Evolutionary History of a Large-Genome Salamander Across Five Disjunct Regions of the Southeastern United States

The southeastern United States has a dynamic geologic history. Mountain range uplift, sea level fluctuations, and river basin evolution have shaped species geographic distributions in the region. My dissertation objectively identifies amphibian species with highly fragmented distributions in the Southeast (Chapter 2) and examines the phylogeographic history of one of those species, Plethodon serratus. This salamander species has a widely disjunct range across five regions: the Appalachians, the Ozarks, the Ouachitas, and two allopatric sites in Louisiana. Analyses of mitochondrial and nuclear loci (Chapter 3) showed that P. serratus is comprised of multiple genetic lineages, and the five regions are not reciprocally monophyletic. Instead, there was evidence of historical gene flow between one of the Louisiana sites and the Ouachitas. Niche and paleodistribution modeling results suggested that P. serratus expanded from the Appalachians during the cooler Last Glacial Maximum and has since been restricted to its current disjunct distribution by a warming climate. These data reject the universal applicability of the glacial contraction model to temperate taxa and reiterate the importance of considering the natural history of individual species. Using a large next-generation sequencing data set of ultraconserved elements (Chapter 4), I estimated a fully resolved species tree that confirmed the non-sister relationship of the two Louisiana populations. I successfully generated this data set without modifying the established laboratory protocols; this is an important note, as large genomes can present challenges for next-generation sequencing. I found that P. serratus has a genome size of 21 pg (Chapter 5) and that this species, along with its closest relatives, has undergone genome size reduction since diverging from the ancestor of Plethodon. This dissertation demonstrates that established methods of next-generation sequencing can be used in studies of large-genome salamander phylogeography. This is especially important, as many salamander populations are declining in the face of habitat loss and climate change. Plethodon serratus is only one of many amphibian species in the Southeast with fragmented ranges. Future research on the biogeography of these organisms will be crucial to conservation

Parameter identifiability in a class of random graph mixture models

We prove identifiability of parameters for a broad class of random graph mixture models. These models are characterized by a partition of the set of graph nodes into latent (unobservable) groups. The connectivities between nodes are independent random variables when conditioned on the groups of the nodes being connected. In the binary random graph case, in which edges are either present or absent, these models are known as stochastic blockmodels and have been widely used in the social sciences and, more recently, in biology. Their generalizations to weighted random graphs, either in parametric or non-parametric form, are also of interest in many areas. Despite a broad range of applications, the parameter identifiability issue for such models is involved, and previously has only been touched upon in the literature. We give here a thorough investigation of this problem. Our work also has consequences for parameter estimation. In particular, the estimation procedure proposed by Frank and Harary for binary affiliation models is revisited in this article

The dynamic evolutionary history of genome size in North American woodland salamanders

© 2017 Published by NRC Research Press. The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders

Local political leadership and the modernisation of local government

Political leadership has been a key element of central government’s attempts to ‘modernise’ local government over the past decade, within a discourse that emphasised ‘strong’ and ‘visible’ leadership and the role of leaders and leadership in driving change within local authorities. In the context of such an approach, and also taking account of academic discourse, this article draws upon interviews with nearly thirty individuals in leadership positions in local authorities in England, Scotland and Wales to assess their experiences of leadership and their views of some aspects of the role and work of councils. It suggests that whilst there is broad convergence between the aspirations of government and the narratives that emerge from these leaders on some aspects of local political leadership, there are also differences, perhaps most notably over the relationship between changes to decision making structures and the loci of political power

Bayesian stochastic blockmodeling

This chapter provides a self-contained introduction to the use of Bayesian inference to extract large-scale modular structures from network data, based on the stochastic blockmodel (SBM), as well as its degree-corrected and overlapping generalizations. We focus on nonparametric formulations that allow their inference in a manner that prevents overfitting, and enables model selection. We discuss aspects of the choice of priors, in particular how to avoid underfitting via increased Bayesian hierarchies, and we contrast the task of sampling network partitions from the posterior distribution with finding the single point estimate that maximizes it, while describing efficient algorithms to perform either one. We also show how inferring the SBM can be used to predict missing and spurious links, and shed light on the fundamental limitations of the detectability of modular structures in networks.Comment: 44 pages, 16 figures. Code is freely available as part of graph-tool at https://graph-tool.skewed.de . See also the HOWTO at https://graph-tool.skewed.de/static/doc/demos/inference/inference.htm

Physiotherapy rehabilitation for osteoporotic vertebral fracture (PROVE) : study protocol for a randomised controlled trial

Background: Osteoporosis and vertebral fracture can have a considerable impact on an individual’s quality of life. There is increasing evidence that physiotherapy including manual techniques and exercise interventions may have an important treatment role. This pragmatic randomised controlled trial will investigate the clinical and cost-effectiveness of two different physiotherapy approaches for people with osteoporosis and vertebral fracture, in comparison to usual care. Methods/Design: Six hundred people with osteoporosis and a clinically diagnosed vertebral fracture will be recruited and randomly allocated to one of three management strategies, usual care (control - A), an exercise-based physiotherapy intervention (B) or a manual therapy-based physiotherapy intervention (C). Those in the usual care arm will receive a single session of education and advice, those in the active treatment arms (B + C) will be offered seven individual physiotherapy sessions over 12 weeks. The trial is designed as a prospective, adaptive single-blinded randomised controlled trial. An interim analysis will be completed and if one intervention is clearly superior the trial will be adapted at this point to continue with just one intervention and the control. The primary outcomes are quality of life measured by the disease specific QUALLEFO 41 and the Timed Loaded Standing test measured at 1 year. Discussion: There are a variety of different physiotherapy packages used to treat patients with osteoporotic vertebral fracture. At present, the indication for each different therapy is not well defined, and the effectiveness of different modalities is unknown

Teaching to learn and learning to teach : a case study of multilevel, interdisciplinary education in natural resources

The University of Vermont’s School of Natural Resources (SNR) has linked undergraduate and graduate education through a recent update of a sophomore-level class in SNR’s core curriculum: “Environmental Problem Analysis” (NR105). As a result of a series of collaborative workshops, NR105 now includes explicit links to two other courses: “Ecology, Ecosystems and Environment” (NR103) and “Social Processes and the Environment” (NR104), and students must take these three courses concurrently. NR105, a multidisciplinary, integrative course, is taught collaboratively by two SNR Ph.D. students (an ecologist and a social scientist), and fulfills their graduate teaching requirement. Through direct course development and oversight, regular meetings with faculty members who teach the concurrent courses, and participation as members of the core faculty development group, this model places Ph.D. students into a “faculty apprentice” role. The three- course sequence thus combines integrative, cross-disciplinary education with a multilevel approach to education. At both undergraduate and graduate levels, it also includes an explicit focus on group work and interdisciplinary team collaborations

Empirically-Driven Multiwavelength K-corrections At Low Redshift

K-corrections, conversions between flux in observed bands to flux in rest-frame bands, are critical for comparing galaxies at various redshifts. These corrections often rely on fits to empirical or theoretical spectral energy distribution (SED) templates of galaxies. However, the templates limit reliable K-corrections to regimes where SED models are robust. For instance, the templates are not well-constrained in some bands (e.g., WISE W4), which results in ill-determined K-corrections for these bands. We address this shortcoming by developing an empirically-driven approach to K-corrections as a means to mitigate dependence on SED templates. We perform a polynomial fit for the K-correction as a function of a galaxy's rest-frame color determined in well-constrained bands (e.g., rest-frame (g-r)) and redshift, exploiting the fact that galaxy SEDs can be described as a one parameter family at low redshift (0.01 < z < 0.09). For bands well-constrained by SED templates, our empirically-driven K-corrections are comparable to the SED fitting method of Kcorrect and SED template fitting employed in the GSWLC-M2 catalogue (the updated medium-deep GALEX-SDSS-WISE Legacy Catalogue). However, our method dramatically outperforms the available SED fitting K-corrections for WISE W4. Our method also mitigates incorrect template assumptions and enforces the K-correction to be 0 at z = 0. Our K-corrected photometry and code are publicly available.Comment: 15 pages, 9 figures, submitted to MNRA