Species Delimitation in the Genomic Era and Its Implications for Taxonomy, Biogeography, Fisheries and Conservation of North American Freshwater Fishes
Date of Award
Fall 2023
Document Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Ecology and Evolutionary Biology
First Advisor
Near, Thomas
Abstract
Understanding the mechanisms that generate biodiversity is a fundamental goal of evolutionary biology. However, a prerequisite for such investigations is a thorough and accurate inventory of species diversity. The recent availability of genomic-scale DNA sequence data and advances in analytical methods has complemented traditional species delimitation based on morphology. With such advances in data availability and methods, researchers are revisiting long-standing species delimitation problems that involve geographically widespread and phenotypically variable species, which often result in the recognition of multiple independent evolutionary lineages masquerading as traditionally delimited species.In chapter one, we test the hypothesis that the Lepomis megalotis complex (Teleostei: Percomorpha: Centrarchidae) is limited to two species: L. megalotis and L. peltastes, through analysis of a double digest restriction-site associated DNA (ddRAD) genomic dataset and morphological traits traditionally used in ichthyology to delimit species. Our analyses reveal that L. peltastes is nested in a paraphyletic L. megalotis and there are six relatively ancient lineages ranging in age from 5.19 to 2.56 Ma, currently referred to as L. megalotis or L. peltastes. These six lineages have moderate to high degrees of genomic and phenotypic divergence, exhibiting geographic distributions consistent with the hypothesized paleodrainage patterns for central and southern North America between the Great Plains and Appalachian Mountains. We also discover patterns of introgression and localized hybridizing populations, some of which may have been facilitated by a post-glacial range expansion. When specimens from populations characterized by genetic admixture are segregated, each of the six delimited species has higher probability of correct identification using systematically important morphological traits. Our study shows the important synergy of genomic and traditional morphological data in discovering and delimiting species. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. In chapter two, we investigate the phylogeny and delimitation of species of Micropterus (Centrarchidae) using a ddRAD dataset sampled with comprehensive geographic coverage of all recognized species in the clade. We rely on an operational species concept that views separately evolving metapopulation lineages as the sole criterion for the recognition of species. Our analyses not only provide a perspective on species diversity in Micropterus that differs from those accepted by both ichthyologists and fisheries scientists, but also dramatically reveal that the scientific names Micropterus salmoides and Micropterus floridanus have been incorrectly applied to the Largemouth Bass and Florida Bass over the past 75 years. In addition to a new delimitation of Black Bass species, the genomic analyses provide a reconstruction of their evolutionary history and an important basis for the management and conservation of this economically and culturally important recreational fishery resource. In chapter three, we investigate the history of human mediated introductions of Lepomis auritus (Centrarchidae) using a ddRAD dataset sampled with comprehensive geographic coverage of the species. Our analyses verify the populations of L. auritus in rivers in Texas, the Tennessee River system, and the Mobile River Basin as non-native. The complicated history of human-mediated introductions of L. auritus suggests the populations in rivers in Texas are the result of a single source of introduction from the Suwannee River in northern Florida, and the populations in the Tennessee River system and the Mobile River Basin are genetic admixtures resulted from multiple introductions from different source populations. Ecological and evolutionary investigations of the non-native populations of L. auritus will broaden the understanding of biological invasions. Finally, in chapter four, we analyze a ddRAD dataset sampled from all known populations of Etheostoma bellator and E. chermocki (Teleostei: Percomorpha: Percidae). My analyses reveal that E. chermocki is nested phylogenetically within a clade composed of undescribed species currently delimited as E. bellator. The Etheostoma chermocki complex consists of six independent evolutionary lineages that diversified over a period of 4.43 to 0.97 million years ago. The disjunct, narrow distribution of the six species, along with their high levels of genetic divergence, suggest urgent conservation needs for the currently unprotected lineages of E. bellator. These newly delimited species are distributed exclusively in tributaries with a carbonate rock substrate and are separated from the other closely related lineages by channels flowing over siliciclastic rock. However, as rivers erode through geologic structures and strata, the spatial distribution of rock-types at the surface changes over time. Our results show that surface exposure of carbonate rock either pre-existed or was generated during the diversification of the species complex, suggesting that geomorphic processes and episodic dispersal events set the stage for subsequent allopatric speciation.
Recommended Citation
Kim, Daemin, "Species Delimitation in the Genomic Era and Its Implications for Taxonomy, Biogeography, Fisheries and Conservation of North American Freshwater Fishes" (2023). Yale Graduate School of Arts and Sciences Dissertations. 1220.
https://elischolar.library.yale.edu/gsas_dissertations/1220
