Genbank. I narrowed the sequence data to genes that had sequences for at least 3 taxa included in the analysis (5 pelicans and 1 outgroup a shoebill, Balaeniceps rex). Genes included in my analysis were cytochrome oxidase subunit 1, ATP synthase subunit 8 and 6, 12s, Fibrinogen beta chain gene, cytochrome b, and ornithine decarboxylase gene. A total of 3893 bases were included in the analysis of which 3409 were constant. Of the remaining characters 313 were parsimony uninformative leaving 171 characters as parsimony informative. Because sequences were not from the same specimen they were combined at random in order to have one sample of each taxa with the most possible sequences for analysis.

Taxon sampling

Data were only available for 5 of the 8 species of Pelecanus. Included taxa were the brown pelican (P. occidentalis), American white pelican (P. erythrorhnchous), great white pelican (P. onocrotalus), Dalmatian pelican (P. crispus), and the Australian pelican (P. conspicillatus). Only a single gene (which was not available for any other species) was available for the spot-billed pelican (P. phillippensis). The remaining two species, the Perunvian pelican (P. thagus) and the pink-backed pelican (P. rufescens) lacked any sequence data.

Data analysis

Data were extracted from genbank, aligned in clustal w (using bioedit) then manually checked by eye. Data were then analyzed using parsimony in PAUP*. A heuristic search was done using 1000 random adition sequences. Next duplicates of taxa were removed and an exhaustive search performed (tree shown below)

Results

A single most parsimonious tree was recovered with a length of 547. CI and RI were 0.956 and 0.870 respectively. The ingroup was monophyletic with a bootstrap value of 95. The Australian pelican was the most basal of the ingroup sampled. I haven't done bremer supports or looked at the Ti/Tv ratios etc if people are curious though it could be arranged.

What were they thinking?

The alleged Brazilian wandering spider in Tulsa is a great example as to why we need collections (and taxonomists to work in them). A brief summary of the story: spider found in banana section of whole foods in Tulsa, OK. Manager is concerned its dangerous and commits mistake number 1- taking it to University of Tulsa. Now I'm sure U. of Tulsa is well known for something, but trust met arachnid identification is not it. Once there the spider is shown to the animal facilities manager- mistake number 2. I'm not exactly sure what animal facilities managers do but I expect their knowledge of exotic spider taxonomy is rather limited. Rather than sending the manager off to an actual expert he gave an ID. I'm not sure what his id was based on but whatever the case he made an identification as a Brazilian wandering spider. To be fair if you don't know what something is (and you've made the decision somehow to still answer the question) I guess its safer for all involved to go with it being the more dangerous option rather than saying its not dangerous and finding out the hard way it was (like the assumption an unidentified snake is venomous until it is identified as otherwise). After the determination was made mistake number 3 occurred. According to the new articles after identification the specimen was destroyed at urging of an administrator at the school making it impossible to figure out what species the spider actually was. Based on photos and videos of the spider in question various scientists are questioning the identification.

Although the first two mistakes caused the problem in the first place (taking the specimen to a diagnostic lab at major university or the USDA would have allowed identification by either a trained personal or if that was not possible sent to a specialist for determination) they are not the biggest problem. That distinction goes to mistake number 3. The first two mistakes could have been easily fixed if the specimen was available for study. Destroying the specimen compounded the previous errors by preventing a formal identification by experts. Instead they are stuck watching videos trying to look for distinguishing characters, a process which would take seconds with the specimen in hand.

Incidents like these highlight the need for taxonomists and collections. One of the cardinal rules of taxonomy is always keep the specimens. If the spider had been shown to a taxonomist of any flavor be it spiders or sea-slugs the importance of keeping the specimen in good condition would have been known. Related to the retention of specimens is the need for well maintained collections. If the manager of Whole Foods had taken the spider to Oklahoma State it could have been compared to known specimens held in the collection, making identification (even by someone with limited spider knowledge) more possible.

another month have passed

Well another month has passed and my life can pretty much be summarized with a few brief statements.
1. I defend my first thesis next month, i sank about have the members of the genus, and described a new species. Additionally I'm working on the description of 2 species in a related genus. No names posted so as not to cause confusion.
2. I got a 3 year fellowship to University of Illinois Urbana-Champaign to get my PhD in Ecology, Evolution, and Conservation. Start up there in August doing leafhopper systematics, hopefully some biogeography, and of course still playing in avian ecology
3. My peregrine is molting like its going out of style, if this continues he should be ready to go in September. I flew him in the Texas Sky Trials and learned an important lesson about greedy pitches. My kestrel is still weak from WNV but she is finally flying pretty strongly
4. I go back to africa in May. Will get my plane tickets next week, but it looks like I'll be there for 2.5 months, plenty of time to get the black spar hunting.
5. My pointer is going to be awesome, hes 9 months and already holding point like a pro.

Thats all for now, maybe I'll really start updating this thing now that its spring break and i have time to find cool stories to talk about...