UC Santa Cruz

Damselfishes (Family: Pomacentridae) are a group of ecologically important, primarily coral reef fishes that include over 400 species. Damselfishes have been used as model organisms to study recruitment (anemonefishes), the effects of ocean acidification (spiny damselfish), population structure and speciation (Dascyllus). The genus Dascyllus includes a complex of relatively larger bodied species, the Dascyllus trimaculatus species complex. This complex is comprised of several species including D. trimaculatus itself. The three-spot damselfish, D. trimaculatus is a widespread, common, and well-studied coral reef fish species found across the tropical Indo-Pacific that has served as a model species for coral reef fish research. In this dissertation, we expand on what is known of population dynamics of the complex while providing valuable genomic resources to support future research into this model system. In Chapter 1 of this dissertation, we explore populations at the margins of a species’ distribution which tend to be smaller, more isolated, and importantly, exist in habitats at the edge of the species’ physiological limit. These conditions make such populations particularly vulnerable to extirpation, especially amid accelerating environmental changes. We focus on population structure based on mitochondrial DNA markers and inferred dynamics of an understudied, potentially vulnerable, population of an otherwise well studied and widespread coral reef fish. We present phylogeographic results using the most robust set of samples collected in the Ryukyu Archipelago and gain insight into edge population dynamics by comparing to another more well-studied edge population in French Polynesia. We found that despite its proximity to the Coral Triangle and position along the Kuroshio Current, the Ryukyu population of D. trimaculatus seems to be a relatively young and closed, suggesting that it may be more vulnerable to extinction than might be otherwise expected. In Chapter 2 we present the first genome assembly of Dascyllus trimaculatus. This assembly contains 910 Mb, 90% of the bases are in 24 chromosome-scale scaffolds, and the BUSCO score of the assembly is 97.9%. Our findings confirm previous reports of a karyotype of 2n = 47 in D. trimaculatus in which one parent contributes 24 chromosomes and the other 23. We find evidence that this karyotype is the result of a heterozygous Robertsonian fusion. This assembly was a necessary resource for research in Chapter 3 and will be a valuable resource in the population genomics and conservation of Damselfishes, and continued studies of the karyotypic diversity in this clade. In Chapter 3, we use low coverage whole genome sequencing to examine the population structure of its Pacific distribution, and again, focus on dynamics of the Ryukyu Archipelago in southern Japan. We find evidence of clear divergence between the Pacific and Indian Ocean populations as well as between the Pacific and the restricted edge population in the Society Islands at the eastern edge of its range. We see a clear signal of introgression of one species within the complex, D. auripinnis described from the Line and Phoenix islands into D. trimaculatus that extends across to the west Pacific - further than previously reported. We also find that there is directional but restricted gene flow of Philippine genotypes into the Ryukyu Archipelago. While we have not yet identified specific isolation and speciation mechanisms, we propose some likely scenarios. This dissertation builds upon previous research of this complex which had made it a model system in its own right and adds genomic resources to ensure that we continue to further our understanding of this important model system in this genomic age. There are now resources for endless directions and questions to follow regarding this species complex and evolutionary processes. Understanding mechanisms of dispersal, the role of selection, and the capabilities of local adaptation in a species with relatively restricted gene flow are some of the exciting questions that this project has uncovered, thus placing Dascyllus trimaculatus as an ideal model species to address fundamental questions in the ecology and evolution of coral reef fishes.