The Catostomidae, colloquially known as the suckers, is a family of freshwater fish endemic to North America and Asia. This family is hypothesized to have evolved sometime before or during the Paleocene (56-66 Mya) from a single tetraploid ancestor, which is thought to be the product of a hybridization event between two closely related, diploid cypriniforms. Currently, there are 79 recognized, extant species, some of which are difficult to discriminate between in the field. Despite the numerous studies that have aimed to reconstruct the evolutionary history of this family, little consensus exists for the relationships of the subfamilies within the Catostomidae, with practically every combination of subfamilial relationships having been proposed in the past. Additionally, and of importance to our understanding of the evolution of the catostomids, little is still known about the consequences of whole genome duplication on molecular evolution, especially for polyploid animals. In this study, we sought to reconstruct the evolutionary history of the Catostomidae as well as characterize the patterns of molecular evolution of lineages within this family. Two nucleotide sequence, genome-scale data sets were generated with the aim to reconstruct the evolutionary history of the Catostomidae as well as characterize patterns of molecular evolution of their polyploid genomes. These data sets, an unphased data including one sequence for each taxon and a phased data with the number of sequences per taxon representative of their ploidy level, included 179 and 267 loci, respectively. From the reconstruction of the evolutionary history of the family, we recovered a topology which places Myxocyprinus asiaticus as the sister taxon to all other extant catostomids and Cycleptus elongatus as the sister taxon to an Ictiobinae + Catostominae clade. Additionally, we found that Catostomus was recovered as paraphyletic, with Deltistes luxatus, Chasmistes liorus, and Xyrauchen texanus forming strongly supported sister species relationships with species within Catostomus. In the second chapter, we found that the ictiobines, cycleptines, and myxocyprinines tended to have more polymorphic alleles than taxa within Catostominae. We also found that rates of molecular evolution were significantly greater within catostomine lineages than all other catostomid lineages
