História evolutiva do gênero Caiman Spix, 1825 (Crocodylia, Alligatoridae): delimitação de espécies através de uma abordagem integrativa.

Abstract

The Caiman genus is composed of the largest diversity of taxa among Neotropical crocodilians, composed of three species: Caiman crocodilus (four subspecies), Caiman yacare and Caiman latirostris. Despite this, there is a big gap about the real diversity of evolutionary lineages and species within the genus, especially due to the lack of sampling throughout the distribution of all taxa. The use of coalescent-based species discovery methods has enabled the delimitation of a high diversity of cryptic species, being fundamental for studies of integrative taxonomy of complexes of morphologically conserved species, as in the case of crocodilians. The main goals of this thesis was to unveil the evolutionary history of the genus Caiman, using coalescent-based methods of species discovery and validation using mitochondrial and genomic markers, incorporated later in an integrative taxonomy framework, making it possible to verify the real number of species, the relationships between them and how this diversification occurred within the genus. In the first chapter, we used for the first time a representative sampling throughout the entire distribution of the genus, and with the use of mitochondrial marker Cytb and coalescent species discovery methods, it was possible to verify a high diversity of lineages (10-13) in the genus Caiman. In addition to making a dated phylogeny for the genus and showing that, geological events during the Oligocene and Miocene shaped the diversification of the major lineages within Caiman. We also discuss the threats and conservation measures necessary for the conservation of those evolutionary lineages. In the second chapter, we sub-sampled the mitochondrial lineages found in the Caiman crocodilus/yacare and C. latirostris species complex and performed a new generation sequencing to incorporate multiloci data (ddRADs) in our species validation analyzes. In addition, we used morphological data such as cranial sutures, scalations and geometric morphometrics to verify differences in the shape of the skull between the lineages, through an integrative taxonomy approach. Species discovery methods using SNPs and ddRAD were similar to mitochondrial results. In addition, associated with the differences found in the shape of the skull, cranial sutures and the pattern of scales on the flanks, it was possible to verify significant differences that suggest the recognition of Caiman fuscus as full species, occurring in the Magdalena River basin throughout the Central América, in addition to proving the taxonomic status of Caiman yacare as full species. In the third chapter, we used the same database as the first chapter and incorporated samples of the exotic populations of Caiman crocodilus in South Florida to verify the real taxonomic status of the species and determine the possible origin of this population. We found that this introduced population is composed of only one lineage, Caiman crocodilus fuscus, with possible origin from the Magdalena River basin in Colombia.