Biology Theses and Dissertations

Permanent URI for this collectionhttp://hdl.handle.net/1903/2749

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    GENOMIC AND REPRODUCTIVE CONSEQUENCES OF SELF-FERTILITY IN CAENORHABDITIS NEMATODES
    (2019) Yin, Da; Haag, Eric S; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The evolution of a new reproductive strategy is expected to be reflected in an organism's genome and impact mating-related traits. Several species of Caenorhabditis nematodes have evolved the ability to self-fertilize from their outcrossing ancestors. Comparisons of species with different reproductive strategies may therefore reveal consequences of transition to self-fertilization. We compared chromosome-scale genome assemblies for the outcrossing nematode Caenorhabditis nigoni and its recently self-fertile sister species, C. briggsae. C. nigoni genome resembles that of outcrossing relatives but encodes 31% more protein-coding genes than C. briggsae. C. nigoni genes lacking C. briggsae orthologs were disproportionately small and male-biased in expression, including the male secreted short (mss) gene family that encodes sperm surface glycoproteins conserved only in outcrossing species. Sperm of mss-null males of an outcrossing species failed to compete with those of wild-type males, despite having normal fertility in non-competitive situations. Restoration of mss to C. briggsae males was sufficient to enhance sperm competitiveness. These results reveal the pervasive influence of sex on genome content that can be used to identify sperm competition factors. Further I found the fitness of mss+ genotype was influenced by mating system and population subdivision. Specifically, mss+ is sufficient to increase male frequency and depress population growth in genetically homogenous androdioecious populations. Using experimental evolution, I demonstrated that when mss+ and mss-null (i.e. wild-type) genotypes compete, mss+ is positively selected in both mixed-mating and strictly outcrossing situations, though more strongly in the latter. I suggest that the lack of inbreeding depression and the strong subdivision thought to characterize natural Caenorhabditis populations impose selection on sex ratio that makes loss of mss adaptive in self-fertile species.
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    STRUCTURAL EVOLUTION OF AFRICAN CICHLID GENOMES
    (2018) Conte, Matthew A; Kocher, Thomas D; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    An unanswered question in biology is how the evolution of genome structure supports or accompanies diversification and speciation on different time scales. African cichlid fishes are a well-documented system ideal for studying rapid evolution, due to their phenotypic diversity and high number of speciation events over the last several million years. I generated two de novo genome assemblies of the riverine cichlid Oreochromis niloticus (tilapia) and the Lake Malawi cichlid Metriaclima zebra using high-coverage long-read sequencing data and anchored the assemblies to chromosomes using several genetic and physical maps, to produce two high-quality anchored references. By comparing these chromosome-scale assemblies to integrated recombination, transcriptome, and resequencing data of multiple genera and species, I identified and characterized many large novel genome rearrangement events. These rearrangements included multiple novel sex-determination inversions, several metacentric-acrocentric karyotype differences via centromere assembly and placement, and wide regions of suppressed recombination in genera- and species-level crosses of Lake Malawi cichlids. Karyotype evolution in cichlids was further analyzed with long-read sequencing, specifically revealing the complex structure and content of a highly repetitive supernumerary chromosome present in some but not all individuals of a population across a wide range of eukaryotes, including many cichlid species. These supernumerary "B" chromosomes are shown to be limited to female Lake Malawi cichlids and have a unique evolutionary history with B chromosomes present in Lake Victorian cichlids male and females. This work reveals how structural genomic changes impact a rapidly evolving clade, while providing high-quality resources for the community, a context for previous genetic studies, and a robust platform for future genome research in cichlids.