A New Look At F. Similis And F. Majalis DNA

I've been on a new burst of activity analyzing cytochrome b DNA sequences using the Geneious software package. I've realized that Bayesian inference, a somewhat quirky statistical method, is the best approach to comparing sequences of DNA and building a tree so as to easily visualize patterns of relatedness and divergence. The image above is a cleaned-up, simplified analysis of what I have to date in my quest for looking at the relatedness between two very similar coastal killifishes, Fundulus majalis and F. similis. The two fish at the top of the cladogram are related species present to serve as outgroups, for comparison purposes to "root" this analysis. The numbers at the nodes of the branches are consensus numbers, basically a measure of how strong the decision to put a branch at that spot on the tree is from running lots of replicates of the tree building algorithm.

The two species separate out cleanly in this tree, but there's not very much distance between them; the scale bar showing 0.03 (substitutions per base, really) is about how different they are, and that's not a big difference between species. The other interesting feature of this tree is that the Key West, Florida, F. similis is relatively removed from others of that species. There has been discussion over the years about whether the Key West population is really a separate species. I would say that it doesn't appear to be, but it does rate consideration as a distinct population about halfway to being a distinct species, with the other Florida group being close to it (I'm not sure where in Florida that's from, I downloaded that sequence from GenBank and it was only labeled Florida). I have a thought that because Florida has so much coastline that has been suitable habitat for a long period of time (even during the last glaciation) that Florida populations are more ancient and have had time to diversify. Conversely, F. majalis is only found on the Atlantic coast and has probably been affected by glacial cycles that greatly reduce available habitat, leading to lower genetic diversity as a result of long periods of reduced population. That's my working theory, anyway. I hope to have more DNA sequences in the not-so-distant future (thanks, Tony!) and see how this plays out with more localities.