Applied Environmental Genomics

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

Biography

Oliver F. Berry is 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.