At this point in my project, I’m playing around with different methods to analyze the collected data. I’ve translated my Mesquite matrix to a MacClade matrix so that it’s more compatible with StrataPhy, a program that incorporates stratigraphic data into a cladistic analysis. The drawback is that this is a very slow program (given that it does include the stratigraphic data) and it’s a bit odd to handle. The upcoming week will be spent figuring things out on my own as my adviser is in Australia until next Tuesday. Thankfully if I run into any issues, Gene is right down the hall and acts very well as a stand-in adviser.
Altogether, I coded for 29 taxa within the Knightites genus with ranges from the Lower Pennsylvanian to the Lower Triassic—this includes the Retispira, Knightites, and Cymatospira subgenera. I did go ahead and code an extra species, an Upper Mississippian Patellilabia, to be used as an outgroup if necessary (really, that just makes the program run much more quickly). I’ll run it with and without the outgroup to see if there are any significant differences. Currently I’ve only done small test runs with MrBayes and StrataPhy, producing several preliminary trees. So far, even within the test runs, some really interesting (and consistent) clades have been popping up. On the other hand, the Retispira group really is a monster of a polyphyletic mess—one of which I cannot sufficiently tease apart during my stay here. We’ll see how it changes (if at all) when I do complete runs next week.
In short, I’m still goin’ strong!