Comparative Phylogenomics, Cryptic Species and Evolution of Lizards in the Cerrado Biodiversity Hotspot

Author: Fabricius Maia Domingos

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Domingos, Fabricius Maia, 2015 Comparative Phylogenomics, Cryptic Species and Evolution of Lizards in the Cerrado Biodiversity Hotspot, Flinders University, School of Biological Sciences

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The evolution and diversification patterns of the Neotropical biota are a matter of extensive scientific debate. Despite centuries of research interest in this region, the levels of biodiversity in the Neotropics are still largely underestimated. This is particularly true for the Cerrado, the largest Neotropical savannah and a formally recognized biodiversity hotspot. The Cerrado landscape is dominated by ancient plateaus and younger valleys that were excavated by river catchments. Throughout the Quaternary climatic fluctuations, during moister periods, the savannah vegetation was restricted to refugia in the plateaus, while the valleys were invaded by forest-like vegetation. Both the landscape compartmentalisation caused by the uplift of the Central Brazilian Plateau and the Quaternary climatic fluctuations have been proposed as drivers of diversification of the Cerrado biota. However, these hypotheses have not been properly tested in a phylogeographic perspective, and the understanding of processes that shaped the distribution of biological diversity within the Cerrado is still incipient. Lizards have for long been used as model organisms in evolutionary studies. They are generally poor dispersers and thus can be used as indicators of fine-scale biogeographic history. The study of endemic Cerrado lizards has the potential to elucidate the influence of historical changes in the landscape on the ecological characteristics of lineages, and to clarify the resulting patterns of biodiversity. In this thesis, I employed a comparative phylogeography approach and used species delimitation methods to address knowledge gaps of Cerrado endemic lizards, and to clarify diversification patterns in the Cerrado. Three codistributed endemic lizard species were targeted: Gymnodactylus amarali (Phyllodactylidae), Micrablepharus atticolus (Gymnophtalmidae) and Tropidurus itambere (Tropiduridae). For each species, I used a combination of phylogenetic analyses, Bayesian species delimitation analyses, coalescent statistical phylogeography and population genetic estimates based on sequences of one mitochondrial DNA gene and of ~400 nuclear loci obtained using an anchored phylogenomics protocol. Morphological data for one of the three taxa were also integrated into the analyses. The results suggested the existence of several cryptic species within each taxon. Statistical phylogeographic analyses coupled with species distribution modeling indicated that endemic lizards exhibit a degree of concordant phylogeographic history but also taxon-specific evolutionary patterns within the Cerrado. The two species groups that use similar habitats, G. amarali and T. itambere, displayed similar geographic distribution of basal clades, and similar estimated ancestral distributions. On the other hand, results also indicated that landscape compartmentalisation probably played different roles in the evolution of each taxon. The ecologically distinct M. atticolus and T. itambere had very similar palaeodistributional shifts throughout the Quaternary, while G. amarali presented a different refugia pattern. Overall patterns of diversification are associated with geologic processes during the Neogene and with a complex history of colonisation of plateaus and valleys during the Quaternary. This thesis pioneered the investigation of several competing diversification hypotheses about the Cerrado in a comparative context, and is the first example of species delimitations methods using next- generation sequencing for Cerrado organisms. The results will guide the description of several new species for the biome and directly contribute to conservation planning. Future research on the evolution of Cerrado biota should focus on linking patterns of genetic diversity and speciation with climatic and geomorphological processes of the biome.

Keywords: Evolution, Neotropics, Savanna, Reptiles, Next-Generation Sequencing.
Subject: Biological Sciences thesis

Thesis type: Doctor of Philosophy
Completed: 2015
School: School of Biological Sciences
Supervisor: Professor Luciano B. Beheregaray