Phylogenetics, Macroevolution, Biogeography, and Herpetology
Welcome to the Skipwith lab in the Biology Department at the University of Kentucky. Research in this lab focuses squamate reptiles to understand the mechanisms of diversification within lineages. Specifically, the processes impacting the tempo of speciation and phenotypic change, the relationship between speciation and phenotypic diversification, and the phenomenon of convergent evolution. These are particularly pertinent subject areas when it comes to understanding the forces responsible for the generation of adaptive radiations. To date, I have used a variety of techniques, including phylogenomics and CT-scanning, and analytical methods to better understand the processes governing macroevolutionary dynamics.
Lab News: Now Looking for Students 2022!
I'm pleased to say that the Biology Department will have slots open for new Ph.D. students for the fall of 2022. For prospective students interested in phylogenomics, macroevolution, and adaptive radiations, email me at pskipwith@uky.edu. My lab currently has projects focusing on the phylogenomics and comparative phylogenetics of geckos and caenophidian snakes with the aim of foraying into whole genome sequencing in the coming year.
Featured Research
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All critters are welcome, even molluscs
Lucy Chang and I have a manuscript on bivalve evolution coming out in Paleobiology soon, so keep a look out. Here, we combine molecular phylogenetics, fossil occurrence data, and community assembly methods to test whether competitive exclusion or environmental filtering influenced the composition of the San Joaquin Basin (SJB) bivalve community. New velvet gecko species!
Chris Jolly, Paul Oliver, and I recently described a new Australian velvet gecko, Oedura nesos, from the island of Groote Eylandt. This species is morphologically similar to other certain other species from the marmorata complex on the mainland, but is very distinct genetically. This finding supports that this small island from the northwest corner of the Gulf of Carpentaria serves as an area of endemism for various squamates. Ecomorphological diversification of snakes
For the last two years, I have been working at the American Museum of Natural History with Frank Burbrink on the phenotypic evolution of unique group of snakes, the pseudoxyrhophiine lamprophiids of Madagascar. More simply, the Malagasy gemsnakes. I've made the transition from mostly phylogenomic work to working with high-res micro CT scans to examine ecomorphological diversification. We've found that while the Malagasy gemsnakes have generated an astounding degree of ecological diversity, they've managed to replicate phenotypes seen elsewhere in unrelated colubroids (advanced snakes). Australasian gecko phylogenomics
The first chapter of my dissertation just came out in Molecular Phylogenetics and Evolution. Here, we looked at the entirety of the Diplodactyloidea, the group of geckos that includes pygopods and the New Caledonian radiation, using a massive phylogenomic dataset. We implemented over 4,000 Ultraconserved Elements to fully resolve relationships in this clade of over 200 . species. Comparisons of topological metrics support that this is the most well-supported phylogenetic estimate for this clade and that the relationships recovered here differ markedly from those proposed in earlier, Sanger-based, molecular studies. Divergence dating supports multiple mid-Cenozoic over-water dispersal events into Oceania but fails to support any mass extinction events, something that has been proposed previously. 
Map of Oceania with species counts for each of the three diplodactyloid families.
New Caledonian gecko diversification
My interest in herpetology began with my Masters at Villanova University with Aaron Bauer. I had the good fortune of working on the phylogenetics of New Caledonian diplodactylid geckos, a diverse radiation of 36 described species. Well, that study is finally out! We present a revised phylogeny using a multilocus dataset implementing multispecies coalescent methods. Turns out this group is very young, much younger than previously thought and probably dispersed to New Caledonia sometime during the Miocene. We also demonstrate that this clade experienced rapid initial speciation followed by a gradual slow down. |
Time calibrated phylogeny of bivalves in the SJB during the Cenozoic. Colored boxes to the right indicate the presence of a given genus in the SJB during a given time bin.
Live Oedura nesos from figure 2 of Jolly et al. (2020). Taken by Chris Jolly.
Phylogenies of the Diplodactyloidea based on 4,268 UCEs. Red tips indicate discordant placements between the multispecies coalescent and concatenation. Left: Timetree from MCMCtree constrained on the species tree topology from ASTRAL. Right: Concatenated RAxML phylogram.
Timetree from *BEAST for the New Caledonian clade. Note the young crown age.
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