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Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC Santa Cruz Electronic Theses and Dissertations (2022)

While the immediate impacts of global climate change are of serious concern, the outcomes of these environmental changes for populations will ultimately play out over multiple generations. Despite this, our understanding of the evolutionary impacts of climate-related environmental change is still in its early stages, particularly in the marine realm. Furthermore, evolutionary processes can act over short, ecological timescales, such that they may play a key role in both the short-term resistance and long-term resilience of natural populations. Therefore, the objective of this dissertation is to better incorporate evolutionary processes into the developing understanding of the ecological effects of global change. In particular, I focus my investigations on the relationships between genetic diversity, local adaptation, and environmental change to better understand the evolutionary factors that contribute to a population’s adaptive capacity and resilience. A population’s genetic diversity may translate to response (phenotypic) diversity, the level of which will determine the likelihood of evolutionary rescue via the portfolio effect. Adaptation of subpopulations to their local conditions (local adaptation) has the potential to enhance broad-scale genetic diversity within a species, potentially increasing resilience in the face of environmental change, but can simultaneously reduce local diversity, increasing the risk of extinction for subpopulations if gene flow is low. In this dissertation, I use a pair of marine fish species with unique life-histories (Embiotoca jacksoni and Brachyistius frenatus; family Embiotocidae) to 1) test the molecular impact of environmental change on an important temperate fish group, 2) investigate the scale of genetic diversity and admixture along the Pacific coast of North America, 3) provide evidence of local adaptation among subpopulations, and 4) associate genomic differences between subpopulations with regional environmental differences to better understand the physiological pressures imposed by climate variables and form hypotheses for the genetic mechanisms that may underlie ongoing adaptation to climate change.

  • 3 supplemental ZIPs
Cover page: Adaptation Genomics of Surfperch Populations in the Context of Rapid Environmental Change
  • Article
  • Peer Reviewed
UC Santa Cruz Previously Published Works (2023)
The surfperches (family Embiotocidae) are a unique group of mostly marine fishes whose phylogenetic position within the Ovalentaria clade (Percomorpha) is still unresolved. As a result of their viviparity and lack of a dispersive larval stage, surfperches are an excellent model for the study of speciation, gene flow, and local adaptation in the ocean. They are also the target of an immensely popular recreational fishery. Very few high-quality molecular resources, however, are available for this group and only for a single species. Here, we describe a highly complete reference genome for the kelp surfperch, Brachyistius frenatus, assembled using a combination of short-read (Illumina, ~47× coverage) and long-read (Oxford Nanopore Technologies, ~27× coverage) sequencing. The 596 Mb assembly has a completeness level of 98.1% (BUSCO), a contig N50 of 2.6 Mb (n = 56), and a contig N90 of 406.6 kb (n = 293). Comparative analysis revealed a high level of synteny between B. frenatus and its close relative, Embiotoca jacksoni. This assembly will serve as a valuable molecular resource upon which future evolutionary dynamics research will build, such as the investigation of local adaptation and the genomic potential for climate adaptation in wild populations.
    Cover page: A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage
    • Article
    • Peer Reviewed
    UC Santa Cruz Previously Published Works (2022)
    Acidification-induced changes in neurological function have been documented in several tropical marine fishes. Here, we investigate whether similar patterns of neurological impacts are observed in a temperate Pacific fish that naturally experiences regular and often large shifts in environmental pH/pCO2 . In two laboratory experiments, we tested the effect of acidification, as well as pH/pCO2 variability, on gene expression in the brain tissue of a common temperate kelp forest/estuarine fish, Embiotoca jacksoni. Experiment 1 employed static pH treatments (target pH = 7.85/7.30), while Experiment 2 incorporated two variable treatments that oscillated around corresponding static treatments with the same mean (target pH = 7.85/7.70) in an eight-day cycle (amplitude ± 0.15). We found that patterns of global gene expression differed across pH level treatments. Additionally, we identified differential expression of specific genes and enrichment of specific gene sets (GSEA) in comparisons of static pH treatments and in comparisons of static and variable pH treatments of the same mean pH. Importantly, we found that pH/pCO2 variability decreased the number of differentially expressed genes detected between high and low pH treatments, and that interindividual variability in gene expression was greater in variable treatments than static treatments. These results provide important confirmation of neurological impacts of acidification in a temperate fish species and, critically, that natural environmental variability may mediate the impacts of ocean acidification.
      Cover page: Upwelling‐level acidification and pH/pCO2 variability moderate effects of ocean acidification on brain gene expression in the temperate surfperch, Embiotoca jacksoni
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      • Peer Reviewed
      Publications (2022)
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