Evolutionary studies in South American marsh rats (Rodentia: Holochilus)

• Autor(a) principal: Prado, Joyce Rodrigues do
• Data de Publicação: 2017
• Tipo de documento: Tese
• Idioma: eng
• Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
• Texto Completo: http://www.teses.usp.br/teses/disponiveis/91/91131/tde-14032018-110612/
• topic: Biogeografia; Biogeography; Clade D; Clado D; Genômica; Genomics; Morfometria; Morphometrics; Next generation sequencing; Oryzomyini; Oryzomyini; Rodents; Roedores; Sequenciamento de nova geração

An interdisciplinary approach integrating micro and macroevolution, genomic, morphometric and morphological variation, systematics, quantitative genetics, and biogeography was employed to investigate the evolutionary history of the genus Holochilus (Rodentia: Sigmodontinae). Holochilus presents poorly defined species, with nomenclatural problems and phylogenetic relationships on species level unknown. The current species number possibly does not reflect its real diversity, and no work combining genetic and morphometric evidences from all its geographic range was performed. This genus belongs to the tribe Oryzomyini, and along with other 14 genera constitute the Oryzomyini clade D, the most comprehensive generic diversity of the tribe, occupying distinct environments. The internal phylogenetic relationship within this clade is still unclear and variable. Due to its broad geographic distribution, Holochilus also represents a key piece on the study of the evolution of oryzomines of open formations of South America. Based on a comprehensive sampling, I analyzed patterns of morphometric and genomic variation within Holochilus, in order to delimit the species belonging to this genus, as well as access the phylogenetic relationship between these lineages. I investigated the sexual and ontogenetic variation in this group, comparing natural and captive populations, seeking for understand the effect of the environmental differences in the pattern of variation and ontogenetic trajectories (Chapter 1). I also evaluated and compared the genomic variation among three species of Holochilus to verify the influence of the biomes and the climatic changes in the genomic signatures (Chapter 2). I applied a model-based approach to delimit species (Chapter 3). And finally, additional investigations were made to propose the phylogenetic relationship between members of clade D, and provide date intervals for the main diversifications events, as well as the possible process responsible for the biogeographic pattern current observed related with the forest and open areas occupation (Chapter 4). Sexual dimorphism exhibited small degree of variation among populations. The greater ontogenetic variation is found in the younger age classes, but oldest individuals also show larger degree of differentiation. There are also great differences in the ontogenetic trajectories among samples, where individuals from the captive population exhibited the lower degree of variation between all age classes. The quantitative genetic analysis showed that genomic differences are observed across the taxa, and it was associated with geography. Ecological niche models revealed that biomes with larger areas of stability also presented more genomic structure, suggesting that historical dimension impacted population isolation/connectivity. Results also shows that biomes not only differ geographically and environmentally (based on past climatic conditions), but also show significant association between the environmental space and the genetic variation that is not related with geography. Eight independent lineages within Holochilus were recovered, and the phylogenetic arrangement partially corroborates previous studies. Finally, the phylogeny proposed for the clade D presented some differences in comparisons with other previously reported, and suggest that most of the cladogenetic events happened during the Pleistocene, being the expansion of open environments an important driver of diversification in this group.