Phylogenomics, diversification, and biogeography of Neotropical squirrels (Sciurillinae and Sciurinae: Sciurini)

• Autor(a) principal: Abreu Júnior, Edson Fiedler de
• Data de Publicação: 2020
• Tipo de documento: Tese
• Idioma: eng
• Título da fonte: Biblioteca Digital de Teses e Dissertações da USP
• Texto Completo: https://www.teses.usp.br/teses/disponiveis/91/91131/tde-07012021-171352/
• topic: Biogeografia; Biogeography; Filogenia; Phylogeny; Sciuridae; Sciuridae; Sistemática; Systematics; Taxonomia; Taxonomy

Squirrels are conspicuous inhabitants of most Neotropical forests, where they play ecologically crucial roles as seed predators and dispersers. Two distinct radiations are found in this region: the subfamily Sciurillinae, represented exclusively by the Neotropical pygmy squirrel (Sciurillus pusillus); and the tribe Sciurini (subfamily Sciurinae), a speciose group composed of about 45 species of tree squirrels that also occur throughout the Nearctic and Palearctic regions. Despite their unquestionable importance to ecosystems dynamics and representing a substantial portion of the diversity of rodents in the Neotropics, squirrels have been largely neglected by taxonomists and systematists. As a result, basic information on number of genera and species is still ambiguous for the group, and also most aspects of their evolution and diversification remains unclear. In the present thesis, I employed mitochondrial genomes and Ultraconserved Elements to undertake the molecular systematics and the evolutionary history of the two radiations of Neotropical squirrels. In the Chapter 1, I used mitogenomic data sequenced from 232 historical and modern museum specimens to provide the first comprehensive phylogeny of tree squirrels. I contrasted the phylogenetic results with generic arrangements proposed for the tribe Sciurini, discussed the taxonomic implications, and suggested a tentative new classification at genus level employing 13 generic names used by previous authors. I also found evidence that the diversity of Neotropical tree squirrels is underestimated, with at least six lineages that represent taxa to be named or revalidated. In the Chapter 2, my main objective was to test current hypotheses on the tempo and mode of diversification of tree squirrels, employing the mitogenomic dataset including 43 of the 46 putative species of Sciurini. I estimated the date of origin of the tribe Sciurini around 14 Mya and suggested that its ancestral area was most likely in North America. The origin of the Neotropical radiation was estimated to have occurred around 6 Mya in northwestern South America, in the Pacific dominion. The majority of Neotropical cladogenetic events occurred along the Pliocene--right after the South American invasion. A fairly constant speciation rate was estimated for tree squirrels, which contrasts with the peak of lineage accumulation observed in the Pliocene. In the Chapter 3, I provided a nuclear genome-wide perspective of the Neotropical squirrels (Sciurillinae and Sciurinae: Sciurini) phylogeny, employing over 3,700 Ultraconserved Elements sequenced from 184 historical and modern samples. Phylogenetic analyzes estimated with strong support the relationship among the five subfamilies of Sciuridae, and also provided consistent and well-supported results for the relationships among the deepest branches of Sciurini. For the Neotropical radiation, which experienced a rapid diversification, conflicting relationships at both genus- and species-level were estimated upon data filtering and inference method. Inconsistences were also recovered with regards to the mitogenomic hypothesis. Finally, in both chapters 1 and 3, I took advantage of the large sampling across a diverse lineage of mammals to investigate how distinct aspects of historical samples might influence the recovery of genomic data, providing useful information for future genetic studies sampling from historical specimens.