Wildlife Population Genomics: Applications and Approaches
Population genomics provides a powerful and growing set of approaches for wildlife biology, revealing new insights into demographic history, population structure, adaptation, and the consequences of genetic diversity. Given the multiple threats faced by g
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Abstract Population genomics provides a powerful and growing set of approaches for wildlife biology, revealing new insights into demographic history, population structure, adaptation, and the consequences of genetic diversity. Given the multiple threats faced by global biodiversity, it is critical for researchers to advance efforts to manage and conserve wildlife populations. In this chapter we provide an overview of the research questions that can be addressed in wildlife population genomics, applications to specific conservation and management issues, and the variety of technical methods at all stages from sampling to sequencing and data analysis. Wildlife species, here defined as vertebrate species of specific conservation or management concern, present unique challenges and opportunities. These include not only the necessity of using poor-quality samples from non-invasive or archival collections, but also the availability of genomic reference data from closely related domestic species. We highlight a number of case studies in particular taxa that illustrate recent progress in wildlife population genomics, including how population genomics approaches have been applied to date, and also how the field can continue to connect research to urgent conservation actions in wildlife populations. We also discuss prospects for applications of population epigenomics, transcriptomics, metagenomics, and eDNA approaches in wildlife.
Soraia Barbosa and Sarah A. Hendricks contributed equally to this work. S. Barbosa · S. A. Hendricks · P. A. Hohenlohe (*) Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA e-mail: [email protected] W. C. Funk Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA O. P. Rajora Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada Paul Hohenlohe and Om P. Rajora (eds.), Population Genomics: Wildlife, Population Genomics [Om P. Rajora (Editor-in-Chief)], https://doi.org/10.1007/13836_2020_83, © Springer Nature Switzerland AG 2020
S. Barbosa et al.
Keywords Adaptive potential · Conservation units · Effective population size · Genetic rescue · Inbreeding depression · Population epigenomics · Population genomics · Population transcriptomics · Whole-genome sequencing · Wildlife
1 Introduction Wildlife species face a number of threats, such as habitat loss and fragmentation, direct mortality from exploitation, invasive species, pollution, and climate change. The genomic revolution has democratized the field of population genomics, allowing high-throughput sequencing to be applied in nearly any organism, including natural populations of rare or difficult-to-study wildlife species (Luikart et al. 2019; Rajora 2019). Wildlife biology can benefit from population genomics in several ways: first, by improving our basic understanding of wildlife species and populations, including their evolutionary history and relationships, adaptati
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