DEMOGRAPHIC, SPATIAL, AND EPIGENETIC RESPONSE OF THE LOUISIANA WATERTHRUSH (PARKESIA MOTACILLA) TO SHALE GAS DEVELOPMENT

My study centered on a bioindicator songbird, the Louisiana Waterthrush (Parkesia motacilla), hereafter waterthrush, an organism that co-occurs in both forested and aquatic habitat across the aquatic-terrestrial interface. This enabled the opportunity to quantify demographic, spatial, and epigenetic (i.e., DNA methylation) responses in a highly forested watershed of the Central Appalachians, the areas that have undergone the most rapid transformations over the last decade from unconventional shale gas development and activities. I organized my dissertation into 4 parts (Part 1: Introduction, Part 2: Louisiana Waterthrush Demography, Part 3: Spatial Assessment of Louisiana Waterthrush Foraging, Part 4: Louisiana Waterthrush Molecular Ecology) including 6 chapters that indicate multiple biotic and abiotic factors interacted with or were altered by shale gas development resulting in atypical, negative disturbances that drove a steep decline in a waterthrush population in West Virginia. Part 1 includes Chapter 1 and is an introduction to my dissertation. I introduce the reader to the rationale for my study, the focal species, research objectives, and the study area. I also mention some limitations to my study that can be considered in any future research endeavors. Part 2 comprises Chapters 2–3 which are a comprehensive examination of demographic parameters over a six-year period (2009–2011, 2013–2015). In Chapter 2, I examined demographic response to shale gas development for nest abandonment, nest survival, nest productivity, a source-sink threshold, riparian habitat quality, and territory density and length. Nest productivity was lower in areas disturbed by shale gas where a source–sink threshold suggested these areas were more at risk of being sink habitat. Overall results suggest a decline in waterthrush site quality as shale gas development increased. In Chapter 3, I focused on first-year return rates (site fidelity), site fidelity factors, and apparent survival. I related natal fidelity and pairing rates to territory density, and also compared # of breeding attempts between return and non-returning females with and without territory shale gas disturbance. The study identified potential conflicts between factors that influence adult survival and site fidelity that may affect long-term population persistence. Part 3 includes Chapters 4–5 and focuses on utilizing and accounting for spatial properties intrinsic to stream ecosystems to make informed decisions regarding waterthrush foraging. Chapter 4 was a follow-up to a waterthrush aquatic prey study at our site in 2011 that suggested shale gas development negatively affected waterthrush demography from alterations in their aquatic prey at a watershed scale. During 2013–2014, I quantified waterthrush demographic response and nest survival in relation to potential changes in its aquatic prey due to shale gas development. I utilized spatial generalized linear mixed models that accounted for both spatial and non-spatial sources of variability. I found waterthrush aquatic prey was negatively affected by shale gas development at the nest and territory level, and that there may be a disturbance threshold at which waterthrush can no longer adapt and respond negatively to changes in its aquatic prey. In Chapter 5, I used spatial stream network models (SSNMs) to explore relationships among the waterthrush, stream channel and monitoring data, and the aquatic prey of the waterthrush. I compared the spatial models to traditional regression models to see which ones performed best. We sampled aquatic prey in waterthrush territories and collected wetted perimeter stream channel and water chemistry data along a 50m fixed point stream grid that mapped the foraging substrate or stream channel where waterthrush forage. By relating foraging observations and data collected to the stream grid, I was able to develop a foraging probability index that determined what conditions or variables create or affect ideal foraging locations. Spatial models outperformed traditional regression models and made a statistical difference in whether stream covariates of interest were considered relatable to waterthrush foraging. My study also indicated waterthrush forage in areas of higher biotic stream integrity. Lastly, Part 4 includes Chapter 6 where I examined epigenetic modifications. These are alterations to genes without changing the gene sequence and can be thought of as an evolutionary soft inheritance of gene expression that can either be adaptive or maladaptive for the individual. DNA methylation is one type of epigenetic modification that may vary in response to environmental stressors. We examined the association between DNA methylation and demographic characteristics in addition to potential differential methylation from shale gas development. There was differential methylation for demographic characteristics as well as for adult males between shale gas undisturbed and disturbed areas. Barium (Ba) and strontium (Sr) data were collected in 2013 feather samples where adult males had fewer methylated sites at higher concentrations of Ba and Sr, while nestlings displayed no correlation of methylation to Ba and Sr concentrations. Females displayed increased methylation with increased Ba and Sr, a trend reflected in adult female recaptures. Overall, results of our study suggest sex-specific influences of shale gas development on gene expression that may affect long-term population survival and fitness

Spatial stream modeling of Louisiana Waterthrush (\u3ci\u3eParkesia motacilla\u3c/i\u3e) foraging substrate and aquatic prey in a watershed undergoing shale gas development

We demonstrate the use of spatial stream network models (SSNMs) to explore relationships between a semiaquatic bioindicator songbird, Louisiana Waterthrush (Parkesia motacilla), and stream monitoring and benthic macroinvertebrate data in an area undergoing shale gas development. SSNMs allowed us to account for spatial autocorrelation inherent to these environmental data types and stream properties that traditional modeling approaches cannot capture to elucidate factors that affect waterthrush foraging locations. We monitored waterthrush along 58.1 km of 1st- and 2nd-order headwater stream tributaries (n = 14) in northwestern West Virginia over a two year period (2013–2014), sampled benthic macroinvertebrates in waterthrush territories, and collected wetted perimeter stream channel and water chemistry data along a 50 m fixed point stream grid. Spatial models outperformed traditional regression models and made a statistical difference in whether stream covariates of interest were considered relatable to waterthrush foraging. Waterthrush foraging probability index (FPI) was greater in areas where family and genus-level multi-metric indices of biotic stream integrity were higher (i.e. WVSCI and GLIMPSS). Waterthrush were found foraging both among stream flow connected and unconnected sampled sites on relatively further upstream locations where WVSCI and GLIMPSS were predicted to be highest. While there was no significant relationship found between FPI and shale gas land use on a catchment area scale, further information on waterthrush trophic dynamics and bioaccumulation of surface contaminants is needed before establishing the extent to which waterthrush foraging may be affected by shale gas development

Do Mitigated Wetlands Support Similar Small Mammal Communities as Natural Wetlands?

Wetlands provide many ecosystem services and play an important ecological role in wildlife communities. Although wetland mitigation is a standard tool to combat losses to natural wetlands, it is essential to understand if mitigated wetlands are truly replacing natural wetlands in their full capacity. Because one important role of wetlands is to provide habitat for wildlife communities, it is important to determine if these created or restored wetlands can foster a wildlife community that is similar to natural wetlands. One understudied taxa in the realm of wetland mitigation research is small mammals. Our objectives are to examine community composition, occupancy, abundance, species diversity, species richness, and species evenness of small mammals at mitigated and natural wetlands to determine if there exists a difference between the two types of wetlands. To conduct this research, we are using Sherman traps for a capture-mark-recapture study on small mammals at mitigated and natural wetlands that are paired by similarities in ecoregion, elevation, geology, and wetland classification. In 2020, ten wetland sites were sampled with a total of 3,875 trap nights and 249 captures. Preliminary data analyses show Peromyscus spp. to be more abundant in natural wetlands than mitigated wetlands, and species richness between the two wetland types not to be statistically different. Results will determine if mitigated wetlands are successful in terms of providing habitat for small mammal communities, and in turn will contribute to whether current wetland mitigation is truly fulfilling its intended purpose. These findings could inform future management decisions

Demographic characteristics of an avian predator, Louisiana Waterthrush (Parkesia motacilla), in response to its aquatic prey in a Central Appalachian USA watershed impacted by shale gas development

We related Louisiana Waterthrush (Parkesia motacilla) demographic response and nest sur- vival to benthic macroinvertebrate aquatic prey and to shale gas development parameters using models that accounted for both spatial and non-spatial sources of variability in a Central Appala- chian USA watershed. In 2013, aquatic prey density and pollution intolerant genera (i.e., pollu- tion tolerance value \u3c4) decreased statistically with increased waterthrush territory length but not in 2014 when territory densities were lower. In general, most demographic responses to aquatic prey were variable and negatively related to aquatic prey in 2013 but positively related in 2014. Competing aquatic prey covariate models to explain nest survival were not statistically significant but differed annually and in general reversed from negative to positive influence on daily survival rate. Potential hydraulic fracturing runoff decreased nest survival both years and was statistically significant in 2014. The EPA Rapid Bioassessment protocol (EPA) and Habitat Suitability Index (HSI) designed for assessing suitability requirements for waterthrush were posi- tively linked to aquatic prey where higher scores increased aquatic prey metrics, but EPA was more strongly linked than HSI and varied annually. While potential hydraulic fracturing runoff in 2013 may have increased Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness, in 2014 shale gas territory disturbance decreased EPT richness. In 2014, intolerant genera decreased at the territory and nest level with increased shale gas disturbance suggesting the potential for localized negative effects on waterthrush. Loss of food resources does not seem directly or solely responsible for demographic declines where waterthrush likely were able to meet their foraging needs. However collective evidence suggests there may be a shale gas dis- turbance threshold at which waterthrush respond negatively to aquatic prey community changes. Density-dependent regulation of their ability to adapt to environmental change through acquisition of additional resources may also alter demographic response

Protective Microbiota: From Localized to Long-Reaching Co-Immunity

Resident microbiota do not just shape host immunity, they can also contribute to host protection against pathogens and infectious diseases. Previous reviews of the protective roles of the microbiota have focused exclusively on colonization resistance localized within a microenvironment. This review shows that the protection against pathogens also involves the mitigation of pathogenic impact without eliminating the pathogens (i.e., “disease tolerance”) and the containment of microorganisms to prevent pathogenic spread. Protective microorganisms can have an impact beyond their niche, interfering with the entry, establishment, growth, and spread of pathogenic microorganisms. More fundamentally, we propose a series of conceptual clarifications in support of the idea of a “co-immunity,” where an organism is protected by both its own immune system and components of its microbiota

Is spot mapping missing important aspects of golden-winged warbler (Vermivora chrysoptera) breeding habitat?

The Golden-winged Warbler (Vermivora chrysoptera) is an imperiled migratory songbird that nests in young forest habitats of eastern North America. As such, this species has recently been the focus of an intensive multi-year, range-wide, breeding ecology study. A major focus of this research involved spot-mapping color banded males to examine relationships between nesting success and territory-scale habitat variables. I compared differences in space and habitat use of individual male Golden-winged Warblers that were monitored using both spot mapping and radio telemetry. An individual's telemetry delineated use area was on average 3.6 times larger than its spot-mapped territory. Almost half (46%) of all telemetry locations were located outside their respective male's spot-mapped territory. Number of saplings was higher in telemetry use areas (22.49 ± 2.14) than spot-mapped territories (11.80 ± 1.86). Although the exact motive for extra-territorial movements is unknown, foraging and/or suggestive observations of extra-pair copulation are likely motivating factors. The results of my study suggest Golden-winged Warblers are seeking resources outside their spot-mapped delineated territories. Furthermore, Golden-winged Warblers were found to have more telemetry locations in mature forest than found through spot-mapping. Ultimately, spot mapping alone does not accurately reflect Golden-winged Warbler space use and habitat needs

Demographic characteristics of an avian predator, Louisiana Waterthrush (Parkesia motacilla), in response to its aquatic prey in a Central Appalachian USA watershed impacted by shale gas development.

We related Louisiana Waterthrush (Parkesia motacilla) demographic response and nest survival to benthic macroinvertebrate aquatic prey and to shale gas development parameters using models that accounted for both spatial and non-spatial sources of variability in a Central Appalachian USA watershed. In 2013, aquatic prey density and pollution intolerant genera (i.e., pollution tolerance value <4) decreased statistically with increased waterthrush territory length but not in 2014 when territory densities were lower. In general, most demographic responses to aquatic prey were variable and negatively related to aquatic prey in 2013 but positively related in 2014. Competing aquatic prey covariate models to explain nest survival were not statistically significant but differed annually and in general reversed from negative to positive influence on daily survival rate. Potential hydraulic fracturing runoff decreased nest survival both years and was statistically significant in 2014. The EPA Rapid Bioassessment protocol (EPA) and Habitat Suitability Index (HSI) designed for assessing suitability requirements for waterthrush were positively linked to aquatic prey where higher scores increased aquatic prey metrics, but EPA was more strongly linked than HSI and varied annually. While potential hydraulic fracturing runoff in 2013 may have increased Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness, in 2014 shale gas territory disturbance decreased EPT richness. In 2014, intolerant genera decreased at the territory and nest level with increased shale gas disturbance suggesting the potential for localized negative effects on waterthrush. Loss of food resources does not seem directly or solely responsible for demographic declines where waterthrush likely were able to meet their foraging needs. However collective evidence suggests there may be a shale gas disturbance threshold at which waterthrush respond negatively to aquatic prey community changes. Density-dependent regulation of their ability to adapt to environmental change through acquisition of additional resources may also alter demographic response

Restored and Natural Wetland Small Mammal Communities in West Virginia, USA

Wetland restoration is a common practice, and, in many cases, it is for mitigation to offset losses of natural wetlands due to human interference. Researchers commonly compare bird, amphibian, and reptile communities between these wetlands and natural wetlands but overlook small mammals. However, terrestrial small mammals are essential to consider as they serve a fundamental role in the ecosystem as seed dispersers and prey for larger wildlife. We conducted small mammal trapping on 26 wetlands (n = 14 restored, n = 12 natural) in West Virginia, USA, in the summers of 2020 and 2021 to obtain and compare community metrics between wetland types. We found that mass, occupancy probability, and community composition were similar between restored and natural wetlands. However, the apparent abundance of deer mice (Peromyscus maniculatus) was higher in natural wetlands (p &lt; 0.001). Because we captured the three rarest species exclusively in natural wetlands, the ability of restored wetlands to provide an adequate habitat for rare or wetland-obligate species may be biologically significant. Restored wetlands mainly offer sufficient habitat for small mammal communities, but apparent abundance in restored wetlands may differ from natural wetlands depending on species

Restored and Natural Wetland Small Mammal Communities in West Virginia, USA

Wetland restoration is a common practice, and, in many cases, it is for mitigation to offset losses of natural wetlands due to human interference. Researchers commonly compare bird, amphibian, and reptile communities between these wetlands and natural wetlands but overlook small mammals. However, terrestrial small mammals are essential to consider as they serve a fundamental role in the ecosystem as seed dispersers and prey for larger wildlife. We conducted small mammal trapping on 26 wetlands (n = 14 restored, n = 12 natural) in West Virginia, USA, in the summers of 2020 and 2021 to obtain and compare community metrics between wetland types. We found that mass, occupancy probability, and community composition were similar between restored and natural wetlands. However, the apparent abundance of deer mice (Peromyscus maniculatus) was higher in natural wetlands (p < 0.001). Because we captured the three rarest species exclusively in natural wetlands, the ability of restored wetlands to provide an adequate habitat for rare or wetland-obligate species may be biologically significant. Restored wetlands mainly offer sufficient habitat for small mammal communities, but apparent abundance in restored wetlands may differ from natural wetlands depending on species