Chromosome-scale genome assembly and investigation of the Hypomesus transpacificus genome for sex-specific markers, and association of the lactase persistence haplotype block with disease risk in populations of European descent.

Delta smelt, Hypomesus transpacificus (McAllister, 1963), is a federally threatened and California State endangered fish endemic to the San Francisco Estuary and Sacramento-San Joaquin Delta of North America (SFE). The species is a small, pelagic, mostly annual fish with freshwater resident, migratory, and semi-migratory life histories (Campbell et al., 2022; Hobbs et al., 2019). They have historically been considered an indicator species for water quality in the SFE. Over the last few decades, the species has undergone a population collapse associated with drought and anthropogenic disturbances, and it is now believed stochastic processes may push the species to extinction (Fisch et al., 2011; Moyle, Peter B., Brown, Larry R., Durand, John R., Hobbs, 2016). Meaningful conservation management of the species must encompass gaining a better understanding of the life history, ecology, demography, and physiology of the species so biological components contributing to success in the wild can be preserved. Because genetics, in combination with the environment, influence many aspects of individual and population level phenotypes, building a framework to better understand the species requires the development of genetic resources and monitoring of genetic diversity. Chapter one of this dissertation presents two chromosome-level genome assemblies -- one male and one female -- which are necessary resources for current and ongoing evolutionary and conservation genetics research concerning delta smelt and other declining and vulnerable species in the Osmeridae family, such as longfin smelt. Chapter two investigates three methods for identifying sex marker(s) within the assembled female and male delta smelt reference genomes. While ultimately no diagnostic sex-specific sequences were found in our RAD-sequencing dataset, abundance discrepancies in k-mers from female and male linked-read sequence data were identified. Chapter three is a first author paper I wrote titled "Association of the lactase persistence haplotype block with disease risk in populations of European descent" published in Frontiers in Genetics. This chapter switches organisms and investigates the potential for deleterious mutations to hitchhike in haplotype blocks which were heavily selected for in humans. This paper is a result of the work I completed in the first year and a half of my doctoral studies. Together this work contributes to the fields of evolutionary, comparative and conservation genomics. This work specifically contributes to delta smelt monitoring, management and research, and human disease risk studies. \nIn summary my doctoral work has provided a novel delta smelt genome assembly which is the first chromosome-level and least fragmented publicly available male and female reference genomes within the Osmeridae (smelt) family; an examination of female and male delta smelt sequencing data showing a discrete difference between sexes and establishes a framework for further investigation; and results suggesting that despite the fact that the human lactase persistence haplotype block harbors increased deleterious mutations compared to the rest of the genome, they seem to have little effect on prostate cancer, cardiovascular disease, and bone mineral density disease phenotypes.\n

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