Dissertation/Thesis Abstract

Phylogenetic and coalescent approaches to understanding North American freshwater fish diversity
by Harrington, Richard Charles, Ph.D., Yale University, 2012, 175; 3535397
Abstract (Summary)

North America is home to the most diverse assemblage of temperate freshwater fishes. Darters (Percidae: Etheostomatinae), with approximately 248 species, are the second-largest component of this assemblage and are endemic to eastern North America. Accurate phylogenetic hypotheses of the relationships among species of darters are integral tools for understanding the role of paleogeological events and biological processes that generated this astounding diversity. There is a long history of taxonomic and systematic study of darters—based primarily on morphological data. Unfortunately in many cases, there has not been enough morphological data generated to resolve and strongly support phylogenetic hypotheses or unambiguous taxonomic descriptions. Here, phylogenetic hypotheses, ranging from very recent (species delimitation) to much deeper evolutionary time (relationships among major lineages in a clade of approximately 54 species), are tested with multi-locus datasets in phylogenetic and coalescent frameworks. These phylogenies are applied to macro-evolutionary hypotheses regarding the evolution of morphological traits and ecological niche. These studies demonstrate the importance of utilizing an appropriate framework with which to address phylogenetic challenges at an array of evolutionary timescales.

A recent revision of the taxonomy of Etheostoma simoterum species complex described four new species in this clade. Descriptions were based largely on color patterns of nuptial males, and initial phylogenetic analysis suggested that many of the newly described species were not monophyletic. With expanded genetic sampling of multiple loci and re-examination of diagnostic morphological traits in nuptial males, these species descriptions were tested in a phylogenetic and coalescent framework. Morphological data and coalescent simulation analyses supported a scenario in which there are only three distinct species in the E. simoterum species complex, instead of six.

Catonotus is one of the largest subclades of darters, yet its monophyly has been largely untested with molecular data, and morphological data do not strongly support any hypotheses of relationships among Catonotus, or its relationships with other lineages within the larger Goneaperca clade. A dataset comprising 15 nuclear genes sampled for every species in Goneaperca is used to construct a phylogeny using Bayesian species tree and concatenated methods. These analyses strongly support the monophyly of Catonotus. With expanded infra-specific sampling in Stigmacerca, a subclade of Catonotus , hypotheses of gene flow and the evolution of putative egg-mimic structures are tested in a Bayesian coalescent framework. These analyses strongly support a single origin of egg-mimic structures in Stigmacerca, but also several instances of introgressive hybridization between egg-mimic species and those without egg mimics.

Using gut-content data from the literature, recently developed comparative methods, and a multi-locus phylogeny of all darter species, hypotheses regarding differences in trophic niche among major darter subclades were tested. These analyses reveal that there are significant differences in trophic niche among major darter subclades. Percina was shown to utilize a smaller set of benthic prey taxa than expected from a Brownian model of evolution. The observed differences in trophic niche evolution may be related to important contrasts in morphology and life history traits, such as the degree to which species are benthic.

Indexing (document details)
Advisor: Near, Thomas J.
Commitee: Burbrink, Frank, Donoghue, Michael, Post, David
School: Yale University
Department: Ecology and Evolutionary Biology
School Location: United States -- Connecticut
Source: DAI-B 74/05(E), Dissertation Abstracts International
Source Type: DISSERTATION
Subjects: Genetics, Systematic, Zoology
Keywords: Diverse assemblage, Freshwater fish diversity, Gene trees, Introgression, Species delimitation
Publication Number: 3535397
ISBN: 9781267856777
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