Evolutionary Studies of Two Major Groups of Teleost Fishes (Otophysi and Tetraodontiformes) Integrating Phylogenomic and Paleontological Information
Open AccessThe Teleostei is a spectacularly diverse group of fishes that comprise over 32,000 species that inhabit freshwater, marine and estuarine waters. Many recent molecular phylogenetic studies have unraveled the evolutionary relationships of teleost fishes; however, for some groups their interrelationships remain unresolved. In this dissertation, I address the evolutionary history and systematics of two major groups of teleosts: Otophysi and Tetraodontiformes. I address the phylogenetic relationships among lineages of Otophysi, the largest radiation of freshwater fishes with over 10,000 species. I collected genome-wide sequence data from 1,051 exons using target capture and Illumina sequencing for 225 species representing all major lineages. I also introduced a new practical phylogenomic approach (namely, Gene Genealogy Interrogation or “GGI”) to studying ancient divergences in the face of high levels of phylogenetic conflict among gene trees. The results of this section resolve a longstanding conundrum in fish systematics regarding the branching order of major otophysan lineages, reconciling a long history of conflict observed in many recent molecular studies. Ultimately these results are congruent with the null morphological hypothesis about otophysan relationships, providing support for the monophyly of the order Characiformes. Finally, I tested the generality of the GGI approach in other distantly related groups with controversial resolution in the Tree of life. GGI supported the notion that ctenophores are the earliest branching animal lineage, and adds insights into the relationships within clades of yeast, birds, and mammals. I also assessed the monophyly and relationships of Stevardiinae, a species rich Neotropical subfamily of otophysan fishes in the family Characidae (order Characiformes), and I investigated the evolutionary origins of internal insemination in the group. To tackle these questions, I examined 355 specimens representing 153 species in 32 genera, and sequenced three mitochondrial and 4 nuclear genes. My results support the monophyly of the Stevardiinae and provide a framework to address the taxonomic limits within the subfamily, leading to a revised classification that recognizes 50 genera. Finally, I include a taxonomic revision of the stevardiine genus Acrobrycon, with the description of two new species. I estimated multi-locus phylogenies of the predominantly marine tetraodontiform fishes (Percomorphaceae: Eupercaria) complemented with morphological data of extant and fossil taxa to reassess the time-scale of tetraodontiform evolution. I also use tetraodontiforms as case study to provide an empirical comparison of phylogenetic dating approaches, including node dating and tip dating methods, as implemented in different programs (MrBayes and BEAST), and using different models (e.g., Fossilized Birth Death). Finally, I investigated the phylogenetic placement of 16 recently described fossil species and assessed macroevolutionary dynamics in the group based on inferences that combine paleontological and neontological data. The results of this section reveal robust estimates for the origin of tetraodontiforms, indicating a complex evolutionary history during the late Cretaceous and Cenozoic, shaped by mass-extinctions and changes in speciation and extinction rates.
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