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Despite the incredible diversity of lowland tropical rainforests; we still have limited understanding of the drivers of speciation in these ecoregions. In these difficult-to-access habitats that maintain a significant reservoir of the world’s biodiversity, it is widely accepted that a vast amount of species would remain undescribed and that some of them will likely go extinct before they have a chance to be properly described and studied. The present work studies the ecological, phenotypic and genetic diversification of Neotropical Harlequin poison frogs of the genus Oophaga, a group of organisms where a perplexing variation in colouration and patterns have led to taxonomic uncertainty. First, in order to investigate the relative contribution of geographical and environmental factors to the diversification of these frogs, I combined phylogenetic methods with detailed geographic data and environmental niche modelling (ENM) to test the role of geographic isolation, climatic niche divergence and altitudinal gradients. Overall, my results suggested that speciation along climatic gradients on a structured landscape has been a major evolutionary force behind the diversification of Oophaga poison frogs. Second, by using an integrative taxonomy framework and different lines of evidence derived from environmental data and intrinsic biological attributes (phenotypic variation, genetics), I statistically tested competing lineage-boundary hypothesis within the currently known Oophaga histrionica species. I found that diversity within the complex has been underestimated and proposed the existence of at least three independent evolutionary lineages of Oophaga poison frogs that should be further studied as they potentially represent new species to science. These results have important conservation implications as some of its members are considered amongst the most endangered species of all amphibians. Third, I hypothesized that the genes, pathways, and/ or gene networks potentially associated with colouration, alkaloid metabolism, transport and storage, should be highly expressed in skin tissue. Then, by taking advantage of the high coverage offered by Next Generation sequencing (NGS), I investigated the common transcriptional profiles of five Oophaga lineages. To my knowledge, this represent the first transcriptome dataset for Dendrobatid frogs where a functional annotation and comparative analyses allowed the identification of potential candidate genes in important adaptive traits. The identification of more than 250 orthologous contigs across lineages allowed testing the current phylogenetics hypothesis for this group. Overall, in this part of my work I provide an important molecular resource not only for the study of aposematism within Dendrobatids but for the future assembling and annotation of Dendrobatid genomes. Finally, Harlequin poison frogs represent an excellent group, yet underexplored, to study the ultracellular structural basis of colour variation and the role of candidate genes in colour variation. In this final part of my dissertation, I report the basis of histological-cellular components of colouration and provide initial hypothesis of the functional effect of mutations at the Melanocortin-1 receptor gene (MC1R) and the genetic mechanisms of colour variation in this frogs. One of the most interesting findings was the observation of similar phenotypes appearing independently in nature as a consequence of different mutations of the same gene, a classical example of convergent phenotypic evolution and genetic repeatability. Broadly, I provided evidence to suggest that variation at the MC1R receptor could potentially be a major factor responsible for the high phenotypic variation of aposematic signals of Harlequin poison frogs.



Dendrobatids, Niche modelling, Transcriptome, NGS



Doctor of Philosophy (Ph.D.)







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