Subterranean Fishes of the World

7098

2025

UC Santa Cruz This work is made available under the terms of a Creative Commons Attribution- Non Commercial-ShareAlike License, available at: https://creativecommons.org/licenses/bync-sa/4.0/ Copyright © by Kara Ryan 2025 All rights reserved

A central question in evolutionary biology is whether evolution is predictable – driven by similar selective pressures leading to repeated outcomes – or contingent on historical and stochastic processes. While convergent traits are widespread across the tree of life, the underlying genetic mechanisms often vary, raising questions about how different sources of variation can influence evolutionary trajectories. In this dissertation, I use the Poecilia mexicana species complex, which includes multiple sulfide-adapted and non-sulfide-adapted populations across four river drainages, as a model for repeated adaptation to extreme environments. In Chapter One, I used targeted capture sequencing to test for selection in 250 candidate genes, identifying shared signatures of selection in key sulfidic detoxification genes across independent sulfidic lineages. In Chapter Two, I generated new genome assemblies for six Poecilia and Gambusia species, assessed synteny and demographic history, and tested hypotheses about population size changes and the genomic architecture in sulfidic lineages. Chapter Three investigated the role of structural variants in adaptation by integrating long- and short-read DNA sequencing with transcriptomic data. This work identified many structural variants under selection, including a deletion in ethe1 associated with gene expression differences that was fixed in sulfidic individuals and at low frequency in nonsulfidic individuals. Finally, Chapter Four, using whole genome resequencing data from 172 individuals, revealed that gene flow has facilitated repeated adaptation to sulfide springs by shaping allele frequencies and patterns of divergence for both SNPs and structural variants. Collectively, this dissertation shows that while a defined set of genes and pathways involved in sulfide detoxification recurrently underpin adaptation, this is the result of the interplay of de novo mutation, gene flow and selection. This work highlights how predictable and contingent processes jointly shape evolutionary outcomes, proving new insight into convergent adaptation in extreme environments

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