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DNA is the essence of life and the original 'big data'. New technologies are allowing scientists to access and make sense of this information like never before, and they are using it to solve the world's greatest environmental challenges.
Applied Environmental Genomics synthesises the latest and most exciting uses of genomic technologies for environmental science and management. With an emphasis on diversity of applications and real-world demonstrations, leading researchers have contributed detailed chapters on innovative approaches to obtaining critical management-relevant information about the natural world. Examples of this include DNA barcoding surveys and estimating biodiversity using environmental DNA (eDNA); estimating population abundance, health, and dispersal; detecting invasive species and infectious diseases; or helping to make tough decisions on what species to prioritise in conservation efforts. These chapters are complemented by perspective sections written by environmental managers who describe their experiences using genomics to support evidence-based decisions.
Ideal for students, researchers and professionals working in natural resource management and policy, Applied Environmental Genomics is a comprehensive introduction to a fast-moving field that is transforming the practice of environmental management, with profound relevance to industry, government and the public.
Section A: Biodiversity 1. Design considerations for eDNA metabarcoding surveys 2. Measuring biodiversity with eDNA metabarcoding 3. Perspective - eDNA and metagenomics: a story of a disruptive technology for biodiversity monitoring 4. Revealing animal diet and food webs through DNA metabarcoding 5. Approaching ecological questions using DNA barcodes Section B: Life history and population biology 6. Lifespan estimation from genomic analysis 7. Development of epigenetic clocks 8. Molecular sex identification for applications in conservation, industry and veterinary medicine 9. Perspective - Whole genome assemblies, devils and disease 10. Genetic-based inventories of wildlife abundance 11. The practical magic of close-kin mark-recapture 12. Perspective - Genomics and bear management 13. How can we use genomics to predict and improve population viability? Section C: Adaptation and change 14. Adaptive responses to the environment and environmental change 15. Perspective - The power of genomics for guiding reintroductions 16. Palaeo- and museo-genomics: perspectives on modern species 17. Perspective - Genomics and the prioritisation of taxa and populations for conservation Section D: Environmental molecular physiology 18. Applied epigenomics in a rapidly changing world 19. DNA-based microbial bioindication of environmental state 20. Perspective - The promise of ecotoxicogenomics for assessing aquatic health Section E: Spatial genomics 21. Unravelling plant-pollinator interactions through pollen DNA analysis 22. Genomic approaches to study
Acknowledgements
List of contributors
Introduction to applied environmental genomics
Section A: Biodiversity
1. Design considerations for eDNA metabarcoding surveys / William Bernard Perry, Kirthana Pillay, Paul George, Georgina Brennan, Abigail Lowe, Laura Jones, Luke Holman, Tom Gibson, Natasha de Vere and Simon Creer
2. Measuring biodiversity with eDNA metabarcoding / Antton Alberdi, Iñaki Odriozola, Raphael Eisenhofer and Ostaizka Aizpurua
3. Perspective – eDNA and metagenomics: a story of a disruptive technology for biodiversity monitoring / Peter Gilchrist
4. Revealing animal diet and food webs through DNA metabarcoding / Bruce E. Deagle, Johan Pansu, Julie McInnes and Michael Traugott
5. Approaching ecological questions using DNA barcodes / Michael Stat and Katrina West
Section B: Life history and population biology
6. Lifespan estimation from genomic analysis / Benjamin Mayne and Christopher Faulk
7. Development of epigenetic clocks / Simon Jarman, Benjamin Mayne and Tom Little
8. Molecular sex identification for applications in conservation, industry and veterinary medicine / Clare E. Holleley, Sarah L. Whiteley, Floriaan Devloo-Delva, Andreas Bachler, Joshua Llinas and Arthur Georges
9. Perspective – Whole genome assemblies, devils and disease / Carolyn J. Hogg, Emma Peel, Yuanyuan Cheng and Katherine Belov
10. Genetic-based inventories of wildlife abundance / Garth Mowat, Joseph D. Clark, Alexander Kopatz, Clayton Lamb and Anita J. Norman
11. The practical magic of close-kin mark-recapture / Mark V. Bravington and Emma L. Carroll
12. Perspective – Genomics and bear management / Michael Proctor
13. How can we use genomics to predict and improve population viability? / Fred W. Allendorf, Nils Ryman and Marty Kardos
Section C: Adaptation and change
14. Adaptive responses to the environment and environmental change / Orly Razgour, Jesse R. Lasky, Thibaut Capblancq and Brenna R. Forester
15. Perspective – The power of genomics for guiding reintroductions / Helen Taylor
16. Palaeo- and museo-genomics: perspectives on modern species / Alicia Grealy, Lauren C. White, Emily Roycroft and Jeremy J. Austin
17. Perspective – Genomics and the prioritisation of taxa and populations for conservation / Catherine Darst
Section D: Environmental molecular physiology
18. Applied epigenomics in a rapidly changing world / M. Teresa Boquete, Sabrina M. McNew and Christina L. Richards
19. DNA-based microbial bioindication of environmental state / Jodie van de Kamp, Ángel Borja and Andrew Bissett
20. Perspective – The promise of ecotoxicogenomics for assessing aquatic health / Alvine C. Mehinto
Section E: Spatial genomics
21. Unravelling plant-pollinator interactions through pollen DNA analysis / Liz Milla and Francisco Encinas-Viso
22. Genomic approaches to study dispersal in wild animal populations: implications for wildlife management / Liz Milla and Francisco Encinas-Viso
23. Conservation prioritisation based on evolutionary distinctiveness of communities / Renee A. Catullo, Christiana McDonald-Spicer and Craig C. Moritz
Section F: Biosecurity and disease monitoring
24. Invasive species detection and management using genomic methods / Katarina C. Stuart, Andrew P. Woolnough and Lee A. Rollins
25. Genomic identification and surveillance of infectious diseases in natural systems / Jocelyn P. Colella, Stephen E. Greiman, Susan Kutz, Holly L. Lutz and Joseph A. Cook
26. Management of vertebrate pests using genetic control techniques / Anna C. Clark, Alana Alexander, Jackson Champer, Rey Edison, Mandira Katuwal and Neil J. Gemmell
27. Perspective – The ‘E’ in RD&E and the application of genomics for environmental and biosecurity risk management / Geoff Grossel
Glossary
Index
Oliver F. Berry is the Director of the Environomics Future Science Platform at CSIRO. His career has featured a diversity of genomics techniques from population genomics to environmental DNA, and he has worked in application domains from conservation biology to invasive species management.
Clare E. Holleley is a Principal Research Scientist at National Research Collections Australia (CSIRO). She is an expert in vertebrate sex determination and an innovator in the field of historical epigenomics. Her work characterises rates of evolutionary change in ecological, reproductive and disease research.
Simon N. Jarman is Professor of Environmental Genomics at Curtin University. He is an expert in analysis of animal age and life cycles with genomic methods, and environmental DNA analyses of species diversity.
