Using Ecological Niche Modeling and Genetics to Evaluate the Conservation Status of the Texas Gartersnake, Thamnophis Sirtalis Annectens

The definition of a species has been argued extensively by philosophers and biologists resulting in the development of many different concepts which often contradict each other. An integrative approach using multiple types of data (e.g, morphological, ecological, behavioral, genetic) may be the most successful at correctly assigning taxonomic levels.Here, we use an integrative approach of ecological niche modeling and molecular genetics to investigate the taxonomy of a state imperiled gartersnake subspecies, Thamnophis sirtalis annectens, using ecological niche modeling and molecular phylogenetics analyses. Recently, it was given a conservation rank of S2 (imperiled) in the state of Texas and those that are familiar with it have suggested that its numbers are dwindling. Using ecological niche modeling and mtDNA sequence data we begin to understand the natural and evolutionary history of T. s. annectens. The results of this study provided additional information on the ecology and potential habitat range of T. s. annectens as well as information on the phylogenetic systematics of this subspecies. Our ecological niche model indicates areas where conservation efforts for T. s. annectens should be focused as well as important environmental variable such as landcover and geology that T. s. annectens prefers. When including T. s. annectens in a comparative niche model, this subspecies primarily occupies distinctly different habitat than the red-sided gartersnake, T. s. parietalis, which also occurs in Texas. Statistical analysis indicated that T. s. annectens occupies as significantly different ecological niche than T. s. parietalis. Similarly, the genetic data indicate that T. s. annectens can be differentiated from T. s. parietalis and T. s. sirtalis, however this difference is greatest between T. s. sirtalis. While this work has told us much about T. s. annectens, more is left to be learned including ground-truthing our ecological niche model. Collecting additional genetic data to verify the phylogenetic relationships we have hypothesized here should also be done in the future. Regardless, this work indicates T. s. annectens may be distinct both genetically and ecologically and provides conservation managers with niche models that will assist in locating the optimal habitat required by this subspecies

A Spatial Assessment of the Status and Risks to Mussel Concentrations in the Meramec Drainage of Missouri

Effective conservation of a taxonomic group requires the identification of the fundamental requirements that allow it to persist and factors best suited to predict its distribution. Freshwater mussels are among the most imperiled taxa in the United States. The unique life history and habitat requirements of unionid mussels complicate efforts to model their distributions, an obstacle to mussel conservation. Given limited resources, a strategic approach including these factors to describe mussel requirements and spatially-explicit identification of threats will improve effectiveness and lower cost of mussel conservation and monitoring programs. In this dissertation, I review existing knowledge regarding mussel ecology, how this information has influenced modeling successes and failures in the past, a consensus of the importance of physical stream characteristics and their impacts on mussel distributions, and limitations to mussel monitoring and modeling, concluding with an approach to mussel conservation to address limitations and complications. Finally, I outline a two-part study that follows this approach and is part of a long-term mussel monitoring and conservation program in Missouri. The overarching goal of this study is to spatially describe the status and risks to mussel communities in the species-rich Meramec River Drainage. Elucidating relationships between community metrics (e.g., species richness) within otherwise fundamentally suitable habitats helps to inform management and pinpoint threats to mussel communities. Information on threats to mussels gained through this process is used to categorize reaches suitable for mussel communities, with conservation prioritization as the focus. Monitoring suggestions tailored to these categories are provided, and areas of potential reintroduction and restoration are identified. The results of this project provide information for managers on where mussel strongholds occur, why mussels are not present in areas that are otherwise fundamentally suitable, what threats affect mussel communities, and what monitoring strategies will efficiently track mussel communities through time

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu