Spatial and temporal patterns of adaptation and adaptive potential in a changing ocean
Creators: name: Clark, Rene Delight
Publisher: name: No Publisher Supplied
Year: 2023

description: Genetic diversity is a fundamental component of biodiversity, a proxy for adaptive potential, and the medium for speciation events. Understanding how evolutionary forces interact to distribute and maintain genetic diversity across both space and time is of great interest in ecology and evolution, especially in an era of global change. While many processes, including life history traits, demographic histories, connectivity patterns, and phylogenetic relationships are known to influence genetic diversity to varying degrees, our understanding of how these forces collectively shape such patterns is less well established. Here, I characterize spatial and temporal patterns of adaptation and adaptive potential in marine systems, to enable a better understanding of how demographic processes, environmental conditions, and anthropogenic pressures separately and synergistically create and maintain such distributions.Chapter 1 of my dissertation addresses the spatial component of these patterns and investigates how evolutionary forces combine to facilitate local adaptation at range margins. I investigated the relationship between selection, gene flow, and genetic drift in three populations of the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of its species range. I found low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism, and translation. My observations illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.In Chapter 2, I extend these spatial analyses to encompass marine populations worldwide, and compiled 6862 observations of genetic diversity from 492 species of marine fish globally, assessed their associations with macroecological drivers, and tested among three hypotheses for diversity gradients: the founder effect hypothesis, the kinetic energy hypothesis, and the productivity-richness hypothesis. I found that mitochondrial genetic diversity follows latitudinal and longitudinal gradients similar to those of species diversity, being highest near the equator, particularly in the Coral Triangle, while nuclear genetic diversity did not follow clear geographic patterns. Despite these differences, all genetic diversity metrics were significantly and positively correlated with chlorophyll, while mitochondrial diversity was also positively associated with sea surface temperature. Overall, these findings reveal how environmental controls on mutation and drift in the ocean combine to establish global gradients of genetic diversity within species, and in turn, species and community assemblages.Finally, in Chapter 3, I explore temporal, rather than spatial, patterns in genetic diversity. I assess the degree to which genetic diversity has declined in tropical marine fish species over the past century of intense exploitation and rapid anthropogenic industrialization. Although such losses have been well-documented in temperate systems, the degree to which similar reductions have occurred in tropical species remains an open and important question, particularly as these environments are currently undergoing some of the most intense rates of environmental change. Here, I compare capture-enriched genomic data from three tropical near-shore marine fish species (Atherinomorus endrachtensis, Equulites laterofenestra, and Gazza minuta) collected from a single location in the Philippines at the beginning of the 20th and 21st centuries, bookending a period of intense environmental change. I found a marked loss in genetic diversity and evidence for sharp reductions in effective population size (Ne) across all three species, suggesting the past century of intensifying industrialization has resulted in substantial genomic erosion. Such a decline highlights the ability of anthropogenic impacts to translate into long-lasting genomic consequences and potentially limit future adaptive capacity, particularly in some of the most biodiverse portions of the oceans.In total, my dissertation helps to build a better understanding of how evolutionary processes interact to drive large-scale patterns in adaptive potential, as well as the evolutionary consequences of anthropogenic change in marine systems.