Genomics Commons^™

The Island Biogeography Of Mangrove-Dwelling Vertebrates: Isolation, Specialisation, And Extinction, Jian Xiong David Tan

Biology ETDs

Mangroves are highly dynamic ecosystems that are widely distributed across the coastlines of the tropics and subtropics. Despite their low plant diversity, mangroves host a disproportionately high number of terrestrial vertebrate taxa. However, mangrove specialists — taxa that only occur in mangrove habitats — exhibit a global distribution that is incongruous with the broader background distribution patterns of mangrove-associated fauna, exhibiting higher diversity in Australia and Southeast Asia. This dissertation therefore aims to assess how the diversity and distribution of mangrove specialist fauna may have been shaped by the historical biogeography of mangroves, and the effects of mangrove specialisation on …

The Role Of Elevation In The Migration, Physiology, And Genomic Diversification Of Birds, Jessie L. Williamson

Biology ETDs

Elevational gradients cause profound eco-climatic variation across short distances. Partial pressure of oxygen (PO₂) is a severe challenge that organisms face at high elevations; due partly to specialization on PO₂, most Neotropical bird species have narrow elevational ranges. However, a small fraction are elevational generalists that span sea level to high elevations, and a subset undertake extreme migratory journeys from low to high elevations biannually. My dissertation combines diverse approaches across levels of biological organization to understand how elevation impacts the ecology, evolution, physiology, and migration of montane birds. I examined ‘extreme’ elevational …

Conservation Genomic Investigation Of A Threatened Trout Species Endemic To The Gila River, David Thomas Camak

Biology ETDs

Climate change is a looming threat to the persistence of species, especially aquatic, imperiled species. Species native to desert streams are at a particular disadvantage, as many species already face drought, floods, wildfires, and threats from nonnative species, all of which are thought to be exacerbated by climate change. Species such as the threatened Gila Trout (Oncorhynchus gilae) already have small ranges and persist in fragmented and isolated habitats that limits gene flow between populations. Therefore, it is important to understand the current genomic status of such populations to be able to predict the future effects of climate …

Crossing The Ocean: The Importance Of Gene Flow In Island Evolution, Ethan F. Gyllenhaal

Biology ETDs

Islands have long been a critical arena for the development of ecological and evolutionary theory, particular due to persistent open-water gaps between them. In this dissertation I demonstrates how these caps are permeable, which can be leveraged to understand evolution on islands and more broadly. The first chapter develops this connection between ongoing, overwater gene flow and island biogeographic theory, and tests it on an archipelago species. The second take a three-pronged approach in demonstrating how over-water gene flow can bias phylogenetic inference, and how many phylogeographic metrics in islands are likely shaped by long-term gene flow. The final two …

Evolutionary Ecology Of Host-Parasite Relationships: Role Of Host Ecology, Phylogeny, And Demographics In Shaping Parasite Evolution, Erika Taylor Gendron

Biology ETDs

Host-parasite systems exist across complex and ecologically heterogeneous landscapes, and may occur across taxonomically and ecologically disparate host species. Under these conditions, mechanisms underlying microevolutionary processes (i.e. gene flow, genetic drift) are not always clear, and may be mediated by numerous co-occurring factors specific to individual hosts. Host traits such as host immunology, demographics, phylogeny and ecology may act in concert to shape host-parasite relationships, and ultimately evolutionary processes. The research described herein used phylogeographic, phylogenomic, and population genetic methods to further understanding of how host traits impact the evolutionary ecology of trematode systems, using avian schistosomes (Digenea: Schistosomatidae) as …

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Physella Acuta, Comparative Immunology And Evolutionary Aspects Of Gastropod Immune Function, Jonathan H. Schultz

Biology ETDs

Gastropod immunobiology has benefitted from investigations focused on the planorbid snail Biomphalaria glabrata, intermediate host for the human parasite Schistosoma mansoni. Though such concentrated efforts have elucidated fascinating aspects of invertebrate immunity, they have not provided full knowledge regarding the evolution of immune function among other gastropod species. This dissertation presents the importance of making strategic choices regarding which organisms to select for comparative immunology. Herein, the choice was made to investigate the immunobiology of Physella acuta, a freshwater snail species of the Physidae, a sister family to Planorbidae to which B. glabrata belongs. Benefiting greatly from …

Genomic Signatures Of Adaptive Evolution, Jessica A. Weber

Biology ETDs

Comparative genomics has revolutionized virtually all fields of biology including the study of evolution. In this dissertation, I used next-generation sequencing to explore the evolutionary histories and adaptive evolution of a diverse set of taxa. Comparisons ranged across time scales, from population-level genetic diversity studies to questions spanning the deepest branches of the metazoan lineage. Whole genome sequencing of 50 unrelated Korean individuals revealed that Koreans have a distinct genetic history from the Chinese and Japanese populations. Our Korean-specific variome database was used to identify novel disease-causing variants in the Korean population, highlighting the value of high-quality ethnic variation databases …

Systematics And Diversification Of The Pantropical Avian Order Coraciiformes, Jenna Merle Mccullough

Biology ETDs

How and why species diversify is a central theme of evolutionary biology. Species-rich, morphologically diverse, pantropical clades provide rare opportunities to explore questions about drivers of diversification in the tropics. Here, we present the first complete species tree of Coraciiformes (6 families, ~177 species of kingfishers, motmots, bee-eaters, and allies), produced with thousands of ultraconserved elements. We recovered a well-supported tree which shows that there are two clades within Coraciiformes: 1) bee-eaters sister to rollers + ground- rollers and 2) todies sister to motmots + kingfishers. We estimated the biogeographical history of the group, explored bill shape evolution with a …