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Conservation Genetics in the Age of Genomics

Conservation Genetics in the Age of Genomics

George Amato
Oliver Ryder
Howard Rosenbaum
Rob DeSalle
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  • Book Info
    Conservation Genetics in the Age of Genomics
    Book Description:

    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.

    eISBN: 978-0-231-50231-3
    Subjects: Ecology & Evolutionary Biology, Environmental Science, Biological Sciences

Table of Contents

  1. Front Matter
    (pp. i-iv)
  2. Table of Contents
    (pp. v-vi)
  3. List of Illustrations
    (pp. vii-vii)
  4. List of Tables
    (pp. viii-viii)
  5. FOREWORD: The Continuity of Genomes and Genetic Resources for the New Century
    (pp. ix-x)
    Sydney Brenner

    Genomics promises to solve previously intractable problems in the biology of complex organisms, and in this context I believe genomics will be of high utility to conservation biology. Two important components of modern genomics can enhance the expansion of modern biology to address these important biological problems. The first concerns a new paradigm for studying organisms at a variety of levels gleaned from genomic studies. This paradigm uses the evolutionary process and evolutionary principles. The second concerns the potential availability of genetic resources from as broad an array of organisms as possible. Both of these components are relevant to conservation...

    (pp. xi-xii)
    (pp. xiii-xvi)
    George Amato, Oliver Ryder, Howard Rosenbaum and Rob DeSalle

    This collection of essays is the result of two meetings held on opposite coasts of the United States, in San Diego and New York. Both symposia addressed the role of expanding technology in the conservation of endangered species, and both were sponsored by preeminent institutions with a focus on biodiversity and wildlife conservation. The San Diego meeting was sponsored by the San Diego Zoological Park, and the New York meeting was sponsored by the Wildlife Conservation Society and the American Museum of Natural History Center for Biodiversity and Conservation. During the two meetings, speakers discussed the role of expanding genomic...

  8. Part I. Perspectives on the Union of Conservation and Genetics

    • 1 The Expansion of Conservation Genetics
      (pp. 3-24)
      Rob DeSalle and George Amato

      Conservation biology has been accurately described as a crisis discipline. Much like the human disease crisis disciplines of HIV biology and cancer biology, conservation biology requires an immediate understanding of the patterns and processes that make it such a critical subject. The urgency of the crises that are the subject of conservation biology are manifest in the large number of species facing imminent extinction. In fact, the last two centuries of human activity have been described as one of the most severe periods of mass extinction of all time, challenging even the most extreme periods of extinction in the long...

    • 2 Conservation Genetics and the Extinction Crisis: A Perspective
      (pp. 25-33)
      William Conway

      Max Frisch (1957) observed, “Technology is a way of organizing the world so that man does not have to experience it.” Nevertheless, these are heady times for genomics. The significance of the sequencing of the human genome has been compared with our first landing on the moon. New computational power has brought genetic insights to our perception of species survival (Lacy, 1993). Embryo transfer, cloning, artificial insemination, and a host of other techniques offer a new level of control of animal reproduction. Serendipitously, all this is taking place at a time when wildlife populations are facing a desperate extinction crisis....

    • 3 Moving Toward a More Integrated Approach
      (pp. 34-38)
      George Amato

      The debate over reductionism versus holism has been ubiquitous in the different disciplines within biology (Hagen, 1989). This debate dominated my intellectual environment while I was being trained as a geneticist and conservation biologist in the early stages of genetic studies of populations. In the 1970s we explored population biology and genetics using the “cutting-edge” technologies of isoelectric focusing. We quickly leapt to Southern blotting as we sought to understand evolutionary processes by examining and characterizing genetic variation, admittedly a bit indirectly at times.

      As a contrast, consider the university where I spent most of my formative years: Yale University....

  9. Part II. Conservation Genetics in Action:: Assessing the Level and Quality of Genetic Resources in Endangered Species

    • 4 Neutral, Detrimental, and Adaptive Variation in Conservation Genetics
      (pp. 41-57)
      Philip W. Hedrick

      Because of the new molecular genetic information from various genome projects, new applications and insights for genetic studies in endangered species are being developed. Neutral variants are generally used for conservation applications and for estimating evolutionary parameters, and with highly variable loci, greater availability of markers, or extensive sequence data, these approaches should become much more informative. Detrimental and adaptive variations are also important in conservation genetics, but identification and characterization of such variations are more difficult. Neutral variants might be used to identify adaptive variants, but the overlay of different mutational processes and selective regimes suggests that great caution...

    • 5 Stopping Evolution: Genetic Management of Captive Populations
      (pp. 58-81)
      Robert C. Lacy

      We need to conserve the diversity of the natural world at multiple levels. Biodiversity conservation is most often discussed in terms of species loss, because the loss of unique evolutionary lineages is irreversible. Below the species level, we are also concerned with the stability and sustainability of populations within species and with the diversity of genes within populations. Population and gene diversity often have value to us directly, and they are also critical to the persistence of the species they make up (Bijlsma et al., 2000; Frankham, 1995; Frankham et al., 1999; Lacy, 1997; Saccheri et al., 1998; Taylor et...

    • 6 The Emerging Theme of Ocean Neighborhoods in Marine Conservation
      (pp. 82-95)
      Stephen R. Palumbi

      The oceans evoke a sense of mystery and vastness that pervades our literature and colors our perception of the nature of marine life. Deep beneath the ocean surface roils a dangerous ecology that is portrayed to be more exotic and more predatory than the mostly tamed ecosystems on land. With effort and technology we can breach the surface and dive down to observe, catalogue and understand marine life, but many crucial aspects of it remain hidden or obscure. In this obscurity lies much of the charm of the sea, but in it also lies a great deal of danger because...

    • 7 Genetic Data and the Interpretation of Restoration Priorities of the Cicindela dorsalis Say Complex (Coleoptera: Carabidae): The Components of Conservation Genetics Revisited
      (pp. 96-105)
      Paul Z. Goldstein

      Known historically to have occurred “in great swarms” on coastal beaches from Massachusetts to Chesapeake Bay (Leng, 1902:161), the northeastern beach tiger beetle Cicindela d. dorsalis, one of four named subspecies, all but disappeared from its recorded range in the latter half of the twentieth century. Since the recognition of its decline in the early 1970s (Stamatov, 1972), the animal has received attention from biologists and conservationists as an important flagship species for issues in invertebrate conservation, beach stewardship, and, most recently, conservation genetics. Knisley et al. (1987) illustrated the precipitous decline of collection records of this insect, which appears...

    • 8 Range Collapse, Population Loss, and the Erosion of Global Genetic Resources
      (pp. 106-112)
      James P. Gibbs

      Much of the current scientific and public concern over the extinction crisis centers on loss of species, and rightly so: Extinction of each species corresponds to the loss of all genetic variation that uniquely characterized it. This “pruning of the tree of life” is occurring at an alarming rate, with global extinction rates estimated at 1,000 to 10,000 times higher than at any time in the last 65 million years (Lawton and May, 1995). Because so much of aggregate genetic diversity is lodged in the branches rather than the twigs of the tree of life, the tree of life may...

  10. Part III. Saving Genetic Resources

    • 9 Biodiversity, Conservation, and Genetic Resources in Modern Museum and Herbarium Collections
      (pp. 115-123)
      Robert Hanner, Angélique Corthals and Rob DeSalle

      The biodiversity that exists today is the result of 3.5 billion years of evolution. Its preservation is of critical importance for many reasons, including the intrinsic value of functional ecosystems, species, and, ultimately, genes. The conservation of biological diversity is one of the most critical problems of our time. Unfortunately, our window of opportunity for sampling and studying this diversity is closing as habitats and the organisms they contain are lost to extinction at an ever-increasing rate. Much work lies ahead in simply documenting the existence of the world’s remaining unknown species, as perhaps less than 10 percent of all...

    • 10 Banking of Genetic Resources: The Frozen Zoo at the San Diego Zoo
      (pp. 124-130)
      Leona G. Chemnick, Marlys L. Houck and Oliver A. Ryder

      It is a testimony to the rapid advances in the field of genetics that the banking efforts for genetic samples envisioned more than thirty years ago largely anticipated the need for germplasm resources. In the intervening years, the importance of saving biomaterials in a form that can be propagated has not diminished, and the value of saving samples of DNA as resources for studying genome organization, genome evolution, and the molecular basis for adaptation has been seen as a worthwhile goal in and of itself (Ryder et al., 2000).

      The importance of collecting and providing access to biological samples from...

    • 11 The Role of Cryopreserved Cell and Tissue Collections for the Study of Biodiversity and Its Conservation
      (pp. 131-140)
      Vitaly Volobouev

      The Rio de Janeiro Convention on Biodiversity (1992) was the first and most complete document substantiating the importance of biodiversity conservation on a global scale, presenting an integrated program on the study, protection, and use of species diversity. This initiative was taken up and developed in Systematics Agenda 2000 (1994) (hereafter SA 2000), an ambitious program of research with the aim of answering four major questions over the next twenty-five years: What are the earth’s species? Where do they occur? What properties do they have? How are they related? This document made evident the fact that that we can realize...

    • 12 The Silent Biodiversity Crisis: Loss of Genetic Resource Collections
      (pp. 141-159)
      Deborah L. Rogers, Calvin O. Qualset, Patrick E. McGuire and Oliver A. Ryder

      For many centuries biological materials have been collected to meet human needs—originally for sustenance and utility but later to satisfy scientific curiosity. Later collections of living plants, animals, and microbes were classified, curated, conserved, and shared in parallel with public and private collections of human artifacts and natural history materials. Biological resource collections may be viewed as genetic resource collections when they encompass genetically definable material. Genetic resource collections provide a basis for contributing to the conservation of species and the diversity within species. It is our goal to provide an understanding of genetic resource collections and their place...

    • 13 Who Owns the Ark, and Why Does It Matter?
      (pp. 160-166)
      Cathi Lehn, Rebecah Bryning, Rob DeSalle and Richard Cahoon

      Animal diversity from around the globe can be found in institutional collections accredited by the Association of Zoos and Aquariums (AZA). As stewards of this diversity we hold a responsibility to care for and exhibit these animals to the best of our knowledge and ability. Therefore, while they are in our care we also have a responsibility to learn as much as we possibly can from our animals so that they may be best cared for in captivity and conserved in their natural habitats. We learn about our animals from careful scientific study, which may include behavioral observations but also...

  11. Part IV. Genomic Technology Meets Conservation Biology

    • 14 Conservomics? The Role of Genomics in Conservation Biology
      (pp. 169-178)
      George Amato and Rob DeSalle

      The suffixes “-omics” and “-genomics” have been added to a wide range of root words in the past decade to reflect the impact genomics has had on these areas of biological research. A good example of this suffix addition is sociogenomics (Robinson, 1999, 2002; Robinson et al., 2005), the study of social behavior as illuminated by genomic approaches. This chapter addresses whether we need to add the suffix to conservation biology. Specifically, we examine the genomic technologies that are most pertinent to conservation biology and then assess which technologies will have the biggest impacts on conservation of biological species.


    • 15 Genomics and Conservation Genetics
      (pp. 179-186)
      Judith A. Blake

      The Human Genome Project was launched with the ultimate goal of obtaining the complete sequence of the human genome. Along the way, this initiative has accelerated the scientific endeavor in novel and exciting ways. As would be anticipated from such a well-funded and compelling endeavor, the developments and results of this work have influenced many scientific fields, including conservation genetics. Of course, advances in technology were expected and essential. Scientific fields from biochemistry to biomedicine to computer science and engineering devoted resources to the development of informatics and analysis systems to maintain, manipulate, and interpret the flood of genome information....

    • 16 Crop Transgenes in Natural Populations
      (pp. 187-198)
      Norman C. Ellstrand

      Public discussion of concerns surrounding the products of crop biotechnology has increased steadily over the past few years. One of the most frequently cited scientifically based concerns is that hybridization between engineered crops and wild plants may permit transgenes to escape into the environment (Ellstrand, 2003; Ellstrand and Hoffman, 1990; Hancock et al., 1996; Snow and Moran-Palma, 1997). The basis for this concern is that once transgenes move into unmanaged populations, they have the opportunity to multiply and spread via sexual reproduction. If the transgenes have unintended, unwanted effects in the wild, they may be difficult or impossible to contain....

    • 17 The Role of Assisted Reproduction in Animal Conservation
      (pp. 199-203)
      Anne McLaren

      In the 1960s and 1970s, the exponential increase in world population at last penetrated social consciousness. The regulation of human fertility, the prevention of unwanted pregnancies, became a major target of scientific funding bodies. In the 1980s and 1990s, however, social consciousness tended to shift away from the world population problem and toward problems of the environment, sustainable development, and biodiversity. At the same time, the motivation for research of human reproduction shifted away from the regulation of fertility toward the alleviation of infertility. Louise Brown, born in 1978, was the first baby conceived by in vitro fertilization (IVF) and...

    • 18 Conservation and Cloning: The Challenges
      (pp. 204-210)
      Ian Wilmut and Lesley Paterson

      The birth of Dolly the cloned sheep created many new opportunities in medicine, biology, and research, many of which are discussed elsewhere. There has also been a great deal of discussion about the use of cloning techniques to create copies of endangered or even extinct species. In order to consider this suggestion, we will first describe briefly the method of nuclear transfer and summarize the achievements and limitations of the present procedures. The resources and techniques needed if cloning is to be used in conservation will become apparent from these descriptions.

      Cloning is the technique of transferring a nucleus from...

  12. Part V. Policy, Law, and Philosophy of Conservation Biology in the Age of Genomics

    • 19 Can Our Laws Accommodate the New Conservation Genetics?
      (pp. 213-223)
      Gerald J. Flattmann Jr., Barbara A. Ruskin and Nicholas Vogt

      The importance of genomics and its central role in the future of biotechnology is widely recognized. Some have gone so far as to call genomics the world’s third technology revolution, after the industrial and information revolutions.¹ As discussed in detail during the symposium “Conservation Genetics in the Age of Genomics,” these new genetic technologies may enable society to recoup some of the losses suffered as a consequence of the severe depletion of the world’s ecosystems and modern agricultural practices. They could even allow conservation biologists to clone endangered or extinct species from somatic cells, such as skin cells, in the...

    • 20 The Import of Uncertainty
      (pp. 224-234)
      Sandra D. Mitchell

      As new technologies develop, new questions for ethics and social policy are generated. As our understanding of the consequences of human action changes, we need to revise our view on how to implement the values we hold.

      What is most worrying about the present discourse is the near exclusion of an open scientific debate with clearly stated arguments. The arguments are highly emotional and fed by motives which are far removed from the actual issues on biotechnology. Diverse organizations use the debate for increasing their political influence without any useful result for the population. A democratic process functioning in an...

  13. Further Reading
    (pp. 235-236)
  14. List of Contributors
    (pp. 237-238)
  15. Index
    (pp. 239-248)