Applied Environmental Genomics

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. 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. 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.

Acknowledgements

List of contributors

Introduction to applied environmental genomics

Acknowledgements



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 dispersal in wild animal populations: implications for wildlife management

23: Conservation prioritisation based on evolutionary distinctiveness of communities



Section F: Biosecurity and disease monitoring

24: Invasive species detection and management using genomic methods

25: Genomic identification and surveillance of infectious diseases in natural systems

26: Management of vertebrate pests using genetic control techniques

27: Perspective – The ‘E’ in RD&E and the application of genomics for environmental and biosecurity risk management



Glossary

Index