No description available.

Adjacent terrestrial habitat surrounding wetlands are critical for the survival and success of many species that use them. The primary purpose of this study was to determine amphibian movement from adjacent habitats into Orchard Bog, a restored bog located in Shady Valley, Johnson County, Tennessee. In addition, a secondary bog, Quarry Bog, was also studied determining baseline presence/absence data A total of 16 species from six families were observed throughout the study sites. Seven species of anurans, Bufonidae, Hylidae, and Ranidae and nine species of caudates in the families Plethodontidae, Ambystomatidae and Salamandridae were identified. Fourteen of the 16 species were found within Orchard Bog. Data collected can be used to help determine more beneficial land acquisitions and management strategies. Survey methods included pitfall traps, funnel traps, coverboard arrays, and opportunistic surveys.

No description available.

No description available.

Amphibians, because of their semi-permeable skin, sensitivity to changing microclimates, and important role in ecosystems, are often viewed as indicators of ecosystem health. They make excellent organisms for studies on the effects of silvicultural practices. My goal was to provide recommendations for forest management in the southern Appalachians so that harvesting operations are compatible with maintaining healthy populations of forest amphibians. I tested previously created habitat models that determined the most important habitat characteristics for salamanders. I counted salamanders in 240 10 x 10 m plots located in the MeadWestvaco Wildlife and Ecosystem Research Forest in north-central West Virginia. We also collected a variety of habitat data in these plots to predict salamander abundance with previously created models. These simple linear regression analyses of predicted versus observed values suggest for most models (7 out of 9) a weak relationship between predicted and observed values (R2 from 0.0033 to 0.2869, p from < 0.0001 to 0.7490). However, one of the models showed characteristics suggesting that it predicted new data as well or better than the original data, and therefore was the most accurate at predicting salamander abundance, and could be used for management purposes, although there was still much unexplained variation. This model included the variables woody stems (< 7.5 cm DBH), available rock, riparian status (i.e., within 15 m of a stream), percent overstory canopy cover, and available highly decomposed woody debris (decomposition classes 3 to 5). All of these relationships were positive except for woody stems, suggesting that in order to maintain healthy populations of salamanders, we should protect areas next to streams, with high amounts of rock, decomposed woody debris, overstory canopy cover, and few woody stems. I also examined the immediate effects of clearcuts on salamander movement and population estimates. I batch marked salamanders in plots at the edges of a clearcut, and in a control plot. Using the Schnabel estimator, I estimated population sizes in each plot. I then compared population estimates pre- and post-harvest on the interior (harvested) and exterior (unharvested) sides of the plots, taking into account the control plot. I also examined adult-juvenile ratios and movements from one side of the plot to the other. I found no significant changes (p > 0.05) following harvest in any of these measures, suggesting that salamanders do not move out of the harvested area post-harvest, at least over the short term (10 months of this study). This suggests that a longer period of time (> 1 year) is required to observe the population declines detected in most studies. / Master of Science

Large-scale land uses such as residential wastewater discharge and coal mining practices, particularly surface coal extraction and associated valley fills, are of particular ecological concern in central Appalachia. Identification and quantification of both large-scale land use and microhabitat alterations to ecosystems are a necessary first-step aid in mitigation of negative consequences to biota. In central Appalachian headwater streams absent of fish, salamanders are the dominant, most abundant vertebrate predator providing a significant intermediate trophic role. Stream salamander species are considered to be sensitive to aquatic stressors and environmental alterations with past research having shown linkages among microhabitat parameters, and large-scale land use such as urbanization and logging to salamander abundances. However, there is little information examining these linkages in the coalfields of central Appalachia. In the summer of 2013, I visited 70 sites (sampled three times each) in the southwest Virginia coalfields to collect salamanders and quantify stream and riparian microhabitat parameters. In an information-theoretic framework I compared the effects of microhabitat and large-scale land use on salamander occupancy and abundances. My findings indicate that dusky salamander (Desmognathus spp.) occupancy and abundances are more correlated to microhabitat parameters such as canopy cover than to subwatershed land uses. Brook salamander (Eurycea spp.) occupancy show negative associations to large-scale land uses such as percent recent mining and percent forested. Whereas Eurycea spp. abundances are negatively influenced by suspended sediments, stream bank erosion and stream substrate embeddedness. Management implications of these findings include erosion prevention and control as well as protection and management of riparian habitats. However, quantifying physical environmental quality such as stream and riparian habitat often can be quite difficult, particularly when there are time or fiscal limitations. In order to accurately assess stream and riparian habitat in a time- and cost- effective manner, the U.S. Army Corps of Engineers (USACE) developed a functional condition index (FCI) assessment for streams that measures 11 stream and riparian parameters along with watershed land use to calculate three different scores: a hydrology score, biogeochemical score, and habitat score (Noble et al 2010). Using the salamander data from 2013, I then analyzed the FCI scores using collected occupancy and abundance analyses. Both analyses supported the Habitat FCI score as it had strong correlations with both occupancy and abundance of three Desmognathus spp., and support the use of the USACE protocol for stream and riparian habitat assessment. / Ph. D.

In this dissertation, I report new information that is necessary for future mating system studies in a little studied species, the marbled salamander (Ambystoma opacum). I studied female mating behavior, sexual selection, and the consequences of polyandry for individual females and salamander populations. I also compared the performance of several statistical approaches for analyzing genetic mating system data. The first chapter summarizes the characteristics of several novel microsatellite DNA loci as well as cross-amplified loci for marbled salamanders and mole salamanders that may be used for future studies. In the second chapter, I report estimates of sire number for 13 marbled salamander clutches based on microsatellite data from 32 hatchlings per clutch. Females mated with as many as three different males as indicated by conservative techniques. Less than half of females mated with multiple males. Based on comparative analyses, I recommend the parental reconstruction approach with the computer program GERUD for assessing multiple paternity. The third chapter describes an experiment designed to study sexual selection. As expected, in breeding mesocosms, the potential for sexual selection was much higher for males than for females. Size was unrelated to variance in male reproductive fitness. Only opportunity for selection and Morisita’s index conformed to theoretical expectations of the relationship between operational sex ratio and the potential for sexual selection among males. Because opportunity for selection has intuitive links to formal sexual selection theory, I recommend its continued use. In the fourth chapter, I compared polyandrous and monandrous females to explore the potential fitness consequences of multimale mating. No fitness measure at the egg or hatchling stage (clutch size, hatching success, hatchling size, etc.) differed between the two types of clutches. Size of metamorphs was not different, but polyandrous clutches had significantly higher survival to metamorphosis. In the fifth chapter, I analyzed effects of increased polyandry and male availability on genetic diversity, effective population size (Ne), and fitness of experimental populations. Although no analyses were significant, some effects were moderate to high in size. Ne was higher when estimated from hatchlings than with metamorphs.

Classified in the Lissamphibia, modern amphibians are the only non-amniote tetrapods living today. They consist of three morphologically distinct groups: the tailless frogs and toads (Anura), the limbless caecilians (Gymnophiona), and the tailed salamanders and newts (Urodela). With 205 species, the caecilians are highly specialized worm-like forms that live a fossorial lifestyle, with a relatively narrow distribution in the tropic rainforests of South America, Africa and Asia (Duellman and Trueb, 1994; Amphibiaweb, 2015). Salamanders, with 683 species, are widely distributed in the North America, Asia and Europe, with a few plethodontids extending to Central and South America (Duellman and Trueb, 1994; Amphibiaweb, 2015). Frogs are the most diverse amphibian groups, with 6644 species distributed over all continents except Antarctica (Duellman and Trueb, 1994; Amphibiaweb, 2015). Both frogs and salamanders develop a wide array of lifestyles, ranging from terrestrial, aquatic, fossorial to aboreal lifestyles (Duellman and Trueb, 1994). During ontogeny, amphibian larvae usually undergo a drastic post-embryonic shift into an adult form, a term known as metamorphosis. In salamanders, another developmental pathway – neoteny – also occurs, in which the larval morphology is retained in sexually mature adults (Duellman and Trueb, 1994; Rose, 2003). Because of the diverse lifestyles and developmental pathways, frogs and salamanders are often used as model systems in many fields of biology (e.g., evo-devo). Over a century, but especially in the past two decades, a wealth of frog and salamander fossils has been discovered from the Mesozoic and Cenozoic of East Asia (e.g., Noble, 1924; Young, 1936; Borsuk-Bialynicka, 1978; Gao, 1986; Dong and Wang, 1998; Gao and Shubin, 2001, 2003, 2012; Gao and Wang, 2001; Gao and Chen, 2004; Wang and Rose, 2005; Wang and Evans, 2006b; Zhang et al., 2009; Chen et al., 2016; this study). Some of these fossils represent the earliest members of many crown clades, including the earliest crown salamanders from the Middle Jurassic (~165 Ma, Gao and Shubin, 2003), the earliest salamandroid from the Late Jurassic, the earliest sirenid from the Late Jurassic (this study), and the earliest spadefoot toads from the late Paleocence (Chen et al., 2016). Other fossils also bear important anatomical, temporal and geographical information in understanding their evolution. Unfortunately, the importance of many of these fossils remains obscure in a phylogenetic context. For example, an early-middle Oligocene Mongolian spadefoot toad Macropelobates osborni (Noble, 1924) was discovered outside the current distribution of spadefoot toads, yet its phylogenetic position and its implication on spadefoot toad biogeography remain not well understood. A major reason for the poor understanding of these fossils can be attributed to a trend of dichotomy between morphological and molecular phylogenies on amphibians. Whereas morphologists and paleontologists sometimes use a relatively small morphological dataset to reconstruct relationships (e.g., Gao and Shubin, 2012; Henrici, 2013), large-scale phylogenies are almost always conducted with molecular data with only living taxa (e.g., Roelants and Bossuyt, 2005; Pyron and Wiens, 2011). Very few studies on amphibian phylogeny have combined morphological and molecular data together, and even fewer also combined fossils. Because of this, the positions of many important fossils remains unclear, and the evolutionary scenarios inferred from only living species can sometimes be inconsistent with fossil evidence. In this thesis, I adopt a total-evidence approach to understand the evolution of amphibians, especially frogs and salamanders. I will incorporate information from fossils, morphology and molecules together to reconstruct the relationships. Compared with studies with each individual datasets, this approach incorporates all available data in a single analysis, with a goal to reach robust and congruent results that allow further discussions on character evolution and biogeographic reconstruction. The inclusion of fossils directly into the combined analysis provides the time dimension that is independent from molecular data (Norell, 1992). The anatomical combination of fossils can represent intermediate forms that help to solve the “long branch” problems caused by highly specialized modern taxa. The morphological dataset, despite its much smaller size with molecular data, is the only link between fossils and modern taxa. The inclusion of key morphological characters in both reconstructing phylogenetic hypotheses and examining character evolution provide consistent results that allow discussion on the homology/homoplasy of a certain character without ambiguity. The molecular sequence data provides overwhelmingly large data on modern taxa for phylogenetic reconstructions compared with morphological data, which helps to reach a robust hypothesis. Although fossils contain no molecular data, the inclusion of molecular sequence data into the combined analysis does have an effect on the positions of fossil taxa. By altering the relationship “framework” of modern taxa, the character optimization of fossils and other taxa of a combined analysis also varies compared with results of morphology-only analysis, thus changing the positions of fossils. In the following five chapters, I will describe a number of fossil amphibian species, reconstruct three combined phylogenies, and use the results for discussions on character evolution and biogeography. In Chapter 1 and Chapter 2, I focus on a frog clade called spadefoot toads (Anura: Pelobatoidea). In Chapter 1, I provide descriptions on three important fossil spadefoot toads from the Cenozoic of East Asia and North America: Macropelobates osborni from the early-middle Oligocene of Mongolia, Prospea holoserisca from the latest Paleocene of Mongolia, and Scaphiopus skinneri from the middle Oligocene of the United States. In Chapter 2, I conduct a combined phylogenetic analysis of archaeobatrachian frogs, and discuss the evolution of the bony spade and the historical biogeography of spadefoot toads based on the results of the phylogeny. In Chapter 3, I describe a new fossil frog from the Early Cretaceous of Inner Mongolia, China. The unique morphology of the new fossil is distinct from previous Early Cretaceous frogs from the Jehol Biota of China. Results of the combined analysis show that the new frog represents a basal member of the Pipanura. Comparisons between the Early Cretaceous frogs from China, Spain and Brazil show a high diversity of species coupled with a high degree of endemism during the Early Cretaceous. I discuss in the phylogenetic context how early frogs gradually reach their postcranial body plan with a shortened vertebral column, loss of ribs, and specialized pelvic regions. In Chapter 4, I provide a brief review of Mesozoic fossil salamanders from northern China, and describe a new fossil from the Late Jurassic of Liaoning Province, China. I conduct a combined phylogeny of higher-level relationships of salamanders. The new fossil, despite its general-looking appearance, represents a basal member of the highly specialized eel-like neotenic family Sirenidae on the cladogram. I discuss character evolutions in the Sirenidae, and how the neotenic developmental pathway evolved in early salamanders. In Chapter 5, I conduct a combined phylogenetic analysis of the salamander suborder Cryptobranchoidea, consisting of the neotenic giant salamanders (Cryptobranchidae) and the metamorphic Asiatic salamanders (Hynobiidae). The new morphological matrix includes new characters that were previously less sampled in the hynobranchial region. The monophyly of the Hynobiidae are confirmed by the new analysis, and four unequivocal synapomorphies are found for the clade. An S-DIVA biogeographic reconstruction is conducted to disscuss the distributional patterns of the Hynobiidae.

The Southern Appalachian hardwood forests contain a wide diversity of flora and fauna. Understanding processes that affect nutrient availability in these forests is essential for sound forest management. Three interconnected research projects regarding soil resource heterogeneity were designed to increase our understanding of this ecosystem. The objective of these projects were as follows: 1) to examine and quantify the role of decaying stumps in regards to total carbon (C) and nitrogen (N) pools and fine-root dynamics, 2) compare and contrast the use of ground-penetrating radar (GPR) vs. a soil auger for estimating soil depth and site quality and 3) to evaluate how eastern red-backed salamanders (Plethodon cinereus) affect N-availability. For the stump study, results show that decomposing stumps occupy approximately 1.2% of the total soil volume and constitute 4% and 10% of total soil N and C pools. Significant differences in N (p = 0.0114), C (p = 0.0172), microbial biomass C (p = 0.0004), potentially mineralizable N (p = 0.0042), and extractable NH4+ (p = 0.0312) concentrations were observed when compared to mineral soil horizons. In particular, potentially mineralizable N was 2.5 times greater in stump soil than the A-horizon (103 vs. 39 mg kg-1), 2.7 times greater for extractable NH4+ (16 vs. 6 mg kg-1) and almost 4 times greater for MBC (1528 vs. 397 mg kg-1). These measured properties suggest higher N-availability, organic matter turnover and N uptake in stump soil versus the bulk soil. 19% of the total fine root length and 14% of fine root surface area also occurred in the stump soil. The increased fine root length suggests higher concentrations of labile nutrient in the stumps since roots often proliferate in areas with higher nutrient availability. Significant differences occurred in N and C concentrations between all four decay classes and the A-horizon, which validated the use of this system and the need to calculate weighted averages based on the frequency and soil volume influenced by each decay class. In the GPR Study, depth estimations were shallower using a soil auger compared to estimates obtained using GPR across all plots (p = 0.0002; Figure 3.4). On a soil volume basis, this was equivalent to about 3500 m3 of soil per hectare unaccounted for using traditional methods. In regards to using soil depth as a predictor for site quality, no significant relationships were observed with soil depth estimations obtained from the auger (Table 3.3). On the other hand, depth measurements from GPR explained significant amounts of variation across all sites and by physiographic region. Across all sites, soil depth estimates from GPR explained 45.5% of the residual variation (p = 0.001; Table 3.3). When the data were stratified by physiographic region, a higher amount of variation was explained by the regression equations; 85% for the Cumberland Plateau (p = 0.009), 86.7% for the Allegheny Plateau (0.007) and 66.7% for the Ridge and Valley (p = 0.013), respectively (Table 4.2). Results from this study demonstrate how inaccurate current methods can be for estimating soil depth rocky forests soils. Furthermore, depth estimations from GPR can be used to increase the accuracy of site quality in the southern Appalachians. In the salamander study, no significant salamander density treatment or treatment by time effects were observed over the entire study period (p < 0.05). However, when the data were separated by individual sampling periods a few significant treatment by time interactions occurred: 1) during August 2006 for available NH4+ under the forest floor (i.e. horizontal cation membranes; p = 0.001), 2) August and 3) September 2006 for available NH4+ in the A-horizon (p = 0.026), and 4) May 2007 for available NO3- under the forest floor (p = 0.011). As a result of these trends, an index of cumulative N-availability (i.e. NH4+ and NO3-) under the forest floor and in the A-horizon was examined through the entire study period. Cumulative N-availability under the forest floor was consistently higher in the low- and medium-density salamander treatments compared to the high-density treatment. For cumulative N-availability in the A-horizon, a gradient of high to low N-availability existed as salamander density increased. Factors such as a prolonged drought in 2007 may have affected our ability to accurately assess the effects of salamanders on N-availability. We concluded that higher salamander densities do not increase N-availability. Implementing methodologies that accurately account for soil nutrient pools such as stump soil, physical properties such as depth and fauna such as salamanders, increase our understanding of factors that regulate site productivity in these ecosystems. As a result, landscape-level and stand-level management decisions can be conducted more effectively. / Ph. D.

No description available.