Phylogeography of the green anole
In the course of our research on transposable element solution, we realized that if we were to fully understand the dynamics of amplification of TEs in our model, the green anole lizard (Anolis carolinensis), it was necessary to know the population structure and demographic history of the species. Using a multi-locus phylogeographic approach we discovered that anole populations were structured into five evolutionarily distinct and geographically restricted lineages that last shared a common ancestor two million years ago (Tollis et al. 2012 pdf). Surprisingly, we found that the distribution of genetic diversity in this species is not consistent with a latitudinal shift caused by climatic oscillations as is observed for many co-distributed organisms. This suggests that the most recent Pleistocene glacial cycles had a limited impact on the geographic distribution of the green anole. We further determined that Florida is the cradle of green anole diversity, and that the early diversification of lineages within this species was probably driven by recurrent sea-level refugia, population fragmentation and divergence via genetic drift (Tollis and Boissinot 2014 pdf). Once the Florida peninsula reconnected to the mainland, two separate dispersal events led to the expansion of green anole populations across the Eastern Seaboard and Gulf Coastal Plain, respectively.
Evolution of Ethiopian frogs
The Ethiopian highlands constitute the largest continuous mountain system in Africa. These highlands are a biodiversity hotspot, particularly in amphibians as 40% of the species found in the highlands are endemic. Surprising little is known about the climatic and geological processes responsible for the large biodiversity encountered in Ethiopia. We used a widespread and abundant genus of frogs, Ptychadena, to investigate the processes of diversification and speciation in the Ethiopian highlands (Freilich et al. 2014 pdf). We resolved the phylogeny of Ethiopian Ptychadena using a species-tree approach and determined that species group on the phylogeny according to their habitat preference. We proposed that the diversity of Ethiopian Ptychadena results from an early phase of specialization to distinct elevations followed by a phase of ecological diversification within each elevational range. We estimated that the early phase of diversification probably occurred in the late Miocene and the most recent speciation events in the late Pliocene or Pleistocene.
Baboons (genus Papio) are distributed over most of sub-Saharan Africa and in the southern portion of the Arabian Peninsula. Six distinct morphotypes, with clearly defined geographic distributions, are recognized (the olive, chacma, yellow, Guinea, Kinda, and hamadryas baboons). The evolutionary relationships among baboon forms have long been a controversial issue. Phylogenetic analyses based on mitochondrial DNA sequences revealed that the modern baboon morphotypes are mitochondrially paraphyletic or polyphyletic. The discordance between mitochondrial lineages and morphology is indicative of extensive introgressive hybridization between ancestral baboon populations. To gain insights into the evolutionary relationships among morphotypes and their demographic history, we performed an analysis of nuclear variation in baboons (Boissinot et al. 2014 pdf). We sequenced 13 noncoding, putatively neutral, nuclear regions, and scored the presence/absence of 18 polymorphic transposable elements in a sample of 45 baboons belonging to five of the six recognized baboon forms. We found that the chacma baboon is the sister-taxon to all other baboons and the yellow baboon is the sister-taxon to an unresolved northern clade containing the olive, Guinea, and hamadryas baboons. We estimated that the diversification of baboons occurred entirely in the Pleistocene, the earliest split dating ∼1.5 million years ago, and that baboons have experienced relatively large and constant effective population sizes for most of their evolutionary history (∼30,000 to 95,000 individuals).