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African clawed frogs (Xenopus) have been scientific and medical model species for decades. These frogs present many curious features, and their genomic history is no exception. As such, a variety of evolutionary genomic questions can be addressed with these species in a comparative framework, owing to the great array of genetic tools available and a large number of abundant species. The sex chromosomes of this group are evolutionarily young, and this thesis establishes that there has been an additional change in what constitutes the sex chromosomes in one species of Xenopus. This allows us to compare the evolutionary trajectory of newly established sex chromosomes. By exploring the genetic content of these systems, profiling their recombinational activity, and assessing the extent of nucleotide divergence between the sex chromosomes, we find that sex chromosome evolution may be predictable in some aspects, and highly unpredictable in others. In addition, this genus is uncharacteristic for vertebrates in the frequency with which lineages undergo whole genome duplication. In this thesis, we explore the selective dynamics operating on duplicate genes over time, and the rate at which duplicate copies are purged from the genome from multiple Xenopus species. These investigations provide an animal perspective on the subject of biased subgenome evolution, characteristic of allopolyploids. The last two chapters of this thesis redefine the species boundaries for the most intensively studied Xenopus species (X. laevis), and explore the genetic extent of hybridization between the common X. laevis and the endangered X. gilli. Overall, this thesis provides a broad look at several aspects of Xenopus evolutionary genomics, providing novel contributions to the fields of sex chromosome research, whole genome duplication, and speciation and hybridization. / Thesis / Doctor of Philosophy (PhD)

The Roanoke logperch (Percina rex) is a federally endangered large darter that occurs only within the Roanoke and Chowan drainages of Virginia. This dissertation examines multi-scale habitat use patterns by logperch in three river systems in Virginia, including comparisons among rivers and life stages. The first study in this dissertation compares microhabitat use patterns of logperch among the Roanoke, Pigg, and Nottoway rivers. My objectives are to: 1) compare available microhabitat and microhabitat use by logperch among these rivers; and 2) examine the transfer of habitat models among rivers. Habitat availability in the three rivers indicates that the Nottoway River is least impacted by human activity, while the Pigg River is most impacted. The Roanoke and Pigg rivers are found within the same region of Virginia and share many habitat characteristics. Logperch consistently use silt free, loosely embedded gravel in all rivers and can occupy a variety of depths and velocities to accommodate substrate requirements. Microhabitat models transfer better between the similar Pigg and Roanoke rivers. The second study in this dissertation compares micro- and meso-habitat use patterns by Roanoke logperch in the Roanoke and Nottoway rivers. My objectives are to: 1) compare micro- and meso-habitat use patterns of logperch in the Roanoke and Nottoway rivers; and 2) examine transfer of habitat models at both scales. An increase in scale from micro- to meso- habitat did not improve model transfer. Habitat selectivity and transfer was strongest at the microhabitat scale. Logperch appear to be microhabitat substrate specialists and mesohabitat generalists. The final study in this dissertation examines ontogenetic patterns of habitat use by Roanoke logperch in the Roanoke and Nottoway rivers. My goals are to: 1) examine habitat use by three age classes of logperch and 2) compare ontogenetic patterns of habitat use between the Roanoke and Nottoway rivers. In the Roanoke River, adult and subadult logperch primarily used run and riffle habitat, often over gravel substrate. Subadults were found in lower water velocities and more embedded microhabitats than adults. Young-of-year logperch were found in shallow, stagnant backwaters and secondary channels. In the Nottoway River, both adult and subadult logperch were found over sand and gravel in deep, low velocity pools and runs. Subadults were observed in slightly more silted, lower velocity habitat. Younger age classes of logperch appear to be more vulnerable to sedimentation caused by human activity. Evidence in this dissertation strongly indicates that logperch have strict substrate requirements and the distribution of habitat types and pathways of dispersal will be critical for completion of the logperch life cycle. A watershed-level conservation approach that addresses sediment loading and preserves ecological processes that provide ephemeral, seasonal, and persistent types of habitat required over logperch ontogeny will be most effective for management geared towards the recovery of this endangered species. / Ph. D.

The southeastern United States is a global biodiversity hotspot but has experienced severe declines of natural ecosystems. The southeast is currently facing widespread change, particularly from an increasing human population and climate change, that is likely to impact all remaining natural areas to some degree. In this work, I examine some of the challenges currently facing imperiled species of reptiles and amphibians in this region. The work is focused on two species, the Reticulated Flatwoods Salamander (Ambystoma bishopi) and the Eastern Indigo Snake (Drymarchon couperi) both of which are listed on the U.S. Endangered Species List. Chapter 1 used Light Detection and Ranging (LiDAR) data to measure wetland bathymetry (basin shape) in flatwoods salamander breeding wetlands. Bathymetry data were used to construct stage–area relationships for each wetland, and a history of water level monitoring data were applied to these relationships to build multi-year time series of flooded area metrics. These metrics were then combined with an assessment of vegetation characteristics to map potentially suitable habitat for flatwoods salamander breeding within each wetland. Chapter 2 focused on flatwoods salamander phenology (the timing of life history events) in response to climate change. I quantified flatwoods salamander movements into and out of breeding wetlands over a 10-year period (2010–2020), identifying temperature and precipitation patterns that were conducive to salamander movements. I then used future climate projections to forecast movement opportunities for flatwoods salamander from 2030–2099 and used an existing hydrologic model built on the same climate data to understand how phenology may interact with hydrology. Overall, only a small number of years are likely to have an ideal intersection of phenology and hydrology as has been observed during recent breeding seasons. Chapter 3 described the construction of a stochastic Integral Projection Model for flatwoods salamanders. I integrated the projections from Chapter 2 with the population model to estimate the viability of two flatwoods salamander populations from 2030–2099 under multiple climate change scenarios. The results indicated that approximately half of the examined scenarios resulted in a high probability (>0.5) of extinction when considering both wetland hydrology and salamander phenology. In Chapter 4, I described the creation of a stochastic Integral Projection Model for indigo snakes. I then demonstrated the utility of this model by examining the effects of initial population size, road density, and removal of individuals to support a captive colony on indigo snake populations. I found that high road densities and high collection rates would likely lead to population declines, although the rate of declines and extinction risk varied across scenarios. Taken together, these projects highlight some of the challenges currently facing herpetofauna in the southeastern United States, demonstrate the difficulty in conserving these often-overlooked species, and provide useful tools for ongoing conservation efforts focusing on these two imperiled species. / Doctor of Philosophy / We are in the midst of a global biodiversity crisis, with rates of species extinction far exceeding normal levels. Species loss is largely driven by global change attributable to human activities. A rapidly changing world can make it challenging to effectively conserve and manage imperiled species. In this work, I studied two species found only in the southeastern United States that are listed on the U.S. Endangered Species List. Chapters 1–3 focused on the Reticulated Flatwoods Salamander (Ambystoma bishopi), while Chapter 4 focused on the Eastern Indigo Snake (Drymarchon couperi). In Chapter 1, I used high resolution elevation data to map the shape of flatwoods salamander breeding wetlands. These data were then used to estimate flooded areas across multiple years. Flooded area metrics were combined with vegetation measurements to map potential flatwoods salamander breeding habitat. In Chapter 2, I examined how flatwoods salamander movements may respond to climate change. I identified time periods and weather conditions that coincided with flatwoods salamander movements into and out of breeding wetlands. I then projected potential movement opportunities based on multiple future climate scenarios for each breeding season from 2030–2099. My results showed that few years are likely to be ideal for flatwoods salamander reproduction, which is similar to trends observed in recent years. In Chapter 3, I built a population model for flatwoods salamanders. I then combined the model with predictions made in Chapter 2 to estimate the probability that populations would go extinct by the end of the century. The results indicated that the two flatwoods salamander populations examined had a high probability (>0.5) of extinction in about 50% of the climate scenarios. In Chapter 4, I constructed a population model for indigo snakes using a variety of available data. I used this model to examine the effects of road density, initial population size, and removal of individuals to support a captive colony on indigo snake populations. The results suggested that populations experiencing high road densities or high collection rates were likely to decline over time. These projects highlight some of the difficulties in conserving often-overlooked reptiles and amphibians in the southeastern United States and provide important tools for ongoing conservation projects working with these two imperiled species.

In order to prevent species extinctions, conservation strategies need to incorporate the identification and mitigation of the root causes of population decline with an assessment of vulnerability to genetic and stochastic factors affecting small populations. Species or populations with small ranges, such as those on islands, are particularly vulnerable to extinction, and deficient knowledge of these species often impedes conservation efforts. The Bahama Swallow (Tachycineta cyaneoviridis) is an endangered secondary cavity-nester that only breeds on three islands in the northern Bahamas: Abaco, Grand Bahama, and Andros. I investigated questions related to population size and distribution, genetic diversity and population structure, breeding biology, and ecological interactions of the swallow, with the goal of informing the conservation and management of the species. Using several population survey methods on Abaco, I found that swallow site occupancy and density is higher in southern Abaco, especially near roads and pine snags. Future research should prioritize identifying the causes of variable and low population densities in parts of the swallow's range. I used microsatellite markers and morphometrics to assess differences between populations on Abaco and Andros. We found a lack of genetic differentiation (G'ST = 0.03) between populations, but differences in morphology suggest that gene flow might be low enough to enable traits under selection to diverge. By locating and monitoring nests, I found that swallows rely on woodpecker-excavated cavities in pine snags and utility poles, and that swallows nesting in pine snags had higher fledging success (92%) than those nesting in utility poles (50-62%). Using a cavity nest-web approach, I assessed how swallows interact with cavity-nesting birds and resources on Abaco. Hairy Woodpeckers (Dryobates villosus) primarily excavated pine snags, while West Indian Woodpeckers (Melanerpes superciliaris) excavated utility poles in non-pine habitat. Only swallows and La Sagra's Flycatchers (Myiarchus sagrae) used nest sites in the pine forest. Swallows in non-pine habitat face competition for cavities with American Kestrels (Falco sparverius), and non-native House Sparrows (Passer domesticus) and European Starlings (Sturnus vulgaris). These results highlight the importance of pine forest and the Hairy Woodpecker for the persistence of the swallow. / Doctor of Philosophy / In order to prevent species extinctions, conservation strategies need to identify and resolve the problems that cause species to decline, as well as address issues characteristic of small populations. Species or populations with small ranges, such as those on islands, are particularly vulnerable to extinction, and lack of knowledge of these species often impedes conservation efforts. The Bahama Swallow is an endangered species that only breeds on three "pine islands" in the northern Bahamas. The swallow is a secondary cavity-nester, which means that it nests in a cavity, usually either a natural tree hole or a hole created by another bird species. In this study, I investigated where swallows are found on the islands, the genetics and body sizes of populations, nesting biology, and connections with other species, with the goal of providing information for the conservation and management of the species. On Abaco, I found that there are more swallows in the southern part of the island, especially near roads and the dead standing pine trees (pine snags) used for nesting. Future research should assess why there are fewer birds in other parts of the swallow's range. I tested whether the genetics and body sizes of populations on Abaco and Andros are different from each other. Populations were genetically similar, but may be separated enough to result in body size differences. I located swallow nests on Abaco, and found that swallows rely on cavities made by woodpeckers in pine snags and utility poles. By visiting some nests repeatedly, I found that swallows nesting in pine snags were more successful than those nesting in utility poles. I also assessed how swallows interact with the other bird species that create and use nesting cavities. Hairy Woodpeckers usually create cavities in pine snags, while West Indian Woodpeckers use utility poles outside of the pine forest. Swallows nesting in the pine forest compete with fewer bird species for cavities than swallows nesting in other habitats. These results show that managing the forest to retain pine snags and Hairy Woodpeckers is important for the conservation of the swallow.

<p dir="ltr">Spotted Turtle (Clemmys guttata) populations are declining dramatically across their range primarily due to habitat alteration, fragmentation, and reduction. Fragmented habitats have the potential to affect a population’s genetic diversity and size through the direct loss of individuals and the reduction of gene flow. Understanding genetic variation in Spotted Turtles can provide insight into population dynamics, the geographic distribution of genetic variants, and conservation needs. I examined the genetic variation in Spotted Turtle populations across the western portion of their geographic range including localities in Illinois, Indiana, Ohio, Michigan, and Ontario, Canada. Using blood samples collected during the 2022 and 2023 field seasons as well as previously collected tissues, I genotyped 611 individuals across 17 or more localities using 16 microsatellite loci. Five of 17 sites across the geographic extent of the sample suggested the presence of inbreeding (positive Fis values). Although the precision of estimates was low in most localities (10 of 17 with incalculable confidence intervals), the remaining localities in Ohio were estimated to have effective population sizes of < 20 individuals. Model-based and ordination-based clustering were conducted to assess population structure. Both types of clustering approaches identified four genetic clusters within the dataset. The two Illinois sites fell distinctly into their own cluster, whereas all other sites show a pattern of admixture. Despite these clustering results, incorporation of spatial information in principal component analysis (sPCA), shows that genetic composition gradually changes from west to east across the landscape, a pattern supported by isolation by distance using a Mantel test of the correlation between genetic and geographic distances. My results show that several Spotted Turtle populations have low levels of genetic variation and could benefit from augmentation. The observed pattern of isolation by distance 9 suggests that any translocations of turtles to support populations should be attempt to draw from viable populations that are in closer proximity.</p>

京都大学 / 新制・課程博士 / 博士(情報学) / 甲第24037号 / 情博第793号 / 新制||情||134(附属図書館) / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 大手 信人, 准教授 小山 里奈, 教授 北島 薫 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

This dissertation addresses critical challenges in forest management and restoration in the Lower Mississippi Alluvial Valley (LMAV) through a series of interconnected studies focused on improving habitat suitability modeling and growth prediction for oak species. The research employs advanced modeling techniques to enhance our understanding of species-habitat relationships and forest dynamics in the context of climate change. Initial studies focused on developing ensemble habitat suitability models for American chestnut (Castanea dentata) and butternut (Juglans cinerea), two historically important but currently threatened tree species. These models predict suitable habitats and potential range shifts under various climate change scenarios, highlighting the species' vulnerabilities and informing conservation strategies. Building on these approaches, the research expands to model habitat suitability for eight key oak species in the LMAV. This multi-species analysis reveals both shared and distinct ecological requirements among the oak species, providing valuable insights for targeted restoration efforts. Niche overlap analysis further elucidates potential species interactions and habitat partitioning within the region. The dissertation culminates in the development of improved climate-sensitive growth and yield models for bottomland oaks. By incorporating habitat suitability predictions as a modifier, these models demonstrate significantly enhanced accuracy compared to traditional approaches. This integrated modeling framework offers a more comprehensive understanding of oak growth dynamics under changing environmental conditions. Throughout the research, the importance of key environmental drivers, such as temperature, precipitation, and soil characteristics, is consistently highlighted. The studies also underscore the potential impacts of climate change on species distributions and forest composition in the LMAV. This research contributes to the advancement of forest modeling techniques and provides practical insights for sustainable forest management, conservation of threatened species, and climate change adaptation strategies. The findings have important implications for decision-making in forestry and conservation, particularly in the LMAV but with potential applications to other regions. Future research directions are suggested, including the use of higher-resolution datasets and validation across diverse ecosystems to further improve model applicability and accuracy.

Ways of understanding, living, and communicating with non-human species, and more specifically endangered species, have been thought of dualistically and hierarchically in Western cultures. This type of thinking is harmful when examining environmental issues that involve more than just humans, which is arguably all environmental issues. By enforcing a nature/culture dichotomy, humans are seen as separate from nature and therefore they can ethically excuse themselves from dealing with environmental issues that happen "out there" in nature. This thesis explores two manifestations of this nature/culture separation as it continues to threaten wild orca populations in Puget Sound. The first is because of an anthropocentric culture and the second is because of the capitalist socio-economic system. The anthropocentric part of this type of thinking raises humans up on a pedestal, above all non-human species. It gives humans the excuse to only care about issues that affect them directly. The capitalistic part of this type of thinking enforces human's exploitation and commodification of nature. I argue that anthropocentrism and capitalism together create a human/nature relationship that harms nature and benefits humans. This relationship is illustrated by a small population of orcas, called the Southern Resident Killer Whales (SRKW), off the coast of Washington State that are endangered because of human interference. Lack of prey, toxic water pollution, and excessive noise from boats caused them to become endangered, and these issues are produced by Western society's anthropocentric attitudes and capitalistic systems. The SRKW's will go extinct if the environmental destruction of Puget Sound doesn't end and it will only end if the anthropocentric attitudes and capitalistic systems are dismantled.

Geographic Information Systems (GIS) and remote sensing technologies were used to identify and describe potential habitat for three species endemic to the Southwestern United States; the Golden-cheeked Warbler (Dendroica chrysoparia), the Black-capped Vireo (Vireo atricapillus), and the Texas kangaroo rat (Dipodomys elator). For each species, the computerized classification of digital satellite imagery was integrated with ancillary spatial information (e.g. soils, geology, and land use) to construct a data base to be used for ecological evaluation as well as habitat protection and management measures.