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Tackling Evolutionary Questions in Fishes with Genome-Wide Data from Recent Speciation to Ancient Divergences Open Access

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Ray-finned fishes (Actinopterygii) form the largest clade of vertebrates with more than 34,000 valid species currently described. Here, I use a variety of sequencing approaches to tackle evolutionary questions in fishes, from recent habitat transitions in a group of silverside fishes, to disentangling over 400 million years of evolutionary change to infer the phylogeny of all ray-finned fishes. Chapter two of my dissertation focuses on silverside fishes in the genus Odontesthes (Atherinopsidae), which have recently and rapidly transitioned from marine to freshwater. Two closely related species, marine O. argentinensis and freshwater O. bonariensis, span this ecological divide, and yet show little genetic divergence in mitochondrial markers. We sequenced gill transcriptomes from wild-caught O. argentinensis and O. bonariensis to look for candidate genes that might be of ecological importance in the adaptation of these fish to freshwater habitats. Chapter three focues on resolving relationships in the genus Odontesthes using a large ddRADseq dataset with more than 150 samples, and cytochrome b haplotype dataset with more than 400 individuals, spanning the geographic range of Odontesthes. This chapter addresses the evolutionary relationships and some species boundaries in this group, which have been difficult to disentangle. Marine O. argentinensis and freshwater O. argentinensis, (discussed in chapter 2), despite having no differentiation in cytochrome b, clearly separate into distinct clades with ddRAD data. Chapter four produced the largest phylogenomic matrix (in basepairs, and backbone taxonomic sampling) to date for Actinopterygiians, using a database of 305 genomes and transcriptomes to address paralogy for an exon-capture set for fish phylogenomics. We developed a heuristic using topology tests to detect paralogs in our marker set based on known genome duplications affecting fishes, and inferred a phylogenetic tree to test our marker set of 1105 exons. We also addressed topological conflict in the literature using the ‘gene genealogy interrogation’ technique.

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