Closer to the molecules

It's been a while since my last post... again!

This semester was full of many things going on: classes, comprehensive exam, ESA meeting, work (in two publications -mostly one- that are not part of my dissertation), finishing one weevil paper (of my queue of 3; nothing to do with dissertation either).

One of the classes I took this semester was Phylogenetic Methods with Dr. Mark Holder at the EEB Department at KU.

Maximum Likelihood phylogeny for part of the Acidocerinae

Overall the course was very well planned and executed. I just kind of wish I have had better computational skills, and that I was less stubborn to begin with. Just after our first two lab sessions I realized I'm strongly attached to WinClada (perhaps by learned habit), not only because (in my opinion) it makes creating/editing matrices way simpler than Mesquite (don't get me wrong, I like Mesquite. It can do many more things than WinClada), but also because I had not used (was probably avoiding) other programs to perform phylogenetic analyses. So far I had only worked with morphological data, and refused to leave my parsimonious comfort zone. After trying the GUI version of PAUP*, I was sold!

Then, when we started using Maximum Likelihood (ML) and Bayesian inference programs, it was really challenging for me to get all the command-line applications to work, and at the same time satisfying when the programs finally ran. Also because, as I mentioned before, I'm stubborn and always try to figure things out by myself, instead of asking for help, which is just time-consuming.

The last task for the class was to apply some of the tools we learned to a dataset, so I performed ML and Bayesian phylogenetic analyses to the current dataset that we have for the Acidocerinae (170 terminals + 11 outgroups). For most of those terminals we have sequence alignments for the mitochondrial loci COI, and the nuclear loci 18S, 28S, H3, and CAD.

For the concatenated dataset the results are highly consistent between methods (and roughly in agreement with the molecular analysis presented by Short & Fikáček (2013)). For the most part the same groupings were recovered with comparable support. Given that some of the clades obtained were not well supported (see the grey box in the figure on the right), I also made ML analyses for each of the genes to check for gene-tree discordance. It was very interesting to see how each gene tells a different story, and then how the tale that each particular gene tells, is very similar to previous classification schemes proposed for what now is known as the Acidocerinae. No wonder why this group of hydrophilids is so confusing!

As a point of information, the clades in the grey box are exclusively Neotropical, and only fairly recently discovered. Some of them have been described in the past 20 years or so, and some are only now being described (although present in collections since the 60's - 80's).
The clade highlighted in orange corresponds to Quadriops, the only known terrestrial acidocerine, that we recently revised. You can find the publication here: https://zookeys.pensoft.net/article/19815/
The clade in green corresponds to Globulosis, whose revision also came out this year: https://biotaxa.org/Zootaxa/article/view/zootaxa.4232.2.10
The clade in purple (at least the Tobochares part of it) was also revised by members of our lab this year: https://zookeys.pensoft.net/article/11773/

So all in all, I feel satisfied with the semester (and glad it is finally over!!). The exercise with the molecular dataset was very rewarding for me, and a good way to make me more comfortable working with molecular data and the many parameters you have to keep in mind, and the tons of resources (people among those) that are available for you to make better decisions and obtain more robust phylogenies. Also, it would be interesting to have more genes (more stories) to add to the mix, but then again, we need a stop-point along the way.

References

Girón, J.C. & Short, A.E.Z. (2017) Revision of the Neotropical water scavenger beetle genus Quadriops Hansen, 1999 (Coleoptera, Hydrophilidae, Acidocerinae). ZooKeys 705: 115–141.

Kohlenberg, A.T. & Short, A.E.Z. (2017) Revision of the Neotropical water scavenger beetle genus Tobochares Short & García, 2007 (Coleoptera: Hydrophilidae: Acidocerinae). ZooKeys 669: 113–146.

Short, A.E.Z. & Fikáček, M. (2013) Molecular Phylogeny, Evolution, and Classification of the Hydrophilidae(Coleoptera). Systematic Entomology 38: 723–752.

Short, A.E.Z., García, M., Girón, J.C. (2017) Revision of the Neotropical water scavenger beetle genus Globulosis García, 2001 (Coleoptera: Hydrophilidae: Acidocerinae). Zootaxa 4232(2): 271–281.