The Added Value Of Large Scale Genomic Data In Conservation

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The Added Value of Large-Scale Genomic Data in Conservation

Author : Evan McCartney-Melstad
Publisher :
ISBN 13 :
Total Pages : 161 pages
Book Rating : 4.:/5 (14 download)

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Book Synopsis The Added Value of Large-Scale Genomic Data in Conservation by : Evan McCartney-Melstad

Download or read book The Added Value of Large-Scale Genomic Data in Conservation written by Evan McCartney-Melstad and published by . This book was released on 2016 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: Large-scale genomic datasets have transformed the way we approach problems in biology. While genomic data are now common in studies of human disease and variation, they are rarely used in molecular ecology and conservation genetics. In this dissertation I investigate the added value of genomic-scale data to answer conservation-relevant questions for threatened and endangered amphibians and reptiles. The first chapter is a synthetic literature review of recent studies that used genetic data to learn about the ecology of amphibian species to aid in conservation. This review reveals that genomic studies in amphibians, likely due to their extremely large and complex genomes, have lagged behind other taxa, and includes future directions aimed squarely at large-genome analyses. Chapter two addresses this deficiency empirically by optimizing a genomic data collection strategy for amphibians with large genomes. This study shows that target capture is feasible in large-genome amphibians and experimentally examines two specific modifications that greatly improve efficiency and substantially reduce cost when gathering population-scale genomic data. Chapter three makes use of advancements from chapter two, and presents empirical results from a genomic exon capture dataset of endangered tiger salamanders (Ambystoma tigrinum) on Long Island, NY. This chapter demonstrates the substantial benefits and insights derived from our genomic dataset for answering conservation-relevant questions compared to a previous study of the same system using traditional microsatellite analyses. The final chapter attempts to elevate conservation genomics to the next level by using whole genomes to quantify the impacts of alternative solar energy development scenarios on gene flow of the Mojave desert tortoise (Gopherus agassizii). We generated 270 low-coverage whole genome tortoise sequences to build a historical map of gene flow for the species across the Mojave Desert, modeled the effects on gene flow of a set of proposed renewable energy development alternatives, and supplied management agencies with a ranked list of impacts of the green energy alternatives. Overall, this dissertation provides context for the current use of genomic tools in conservation biology, methodological advances for their application to large-genome amphibians, and two examples of large-scale studies that showcase the added value of genomic datasets in conservation.

Exploring Genetic Diversity and Bioinformatic Strategies for Complex Data in the Genomic Revolution

Author : Paula Elizabeth Adams
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (134 download)

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Book Synopsis Exploring Genetic Diversity and Bioinformatic Strategies for Complex Data in the Genomic Revolution by : Paula Elizabeth Adams

Download or read book Exploring Genetic Diversity and Bioinformatic Strategies for Complex Data in the Genomic Revolution written by Paula Elizabeth Adams and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past twenty-five years, we have gone from completing the first eukaryotic genome assembly to the new goal of sequencing and completing genome assemblies representing all known taxa on Earth. Genomic data has improved research across fields of biology from evolution and genetics to medicine and conservation. As genomic technologies rapidly improve and the amount of genomic data explodes, the need for complex genomic analysis tools has given rise to the field of Bioinformatics. Strategies are needed to address sequence read quality, sequence alignment, genomic variation estimation from sequence data, de-novo genome assembly, post assembly quality assessments and quantification, and genomic comparisons across species. Here we explore complexities in genomic analyses and how using large-scale genomic data can help us better understand the genomic variation that gives rise to the diversity of life. We show that using pooled-sequencing data we can assess recovery from inbreeding depression in Caenorhabditis remanei and the genomic changes that take place during inbreeding. We find that C. remanei is unable to recover from inbreeding even after 300 generations of recovery at large population size. Despite 23 generations of inbreeding, large portions of the genome remained heterozygous, suggesting that pseudo-overdominance may be preventing the ability to purge deleterious mutations. Our results indicate that recovery from inbreeding in the presence of high genetic load is unlikely. One improvement in genomics is the ability to use long-read sequencing to address complex genomic architecture. Using long-read, third-generation sequencing (TGS) generated with Oxford Nanopore Technologies (ONT) we assembled and identified novel insertions in Caenorhabditis elegans mutants, used for studies of human disease phenotypes. While genome assembly has rapidly improved, identifying contamination post-assembly has remained challenging. We show that using supervised machine-learning ensemble decision tree methods we can quickly and accurately identify contamination in genome assemblies. As genomic resources continue to improve and databases grow, developing new tools and analysis methods that can harness this large-scale genomic data will reveal a greater understanding of organisms across the tree of life.

Conservation and the Genomics of Populations

Author : Fred W. Allendorf
Publisher : Oxford University Press
ISBN 13 : 0192598570
Total Pages : 785 pages
Book Rating : 4.1/5 (925 download)

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Book Synopsis Conservation and the Genomics of Populations by : Fred W. Allendorf

Download or read book Conservation and the Genomics of Populations written by Fred W. Allendorf and published by Oxford University Press. This book was released on 2022-02-10 with total page 785 pages. Available in PDF, EPUB and Kindle. Book excerpt: The relentless loss of biodiversity is among the greatest problems facing the world today. The third edition of this established textbook provides an updated and comprehensive overview of the essential background, concepts, and tools required to understand how genetics can be used to conserve species, reduce threat of extinction, and manage species of ecological or commercial importance. This edition is thoroughly revised to reflect the major contribution of genomics to conservation of populations and species. It includes two new chapters: "Genetic Monitoring" and a final "Conservation Genetics in Practice" chapter that addresses the role of science and policy in conservation genetics. New genomic techniques and statistical analyses are crucial tools for the conservation geneticist. This accessible and authoritative textbook provides an essential toolkit grounded in population genetics theory, coupled with basic and applied research examples from plants, animals, and microbes. The book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, evolutionary response to anthropogenic change, and applications in conservation and management. Conservation and the Genomics of Populations helps demystify genetics and genomics for conservation practitioners and early career scientists, so that population genetic theory and new genomic data can help raise the bar in conserving biodiversity in the most critical 20 year period in the history of life on Earth. It is aimed at a global market of applied population geneticists, conservation practitioners, and natural resource managers working for wildlife and habitat management agencies. It will be of particular relevance and use to upper undergraduate and graduate students taking courses in conservation biology, conservation genetics, and wildlife management.

Conservation Genetics in the Age of Genomics

Author : George Amato
Publisher : Columbia University Press
ISBN 13 : 0231502311
Total Pages : 504 pages
Book Rating : 4.2/5 (315 download)

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Book Synopsis Conservation Genetics in the Age of Genomics by : George Amato

Download or read book Conservation Genetics in the Age of Genomics written by George Amato and published by Columbia University Press. This book was released on 2009-08-07 with total page 504 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genome sequencing enables scientists to study genes over time and to test the genetic variability of any form of life, from bacteria to mammals. Thanks to advances in molecular genetics, scientists can now determine an animal's degree of inbreeding or compare genetic variation of a captive species to wild or natural populations. Mapping an organism's genetic makeup recasts such terms as biodiversity and species and enables the conservation of rare or threatened species, populations, and genes. By introducing a new paradigm for studying and preserving life at a variety of levels, genomics offers solutions to previously intractable problems in understanding the biology of complex organisms and creates new tools for preserving the patterns and processes of life on this planet. Featuring a number of high-profile researchers, this volume introduces the use of molecular genetics in conservation biology and provides a historical perspective on the opportunities and challenges presented by new technologies. It discusses zoo-, museum-, and herbarium-based biological collections, which have expanded over the past decade, and covers the promises and problems of genomic and reproductive technology. The collection concludes with the philosophical and legal issues of conservation genetics and their potential effects on public policy.

Ecological Genomics

Author : Christian R. Landry
Publisher : Springer Science & Business Media
ISBN 13 : 9400773471
Total Pages : 358 pages
Book Rating : 4.4/5 (7 download)

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Book Synopsis Ecological Genomics by : Christian R. Landry

Download or read book Ecological Genomics written by Christian R. Landry and published by Springer Science & Business Media. This book was released on 2013-11-25 with total page 358 pages. Available in PDF, EPUB and Kindle. Book excerpt: Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

Integrating Genomic Conservation Data with Motif Discovery

Author : Timothy William Danford
Publisher :
ISBN 13 :
Total Pages : 198 pages
Book Rating : 4.:/5 (573 download)

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Book Synopsis Integrating Genomic Conservation Data with Motif Discovery by : Timothy William Danford

Download or read book Integrating Genomic Conservation Data with Motif Discovery written by Timothy William Danford and published by . This book was released on 2004 with total page 198 pages. Available in PDF, EPUB and Kindle. Book excerpt: We formalize a probabilistic model of inter-species sequence conservation for motif discovery, and demonstrate that adding large-scale genomic conservation data to an existing motif discovery procedure improves the quality of that procedure's results. Existing motif discovery algorithms reveal binding motifs that are statistically over-represented in small sets of promoter regions. To the extent that binding motifs form a reliable part of a cell's regulatory apparatus, and that apparatus is preserved across closely related species, these binding motifs should also be conserved in the corresponding genomes. Previous studies have tried to assess levels of conservation in genomic fragments of several yeast species. Our approach computes the conditional probability of inter-species sequences, and uses this probability measure to maximize the likelihood of the data from different species with a motif model.

Bridging the Genomics Gap

Author : Billie-Jo Hardy
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (13 download)

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Book Synopsis Bridging the Genomics Gap by : Billie-Jo Hardy

Download or read book Bridging the Genomics Gap written by Billie-Jo Hardy and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Next Steps for Functional Genomics

Author : National Academies of Sciences, Engineering, and Medicine
Publisher : National Academies Press
ISBN 13 : 0309676738
Total Pages : 201 pages
Book Rating : 4.3/5 (96 download)

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Book Synopsis Next Steps for Functional Genomics by : National Academies of Sciences, Engineering, and Medicine

Download or read book Next Steps for Functional Genomics written by National Academies of Sciences, Engineering, and Medicine and published by National Academies Press. This book was released on 2020-12-18 with total page 201 pages. Available in PDF, EPUB and Kindle. Book excerpt: One of the holy grails in biology is the ability to predict functional characteristics from an organism's genetic sequence. Despite decades of research since the first sequencing of an organism in 1995, scientists still do not understand exactly how the information in genes is converted into an organism's phenotype, its physical characteristics. Functional genomics attempts to make use of the vast wealth of data from "-omics" screens and projects to describe gene and protein functions and interactions. A February 2020 workshop was held to determine research needs to advance the field of functional genomics over the next 10-20 years. Speakers and participants discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications that would benefit society. This publication summarizes the presentations and discussions from the workshop.

The New Science of Metagenomics

Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309106761
Total Pages : 170 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis The New Science of Metagenomics by : National Research Council

Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.

Conservation and the Genetics of Populations

Author : Fred W. Allendorf
Publisher : John Wiley & Sons
ISBN 13 : 1444309056
Total Pages : 664 pages
Book Rating : 4.4/5 (443 download)

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Book Synopsis Conservation and the Genetics of Populations by : Fred W. Allendorf

Download or read book Conservation and the Genetics of Populations written by Fred W. Allendorf and published by John Wiley & Sons. This book was released on 2009-03-12 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conservation and the Genetics of Populations gives acomprehensive overview of the essential background, concepts, andtools needed to understand how genetic information can be used todevelop conservation plans for species threatened withextinction. Provides a thorough understanding of the genetic basis ofbiological problems in conservation. Uses a balance of data and theory, and basic and appliedresearch, with examples taken from both the animal and plantkingdoms. An associated website contains example data sets and softwareprograms to illustrate population genetic processes and methods ofdata analysis. Discussion questions and problems are included at the end ofeach chapter to aid understanding. Features Guest Boxes written by leading people in the fieldincluding James F. Crow, Nancy FitzSimmons, Robert C. Lacy, MichaelW. Nachman, Michael E. Soule, Andrea Taylor, Loren H. Rieseberg,R.C. Vrijenhoek, Lisette Waits, Robin S. Waples and AndrewYoung. Supplementary information designed to support Conservationand the Genetics of Populations including: Downloadable sample chapter Answers to questions and problems Data sets illustrating problems from the book Data analysis software programs Website links An Instructor manual CD-ROM for this title is available. Pleasecontact our Higher Education team at ahref="mailto:[email protected]"[email protected]/afor more information.

Rewilding European Landscapes

Author : Henrique M. Pereira
Publisher : Springer
ISBN 13 : 3319120395
Total Pages : 239 pages
Book Rating : 4.3/5 (191 download)

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Book Synopsis Rewilding European Landscapes by : Henrique M. Pereira

Download or read book Rewilding European Landscapes written by Henrique M. Pereira and published by Springer. This book was released on 2015-05-04 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: Some European lands have been progressively alleviated of human pressures, particularly traditional agriculture in remote areas. This book proposes that this land abandonment can be seen as an opportunity to restore natural ecosystems via rewilding. We define rewilding as the passive management of ecological successions having in mind the long-term goal of restoring natural ecosystem processes. The book aims at introducing the concept of rewilding to scientists, students and practitioners. The first part presents the theory of rewilding in the European context. The second part of the book directly addresses the link between rewilding, biodiversity, and habitats. The third and last part is dedicated to practical aspects of the implementation of rewilding as a land management option. We believe that this book will both set the basis for future research on rewilding and help practitioners think about how rewilding can take place in areas under their management.

Conservation and the Genomics of Populations

Author : Fred W. Allendorf
Publisher : Oxford University Press
ISBN 13 : 0198856563
Total Pages : 785 pages
Book Rating : 4.1/5 (988 download)

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Book Synopsis Conservation and the Genomics of Populations by : Fred W. Allendorf

Download or read book Conservation and the Genomics of Populations written by Fred W. Allendorf and published by Oxford University Press. This book was released on 2022 with total page 785 pages. Available in PDF, EPUB and Kindle. Book excerpt: The relentless loss of biodiversity is among the greatest problems facing the world today. The third edition of this established textbook provides an updated and comprehensive overview of the essential background, concepts, and tools required to understand how genetics can be used to conservespecies, reduce threat of extinction, and manage species of ecological or commercial importance. This edition is thoroughly revised to reflect the major contribution of genomics to conservation of populations and species. It includes two new chapters: "Genetic Monitoring" and a final "ConservationGenetics in Practice" chapter that addresses the role of science and policy in conservation genetics.New genomic techniques and statistical analyses are crucial tools for the conservation geneticist. This accessible and authoritative textbook provides an essential toolkit grounded in population genetics theory, coupled with basic and applied research examples from plants, animals, and microbes. Thebook examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, evolutionary response to anthropogenic change, and applications in conservation and management.Conservation and the Genomics of Populations helps demystify genetics and genomics for conservation practitioners and early career scientists, so that population genetic theory and new genomic data can help raise the bar in conserving biodiversity in the most critical 20 year period in the historyof life on Earth. It is aimed at a global market of applied population geneticists, conservation practitioners, and natural resource managers working for wildlife and habitat management agencies. It will be of particular relevance and use to upper undergraduate and graduate students taking coursesin conservation biology, conservation genetics, and wildlife management.

Application of genomics in livestock populations under selection or conservation

Author : Anupama Mukherjee
Publisher : Frontiers Media SA
ISBN 13 : 2832544207
Total Pages : 226 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Application of genomics in livestock populations under selection or conservation by : Anupama Mukherjee

Download or read book Application of genomics in livestock populations under selection or conservation written by Anupama Mukherjee and published by Frontiers Media SA. This book was released on 2024-02-06 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Conservation and the Genetics of Populations

Author : Fred W. Allendorf
Publisher : John Wiley & Sons
ISBN 13 : 0470671459
Total Pages : 636 pages
Book Rating : 4.4/5 (76 download)

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Book Synopsis Conservation and the Genetics of Populations by : Fred W. Allendorf

Download or read book Conservation and the Genetics of Populations written by Fred W. Allendorf and published by John Wiley & Sons. This book was released on 2012-12-17 with total page 636 pages. Available in PDF, EPUB and Kindle. Book excerpt: Loss of biodiversity is among the greatest problems facing the world today. Conservation and the Genetics of Populations gives a comprehensive overview of the essential background, concepts, and tools needed to understand how genetic information can be used to conserve species threatened with extinction, and to manage species of ecological or commercial importance. New molecular techniques, statistical methods, and computer programs, genetic principles, and methods are becoming increasingly useful in the conservation of biological diversity. Using a balance of data and theory, coupled with basic and applied research examples, this book examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, the interpretation of genetic data from natural populations, and how these can be applied to conservation. The book includes examples from plants, animals, and microbes in wild and captive populations. This second edition contains new chapters on Climate Change and Exploited Populations as well as new sections on genomics, genetic monitoring, emerging diseases, metagenomics, and more. One-third of the references in this edition were published after the first edition. Each of the 22 chapters and the statistical appendix have a Guest Box written by an expert in that particular topic (including James Crow, Louis Bernatchez, Loren Rieseberg, Rick Shine, and Lisette Waits). This book is essential for advanced undergraduate and graduate students of conservation genetics, natural resource management, and conservation biology, as well as professional conservation biologists working for wildlife and habitat management agencies. Additional resources for this book can be found at: www.wiley.com/go/allendorf/populations.

Plant Conservation Genetics

Author : Robert J Henry
Publisher : CRC Press
ISBN 13 : 1482293625
Total Pages : 196 pages
Book Rating : 4.4/5 (822 download)

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Book Synopsis Plant Conservation Genetics by : Robert J Henry

Download or read book Plant Conservation Genetics written by Robert J Henry and published by CRC Press. This book was released on 2006-06-21 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: A practical guide that covers both in situ and ex situ techniques for plant diversity conservation The conservation and sustainable use of plant genetic resources is of increasing importance globally. Plant Conservation Genetics addresses this issue by providing an extensive overview of this emerging area of science, exploring various pr

Human Genetics and Genomics

Author : Bruce R. Korf
Publisher : John Wiley & Sons
ISBN 13 : 1118537661
Total Pages : 280 pages
Book Rating : 4.1/5 (185 download)

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Book Synopsis Human Genetics and Genomics by : Bruce R. Korf

Download or read book Human Genetics and Genomics written by Bruce R. Korf and published by John Wiley & Sons. This book was released on 2012-11-19 with total page 280 pages. Available in PDF, EPUB and Kindle. Book excerpt: This fourth edition of the best-selling textbook, Human Genetics and Genomics, clearly explains the key principles needed by medical and health sciences students, from the basis of molecular genetics, to clinical applications used in the treatment of both rare and common conditions. A newly expanded Part 1, Basic Principles of Human Genetics, focuses on introducing the reader to key concepts such as Mendelian principles, DNA replication and gene expression. Part 2, Genetics and Genomics in Medical Practice, uses case scenarios to help you engage with current genetic practice. Now featuring full-color diagrams, Human Genetics and Genomics has been rigorously updated to reflect today’s genetics teaching, and includes updated discussion of genetic risk assessment, “single gene” disorders and therapeutics. Key learning features include: Clinical snapshots to help relate science to practice 'Hot topics' boxes that focus on the latest developments in testing, assessment and treatment 'Ethical issues' boxes to prompt further thought and discussion on the implications of genetic developments 'Sources of information' boxes to assist with the practicalities of clinical research and information provision Self-assessment review questions in each chapter Accompanied by the Wiley E-Text digital edition (included in the price of the book), Human Genetics and Genomics is also fully supported by a suite of online resources at www.korfgenetics.com, including: Factsheets on 100 genetic disorders, ideal for study and exam preparation Interactive Multiple Choice Questions (MCQs) with feedback on all answers Links to online resources for further study Figures from the book available as PowerPoint slides, ideal for teaching purposes The perfect companion to the genetics component of both problem-based learning and integrated medical courses, Human Genetics and Genomics presents the ideal balance between the bio-molecular basis of genetics and clinical cases, and provides an invaluable overview for anyone wishing to engage with this fast-moving discipline.

Genetic Management of Fragmented Animal and Plant Populations

Author : Richard Frankham
Publisher : Oxford University Press
ISBN 13 : 0198783396
Total Pages : 426 pages
Book Rating : 4.1/5 (987 download)

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Book Synopsis Genetic Management of Fragmented Animal and Plant Populations by : Richard Frankham

Download or read book Genetic Management of Fragmented Animal and Plant Populations written by Richard Frankham and published by Oxford University Press. This book was released on 2017 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.