Biology Theses and Dissertations
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Item ECOLOGICAL APPLICATIONS OF MACHINE LEARNING TO DIGITIZED NATURAL HISTORY DATA(2022) Robillard, Alexander John; Rowe, Christopher; Bailey, Helen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Natural history collections are a valuable resource for assessment of biodiversity and species decline. Over the past few decades, digitization of specimens has increased the accessibility and value of these collections. As such the number and size of these digitized data sets have outpaced the tools needed to evaluate them. To address this, researchers have turned to machine learning to automate data-driven decisions. Specifically, applications of deep learning to complex ecological problems is becoming more common. As such, this dissertation aims to contribute to this trend by addressing, in three distinct chapters, conservation, evolutionary and ecological questions using deep learning models. For example, in the first chapter we focus on current regulations prohibiting the sale and distribution of hawksbill sea turtle derived products, which continues internationally in physical and online marketplaces. To curb the sale of illegal tortoiseshell, application of new technologies like convolutional neural networks (CNNs) is needed. Therein we describe a curated data set (n = 4,428) which was used to develop a CNN application we are calling “SEE Shell”, which can identify real and faux hawksbill derived products from image data. Developed on a MobileNetV2 using TensorFlow, SEE Shell was tested against a validation (n = 665) and test (n = 649) set where it achieved an accuracy between 82.6-92.2% correctness depending on the certainty threshold used. We expect SEE Shell will give potential buyers more agency in their purchasing decision, in addition to enabling retailers to rapidly filter their online marketplaces. In the second chapter we focus on recent research which utilized geometric morphometrics, associated genetic data, and Principal Component Analysis to successfully delineate Chelonia mydas (green sea turtle) morphotypes from carapace measurements. Therein we demonstrate a similar, yet more rapid approach to this analysis using computer vision models. We applied a U-Net to isolate carapace pixels of (n = 204) of juvenile C. mydas from multiple foraging grounds across the Eastern Pacific, Western Pacific, and Western Atlantic. These images were then sorted based on general alignment (shape) and coloration of the pixels within the image using a pre-trained computer vision model (MobileNetV2). The dimensions of these data were then reduced and projected using Universal Manifold Approximation and Projection. Associated vectors were then compared to simple genetic distance using a Mantel test. Data points were then labeled post-hoc for exploratory analysis. We found clear congruence between carapace morphology and genetic distance between haplotypes, suggesting that our image data have biological relevance. Our findings also suggest that carapace morphotype is associated with specific haplotypes within C. mydas. Our cluster analysis (k = 3) corroborates past research which suggests there are at least three morphotypes from across the Eastern Pacific, Western Pacific, and Western Atlantic. Finally, within the third chapter we discuss the sharp increase in agricultural and infrastructure development and the paucity of widespread data available to support conservation management decisions around the Amazon. To address these issues, we outline a more rapid and accurate tool for identifying fish fauna in the world's largest freshwater ecosystem, the Amazon. Current strategies for identification of freshwater fishes require high levels of training and taxonomic expertise for morphological identification or genetic testing for species recognition at a molecular level. To overcome these challenges, we built an image masking model (U-Net) and a CNN to mask and classify Amazonian fish in photographs. Fish used to generate training data were collected and photographed in tributaries in seasonally flooded forests of the upper Morona River valley in Loreto, Peru in 2018 and 2019. Species identifications in the training images (n = 3,068) were verified by expert ichthyologists. These images were supplemented with photographs taken of additional Amazonian fish specimens housed in the ichthyological collection of the Smithsonian’s National Museum of Natural History. We generated a CNN model that identified 33 genera of fishes with a mean accuracy of 97.9%. Wider availability of accurate freshwater fish image recognition tools, such as the one described here, will enable fishermen, local communities, and citizen scientists to more effectively participate in collecting and sharing data from their territories to inform policy and management decisions that impact them directly.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 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 UNRAVELING THE EVOLUTIONARY HISTORY OF NOCTURNALITY IN THE STRISORES(2017) White, Noor; Carleton, Karen L; Braun, Michael J; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tracing the processes of adaptation is a fundamental practice in the study of evolutionary biology. By combining multiple lines of evidence, we can elucidate the processes of diversification, speciation, and ultimately, evolution. For my doctoral dissertation, I studied the evolutionary history of a superorder of birds (Strisores) that have undergone a dramatic life history transition, the shift from a day-living (diurnal) to a night-living (nocturnal) lifestyle. Previous study found that the diurnal Apodiformes (swifts and hummingbirds) are nested deep within the clade of nocturnal or crepuscular Caprimulgiformes (nightbirds). However, resolution of the other major lineages eluded previous efforts, precluding analysis of the evolution of nocturnality in this group. To resolve the phylogeny of Strisores, I utilized a novel class of genome-scale markers, ultraconserved elements (UCEs). UCEs are operationally defined regions of extreme conservation between two or more genomes. I collected and sequenced ~4,000 UCEs from each of 191 species of birds representing every major extant lineage, plus two crocodilian outgroups—a greater number of elements than had ever been collected or studied before. With this data, I have resolved the phylogeny of the largest and oldest (Caprimulgidae and Nyctibiidae, respectively) lineages of nightbirds, as well as the superorder Strisores, and have shed light on best practices for the use of UCEs in phylogenomics. With a phylogeny representing the evolutionary history of Strisores I then ask when, and where, potential adaptations to nocturnality occurred. To this end, I have developed a molecular tool to efficiently enrich 47 genes comprising the phototransduction cascade, a network of genes that converts the absorption of a photon by an opsin into a neural signal. I demonstrated that this tool is effective in 33 bird species chosen to cover extant avian diversity. The data captured using this array will facilitate the identification of potential molecular adaptations to nocturnality, enable the improvement of models predicting opsin sensitivity from sequence data, and allow strong inference about the perception of color across birds and other vertebrates.Item The Ecology of Early Cretaceous Angiosperms: Insights from the Fossil Record(2014) Jud, Nathan A.; Neel, Maile C.; Wing, Scott L.; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The Early Cretaceous diversification of flowering plants was not preceded by a mass extinction event. This suggests that biotic factors intrinsic to flowering plants played an important role promoting diversification, but the rarity of fossils of early flowering plants makes identifying the important features difficult. Here, I present the results of my specimen-based analysis of plant megafossil collections from Lower Cretaceous deposits of the United States. First, I describe previously unrecognized eudicot leaf fossils from a historically important Aptian (Lower Cretaceous) plant fossil site in the Potomac Group, and I provide a set of characters for recognizing the fossil leaves of these plants. Then, I present a morphotype catalog for the fossil plants from and Aptian-early Albian (Lower Cretaceous) site in the Potomac Group. This collection includes one angiosperm morphotype. Next I describe the angiosperm morphotype identified in the previous chapter. I show that it is widely distributed among coeval collections of the Potomac Group and some specimens were previously described as ferns. The preservation of attached stems leaves and root provides direct evidence of weedy, fast-growing, herbaceous angiosperms in the Aptian-early Albian. In the following chapter, I use megafossil data from the literature and museum collections to test the hypothesis that the diversification of flowering plants is associated with an increase in alpha diversity during the Early Cretaceous. Despite the evidence for a high diversification rate among early flowering plants, I found no relationship between collection age and collection richness, but I found strong evidence that angiosperms were consistently rare during the Aptan-middle Albian, and that locally abundant angiosperms became common during the late Albian, long after the initial diversification. Finally, I use new plant megafossil collections that I made from the Cloverly and Sykes Mountain Formations in Wyoming, USA, for a more high-resolution study of early angiosperm diversity, distribution, and abundance. I show that the Cloverly Formation records the appeareance of flowering plants in North America, and that by the Albian angiosperms were widely distributed among available habitats. I test the hypothesis that variation in community composition (beta diversity) increased with the appearance of angiosperms. I did not find strong support for the hypothesis that angiosperms increased beta diversity; however, rarefaction analysis shows that the rate of morphotype discovery in both the pre-angiosperm and the angiosperm interval is high, which means that additional sampling may reveal a difference in beta diversity between the two intervals. Together my findings indicate that flowering plants diversified during the Early Cretaceous not because they had features that allowed them to displace other plant groups, but because they were uniquely able to maintain high diversification rates in the face of rarity and dispersed populations.Item Molecular evolutionary studies on Trypanosoma cruzi, the agent of Chagas disease(2013) Flores Lopez, Carlos Alberto; Machado, Carlos A; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of DNA sequences to address diverse evolutionary questions has increased steadily with the growing availability of genome sequence data. In this study, I make use of DNA sequence data to describe several evolutionary aspects of the protozoan parasite responsible for Chagas disease, Trypanosoma cruzi. Chagas is estimated to infect 7.7 million people and cause the deaths of approximately ten thousand people every year in Latin America. Just like many other parasitic diseases, Chagas does not have a vaccine or an effective drug treatment. In this body of work, I specifically: (1) describe the evolutionary history of the major strains of the parasite through the use of phylogenetic analyses of 32 loci and demonstrate that the parasite's original classification into two major evolutionary lineages does not reflect the evolutionary history of the parasite, (2) demonstrate that there is strong evidence for just one major recent hybridization event during the history of T. cruzi divergence and not two as previously suggested, (3) show that all major extant T. cruzi lineages diverged recently (less than 3 million years ago), well before the arrival of humans in the Americas, (4) describe a new T. cruzi lineage that appears to have diverged in North America ("TcNA"), (5) show that a significantly larger fraction of protein-coding genes have experienced positive selection in T. cruzi than in Leishmania spp., a pattern likely due to the greater versatility of T. cruzi in its host range, cell tropism and cell invasion mechanisms, and (6) illustrate a recent major expansion of a few surface protein families in T. cruzi that seem to be linked to the evolution of the parasite's ability to invade multiple cell tissues and multiple host species. These results demonstrate the applicability and power of molecular evolutionary analyses for understanding parasitic diseases.Item Evolution and Significance of Sexual Display in Ptilonorhynchidae(2012) Coyle, Brian James; Borgia, Gerald; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)There is spectacular diversity of sexual displays among taxa. Charles Darwin was first to suggest that these traits have arisen through sexual selection (Darwin 1871). The theory of sexual selection addresses competition for mates that occurs within and between sexes (i.e. mate choice) and leads to variation in individual reproductive success. Darwin's insights into display evolution and mate choice were largely rejected by Alfred Russell Wallace (1878), who independently conceived of Natural Selection, and were controversial for decades but are now a cornerstone of evolutionary theory. The important role of sexual displays in mate choice has been demonstrated by extensive research in many species (e.g. Andersson 1994). Although the importance of sexual displays is well established, display evolution remains a controversial topic and active area of research. Multiple hypotheses have been offered to explain the evolution of sexual displays. The "good genes" hypothesis suggests displays communicate reliable information about male quality that allows females to make informed comparisons between potential mates and choose the best one (e.g. Fisher, 1915; Hamilton and Zuk,1982; Maynard Smith, 1976). These indicators of male quality may become costly to produce and maintain and expose the bearer to increased risk. The "handicap" hypothesis predicts that the inherent cost of certain displays and the variation among males in their ability to bear those costs ensure that the traits are honest indicators of relative male quality (Zahavi 1975, 1977). "Runaway selection" is a competing hypothesis that suggests displays evolve through a non-adaptive process that, in most models, is sustained by genetic correlation between display and preference (Fisher, 1930; Lande, 1981, 1987). Display elaboration via run-away is driven by open-ended preference and limited by natural selection. Sensory drive is a theory of signal evolution that addresses display design or form, including characteristics such as color, pattern, and frequency (e.g. Lythgoe, 1979; Endler, 1992a,b; Endler and Basolo, 1998). Sensory drive shapes displays to maximize communication efficiency within the particular constraints of local habitat parameters and sensitivities of the sensory system that receive the display. Thus, differences in display design are largely attributed to variation in habitats and sensory abilities among taxa. For example, display color differences among bird species may be due to the variation in habitat light spectral composition and differences in their visual spectral sensitivity (see Hill and McGraw, 2006). A variation of sensory drive called sensory exploitation suggests that males may evolve displays that take advantage of sensory biases which have evolved in other behavioral contexts, such as foraging, to manipulate females into mating (Ryan and Rand, 1990; Kirkpatrick and Ryan, 1991; Endler and Basolo, 1995). Sensory exploitation may be mal-adaptive for females if the display is not somehow correlated with male quality and may therefore lead to selection on females to eliminate or avoid susceptibility to the display. In this dissertation, I explore the evolution and development of sexual displays in species of bowerbirds, family Ptilonorhynchidae. Most bowerbirds are polygynous species with lek-like mating systems. They have long been an important model for studying sexual selection (e.g. Darwin, 1971; Marshall, 1954; Gilliard, 1969; Borgia, 1985; Frith et al, 2004). Females are highly selective in choosing mates and mating success is strongly skewed among males (e.g. Borgia, 1985; Borgia 1992). Males display in various modalities and express morphological, behavioral and off-body elements. They build a courtship structure called a bower that provides protection to females from forced copulation as they attend to behavioral display. Males decorate their bower and the surrounding display court with objects of various type and color that they collect from their environment and arrange in specific patterns (e.g. Borgia, 1985; Diamond, 1987; Lenz, 1994; Madden et al. 2004; Endler et al., 2005; Endler and Day, 2006; Borgia, 2008). They also destroy bowers of other males and plunder decorations (e.g. Borgia, 1985b; Borgia and Mueller, 1992). Courtship consists of vocalizations, behavioral elements and displays of their colorful plumage. All display types are highly differentiated throughout the bowerbird family and studies in multiple species reveal a strong correlation between mating success and many display elements (e.g. Borgia, 1985; Borgia, 1992; Madden, 2003; Frith et al. 2004). Display development in bowerbirds is complex and is thought to involve an extensive learning component (e.g. Marshall, 1954; Borgia, 1986; Loffredo and Borgia, 1986; Diamond, 1988; Frith et al., 2004; Madden, 2008; Endler et al., 2010). Bowerbirds are long lived species and males are not fully mature until more than five years old. During their juvenile period they observe the displays of adult males and practice display with other juveniles. Many species are also excellent vocal mimics demonstrating that learning is involved at least in vocal display acquisition (e.g. Loffredo and Borgia, 1986; Coleman et al., 2007; Kelly and Healy, 2010). In chapter one, I test the sensory drive hypothesis in bowerbirds by investigating the relationship between visual spectral sensitivity and the color of plumage and decoration displays. Bowerbirds have strong and specific color preferences and dislikes that differ between species. Sensory drive suggests that these differences may be driven by variation in spectral sensitivity that has arisen as a result of local adaptation to habitat (Endler 1992b). Spectrophotometry and microspectrophotometry were used to measure spectral transmission through ocular media (lens, cornea, and aqueous humor) and measure sensitivity of retinal photoreceptors that include four spectrally distinct cone receptors involved in color vision. I also used fluorescent microscopy to quantify the relative number of cone types from mounted retinal tissue. Furthermore, I sequenced the genes that code for opsin pigments to estimate photoreceptor spectral sensitivity. I found no differences in spectral sensitivity among 13 species that would explain the large interspecific variation in display coloration. However, I did find that bowerbird's lenses are relatively transparent to ultraviolet (UV) wavelengths which could influence the evolution of UV reflective displays. In chapter two, I investigated the occurrence of natural hybridization between two bowerbird species, Chlamydera nuchalis and C. maculata. In other sympatric species of bowerbirds hybridization is rare or absent which may be attributable to prezygotic reproductive isolation that is due to large differences in appearance and display (see Coyne and Orr, 2004). In this study I detected over 20% hybrid individuals based on phenotype analysis. I also provide evidence of mitochondrial introgression and show that females of both species hybridize. Given that females show a high degree of effort in intraspecific mate choice (Borgia, 1995a; Madden, 2003) it is not clear why they would mate with males of another species. Based on the distribution of bowers throughout the contact zone, it does not appear that females lack access to males of their own species, which is one of the more common reasons that bird species hybridize. Studies of other avian hybrid systems show that display learning between species drives hybridization. I provide behavioral evidence that male bowerbirds in this contact zone may learn displays from the other species. In chapter three I investigate hypotheses about the design of decoration displays. Recent work suggests that great bowerbirds, Chlamydera nuchalis, arrange objects to create a visual illusion called Forced Perspective that attracts females and increases male mating success (Endler et al. 2010; Kelly and Endler, 2012a,b). According to this hypothesis males arrange objects from small to large with distance from the bower to create an even size gradient such that all objects subtend the same visual angle to the female eye. The supposed effect is to make all objects appear the same size and make displays in the foreground appear closer. However, the data from these studies does not support the claim that males do create even size gradients nor does it show a link between the supposed illusion and mating success (Anderson, 2012; Borgia et al., 2012). I hypothesize that males are simply placing smaller objects closer to the bower for the practical purpose of avoiding interference from obstacles during courtship display. I conducted a survey of human subjects who assessed patterns of size-related bower decoration design. Survey participants were instructed to evaluate the size related pattern of object distribution in decoration displays based on visual examination of digital images. I included 40 bowers from great (C. nuchalis) spotted (C. maculata) and western (C. gutatta) bowerbirds, which share similar decoration schemes. Results of this study do not support either hypothesis, however I suggest that the obstacle avoidance hypothesis may be challenging for naive observers to detect.Item FUNCTIONAL AND MOLECULAR EVOLUTION OF THE PUF FAMILY(2012) Liu, Qinwen; Haag, Eric S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The modification of transcriptional regulation is a well-documented evolutionary mechanism in both plants and animals, but post-transcriptional controls have received less attention. The derived hermaphrodite of C. elegans has regulated spermatogenesis in an otherwise female body. PUF family RNA-binding proteins FBF-1 and FBF-2 limit XX spermatogenesis by repressing the male-promoting proteins FEM-3 and GLD-1. For my dissertation research, I examine the function of PUF homologs from other Caenorhabditis species, with emphasis on C. briggsae, which evolved selfing convergently. C. briggsae lacks a bona fide fbf-1/2 ortholog, but two members of the related PUF-2 subfamily, Cbr-puf-2 and Cbr-puf-1.2, do have a redundant germline sex determination role. Surprisingly, this is to promote, rather than limit, hermaphrodite spermatogenesis. I provide genetic, molecular, and biochemical evidence that Cbr-puf-2 and Cbr-puf-1.2 repress Cbr-gld-1 by a conserved mechanism. However, Cbr-gld-1 acts to limit, rather than promote, XX spermatogenesis. As with gld-1, no sex determination function for fbf or puf-2 orthologs is observed in gonochoristic Caenorhabditis. These results indicate that PUF family genes were coopted for sex determination in each hermaphrodite via their long-standing association with gld-1, and that their precise sex-determining roles depend on the species-specific context in which they act. Finally, I document non-redundant roles for Cbr-puf-2 in several aspects of somatic development. I show Cbr-puf-2 is required for reliable embryonic development, and that it is essential for vulval development and normal progression from early larval stage. I provide evidence suggesting that this latter role is related to pharyngeal muscle physiology. Thus, recently duplicated PUF paralogs, while redundant for some roles, can also rapidly acquire distinct non-redundant functions. This is consistent with theoretical models for the preservation of gene duplicates.Item Breaking the A-P axis: Evolution of diverse asexual reproduction strategies in Convolutriloba acoels(2009) Sikes, James M.; Bely, Alexandra E.; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The defining characteristic of the Bilateria is the presence of a distinct head end and tail end, which defines the anterior-posterior (A-P) axis, a feature that is established during embryogenesis and generally remains unaltered during the lifetime of an organism. While a few bilaterians have evolved asexual reproduction strategies that allow them to subdivide the A-P axis, acoels in the genus Convolutriloba have an unparalleled ability to alter the A-P axis during modes of transverse fission, longitudinal fission, and reversed polarity budding. Convolutriloba acoels thus offer an exceptional opportunity to investigate the mechanisms that allow for the radical modification of an already established A-P body axis and to explore the evolution and development of diverse asexual reproduction strategies among related species. In this study, I reconstruct the evolutionary history of asexual reproduction in the Convolutriloba and compare the diverse modes of asexual reproduction at the level of body-wall musculature, nervous system development, and cell proliferation while also exploring the regenerative potentials of tissues across species with different modes of asexual reproduction. In addition, I further explore the unusual process of A-P axis reversal that occurs during reversed polarity budding in C. retrogemma through studies of body patterning and regeneration. The results of these analyses suggest that a rich developmental toolkit of regenerative abilities, including the ability to utilize both epimorphosis and morphallaxis, to regenerate all parts of its body even from a small fragment, and to produce bifurcated A-P axes were present in the ancestor of the Convolutriloba allowing for the evolution of A-P axis modifications unlike any other bilaterian group. This toolkit along with the evolution of a seemingly unpatterned zone of tissue within the body of C. retrogemma capable of generating new anterior axes appear to have allowed this species to evolve the ability to form reversed A-P axes during budding.Item ISOLATION AND CHARACTERIZATION OF CAENORHABDITIS BRIGGSAE TRA MUTANTS.(2005-12-12) Kelleher, Danielle Fay; Haag, Eric S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)In order to aid in the reconstruction of the Caenorhabditis briggsae sex determination pathway, for the purposes of studying the convergent evolution of hermaphroditism and mating system change in nematodes, Cb-tra mutants have been isolated through forward mutagenesis. Based on phenotype, genetic linkage, molecular linkage, and in some cases sequence analysis, the C. briggsae homologs of tra-1, tra-2, and possibly tra-3 have been identified. Upon further characterization, the function of the tra genes during sex determination between C. elegans and C. briggsae appears to be largely conserved. However, notable differences, with respect to the role of tra-1 and potentially the role of tra-3, have been observed between these two species. In addition, intra-species suppression of the putative tra-3 mutant (AF16 background) by genomic variants in the wild-type strain HK104 suggests that molecular interactions underlying sex determination are changing between these two C. briggsae populations.