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Author: Tyler Duncan Hether
Publisher:
ISBN:
Category : Hyla
Languages : en
Pages : 76
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Book Description
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: Tyler Duncan Hether
Publisher:
ISBN:
Category : Hyla
Languages : en
Pages : 76
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Book Description
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: Niko Balkenhol
Publisher: John Wiley & Sons
ISBN: 1118525248
Category : Science
Languages : en
Pages : 288
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Book Description
Despite the substantial interest in landscape genetics from the scientific community, learning about the concepts and methods underlying the field remains very challenging. The reason for this is the highly interdisciplinary nature of the field, which combines population genetics, landscape ecology, and spatial statistics. These fields have traditionally been treated separately in classes and textbooks, and very few scientists have received the interdisciplinary training necessary to efficiently teach or apply the diversity of techniques encompassed by landscape genetics. To address the current knowledge gap, this book provides the first in depth treatment of landscape genetics in a single volume. Specifically, this book delivers fundamental concepts and methods underlying the field, covering particularly important analytical methods in detail, and presenting empirical and theoretical applications of landscape genetics for a variety of environments and species. Consistent with the interdisciplinary nature of landscape genetics, the book combines an introductory, textbook like section with additional sections on advanced topics and applications that are more typical of edited volumes. The chapter topics and the expertise of the authors and the editorial team make the book a standard reference for anyone interested in landscape genetics. The book includes contributions from many of the leading researchers in landscape genetics. The group of scientists we have assembled has worked on several collaborative projects over the last years, including a large number of peer reviewed papers, several landscape genetics workshops at international conferences, and a distributed graduate seminar on landscape genetics. Based on the experiences gained during these collaborative teaching and research activities, the book includes chapters that synthesize fundamental concepts and methods underlying landscape genetics (Part 1), chapters on advanced topics that deserve a more in depth treatment (Part 2), and chapters illustrating the use of concepts and methods in empirical applications (Part 3). This structure ensures a high usefulness of the book for beginning landscape geneticists and experienced researchers alike, so that it has a broad target audience. At least one of the four co editors is involved in almost every chapter of the book, thereby ensuring a high consistency and coherency among chapters.
Author: Laurie Hall
Publisher:
ISBN:
Category :
Languages : en
Pages : 98
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Book Description
Dispersal and gene flow connect habitat patches, linking demographic and genetic processes within metapopulations. Demographic connectivity can prevent local extinctions and increase species persistence. It allows species to colonize new areas, making it possible for them to shift their ranges in response to changes in the environment. Genetic connectivity may impede local adaptation, but is often advantageous because it minimizes the negative effects of habitat loss and fragmentation, such as inbreeding. This research explored different methodologies for estimating dispersal and gene flow, and estimated connectivity for two species of secretive wetland birds, the California black rail (Laterallus jamaicensis coturniculus) and the Virginia rail (Rallus limicola), from an inland metapopulation in the Sierra Nevada foothills and a coastal metapopulation in the San Francisco Bay Area, California. The research presented includes: (1) a synthesis of landscape genetics methods used to examine spatial patterns of genetic variation, (2) a validation of dispersal distances estimated from occupancy models using dispersal distances estimated from genetic parentage assignments within the inland metapopulation, (3) an estimate of the frequency and distance of long-distance dispersal events between the inland and coastal metapopulations, and (4) an assessment of the effects of habitat loss and fragmentation on gene flow within the coastal metapopulation. Despite its importance in ecology and evolution, dispersal distances are poorly understood for many species, especially those that are secretive and rare, such as rails. For these species, indirect methods, including the use of occupancy models, genetics, and isotopic markers, may be optimal for estimating dispersal. In the Sierra Nevada foothills, Black and Virginia rails exhibited contrasting relationships between connectivity metrics and patch colonization. For black rails, model-averaged dispersal distances from occupancy models (Buffer Radius Metric = 3.46 km; Incidence Function Metric = 3.70 km) showed good agreement with the mean dispersal distance from genetic parentage assignments (5.58 ± 1.92 km). For Virginia rails, however, it was difficult to identify a spatial scale with the best fit in occupancy models, and the sample size for estimating dispersal distance from parentage assignments was limited. Combined inference from genetic and isotopic population assignments suggested that long-distance dispersal of black rails between the Sierra Nevada foothills and the San Francisco Bay Area occurred infrequently, but, somewhat surprisingly, three dispersal events greater than 100 km were recorded during the study. The first was recorded from a band return for a black rail that traveled 128 km. Two other long-distance dispersal estimates were obtained using isotopic and genetic population assignments. Within the San Francisco Bay Area, estimates of gene flow for black rails among 11 wetlands (FST range: 0.014 to 0.067) indicated rails dispersed frequently between wetlands at shorter spatial scales (tens of kilometers), but that gene flow at a larger spatial scale (greater than 50 km) between the North Bay and South Bay (FST = 0.018) was limited. Although previously thought to be dispersal-limited, black rails appear to be capable of dispersing and maintaining some level of gene flow at spatial scales less than 50 km. Therefore, wetland mitigation and restoration efforts for rails should focus on protecting and creating habitat at smaller spatial scales (tens of kilometers) to maintain demographic and genetic connectivity and metapopulation viability.
Author: Antoine Guisan
Publisher: Cambridge University Press
ISBN: 0521765137
Category : Computers
Languages : en
Pages : 513
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Book Description
This book introduces the key stages of niche-based habitat suitability model building, evaluation and prediction required for understanding and predicting future patterns of species and biodiversity. Beginning with the main theory behind ecological niches and species distributions, the book proceeds through all major steps of model building, from conceptualization and model training to model evaluation and spatio-temporal predictions. Extensive examples using R support graduate students and researchers in quantifying ecological niches and predicting species distributions with their own data, and help to address key environmental and conservation problems. Reflecting this highly active field of research, the book incorporates the latest developments from informatics and statistics, as well as using data from remote sources such as satellite imagery. A website at www.unil.ch/hsdm contains the codes and supporting material required to run the examples and teach courses.
Author: Niko Balkenhol
Publisher: John Wiley & Sons
ISBN: 1118525299
Category : Science
Languages : en
Pages : 298
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Book Description
LANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS LANDSCAPE GENETICS: CONCEPTS, METHODS, APPLICATIONS Edited by Niko Balkenhol, Samuel A. Cushman, Andrew T. Storfer, Lisette P. Waits Landscape genetics is an exciting and rapidly growing field, melding methods and theory from landscape ecology and population genetics to address some of the most challenging and urgent ecological and evolutionary topics of our time. Landscape genetic approaches now enable researchers to study in detail how environmental complexity in space and time affect gene flow, genetic drift, and local adaptation. However, learning about the concepts and methods underlying the field remains challenging due to the highly interdisciplinary nature of the field, which relies on topics that have traditionally been treated separately in classes and textbooks. In this edited volume, some of the leading experts in landscape genetics provide the first comprehensive introduction to underlying concepts, commonly used methods, and current and future applications of landscape genetics. Consistent with the interdisciplinary nature of the field, the book includes textbook-like chapters that synthesize fundamental concepts and methods underlying landscape genetics (Part 1), chapters on advanced topics that deserve a more in-depth treatment (Part 2), and chapters illustrating the use of concepts and methods in empirical applications (Part 3). Aimed at beginning landscape geneticists and experienced researchers alike, this book will be helpful for all scientists and practitioners interested in learning, teaching, and applying landscape genetics.
Author: Samuel A. Cushman
Publisher: Frontiers Media SA
ISBN: 2889455483
Category :
Languages : en
Pages : 116
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Book Description
Ecosystems are the stage on which the play of evolution is acted, and ecosystems are complex, spatially structured and temporally varying. The purpose of this Research Topic is to explore critical challenges and opportunities for the transition from landscape genetics to landscape genomics. Landscape genetics has focused on the spatial analysis of small genetic datasets, typically comprised of less than 20 microsatellite markers, taken from clusters of individuals in putative populations or distributed individuals across landscapes. The recent emergence of large scale genomic datasets produced by next generation sequencing methods poses tremendous challenge and opportunity to the field. Perhaps the greatest is to produce, process, curate, archive and analyze spatially referenced genomic datasets in a way such that research is led by a priori hypotheses regarding how environmental heterogeneity and temporal dynamics interact to affect gene flow and selection. The papers in the Research Topic cover a broad range of topics under this area of focus, from reviews of the emergence of landscape genetics, to best practices in spatial analysis of genetic data. The compilation, like the emerging field itself, is eclectic and illustrates the scope of both the challenges and opportunities of this emerging field.
Author: Andrew F. Bennett
Publisher: IUCN
ISBN: 2831707447
Category : Corridors
Languages : en
Pages : 261
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Book Description
The loss and fragmentation of natural habitats is one of the major issues in wildlife management and conservation. Habitat "corridors" are sometimes proposed as an important element within a conservation strategy. Examples are given of corridors both as pathways and as habitats in their own right. Includes detailed reviews of principles relevant to the design and management of corridors, their place in regional approaches to conservation planning, and recommendations for research and management.
Author: V. Loeschcke
Publisher: Birkhäuser
ISBN: 3034885105
Category : Science
Languages : en
Pages : 427
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Book Description
It follows naturally from the widely accepted Darwinian dictum that failures of populations or of species to adapt and to evolve under changing environments will result in their extinction. Population geneti cists have proclaimed a centerstage role in developing conservation biology theory and applications. However, we must critically reexamine what we know and how we can make rational contributions. We ask: Is genetic variation really important for the persistence of species? Has any species become extinct because it ran out of genetic variation or because of inbreeding depression? Are demographic and environmental stochas ticity by far more important for the fate of a population or species than genetic stochasticity (genetic drift and inbreeding)? Is there more to genetics than being a tool for assessing reproductive units and migration rates? Does conventional wisdom on inbreeding and "magic numbers" or rules of thumb on critical effective population sizes (MVP estimators) reflect any useful guidelines in conservation biology? What messages or guidelines from genetics can we reliably provide to those that work with conservation in practice? Is empirical work on numerous threatened habitats and taxa gathering population genetic information that we can use to test these guidelines? These and other questions were raised in the invitation to a symposium on conservation genetics held in May 1993 in pleasant surroundings at an old manor house in southern Jutland, Denmark.
Author: C. Ashton Drew
Publisher: Springer
ISBN: 9781489981356
Category : Science
Languages : en
Pages : 0
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Book Description
Most projects in Landscape Ecology, at some point, define a species-habitat association. These models are inherently spatial, dealing with landscapes and their configurations. Whether coding behavioral rules for dispersal of simulated organisms through simulated landscapes, or designing the sampling extent of field surveys and experiments in real landscapes, landscape ecologists must make assumptions about how organisms experience and utilize the landscape. These convenient working postulates allow modelers to project the model in time and space, yet rarely are they explicitly considered. The early years of landscape ecology necessarily focused on the evolution of effective data sources, metrics, and statistical approaches that could truly capture the spatial and temporal patterns and processes of interest. Now that these tools are well established, we reflect on the ecological theories that underpin the assumptions commonly made during species distribution modeling and mapping. This is crucial for applying models to questions of global sustainability. Due to the inherent use of GIS for much of this kind of research, and as several authors’ research involves the production of multicolored map figures, there would be an 8-page color insert. Additional color figures could be made available through a digital archive, or by cost contributions of the chapter authors. Where applicable, would be relevant chapters’ GIS data and model code available through a digital archive. The practice of data and code sharing is becoming standard in GIS studies, is an inherent method of this book, and will serve to add additional research value to the book for both academic and practitioner audiences.
Author: Morgan Gray
Publisher:
ISBN:
Category :
Languages : en
Pages : 76
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Book Description
The built environment, especially roads, urban and suburban development, can reduce the ability for wildlife to move across landscapes. Maintaining landscape connectivity has become a central theme in ecology and conservation, as corridors of intact habitat help maintain ecosystem functionality and, in the face of climate change, may provide migration paths for species. However, the influence of the built environment on connectivity is rarely quantified using empirical data informed by species detection, movement, or genetic structure. Rather, structural connectivity, as opposed to functional connectivity, is estimated using land cover alone. Structural connectivity estimates offer a simple and potentially powerful approach with fewer data requirements for wildlife corridor planning; however, models of structural connectivity are rarely if ever evaluated with empirical species data, limiting our understanding of their reliability and utility. This dissertation fills this gap by investigating the influence of human land use and habitat fragmentation on landscape connectivity using a suite of quantitative modeling approaches and mammals as the focal species, including cross comparisons among these approaches. Specifically, three methods that vary in levels of biological information are used to evaluate how well structural connectivity models perform for individual species, as well as their relationship to functional connectivity. To begin with, the utility of a structural connectivity model based on the distribution and intensity of land use is evaluated by comparing model predictions to observed land use by a generalist carnivore, the puma (Puma concolor). Findings from this study indicate that generic landscape permeability models can be used with confidence as a guide when prioritizing habitat corridors for biodiversity conservation across fragmented landscapes. Next, the utility of structural connectivity models is further evaluated by examining how the inclusion of specific human land use variables affects model accuracy in a species distribution model for gray fox (Urocyon cinereoargenteus). Findings from this study indicate that species distribution models generated in human-dominated landscapes have higher accuracy when informed by indices of land use. Finally, a combination of spatial and genetic methods is used to evaluate the influence of roads on the functional connectivity for a small mammal, California ground squirrels (Otospermophilus beecheyi). Findings from this study indicate that a combined spatial and genetic approach can be used to identify locations where roads act as barriers. Given the importance of habitat fragmentation, there is a pressing need to rapidly develop and utilize connectivity assessment methods in conservation planning. Research findings presented here have already impacted mammal conservation planning and management in California in the following specific ways. The structural connectivity model was used to identify priority habitat linkages for inclusion in the Conservation Blueprint for Santa Cruz County, and the combined genetic and spatial approach was used by the Santa Clara County Open Space Authority, CA to identify corridors and restore connectivity in an area with an existing road network. Beyond these regional impacts, future conservation planning worldwide can benefit from using readily available data collected by citizen scientists as input in predictive mapping to increase the sample size and spatial coverage for species distribution modeling.
