Biology Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2749
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Item Seasonal Migrations of Atlantic Sturgeon and Striped Bass Through the Maryland Wind Energy Area(2019) Rothermel, Ella Rick; Secor, David; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Baseline information is needed on migrations through US Mid-Atlantic Bight shelf waters in advance of offshore wind development. Acoustically-tagged Atlantic sturgeon and striped bass were detected from 2016-2019 in an array of 20 acoustic telemetry receivers centered on the Maryland Wind Energy Area and extending 10-50 km offshore. Both species were transient (mean residency < 3 days), but migration patterns differed seasonally and were related to depth and temperature. Generalized additive models showed that Atlantic sturgeon occur at inshore sites during spring while striped bass shifted toward the outer shelf as inshore waters cooled in winter. The movement of hundreds of tagged striped bass and sturgeon, originating from shelf waters from Maine to South Carolina suggests that the Wind Energy Area is part of a multi-species Atlantic coastal flyway, particularly during spring, fall, and winter periods. Thus, summer presents a potential window for wind tower construction.Item Multi-locus phylogenetic analysis of Amphipoda indicates a single origin of the pelagic suborder Hyperiidea(2019) Biancani, Leann M; Cummings, Michael P; Osborn, Karen J; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Hyperiidea is an exclusively pelagic suborder of amphipod crustaceans, exhibiting a wide array of unique adaptations to life in the dark, open expanse of the oceanic midwater. No common morphological synapomorphy unites approximately 350 described species. Instead, hyperiid amphipods are defined only by their pelagic existence. Hyperiidea exhibits many of the characteristics of an adaptive radiation and could represent a midwater example of this phenomenon. Previous morphological and molecular analyses have led to uncertainty in the shared ancestry of Hyperiidea. The evolutionary history of their diverse adaptations, as well as their relationship to other amphipods, remains unknown. Here we present results of a multi-locus phylogenetic analysis of publicly available amphipod sequences for three nuclear loci (18S, 28S, and H3) and two mitochondrial loci (COI and 16S) from over 300 amphipod genera, 40 of which are hyperiids. We recover strong support for a monophyletic Hyperiidea as well as reciprocally monophyletic hyperiid infraorders Physocephalata and Physosomata (with enigmatic genera Cystisoma and Paraphronima more closely related to Physosomata). We also identify several benthic, commensal amphipods representing potential sister groups for Hyperiidea. These taxa have not previously been considered close hyperiid relatives and include the genera Amphilochus, Colomastix, Anamixis, Paranamixis, and Leucothoe. Our results support the current definition of Hyperiidea and inform the phylogenetic placement of the suborder within Amphipoda.Item 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.Item Proximate and ultimate insights in the evolution of color vision in tropical freshwater fish(2019) Escobar Camacho, Daniel; Carleton, Karen L; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Evolutionary biology aims to understand diversity and the different mechanisms shaping this organismal variation. Furthermore, several animals vary greatly in coloration patterns and the adaptive mechanisms they have to optimally perceive visual signals in their light environment. The visual system of fish, due to their extensive variation in spectral sensitivities and their numerous adaptations to the underwater light environment, offers a unique opportunity to disentangle this phenotypic diversity. Throughout this dissertation, I analyze the visual systems of two major groups of Neotropical teleosts: cichlids and characins. Through transcriptome, genome and physiological experiments, I characterized the extant opsin gene complements of their visual system, which is a product of highly dynamic opsin gene evolution, and their color vision, which is based on the expression of at least three spectrally different visual pigments. The diversity of visual pigments found in these fish is the product of several spectral tuning mechanisms, which they use to fine-tune their spectral sensitivities to specific wavelengths. Our results follow the sensitivity hypothesis because the visual sensitivities of cichlids and characins match the available light in Neotropical ecosystems. Furthermore, through behavioral assays complemented with visual modeling, I show that African cichlids possess true color vision, the capacity of discriminating color regardless of brightness. This is followed by behavioral experiments analyzing the limits of their chromatic discrimination and discussing the adaptive significance of color vision and its relevance in the visual ecology of Lake Malawi. This dissertation enhances our understanding of color vision in freshwater fish using molecular and behavioral methods. This work encompasses experiments analyzing the genetic complement of visual pigments, builds knowledge in the evolution of these molecules and their relationship with aquatic environments, and analyzes the color dimensionality of visual systems through behavioral trials. Overall, this dissertation demonstrates the evolution of fish color vision with several methodologies highlighting the importance of an integrative and comparative approach in vision research.Item Consequences of sexual selection within and between species of phyllostomid bats(2019) Adams, Danielle Margret; Wilkinson, Gerald S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)To understand the myriad effects of sexual selection in the evolution and diversification of life, we must investigate variation within and among diverse animal taxa. Here, I study sexual selection in phyllostomid bats (Family Phyllostomidae), a diverse radiation comprised of 216 species that vary widely in their social behavior and roosting ecology, but whose mating behavior is largely unknown. First, I investigate whether socio-ecological traits predict variation in the intensity of sexual selection among phyllostomid species. In the absence of behavioral data, I use measures of sexual dimorphism as an indicator of precopulatory sexual selection and testes size as a proxy for postcopulatory competition. Taking a phylogenetic approach, I find that roosting aggregation size, but not roost structure permanence, explains family-wide variation in both pre- and postcopulatory sexual selection. Next, I examine the distribution of extra-group paternity in a single species, Phyllostomus hastatus, whose social mating system of female-defense polygyny has been well described. Through molecular parentage assignment of 241 offspring from three wild colonies in Trinidad, West Indies, I find that most harem-holding males are unable to monopolize mating in their social groups, resulting in paternity by extra-group males. Furthermore, variation in the rate of extra-group paternity is associated with harem male body condition as well as the composition of the female group. Finally, I investigate the variation in a male-specific chemical signal found in P. hastatus, which has been implicated in male-male competition and female choice of this species. Results show that in addition to individual variation, harem males have significantly different chemical profiles from males found roosting in all-male groups (bachelors). Through the examination of both family-wide and species-specific patterns, we can broaden our understanding of how sexual selection has contributed to the diversity within the Phyllostomidae.Item The Diversity of Sex Chromosomes within African Cichlids(2018) Gammerdinger, William Jacob; Kocher, Thomas; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Genetic sex-determination is one of the most prevalent systems by which the sex of an organism can be established. The genes that determine sex reside on chromosomes that experience a unique pattern of evolutionarily processes, which often leads to the degradation of genes surrounding these sex-determination loci. The widespread degradation of sex chromosomes has been noted in the relatively old and heteromorphic sex chromosomes of therian mammals and birds. However, with the advent of next-generation sequencing, it is now possible to study the earliest stages of sex chromosome evolution in relatively homomorphic sex chromosomes. African cichlid fishes are a powerful model system for studying the early stages of sex chromosome evolution because of the diversity and young age of their sex chromosomes. This dissertation develops methods for studying young sex chromosomes and employs these approaches to evaluate the sex chromosomes within tilapia and Lake Tanganyika cichlid fishes. Furthermore, this research demonstrates a method for identifying the ancestral state for species sharing a common sex chromosome system and a process for evaluating the functional significance of these shared mutations. Lastly, this dissertation proposes a mechanism for the diversity of sex chromosome systems observed within African cichlid fishes. This analysis not only characterizes the decay of several known young sex chromosomes, but also reveals multiple previously undiscovered sex chromosome systems within the African cichlid fishes. These novel sex chromosome systems likely represent only a fraction of the true variety of sex chromosome systems within this group, and therefore push forward the argument for characterizing the sex chromosome systems of more cichlid species in order to better understand the early stages of sex chromosome evolution.Item Mechanisms contributing to opsin expression divergence in the visual system of African Cichlids(2018) Nandamuri, Sri Pratima; Carleton, Karen L; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Vision is an important sensory modality, guiding fundamental tasks such as foraging, escaping from predators, identification of conspecifics and selection of mates. As such, animals exhibit a wide variety of adaptations to spectrally tune their visual systems to closely match the environment. This extensive variation in visual system tuning is achieved both via genetic changes as well as environmental induced plasticity. Lacustrine cichlids of East Africa are famous for their expedited adaptive radiations. Cichlids in these rift lakes inhabit a diverse range of light environments, from the murky red-shifted waters of Lake Victoria to clear Lake Malawi. Consequently, African cichlids have some of the most diverse visual systems among vertebrates on the planet, with species expressing different combinations of seven cone opsin genes. This differential expression is under genetic control and leads to drastic differences in the visual sensitivities between closely related species. Moreover, cichlid species often exhibit plastic changes in opsin expression due to alterations in environmental light conditions. The diversity of genetically determined visual palettes and the variation in expression due to plastic changes offers an excellent opportunity to study the proximate mechanisms governing opsin expression divergence in this group. Utilizing a hybrid cross between two species varying in opsin expression, we show that divergent expression of cone opsins is regulated by multiple quantitative trait loci (QTLs). Most of these QTLs are located in trans to the opsins, with the exception of one QTL in cis to the SWS1 opsin. Further fine-mapping of the cis-QTL revealed a deletion in the promoter of the SWS1 gene that is associated with a decrease in its expression. Additionally, performing two reciprocal experiments, we show that adult cichlids from Lake Malawi show rapid and reversible plastic changes in opsin expression due to differences in lighting conditions. These studies show that both predetermined genetic factors and environmental inputs contribute to opsin expression divergence in cichlids. These factors enable short term and ultimately long-term adaptation to changing habitats, facilitating the survival and perhaps speciation of these fantastic fishes.Item 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.Item Phylogenomics, Systematics, and Evolution within the Nudibranch Group Cladobranchia (Mollusca: Gastropoda)(2017) Goodheart, Jessica Ann Marie; Cummings, Michael P; Collins, Allen G; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)To truly understand evolution, we must document patterns of variation in traits – ranging from anatomical features of individuals to geographic ranges of species – to gain insights into the mechanisms that lead to changes in diversity through time. This type of work requires a robust historical context of evolutionary relationships in order to make comparisons across taxa and inferences about past events. My dissertation provides a thorough phylogenetic analysis of the marine gastropod group Cladobranchia (Mollusca) to better understand the evolution of defensive capabilities within the clade. In the absence of a protective shell, lineages within Cladobranchia have evolved a diverse array of alternative defense mechanisms, including the use of stinging organelles (nematocysts) acquired from their cnidarian prey. It has been hypothesized that incorporation of nematocysts as a defensive strategy may have been an evolutionarily important event that led to large-scale diversification within this group. As such, understanding the steps involved in the evolution of this ability is necessary for evaluating this hypothesis. A major objective for my dissertation has been to use transcriptome (RNA-Seq) data from 37 species in Cladobranchia in order to generate a well-supported phylogenetic hypothesis of Cladobranchia. This research has produced the most highly supported phylogenetic tree of Cladobranchia thus far and contributes to confidence in the efficacy of genomic data to resolve relationships among gastropod lineages. As I have been able to expand this phylogenetic hypothesis with additional taxon sampling, including molecular data from a further 60 species, I have been able to provide context for understanding the evolutionary steps that led to the ability to sequester nematocysts. This phylogeny was then combined with morphological data from 50 nematocyst sequestering species within Cladobranchia to allow for a more detailed reconstruction of the evolution of nematocyst sequestration and prey preference within this clade. Overall, this work builds knowledge of the relationships among major lineages within Cladobranchia, and has substantially increased understanding of the evolution of morphological and ecological characters in this group.Item POPULATION DYNAMICS OF EASTERN OYSTERS (CRASSOSTREA VIRGINICA) IN THE CHOPTANK RIVER COMPLEX, MARYLAND, DURING 1989 - 2015(2017) Damiano, Matthew; Wilberg, Michael J; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The eastern oyster (Crassostrea virginica) fishery in the Choptank River Complex (CRC) supports a large fraction of Maryland’s harvest. The CRC is also host to some of the largest oyster restoration projects in the world. Yet the relative effects of harvest and restoration on the population dynamics of oysters in the CRC have not been assessed. We developed stage-based population models for each region of the CRC in AD Model Builder using dredge survey and harvest data provided by Maryland Department of Natural Resources from 1989 to 2015. Natural mortality was low during 2004-2015 potentially due to increased resistance to the disease, Dermo. Recruitment was greatest in the late 1990s, 2010, and 2012, which caused an increase in abundance. These models will serve as the foundation of a simulation model that will be used to help fishery stakeholders evaluate management and restoration options in the CRC.