Systematics, biogeography, and phenotypic evolution of the Thamnophilini (Aves, Thamnophilidae): a massive parallel DNA sequencing approach

Abstract

The Thamnophilini are the most species-rich radiation within the antbirds in the family Thamnophilidae. They are ca. 80 species widely distributed from Mexico to Argentina that reach their highest diversity in Amazonia and show high levels of endemism in various Brazilian biomes, such as the Caatinga and the Atlantic Forest. They inhabit a wide variety of habitats and exhibit high phenotypic diversity. Previous work based on Sanger sequencing of nuclear and mitochondrial DNA has successfully unraveled their recent phylogenetic history, but resolution of the early stages of their diversification process has been difficult. Therefore, their biogeographic history and patterns of phenotypic evolution still remain poorly understood. Recent technological advances in massively parallel DNA sequencing (MPS) technologies allow gathering genetic data at very large scales, which provides opportunities to increase resolution power and to assess how these new inferences compare with hypotheses and comparative analyses based on previous DNA sequencing technologies. The fundamental goal of the proposed research is to unravel patterns of phenotypic evolution and the biogeographic history of the Thamnophilini based on a MPS phylogenetic hypothesis of the tribe. Specifically, I will 1) produce a subspecies-level phylogeny of the Thamnophilini by targeting nuclear ultraconserved genomic elements (UCEs) throughout the genome, and massively sequencing adjacent regions that retain the signal of phylogenetic information at different time depths; 2) compare temporal and topological information of the MPS-based phylogenetic hypothesis with one I previously constructed based on Sanger sequencing of six nuclear and mitochondrial genes; and 3) integrate the resulting phylogeny with morphometric, plumage, vocal, and environmental data to perform model-based analyses that evaluate different scenarios explaining the biogeographic history and the process of phenotypic evolution in this diverse group of birds. (AU)