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Using Genomics To Understand Population Demographics In The Context Of Amphibian Conservation, Schyler O. Nunziata
Using Genomics To Understand Population Demographics In The Context Of Amphibian Conservation, Schyler O. Nunziata
Theses and Dissertations--Biology
Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Large single nucleotide polymorphism datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of both model and non-model species. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography, in both simulation and empirical settings. Here, I used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (Ne) in Wright-Fisher populations over the course of stable and declining population trends, and distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Overall, my results reveal that demographic inference using genome-wide data can be successfully applied to estimate Ne, and the detection of population-size declines. Next, I assess these methods in an empirical study from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and …
Axolotl Paedomorphosis: A Comparison Of Juvenile, Metamorphic, And Paedomorphic Ambystoma Mexicanum Brain Gene Transcription, Carlena Johnson
Axolotl Paedomorphosis: A Comparison Of Juvenile, Metamorphic, And Paedomorphic Ambystoma Mexicanum Brain Gene Transcription, Carlena Johnson
Theses and Dissertations--Biology
Unlike many amphibians, the paedomorphic axolotl (Ambystoma mexicanum) rarely undergoes external morphological changes indicative of metamorphosis. However, internally, some axolotl tissues undergo cryptic metamorphic changes. A previous study examined interspecific patterns of larval brain gene expression and found that these species exhibited unique temporal expression patterns that were hypothesized to be morph specific. This thesis tested this hypothesis by examining differences in brain gene expression between juvenile (JUV), paedomorphic (PAED), and metamorphic (MET) axolotls. I identified 828 genes that were expressed differently between JUV, PAED, and MET. Expression estimates from JUV were compared to estimates from PAED and …
When Molecules And Morphology Clash: Revisiting Species Tree Reconstruction Of Ambystomatid Salamanders Using Multiple Nuclear Loci, Joshua Steven Williams
When Molecules And Morphology Clash: Revisiting Species Tree Reconstruction Of Ambystomatid Salamanders Using Multiple Nuclear Loci, Joshua Steven Williams
Theses and Dissertations--Biology
The analysis of diverse data sets can yield different phylogenetic estimates that challenge systematists to explain the source of discordance. The Ambystomatidae are a classic example of this phylogenetic conflict. Previous attempts to resolve the ambystomatid species tree using allozymic, morphological, and mitochondrial sequence data have yielded different estimates, making it unclear which data source best approximates ambystomatid phylogeny. We present the first multi-locus DNA sequencebased phylogenetic study of the Ambystomatidae. Because independent loci can contain discordant gene tree histories, concatenating unlinked loci into a single data matrix can lead to strongly supported and erroneous results. Therefore, we utilized a …