The use of integrative analyses for understanding the evolutionary and ecological determinants of diversity in New World Crocodylia



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The origin and evolution of Neotropical biodiversity is an area of study that has had a tremendous impact on conservation of New World flora and fauna. The lack of comprehensive knowledge in this matter reduces our capability to adequately address current or future environmental changes, due to either natural or anthropogenic causes, which may not only challenge the natural world in general, but may affect our very existence as a species on Earth. The development of predictive models to generate hypotheses about the evolutionary fate of Neotropical lineages in response to environmental changes is crucial for biodiversity conservation and will be inappropriate unless we understand the patterns of evolution consistent with the processes that are fundamental in maintaining lineage distinctiveness in this ecoregion. Important questions like whether species would be able to: (1) tolerate the projected global warming as a result of phenotypic plasticity, (2) migrate to more favorable habitats, (3) be able to respond quickly and adapt to the new conditions, or (4) face mass extinction are central to conservation biology. Due to the stochasticity and complexity of speciation processes in the Neotropics, any single criterion or empirical data used to delimit and characterize independently evolving lineages can lead to misunderstanding biodiversity and ineffective conservation plans. My research investigated the genetic and environmental forces that have contributed to speciation in the Neotropics using as a model two widely distributed New World crocodylian species, Crocodylus acutus (Cuvier 1807) (an estuarine/saltwater crocodile) and Caiman crocodilus (Linnaeus 1758) (freshwater caiman). My studies have focused on: (1) patterns of diversification, (2) the effects of regional tectonic history, climate change, and sea level changes during the Pleistocene and Quaternary on levels of intra-specific and inter-specific genetic diversity, and (3) the effects of secondary contact and biota interchange within the Neotropics on the phylogeographic and phylogenetic relationships within each lineage. This research tested whether each of these two widespread tropical crocodylian species are genetically cohesive or represent species complexes with high levels of genetic divergence. First, this research uses coalescence theory, phylogeography and phylogenetic analysis in combination with ecological and morphological analysis to infer the historical biogeography and patterns of ancestry in both taxa. Second, I integrate geographic, climatic, and genetic data within a Geographic Information System (GIS) framework to identify putative geographic or ecological barriers promoting reproductive isolation, to design predictive models of species geographic distributions and to identify Evolutionarily Significant units (ESU) within their respective ranges. My results have revealed that both genera, Caiman and Crocodylus, are far more diverse and their evolutionary histories far more complex than previously thought and recognized that the species richness in the Neotropics depends on factors such as the geological and ecological history of the region, as well as the physiology and the ethology of the species. The variety of mechanisms affecting the species distribution and richness in the Neotropics implies that biogeographic patterns are in some way species-specific. My data on caiman populations showed significant population structure and supported the biological validity of recognized subspecies, while also revealing two additional lineages that were not predicted by subspecific taxonomy. One of these is a South American lineage of late Miocene origin and one is a Mesoamerican lineage of early Pleistocene origin. Currently there are no obvious geographic barriers between several distinct mtDNA clades; I showed that in general the evolutionary history of C. crocodilus corresponds to geological and geographical changes that occurred in the Neotropics at the end of the Neogene and in the early Pleistocene, e.g., the rise of the Andes ~5 mya and the closure of the Pacific–Caribbean seaway by ~2.5 mya. The geographic distinctiveness and the decreased physiological capability of caimans to live in saline environments suggest that for Caiman crocodylus sea water is a barrier for its dispersion. Conversely, my results strongly suggest that for Neotropical Crocodylus, adaptive radiations and repeated cycles of population isolation and expansion and global climate changes in the Pleistocene were the primary cause of the diversity we see in the true crocodiles today. The only major geological change in the region that had amajor evolutionary effect on Neotropical crocodiles was the closure of the Isthmus of Panamá. Although habitats are currently, in almost all cases, continuous and reproductive barriers are not fully established, each lineage maintains its identity because they occur in different ecological niches, with reproductive cycles that are seasonally controlled (latitudinal gradient of reproduction). The evaluation of the effects of geographic isolation, gene flow, and the time of isolation on populations structuring of crocodile populations [Crocodylus floridanus (Hornaday 1875)] in the Coiba archipelago and the evaluation of the relative effectiveness of the sea as a barrier for dispersal of C. acutus suggested that crocodiles disperse by the sea using currents as pathways. Interestingly, my results also demonstrate that despite varying levels of gene flow, each population still appears to be able to maintain its own “genetic integrity”. Although it was not the scope of this study to understand the roles of reproductive and social behaviors in population diversification, crocodiles have long-term generation time, are highly territorial (both males and females), with apparently significant social structuring. These species characteristics may play a very important role in both population genetic temporal stability and population divergence.



Crocodilians, Genetics, Evolution, Ecology, Crocodylus, Species-delimitation, Population, Genetics, Phylogeography, Neotropics