Gut microbes provide vital functions for animal hosts. While it is known that host ecology and evolutionary history play a role in shaping gut microbiomes, a majority of studies have focused on mammal hosts. Other vertebrates, including fish, have received little attention. Coral reef fish, in particular, exhibit a wide range of distinct feeding behaviors, evolutionary histories, and geographic distributions that likely correlate with gut microbiome composition and diversity. They also inhabit a fragile ecosystem that is highly sensitive to anthropogenic disturbance—disturbances that are known to impact coral microbiomes but may or may not affect fish gut microbiomes. My thesis leverages a large unprecedented coral reef fish gut microbiome dataset (N=550), where I sampled the gut microbiomes of 20 host species of fish with robust replication spanning three islands across the South Pacific, to better understand how host phylogeny, host diet, and host environment shape vertebrate gut microbiomes. Comparing the gut microbiomes of distantly related hosts can reveal evolutionary and ecological dynamics that govern gut microbiomes across the animal kingdom. Chapter 1 investigates the possible similarities between coral reef fish and mammal gut microbiomes to elucidate any microbial features that may have converged between the two distantly related hosts. Through multivariate and Bayesian analyses, I show that fish and mammal gut microbiomes exhibit striking similarities in composition, particularly within carnivores and herbivores. Specifically, carnivores and herbivore gut microbiomes show more similarities within their diet groups than within their host phylogenies, and share a significant number of ASVs. Herbivore fish and mammal gut microbiomes, in particular, share a significant number of amplicon sequence variants (ASVs) associated with the functional requirements of herbivory, such as Ruminococcus and Treponema. My results indicate that despite 365 million years of evolution and two drastically distinct habitats (terrestrial vs. marine), fish and mammal gut microbiomes have converged on the basis of diet. Expanding on Chapter 1, Chapter 2 moves beyond host phylogeny and diet and aims to isolate and analyze the effects of host habitat on gut microbiome composition and diversity. Previous work on environmental effects acting on animal gut microbiomes largely focused on captive hosts or wild hosts of a single species, potentially ignoring any interactions between host environment and host phylogeny in the wild. Here, I leverage my dataset of coral reef fish gut microbiomes from a diverse range of hosts from three geographically distinct habitats to better understand how host habitat shapes vertebrate gut microbiomes. I find that host habitat significantly shapes fish gut microbiome composition and diversity and these effects are highly dependent on host phylogeny. For example, within the same analyses, a fish such as R. aculeatus, had significantly different gut microbiomes between the three islands, whereas E. merra gut microbiomes were largely unaffected by island location. For the fish gut microbiomes that were significantly impacted by host habitat, many of the associated ASVs were ASVs found in Chapter 1, suggesting that host habitat may also shape gut microbiome function. While comparative approaches on wild hosts are crucial in elucidating generalizable rules that govern animal gut microbiomes, experimental approaches are also imperative to unpack the finer-scale qualities and mechanisms of these rules. Chapter 3 builds on Chapter 2 by leveraging a simulated nutrient enrichment experimental design to further investigate the effects of host environment on gut microbiome composition and diversity. Nutrient enrichment is one of the most threatening consequences of anthropogenic stress on coral reef ecosystems, and the effects of nutrient enrichment on reef fauna gut microbiomes are largely unknown. Here, I artificially enrich the territories (N=40) of a highly abundant, territorial gardening fish, Stegastes nigricans, and use multivariate and differential abundance analyses to elucidate how nutrient enrichment impacts animal gut microbiome composition and diversity. I find that nutrient enrichment effectively “enriches” the gut microbiome, with S. nigricans gut microbiomes in enriched territories exhibiting significantly higher alpha diversities than those in control territories. I also find that these changes are specific to the hindgut and do not occur in the microbiomes of the food source that S. nigricans gardens.

The medical field calls for greater diversity in its physician workforce to promote more equitable healthcare and combat health disparities. The Howard Hughes Medical Institute-funded Diversity, Health Equity and the Environment Program at University of California, Los Angeles aims to increase major retention in underrepresented minority (URM) pre-health undergraduates to promote greater diversity in medical school applicants. Qualitative analysis of student interview responses on student program experience was conducted to better understand the impact of program participation. Students most valued the program’s educational content, research experience, community, and mentorship, which advanced new and already present health-related career goals. The program offers a promising approach to increasing representation in medicine through student-centered learning and cultural support in building science identity.

Coral reefs are among the world’s most biodiverse and valuable ecosystems, but they are in global decline. One major concern for the future of reefs is mass coral bleaching, a phenomenon where corals turn white after expelling their endosymbiotic algae (Symbiodinium) during periods of elevated sea surface temperatures. Unfortunately, the frequency and severity of mass coral bleaching is increasing as climate change results in global sea surface temperature rise. Extensive research has examined how Symbiodinium variation influences bleaching susceptibility, yet Symbiodinium is only one part of a complex coral holobiont that also include bacteria and archaea.

This dissertation investigates variation in coral microbiomes in the world’s largest and most diverse coral reef ecosystem, the Indonesian Archipelago. Using a common garden approach, Chapter 1 investigates how the microbiome of Porites lobata varies with water temperature among two nearby reef ecosystems that experience different levels of coral bleaching—Amed and Pemuteran, Bali. Results reveal significant local variation in microbiomes, but no consistent changes in microbiomes with temperature. Chapter 2 examines how the coral microbiomes of three species of coral with different bleaching susceptibility (Acropora millepora, Pocillopora verrucosa, and Porites lobata) respond to elevated water temperatures in a single location, Manokwari, West Papua. Results show significant differences in microbiomes in all three species, indicating species-specific relationships between coral host and microbial symbionts. However, while microbiomes changed with elevated temperature, there were no consistent patterns by species or by propensity to bleach. Lastly, chapter 3 examines natural variation in microbiomes of these same three species of coral across 5000 km of the Indonesian Archipelago, including reefs with historically low, moderate, and high bleaching susceptibility. Results varied by species: microbiomes of Acropora millepora showed no significant geographic variation; microbiomes of Pocillopora verrucosa were significantly different among most locations, but not among regions; and microbiomes of Porites lobata showed significant variation based on regional variation in bleaching susceptibility, but not among individual localities. Combined, these studies show that coral microbiomes are complex, varying by species, reef, and geographic region, providing novel insights into the nature and specific relationship of microbiomes to coral host and their environment.

Although it is commonly assumed that most speciation occurs in allopatry, a growing body of research indicates that natural selection can lead to reproductive isolation and speciation in sympatry. A common mechanism for sympatric speciation is ecological speciation, where diversification is driven by differential selection across ecological niches. New genetic and genomic techniques facilitate the discovery of cryptic ecological divergence, and allow us to examine in detail the relative roles of natural selection and gene flow in speciation, particularly in marine systems, where it is difficult to identify mechanisms for allopatric speciation.

This dissertation combines broad exploratory field sampling with population genetic and phylogenetic methods to tease apart the roles of geographic isolation and natural selection in driving speciation in the Coral Triangle. Using the coral-associated nudibranch genus Phestilla as a model, in chapter 1 we examine the effect of coral host and geography on population divergence in Phestilla lugubris and Phestilla minor. Phylogenetic analyses and analyses of molecular variance of mitochondrial COI sequences indicate very little population structure in Phestilla lugubris, but Phestilla minor has diverged across the Sunda Shelf and across two major clades of coral host. In chapter 2 we use population genomics to test whether natural selection plays a larger role in the divergence of sympatric host-separated populations than allopatric populations of Phestilla minor. Population genetic analyses of genome-wide single nucleotide polymorphisms show host-driven divergence is stronger than that across the Sunda Shelf, despite having occurred more recently. Genomic scans for selection reveal an important role for natural selection in both geographic and host-associated divergence. Finally, in chapter 3 we broadened our approach to examine the roles of geography and host in diversification of all scleractinian-associated nudibranchs. A phylogenetic tree of COI, 16S, and H3 sequences from scleractinian-associated nudibranchs collected across the Indo-Pacific Ocean reveals three times the number of purported species than previously thought, with evidence for host shifting and geographic divergence multiple times throughout evolutionary history. Combined, these three studies demonstrate that both coral host and geography contribute to diversification both within and between species of scleractinian coral-associated nudibranchs.

Indonesia is the heart of the Coral Triangle, the world’s most diverse marine ecosystem. Preserving the biological and economic value of this marine biodiversity requires efficient and economical ecosystem monitoring. This study investigates the effectiveness of environmental DNA (eDNA) to capture fish biodiversity across a pronounced biodiversity gradient in Indonesia. A total of 15,219,431 sequence reads of 12S rRNA from 39 sites spanning 7 regions of Indonesia revealed 774 Amplified Sequence Variants (ASVs). Patterns of fish diversity based on eDNA partially conformed to expectations based on traditional biodiversity survey methods, with highest fish biodiversity in Raja Ampat, with generally lower diversity in Western Indonesia. However, eDNA performed relatively poorly compared to visual survey methods in site by site comparisons, both in terms of total number of taxa recovered and ablity to assign species names to ASVs. This result stands in a stark contrast to eDNA studies temperate and tropical ecosystems with lower diversity. Analysis showed that while sequencing depth was sufficient to capture all fish diversity within individual samples, variation among samples from individual localities was high, and sampling effort was insufficient to capture all fish diversity at a given sampling site. Results of this study highlight two major challenge of eDNA in highly diverse ecosystems such as the Coral Triangle. First, reference databases are incomplete and insufficient to attach species names to ASVs. Second, sampling design based on studies from lower diversity temperate ecosystems may be inadequate to capture the diversity of high diversity ecosystems.

Marine protected areas (MPAs) are important tools for maintaining biodiversity and abundance of marine species. However, key to the effectiveness of MPAs is monitoring of marine communities. Current monitoring methods rely heavily on SCUBA-based visual observations that are costly and time consuming, limiting the scope of MPA monitoring. Environmental DNA (eDNA) metabarcoding is a promising cost effective, rapid, and automatable alternative for marine ecosystem monitoring. However, as a developing tool, the utility of eDNA metabarcoding requires improved bioinformatic techniques and reference barcode databases. Furthermore, it is important to understand how eDNA metabarcoding performs relative to visual surveys to better understand the strengths and limitations of each approach. This thesis improves eDNA metabarcoding approaches to survey the nearshore rocky reef and kelp forest ecosystems within the Southern California MPA network. It then tests the effectiveness of eDNA metabarcoding against visual surveys conducted by the Channel Islands National Park Service Kelp Forest Monitoring Program and Reef Check California. In Chapter 1, I develop FishCARD, a 12S reference barcode database specific to fishes of the California Current ecosystem. FishCARD improves eDNA metabarcoding taxonomic assignments, resulting in the identification of a broader array of marine vertebrate diversity, including invasive, endangered, and mobile species frequently missed by visual surveys. In Chapter 2, I compare eDNA metabarcoding and visual underwater survey methods inside, on the edge of, and outside the Scorpion State Marine Reserve off Santa Cruz Island. We demonstrate that eDNA captures a broader range of fish taxa than visual surveys and detects fine-scale spatial differences in fish communities. In Chapter 3, I demonstrate that eDNA metabarcoding and visual underwater surveys capture similar biogeographic patterns of fish communities across 44 sites within the Southern California Bight. Importantly, eDNA methods distinguished fish communities inside and outside of Southern California MPAs, finding a greater abundance of target species inside MPAs matching patterns observed through visual surveys. These results built off the collaborative development of the Anacapa Toolkit metabarcoding pipeline. Together I demonstrate the utility of eDNA metabarcoding for monitoring MPAs, providing an important complementary tool to visual methods, helping expand MPA monitoring across space, time, and depth.

Globally, rampant harvesting practices have left vital marine resources in sharp decline precipitating a dramatic loss of the biodiversity and threatening the health and viability of natural populations. To protect these crucial resources and ecosystems, a comprehensive assessment of biodiversity, as well as a rigorous understanding of the mechanisms underlying it, is urgently needed. As global finfish fisheries decline, harvest of cephalopod fisheries, squid, in particular, has exponentially increased. However, while much is known about the evolution and population dynamics of teleost fishes, much less is understood about squids. This dissertation provides a robust, in-depth examination of these mechanisms in commercially important squids using a novel approach combining genetics and genomics methods. In the first chapter, a suite of genetic markers is used to thoroughly examine the distribution and evolution of a species complex of bigfin reef squid (Sepioteuthis cf. lessoniana) throughout the global center of marine biodiversity, the Coral Triangle, and adjacent areas. Phylogenetic analyses and species delimitation methods unequivocally demonstrate the presence of at least three cryptic lineages sympatrically distributed throughout the region. While these putative species are reciprocally monophyletic, they are difficult to distinguish morphologically and little is known about how they differ in life history and ecology. To this end, in chapter 2, patterns of population structure over the Coral Triangle and adjacent regions were examined using genetic and genomic methods to identify important processes shaping both genetic and demographic connectivity in two of these cryptic species. Using both mitochondrial DNA (cytochrome oxidase subunit 1) and genome-wide single nucleotide polymorphisms (generated from restriction site associated digest (RAD) sequencing), we find strong, but discordant, patterns of population structure between these sympatric sibling taxa suggesting contrasting dispersal life histories. Moreover, detection of putative outlier loci highlights the possible role of selective pressures from regional environmental differences in shaping ongoing divergence. Given the fine-scale resolution achieved in chapter 2 with using RAD sequencing, in chapter 3, we apply these methods to examine potential population structure in the highly valuable market squid fishery (Doryteuthis opalescens) in California. This fishery has long been hypothesized to be two separate stocks due to different spawning peaks and areas. Using genome-wide SNPs and a rigorous temporal sampling scheme, we determined that northern and southern regions do not represent two distinct spatial stocks. Rather, complex patterns of temporal population structure lend support to continual spawning of genetically distinct cohorts at both sites throughout the 2014 harvest season. Collectively, these results demonstrate that squid biodiversity and population structure is much more complex than previously thought. Through the use of genetic and genomic technologies, we can delineate populations and identify the mechanisms driving connectivity to provide key information for fisheries management and conservation.

The exceptional concentration of marine biodiversity in the Coral Triangle is among the best-known biogeographic patterns in the ocean. Marine biodiversity peaks in the islands of Eastern part of Indonesia and the Philippines, the heart of the Coral Triangle, and significantly decreases moving away from this global biodiversity hotspot. However, data supporting this pattern largely come from fishes, corals and larger metazoans, and exclude smaller organisms that comprise the majority of marine biodiversity. This study utilized Autonomous Reef Monitoring Structure (ARMS) and DNA metabarcoding to examine biodiversity patterns of marine communities across Indonesia, the largest and most biologically diverse region of the Coral Triangle. In Chapter 1, I examine eukaryote biodiversity patterns of marine communities across Indonesia. Results demonstrate that smaller cryptofauna display similar biodiversity patterns to larger metazoans; the most diverse parts of Indonesia had more diversity per unit area, and greater heterogeneity and beta diversity across all spatial scales, individual ARMS, reefs, or regions. The results show that processes shaping biodiversity hotspots appear consistent in marine and terrestrial ecosystems, and across size and spatial scales. In Chapter 2, I examine patterns marine bacterial diversity across Indonesia, comparing microbial diversity to eukaryotic and metazoan diversity from ARMS. Results showed strong regional differentiation in microbial communities. Microbial diversity tracked eukaryote and metazoan diversity, and displayed a significant pattern of isolation by distance, strongly indicating that associations with larger eukaryotes and physical limitations to dispersal differentiate microbial communities in the Coral Triangle. These results are counter to the hypothesis that “everything is everywhere, but the environment selects”, and provide novel insights into the processes shaping marine microbial diversity in the world’s most diverse marine ecosystem. In Chapter 3, I re-examine data from Chapter 1 to determine how strategies for marine ecosystem monitoring in Indonesia could be developed to yield the best results for the least cost, allowing resource managers to harness the power of metabarcoding to better monitor this region’s biodiversity. Comparisons of cytochrome oxidase 1 (COI) and 18S rRNA metabarcoding data across three separate organismal size classes recovered from ARMS indicate that metabarcoding the 100 �m size fraction with COI captures the largest amount of diversity at the highest resolution. Results indicate that metabarcoding the 100 �m size fraction with COI provides the most accurate and economical approach to monitoring diversity in megadiverse regions where limited research investment precludes sequencing multiple size fractions with multiple metabarcoding markers. Combined, the results of this thesis demonstrate the power of ARMS and metabarcoding for the study and monitoring of marine biodiversity, providing new tools for the study and management of the exceptional marine biodiversity of the Coral Triangle.

Our understanding of evolution in marine ecosystems is framed by theories of speciation developed in terrestrial environments. In the ocean, however, speciation processes are likely to be different than on land. A general lack of absolute barriers, and the vast distances certain organisms can travel as larvae, mean that populations likely diverge in the presence of gene flow. The objective of this dissertation is to examine the relative contribution of different mechanisms of divergence in the sea in order to deepen our understanding of speciation. We examined the population genetics of ectoparasitic snails (Coralliophila radula, C. violacea) that specialize on Porites corals, and occupy a vast geographic and environmental range across the Indo-Pacific. In Chapter One, we used a comparative phylogeographic approach to explore whether populations of both taxa diverged across common geographic barriers, or due to adaptation to the host. We found striking evidence of genetic structure with geography for both snail species, and structure concordant with host within C. violacea populations. These findings suggest that in addition to historical sea level fluctuations, symbioses also contribute to diversification of these snails in the Coral Triangle. In Chapter Two, we used genome-wide data (SNPs) to investigate whether the ecological divergence we observed in C. violacea occurred via directional selection on different hosts and identify loci under selection. We saw genetic evidence of snail migration between hosts, as well as hybridization. By testing for FST outliers, we found loci under divergent selection, including a gene involved in the control of xenobiotic detoxification pathway gene expression, perhaps allowing snails to neutralize coral-specific toxins. These findings provide strong support for ecological divergence with gene flow, driven by adaptation to host. In Chapter Three, we focused on one ecomorph of C. violacea that inhabits coral reefs across a range of environmental conditions. Using genome-wide data and a global ocean-climate database, we identified signatures of geographic isolation and local adaptation. We saw four genetically distinct groups, consistent with results from Chapter One, with most divergence in peripheral populations. Searching for genetic associations with ocean climate variables, we found that the strongest driver of local adaptation was sea surface temperature variation. Our results show that local adaption to different environments likely reinforces neutral divergence, especially in peripheral populations.