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| Author | : Stephen Frank Spear |
| Publisher | : |
| Total Pages | : 152 |
| Release | : 2009 |
| Genre | : Ascaphus |
| ISBN | : |
| Author | : Tyler Duncan Hether |
| Publisher | : |
| Total Pages | : 76 |
| Release | : 2010 |
| Genre | : Hyla |
| ISBN | : |
Understanding the nature of genetic variation in natural populations is an underlying theme of population genetics. In recent years population genetics has benefited from the incorporation of landscape and environmental data into pre-existing models of isolation by distance (IBD) to elucidate features influencing spatial genetic variation. Many of these landscape genetics studies have focused on populations separated by discrete barriers (e.g., mountain ridges) or species with specific habitat requirements (i.e., habitat specialists). One difficulty in using a landscape genetics approach for taxa with less stringent habitat requirements (i.e., generalists) is the lack of obvious barriers to gene flow and preference for specific habitats. My study attempts to fill this information gap to understand mechanisms underlying population subdivision in generalists, using the squirrel treefrog (Hyla squirella) and a system for classifying 'terrestrial ecological systems' (i.e. habitat types). I evaluate this dataset with microsatellite markers and a recently introduced method based on ensemble learning (Random Forest) to identify whether spatial distance, habitat types, or both have influenced genetic connectivity among 20 H. squirella populations. Next, I hierarchically subset the populations included in the analysis based on (1) genetic assignment tests and (2) Mantel correlograms to determine the relative role of spatial distance in shaping landscape genetic patterns. Assignment tests show evidence of two genetic clusters that separate populations in Florida's panhandle (Western cluster) from those in peninsular Florida and southern Georgia (Eastern cluster). Mantel correlograms suggest a patch size of approximately 150 km. Landscape genetic analyses at all three spatial scales yielded improved model fit relative to isolation by distance when including habitat types. A hierarchical effect was identified whereby the importance of spatial distance (km) was the strongest predictor of patterns of genetic differentiation above the scale of the genetic patch. Below the genetic patch, spatial distance was still an explanatory variable but was only approximately 30% as relevant as mesic flatwoods or upland oak hammocks. Thus, it appears that habitat types largely influence patterns of population genetic connectivity at local scales but the signal of IBD becomes the dominant driver of regional connectivity. My results highlight some habitats as highly relevant to increased genetic connectivity at all spatial scales (e.g., upland oak hammocks) while others show no association (e.g., silviculture) or scale specific associations (e.g., pastures only at global scales). Given these results it appears that treating habitat as a binary metric (suitable/non-suitable) may be overly simplistic for generalist species in which gene flow probably occurs in a spectrum of habitat suitability. The overall pattern of spatial genetic and landscape genetic structure identified here provides insight into the evolutionary history and patterns of population connectivity for H. squirella and improves our understanding of the role of matrix composition for habitat generalists.
| Author | : Meryl Mims |
| Publisher | : |
| Total Pages | : 183 |
| Release | : 2015 |
| Genre | : |
| ISBN | : |
The study of how population structure and persistence are shaped by attributes of species and the environment is a central scientific pursuit in ecology and conservation. In this dissertation, I explore four themes central to this pursuit. First, I examined the extent to which species' ecological strategies - their life histories, biology, and behavior - predict patterns and drivers of population connectivity. This research represents a critical step in evaluating the potential of multi-taxa inference in landscape genetics. I examined a suite of hypothesized relationships between genetic connectivity and landscape connectivity for three desert anuran species and found a positive relationship between population differentiation and water dependency, e.g. longer larval development periods and site fidelity for reliable water sources. I also found that aquatic connectivity is important across all species, particularly when considered with topography (slope). Second, I built upon the work of my first chapter and proposed more general traits-based frameworks to enhance the utility of landscape genetics in multispecies conservation. I proposed guiding principles for the formal development, testing, and generalization of traits-based frameworks to advance the utility, efficiency, and effectiveness of genetic inference in contemporary ecology and conservation. Third, I employed population genetic techniques to examine the population structure, diversity, and connectivity of Hyla wrightorum, an anuran native to the southwestern United States and Mexico. Hyla wrightorum exists as a Distinct Population Segment (DPS) in the Huachuca Mountains and Canelo Hills of southeastern Arizona, USA. Due to concerns about declining observations of the species within the DPS, its small geographic and isolated extent within the Huachuca Mountains and Canelo Hills, and presumably small population sizes, the DPS is currently a candidate for federal protection under the Endangered Species Act. I found evidence of larger than expected effective population sizes, significant genetic differentiation between populations, and an isolation-by-distance pattern among populations. These results suggest that the DPS may be less vulnerable to extirpation than previously expected, but some small effective population sizes and the limited geographic extent of the DPS justify current concern for the persistence of this DPS. Finally, I used a spatially-explicit individual based model to simulate the response of the Arizona Treefrog (Hyla wrightorum) to reductions in breeding habitat availability in an isolated portion of its range. I found that reductions in breeding habitat resulted in population declines, with the greatest population declines for H. wrightorum associated with both a reduction in breeding habitat availability and recruitment failure. Reduced breeding habitat also resulted in increased synchrony and decreased variability through time, which likely indicates a transition from a metapopulation to isolated populations. Taken together, the four chapters of this dissertation advance the use of landscape and population genetics in multispecies conservation, and they will contribute directly to the conservation of dryland aquatic species.
| Author | : Guinevere October Wogan |
| Publisher | : |
| Total Pages | : 414 |
| Release | : 2011 |
| Genre | : |
| ISBN | : |
Species evolve in landscapes and environments that change through time. This spatial backdrop has profound effects on the diversification and merging of lineages. Populations become isolated by climate change, moving continents, and rising oceans, all of these factors can impact the evolutionary dynamics of lineages. While the spatial dimension of evolution has been a subject of interest since the inception of biogeography, the approaches to addressing how spatial heterogeneities affect lineages have advanced considerably in recent decades as genetic tools, computational tools, and new methodologies have allowed for explicit spatial hypotheses to be generated using GIS methods that can then be tested with genetic data. The focus of this dissertation examines amphibian evolution at deep temporal scales in relation to a changing global landscape, and sets the stage for examining the spatial dimension across the Asian landscape at shallow temporal scales. Chapter one investigates amphibian evolution and diversification within an explicit spatiotemporal framework in order to understand how spatial variation drives evolutionary patterns of amphibians at global scales. At macroevolutionary scales, global amphibian diversity is strongly correlated with the area of forest rather than the longevity of forests, and signatures of the extensive forest area of the Eocene underlies the dramatic amphibian latitudinal diversity gradient. Chapter two models the changing Asian landscape throughout the Pleistocene in order to understand how glacial and interglacial cycles impact the distribution of habitat types throughout the region. Satellite data on current habitats form the basis for this work. Palynological data are used to validate the models, providing a measure of confidence that the palaeo-predictive models are doing a good job in hind-casting habitats through changing climatic conditions. Asia differs from many other systems in not having been covered in extensive ice sheets during glacial periods, and provides a very different set of habitat dynamics, setting a unique stage for evolutionary dynamics. Habitats across Asia responded in dramatic fashion to changing palaeo-climates, with some habitats undergoing massive expansions and others contracting. The past 140 thousand years have witnessed a highly dynamic landscape. Chapter three delves deeper into palaeo-ecological modeling, and spatially locates stable habitat refugia across Asia for multiple tropical forest, temperate forest, and non-forested habitat types. These refugia are examined with respect to climatic stability and latitude to evaluate if stable climates give rise to stable habitats. Refugia are further examined with respect to terrestrial vertebrate species richness to understand if stable refugia have helped structure contemporary diversity patterns. Strong relationships between habitat stability and species richness were found, indicating that the spatial backdrop has played a pivotal role in contemporary diversity patterns. This indicates that these refugia may be important buffers against climate change and are probably important for the conservation of diversity in Asia. Chapter four focuses in on glacial and interglacial habitat dynamics on the Sundashelf, where dramatic changes in sea-level affect the connectivity of landmasses providing potential migration corridors between mainland SE Asia and insular Asia. I examine how these changing sea levels impact the distribution of habitats across the region and how in turn these habitat changes structure genetic data across the area. I found that high levels of genetic diversity correspond with stable habitats. Chapter five turns its attention to phylogenetics of the family Dicroglossidae, a widespread Old World frog family with high diversity across Asia. This chapter examines the generic assignments and familial monophyly and evaluates how nucleotide substitution models and partitioning affect the phylogenetic informativeness of markers and how this impacts phylogenetic inference. Both partitioning scheme and model selection were found to have profound effects on the phylogenetic informativenss of the genetic data. It was found that there are systemic biases among model selection criteria with the BIC commonly selecting highly parameterized models. It was also found that models of nucleotide substitution are often inadequate in capturing the complexity of empirical data. The monophyly of the Dicroglossidae was supported in these analyses. Many of the genera within the family were found to be monophyletic with the exceptions of the frogs of the Painii group and the Fejervarya. Together, these chapters provide the spatial foundation which sets the stage for research evaluating diversification processes in Dicroglossid frogs across the Old World and within Asia at biogeographic, phylogeographic and population genetics time scales. These analyses provide the first deeper time model-based evaluation of landscape processes for Asia.
| Author | : Sarah Lynn Emel |
| Publisher | : |
| Total Pages | : |
| Release | : 2015 |
| Genre | : |
| ISBN | : |
Global climate change is expected to shift species' suitable habitat toward the poles over this century and beyond. Amphibians and other dispersal-limited taxa may be particularly vulnerable to the effects of climate change due to inability to track suitable habitat. Rhyacotriton kezeri and R. variegatus are two species of torrent salamanders with specific habitat needs and small geographic ranges. This dissertation had three objectives: 1) review and synthesize the results of recent studies of population genetic structure in amphibians, 2) characterize the level of genetic structure and identify landscape features correlated with genetic distance among populations of R. kezeri and R. variegatus, and 3) predict the future distributions of R. kezeri and R. variegatus with climate change through the integration of landscape resistance into range shift models. In Chapter 1, I reviewed 139 studies of amphibians published between 2001-2010 estimating genetic structure, and a meta-analysis revealed that conservation status was the only factor showing a significant relationship with genetic distance. In Chapter 2, I discerned high genetic structure among populations of R. variegatus. Models of landscape resistance revealed that high genetic structure was correlated with low stream and forest cover, high solar radiation, and short growing season. In Chapter 3, I expanded upon Chapter 2 to include R. kezeri and test additional variables, determining that despite subtle differences between species, forest cover, roads, streams, and a correlate of soil moisture best explained patterns of gene flow in both. Lower average genetic diversity in R. kezeri populations is likely due to greater habitat fragmentation. Finally, in Chapter 4, I predicted range shifts of R. kezeri and R. variegatus in response to climate change, incorporating habitat resistance based on the results of Chapter 3 to simulate movement from the current distributions into projected suitable habitat. Although range contraction is only expected for R. kezeri , simulations suggested that neither species would reach a large proportion of its potential range by 2070. Overall, this dissertation demonstrates the importance of understanding the constraints of habitat resistance on dispersal and its consequences for amphibian conservation in the contexts of habitat fragmentation and global climate change.
| Author | : Gage Hart Dayton |
| Publisher | : |
| Total Pages | : |
| Release | : 2006 |
| Genre | : |
| ISBN | : |
The distribution and abundance of organisms is influenced by historical, abiotic, and biotic factors. The goal of my dissertation was to determine the distribution of anurans in the Big Bend region of the Chihuahuan Desert and to examine how abioticand biotic factors shape the composition and structure of anuran communities at multiple spatial scales. My approach relied on extensive field surveys, laboratory and field experiments, and GIS modeling. Results from field surveys and reciprocal transplant studies of tadpoles indicate that abiotic conditions of the breeding site most likely do not play a significant role in causing the segregation of species among individual breeding pools. I used laboratory and mesocosm experiments to test for indirect and direct effects of predators on growth and survival of S. couchii tadpoles. I found that S. couchii tadpoles do not alter their behavior in the presence of predators and are very susceptible to predation. Although tadpoles reared with predators suffered high mortality rates, they metamorphosed significantly faster than tadpoles reared without predators. The reduced time to metamorphose is likely a result of the thinning of intraspecific competitors. Because the primary cause of death for S. couchii tadpoles is desiccation due to pond drying, predators may play an important role in facilitating metamorphosis by decreasing competitors and thus increasing per capita resources, therefore decreasing time to metamorphosis for the surviving tadpoles. At the landscape level anuran distributions seem to be influenced by environmental factors that influence the survival of the adult stage. At the level of the breeding site, microhabitat and abiotic components of the aquatic environment do not seem to play an important role in influencing breeding site use by different species. Rather, it seems likely that predation on tadpoles by predators is important in limiting the distribution of some species and that the fast-developing S. couchii may exclude other species from using sites via oophagy and predation on small tadpoles. My research elucidates the fact that in order to understand factors important in regulating ecological communities it is important to examine both abiotic and biotic factors at multiple spatial scales.
| Author | : Erin Maurine Toffelmier |
| Publisher | : |
| Total Pages | : 147 |
| Release | : 2019 |
| Genre | : |
| ISBN | : |
Examining patterns of diversity at fine and global spatial scales is an important component of to inferring underlying evolutionary mechanisms, understanding species distributional patterns, and informing conservation. Globally, amphibians and reptiles are among the fastest declining taxonomic groups, and now more than ever, it is necessary to quantify diversity and its spatial drivers in order to most effectively conserve species. In this dissertation, I examine the population, landscape, and conservation genomics of several species along a continuum of endangerment, from highly endangered and on the brink of extinction to widespread and abundant. Throughout, I use large-scale molecular data sets coupled with spatial analyses to examine spatial genetic diversity in these varied species. My goals were to contribute to our understanding of how genetic diversity is distributed across a multitude of landscapes and to provide genetic context for the conservation of these species. In Chapters 1 and 2, I examined how genetic diversity is spread across the limited ranges of two ecologically disparate species, California tiger salamanders, Ambystoma californiense, in Santa Barbara County, and the Panamint alligator lizard, Elgaria panamintina, found only in the isolated desert mountain ranges of eastern California, and found surprising parallels. In both, I found populations with exceedingly low levels of genetic diversity and genetic effective population sizes. For tiger salamanders, genetic diversity and divergence is strongly correlated with the number of suitable breeding habitats in regional neighborhoods and presence of natural vernal pools, while divergence across the range of E. panamintina is primarily mediated by geographic distance. In both cases, our findings have important implications for how management and mitigation efforts may more effectively assist the recovery and/or protection of these groups. In Chapter 3, I examined the drivers of spatial genetic structure in the widespread southern alligator lizard, Elgaria multicarinata. I found that patterns of genetic isolation are driven primarily by geographic distances, but that regional ecological niches have also diverged. Collectively, my work demonstrates the utility of integrating genetic and spatial analyses across spatial scales to help elucidate how genetic diversity is distributed across variable landscapes.
| Author | : Chan Kin Onn |
| Publisher | : |
| Total Pages | : 166 |
| Release | : 2017 |
| Genre | : Amolops larutensis |
| ISBN | : |
Elucidating the tempo and mode of diversification is a major goal of evolutionary biology and represents a fundamental step towards understanding how biodiversity is generated and maintained. Achieving this goal is challenging due to the multidimensional complexity of macro- and micro-evolutionary forces that act across time, space and different phylogenetic levels. Furthermore, these evolutionary forces can involve both adaptive and neutral processes that form confounding interactions with landscape/environmental characteristics. Understanding how genes, geography, and ecology interact to generate, maintain and distribute biodiversity, therefore requires numerous datatypes and analytical resources that span different disciplines such as biogeography, population, and landscape genetics. The primary goal of this study is to provide a better understanding of the patterns and processes involved in the diversification of frogs from the family Ranidae through the use of genomic data and recent advances in analytical methods. Malaysia is one of the most biodiverse and environmentally threatened countries in the world. It is part of Sundaland, a biodiversity hotspot that has undergone dramatic climatic fluctuations in the past few million years. The dynamic geological history, coupled with the highly heterogeneous landscape of Malaysia, provides an ideal system to study the patterns and processes of diversification within a spatial and temporal context. Such studies are of particular importance in Malaysia as it is the country with the highest rate of deforestation in the world. Moreover, most biodiversity research in Malaysia revolves around systematic revisions and species descriptions with relatively few studies focused on understanding the evolutionary underpinnings that generate diversity. This study will fill a significant gap in the region’s biodiversity research, especially as it represents the first genomic study on Malaysian amphibians. Chapter 1 examines the broad biogeographic patterns of Ranid diversification at the family and generic level. Using the most comprehensive and robust time-calibrated phylogeny to date, we estimated the timing and patterns of major dispersal events to test the hypothesis that colonization of new geographic areas triggers a concomitant acceleration in diversification rates. Additionally, we determined whether the Eocene-Oligocene extinction event (EOEE) had a significant impact on the diversification of Ranids. Our results showed that the EOEE had no effect on diversification rates; most major dispersal events occurred over a relatively short period of time during the end of the Eocene, and the colonization of new geographic areas was not followed by increased net-diversification. On the contrary, diversification rate declined or did not shift following geographic expansion. Thus, the diversification history of Ranid frogs contradicts the prevailing expectation that amphibian net-diversification accelerated towards the present or increased following range expansion. Rather, our results demonstrate that despite their dynamic biogeographic history, the family Ranidae diversified at a relatively constant rate despite their present high diversity and circumglobal distribution. Chapter 2 compares the efficacy of commonly-used species delimitation methods (SDMs) and a population genomics approach based on genome-wide single nucleotide polymorphisms (SNPs) to assess lineage separation in the Malaysian Torrent Frog Complex currently recognized as a single species (Amolops larutensis). First, we used morphological, mitochondrial DNA and genome-wide SNPs to identify putative species boundaries by implementing non-coalescent and coalescent-based SDMs. We then tested the validity of putative boundaries by estimating spatiotemporal gene flow to assess the extent of genetic separation/cohesion among putative species. Our results show that SDMs were effective at delimiting divergent lineages in the absence of gene flow but overestimated species in the presence of marked population structure and gene flow. However, using a population genomics approach and the concept of species as separately evolving metapopulation lineages as the only necessary property of a species, we were able to objectively elucidate cryptic species boundaries in the presence of past and present gene flow. Chapter 3 builds on the findings of the previous chapter to determine the spatiotemporal factors that generated the genetic differentiation in Amolops. We tested the significance and relative contributions of (1) geographic distance (isolation-by-distance, IBD); (2) landscape/environmental variables including mountain ranges, river basins, forest cover, and habitat suitability (isolation-by-environment, IBE); and (3) historical events (isolation-by-colonization, IBC) towards genetic differentiation. Results showed that interspecies diversification was primarily driven by historical events (IBC); IBD was responsible for intraspecies population structure, and IBE did not play a significant role in the diversification of Amolops. Additionally, demographic analyses detected significant population bottlenecks, indicating that speciation was most likely due to founder effect speciation.
| Author | : Ryan P. O'Donnell |
| Publisher | : |
| Total Pages | : 133 |
| Release | : 2012 |
| Genre | : |
| ISBN | : |
PUBLIC ABSTRACT: Genetic diversity is the raw material for evolution: evolution cannot happen without genetic diversity, and the ability of a population to respond to a changing environment depends directly on how diverse its genes are. Understanding the distribution of genetic diversity is important for many reasons, including predicting whether species will be able to adapt to climate change and predicting the spread of invasive species. Information about the distribution of genetic diversity across the range of the Northern Leopard Frog, a declining species, will not only help us to ensure that the species can continue to evolve in response to changing environmental conditions, but it will also help us gain a better understanding of what factors drive genetic diversity in populations of other species. In Chapter 2, we found that genetic diversity was reduced in edge populations relative to central populations, but was not reduced in populations in previously glaciated areas; therefore position at range edge had a stronger effect in reducing diversity than recent colonization of new habitat. In Chapter 3, we found two distinct lineages within the species that mix in the eastern Great Lakes region, elevating genetic diversity in that area. In Chapter 4, we found that populations in the Stoneman Lake area of Arizona had high genetic diversity, but also contained evidence of introduction of eastern frogs, and we concluded that moving frogs from the Stoneman Lake area to restore diversity in other Arizona populations is not recommended.
| Author | : Roy W. McDiarmid |
| Publisher | : University of Chicago Press |
| Total Pages | : 476 |
| Release | : 1999-11 |
| Genre | : Nature |
| ISBN | : 9780226557625 |
In our own juvenile stage, many of us received our wide-eyed introduction to the wonders of nature by watching the metamorphosis of swimming tadpoles into leaping frogs and toads. The recent alarming declines in amphibian populations worldwide and the suitability of amphibians for use in answering research questions in disciplines as diverse as molecular systematics, animal behavior, and evolutionary biology have focused enormous attention on tadpoles. Despite this popular and scientific interest, relatively little is known about these fascinating creatures. In this indispensable reference, leading experts on tadpole biology relate what we currently know about tadpoles and what we might learn from them in the future. Tadpoles provides detailed summaries of tadpole morphology, development, behavior, ecology, and environmental physiology; explores the evolutionary consequences of the tadpole stage; synthesizes available information on their biodiversity; and presents a standardized terminology and an exhaustive literature review of tadpole biology.
