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Author: Gideon S. Bradburd Publisher: ISBN: 9781339260402 Category : Languages : en Pages :
Book Description
Genetic variation provides the raw materials for both local adaptation and the formation of new species, and understanding the processes generating and maintaining the diversity of living organisms is a fundamental aim across all areas and levels of biological research. The central question that motivated this dissertation research is: what are the patterns of variation within and between populations and species, and what processes, ecological and evolutionary, are generating those patterns? My dissertation is focused on developing statistical methods to infer and visualize spatial patterns of genetic differentiation, and provide clues about the processes that have generated them. In my first chapter, I develop a statistical method to quantify the relative contributions of ecological and geographic distance to patterns of genetic differentiation. The method, BEDASSLE, models the allele frequencies in a set of populations at a set of unlinked loci as spatially correlated Gaussian processes, in which the covariance structure is a decreasing function of both geographic and ecological distance. In my second chapter, I discuss the conceptual framework of Isolation by Environment (IBE, as opposed to Isolation by Distance, or IBD) in a review and synthesis. This work clearly defines IBE as a pattern, rather than a process, and details the different processes that can generate a pattern of IBE. In my third chapter, I extend the statistical framework developed in the first chapter to quantify signals of IBD and IBE to a general method for inferring and visualizing patterns of population structure. This method, SpaceMix, infers, for a set of sequenced samples, a map in which the distances between population locations reflect genetic, rather than geographic, proximity. Together, these chapters represent an advance in the conceptual and statistical framework for analyzing spatial patterns of population genetic structure across landscapes.
Author: Gideon S. Bradburd Publisher: ISBN: 9781339260402 Category : Languages : en Pages :
Book Description
Genetic variation provides the raw materials for both local adaptation and the formation of new species, and understanding the processes generating and maintaining the diversity of living organisms is a fundamental aim across all areas and levels of biological research. The central question that motivated this dissertation research is: what are the patterns of variation within and between populations and species, and what processes, ecological and evolutionary, are generating those patterns? My dissertation is focused on developing statistical methods to infer and visualize spatial patterns of genetic differentiation, and provide clues about the processes that have generated them. In my first chapter, I develop a statistical method to quantify the relative contributions of ecological and geographic distance to patterns of genetic differentiation. The method, BEDASSLE, models the allele frequencies in a set of populations at a set of unlinked loci as spatially correlated Gaussian processes, in which the covariance structure is a decreasing function of both geographic and ecological distance. In my second chapter, I discuss the conceptual framework of Isolation by Environment (IBE, as opposed to Isolation by Distance, or IBD) in a review and synthesis. This work clearly defines IBE as a pattern, rather than a process, and details the different processes that can generate a pattern of IBE. In my third chapter, I extend the statistical framework developed in the first chapter to quantify signals of IBD and IBE to a general method for inferring and visualizing patterns of population structure. This method, SpaceMix, infers, for a set of sequenced samples, a map in which the distances between population locations reflect genetic, rather than geographic, proximity. Together, these chapters represent an advance in the conceptual and statistical framework for analyzing spatial patterns of population genetic structure across landscapes.
Author: Alisa Sedghifar Publisher: ISBN: 9781339542515 Category : Languages : en Pages :
Book Description
Spatial patterns of genetic variation are shaped by a variety of population genetic processes, and can therefore be a rich source of information about population history. The work presented here focuses on two drivers of spatial variation: recent secondary contact after isolation, and responses to spatially varying selection. The first chapter describes expected genome-wide patterns of coancestry resulting from secondary contact between two differentiated populations, with the continuous movement of individuals by diffusive local migration. Using analytic expressions derived for expected linkage disequilibrium (LD), an inference framework was developed to estimate the timing of secondary contact and gene flow. This was applied to genomic data from spatially distributed admixed human populations, providing an alternative to commonly used admixture models. The following chapters examine patterns of spatial variation that are influenced by selection. While continued gene flow acts to homogenize allele frequencies between different populations, differential selection across space can maintain consistent patterns of geographic variation. These patterns are historically well studied, especially in the context of local adaptation. Here, genome-wide patterns of geographic variation in D. simulans is described, in order to better understand the process of local adaptation in this species, and in Drosophlia in general. Chapter two compares and contrasts patterns of differentiation between pairs of northern and southern populations of D. simulans in Australia and North America, with a focus on patterns of convergence and parallelism. There is evidence for parallel differentiation between the two continents in regions of the genome associated with regulation of gene expression. Contrary to patterns observed in the closely related Drosophila melanogaster, the spatial distribution of genetic variation in D. simulans does not support temperate adaptation outside of the species ancestral range. The results of this study suggest that populations on the two continents may have experienced independent, and different, adaptive trajectories, and that there may be limited power to detect parallel differentiation from comparing pairs of populations. Following the results of chapter two, chapter three presents a more detailed examination of genetic variation in D. simulans collected along the North American east coast and Central America. By analyzing patterns of genetic variation in 8 North American and one Panamanian population, this study identifies genetic variants that are associated with environmental gradients along the sampled transect. This study finds some evidence for the potential role of gene regulation in local adaptation, and significant overlap with D. melanogaster of genes containing latitudinally associated alleles. This study also reveals geographically inconsistent patterns of genetic variation along the cline, highlighting the need for further sampling, both temporally and geographically, in order to obtain a better understanding of population dynamics and adaptation in this species. (Gene lists and Gene Ontology enrichments for chapter 3 are available online as Supplemental file 1 and Supplemental file 2).
Author: Stefano Goffredo Publisher: Springer ISBN: 3319313053 Category : Science Languages : en Pages : 842
Book Description
This volume presents a broad panorama of the current status of research of invertebrate animals considered belonging to the phylum Cnidaria, such as hydra, jellyfish, sea anemone, and coral. In this book the Cnidarians are traced from the Earth’s primordial oceans, to their response to the warming and acidifying oceans. Due to the role of corals in the carbon and calcium cycles, various aspects of cnidarian calcification are discussed. The relation of the Cnidaria with Mankind is approached, in accordance with the Editors’ philosophy of bridging the artificial schism between science, arts and Humanities. Cnidarians' encounters with humans result in a broad spectrum of medical emergencies that are reviewed. The final section of the volume is devoted to the role of Hydra and Medusa in mythology and art.
Author: Tong H. Joh Publisher: ISBN: Category : Medical Languages : en Pages : 188
Book Description
The study of the genomic regulation of catecholamine-related enzymes is a new field, emerging from the rapid advances in molecular neurobiology. This text offers detailed summaries of recent progress from the work of leading researchers in molecular genetics and enzymes. It concentrates primarily on the rate- limiting enzyme tyrosine hydroxylase, with several chapters devoted to its complex chemistry, plus an evolutionary view of its structural similarity to certain aromatic amino acid hydroxylases. The book covers the remaining three pathway enzymes and all other enzymes related to catecholamine genes.
Author: Pierre Pontarotti Publisher: Springer Science & Business Media ISBN: 3642382126 Category : Science Languages : en Pages : 295
Book Description
This book presents 19 selected contributions to the 16th Evolutionary Biology Meeting, which took place in September 2012 in Marseilles. The aims of these annual meetings, which gather together leading evolutionary biologists and other scientists, are to promote the exchange of ideas and to encourage interdisciplinary collaborations. The first chapter deals with the history of a great discovery: The first experiments on ascidian and sea urchin egg fertilization. The remaining contributions are grouped under the following categories: · Evolutionary biology concepts · Exobiology and the origin of life · Evolutionary mechanisms Offering an up-to-date overview of recent findings in the field of evolutionary biology, this book is an invaluable source of information for scientists, teachers and advanced students.
Author: Richard Frankham Publisher: Oxford University Press ISBN: 0198783396 Category : Biodiversity Languages : en Pages : 426
Book Description
One of the greatest unmet challenges in conservation biology is the genetic management of fragmented populations of threatened animal and plant species. More than a million small, isolated, population fragments of threatened species are likely suffering inbreeding depression and loss of evolutionary potential, resulting in elevated extinction risks. Although these effects can often be reversed by re-establishing gene flow between population fragments, managers very rarely do this. On the contrary, genetic methods are used mainly to document genetic differentiation among populations, with most studies concluding that genetically differentiated populations should be managed separately, thereby isolating them yet further and dooming many to eventual extinction Many small population fragments are going extinct principally for genetic reasons. Although the rapidly advancing field of molecular genetics is continually providing new tools to measure the extent of population fragmentation and its genetic consequences, adequate guidance on how to use these data for effective conservation is still lacking. This accessible, authoritative text is aimed at senior undergraduate and graduate students interested in conservation biology, conservation genetics, and wildlife management. It will also be of particular relevance to conservation practitioners and natural resource managers, as well as a broader academic audience of conservation biologists and evolutionary ecologists.
Author: Hamid Reza Pourghasemi Publisher: Elsevier ISBN: 0128156953 Category : Science Languages : en Pages : 800
Book Description
Spatial Modeling in GIS and R for Earth and Environmental Sciences offers an integrated approach to spatial modelling using both GIS and R. Given the importance of Geographical Information Systems and geostatistics across a variety of applications in Earth and Environmental Science, a clear link between GIS and open source software is essential for the study of spatial objects or phenomena that occur in the real world and facilitate problem-solving. Organized into clear sections on applications and using case studies, the book helps researchers to more quickly understand GIS data and formulate more complex conclusions. The book is the first reference to provide methods and applications for combining the use of R and GIS in modeling spatial processes. It is an essential tool for students and researchers in earth and environmental science, especially those looking to better utilize GIS and spatial modeling. - Offers a clear, interdisciplinary guide to serve researchers in a variety of fields, including hazards, land surveying, remote sensing, cartography, geophysics, geology, natural resources, environment and geography - Provides an overview, methods and case studies for each application - Expresses concepts and methods at an appropriate level for both students and new users to learn by example
Author: Pavlos Kanaroglou Publisher: Routledge ISBN: 1317051580 Category : Science Languages : en Pages : 344
Book Description
Presenting current research on spatial epidemiology, this book covers topics such as exposure, chronic disease, infectious disease, accessibility to health care settings and new methods in Geographical Information Science and Systems. For epidemiologists, and for the management and administration of health care settings, it is critical to understand the spatial dynamics of disease. For instance, it is crucial that hospital administrators develop an understanding of the flow of patients over time, especially during an outbreak of a particular disease, so they can plan for appropriate levels of staffing and to carry out adaptive prevention measures. Furthermore, understanding where and why a disease occurs at a certain geographic location is vital for decision makers to formulate policy to increase the accessibility to health services (either by prevention, or adding new facilities). Spatial epidemiology relies increasingly on new methodologies, such as clustering algorithms, visualization and space-time modelling, the domain of Geographic Information Science. Implementation of those techniques appears at an increasing pace in commercial Geographic Information Systems, alongside more traditional techniques that are already part of such systems. This book provides the latest methods in GI Science and their use in health related problems.
Author: F. Richard Hauer Publisher: Academic Press ISBN: 0080547435 Category : Science Languages : en Pages : 894
Book Description
Methods in Stream Ecology, Second Edition, provides a complete series of field and laboratory protocols in stream ecology that are ideal for teaching or conducting research. This updated edition reflects recent advances in the technology associated with ecological assessment of streams, including remote sensing. In addition, the relationship between stream flow and alluviation has been added, and a new chapter on riparian zones is also included. The book features exercises in each chapter; detailed instructions, illustrations, formulae, and data sheets for in-field research for students; and taxanomic keys to common stream invertebrates and algae. With a student-friendly price, this book is key for all students and researchers in stream and freshwater ecology, freshwater biology, marine ecology, and river ecology. This text is also supportive as a supplementary text for courses in watershed ecology/science, hydrology, fluvial geomorphology, and landscape ecology. - Exercises in each chapter - Detailed instructions, illustrations, formulae, and data sheets for in-field research for students - Taxanomic keys to common stream invertebrates and algae - Link from Chapter 22: FISH COMMUNITY COMPOSITION to an interactive program for assessing and modeling fish numbers
Author: Gideon S. Bradburd
Author: Gideon S. Bradburd
Author: Alisa Sedghifar
Author: Paula E. Marquardt
Author: Stefano Goffredo
Author: Tong H. Joh
Author: Pierre Pontarotti
Author: Richard Frankham
Author: Hamid Reza Pourghasemi
Author: Pavlos Kanaroglou
Author: F. Richard Hauer