Year of Award

2023

Document Type

Dissertation

Degree Type

Doctor of Philosophy (PhD)

Degree Name

Organismal Biology, Ecology, and Evolution

Department or School/College

Division of Biological Sciences

Committee Chair

Jeffrey M. Good

Commitee Members

Lila Fishman, Zachary A. Cheviron, Jack Sullivan, John R. Demboski

Keywords

adaptation, cryptic species, evolution, genomics, speciation, Tamias

Abstract

Understanding how evolutionary and ecological mechanisms promote speciation and adaptation is one of the central challenges of evolutionary biology. Recent advancements in theoretical, methodological, and computational approaches now allow biologists to test long-standing questions regarding the evolutionary history of species. This includes the genomic underpinnings of reproductive barriers and adaptive phenotypes, and the contribution of ecology, geography, and demography in the generation and maintenance of biodiversity. While great strides have been made in understanding the genetic and ecological factors that underlie speciation and local adaptation, many open questions remain. My dissertation first seeks to address questions about how we define and describe biological diversity, with an emphasis on identifying cryptic species. I then attempt to understand the geographic and ecological context shaping patterns of genomic divergence and the evolutionary history of closely related co-distributed species. Lastly, I seek to understand how ecological divergence and population history has shaped recurrent local adaptation in a wide-spread generalist species.

Chipmunks of western North America (Tamias) provide a rich system to study speciation across a rapid diversification characterized by ecological adaptation, phenotypic convergence, and overlapping geographic distributions. Interest in chipmunk ecology and speciation predates the modern synthesis and they have served as a model system of niche partitioning and competitive exclusion for over a century. Across western North America, western chipmunks are characterized by strong habitat associations and specialization shaped by complex interspecific competition and ecological adaptation. Where ecologically differentiated species come into contact along environmental gradients they occasionally hybridize. In sympatry, ecological associations can break down where chipmunks that occupy similar or transitory habitats show phenotypic convergence (e.g., in size and pelage coloration) between species. Despite this, the rapidly evolving male genital bone (baculum or os penis) provides one general morphological trait that is thought to be strongly diagnostic of species boundaries, presumably reflecting divergence driven by strong sexual selection. In this dissertation, I use extensive sampling of natural populations from fieldwork and museum archives to generate genomic sequence data, phenotypic analyses of traits associated with speciation and ecological adaptation, and ecological niche modeling to study the interplay between ecological and evolutionary processes underlying speciation and adaptation.

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© Copyright 2023 Nathanael David Filer Herrera