Dissertation
Genomic Variation in Extremophile Poeciliid Fishes Adapted to Hydrogen Sulfide-Rich Springs and Caves
Washington State University
Doctor of Philosophy (PhD), Washington State University
2022
DOI:
https://doi.org/10.7273/000005126
Abstract
Extreme environments offer unique opportunities to study adaptation because we can examine the evolutionary basis of a population’s survival in conditions that are intolerable to most species. Poeciliid fishes (family Poeciliidae) have adapted to several extreme environments, including springs containing toxic hydrogen sulfide (H2S) and caves. We asked three major questions to understand adaptation to extremes in this fish system: (1) How does the transcription of genes differ in cavefish populations exposed to near constant darkness versus surface fish exposed to full light? (2) How do regulatory mechanisms affect gene expression differences in sulfidic populations versus non-sulfidic populations? (3) Is there convergence in the rate of evolution and/or amino acid preference in the protein-coding genes of poeciliid lineages that have independently adapted to H2S versus non-sulfidic lineages? For question one, we analyzed eye transcriptomes sequenced from two cave and two surface populations of Poecilia mexicana (the Atlantic molly) from southern Mexico. We found that genes related to visual sensitivity, signaling, and eye structure were downregulated in cavefish compared to surface fish, indicating that differential gene expression is likely involved in early-stage eye regression in the cavefish. For question two, we used nascent sequencing to capture genome-wide patterns in transcription to examine how regulatory mechanisms drive concordant changes in gene expression comparing sulfidic populations to non-sulfidic populations sampled from a species complex of P. mexicana in southern Mexico. We found that changes in nascent transcription largely paralleled those in nearby gene expression, and differential transcription factor binding likely drives expression changes in key H2S-related genes. For question three, we compared H2S- and non-H2S-related genes across lineages of sulfidic and non-sulfidic poeciliids sampled from the Neotropics and examined convergence in their relative rates of evolution and amino acid preference. We found genes involved in antioxidant production showed significantly different rates of evolution in sulfidic lineages versus nonsulfidic lineages but shared amino acid preferences were rare. In sum, our results show that extremophile populations of poeciliids show clear genetic differences from non-sulfidic populations and that adaption to H2S and caves in this fish system has a strong genomic basis.
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Details
- Title
- Genomic Variation in Extremophile Poeciliid Fishes Adapted to Hydrogen Sulfide-Rich Springs and Caves
- Creators
- Kerry Leigh McGowan
- Contributors
- Joanna L Kelley (Advisor)Jeremiah W Busch (Committee Member)William W Dowd (Committee Member)Michael Tobler (Committee Member)
- Awarding Institution
- Washington State University
- Academic Unit
- Biological Sciences, School of
- Theses and Dissertations
- Doctor of Philosophy (PhD), Washington State University
- Publisher
- Washington State University
- Number of pages
- 124
- Identifiers
- 99901019939701842
- Language
- English
- Resource Type
- Dissertation