Conservation genomics of natural and managed populations: building a conceptual and practical framework

Laura Marilyn Benestan; Anne-Laure Ferchaud; Paul A Hohenlohe; Brittany A Garner; Gavin J P Naylor; Iliana Brigitta Baums; Michael K Schwartz; Joanna L Kelley; Gordon Luikart

doi:10.1111/mec.13647

Conservation genomics of natural and managed populations: building a conceptual and practical framework

Mol Ecol. 2016 Jul;25(13):2967-77. doi: 10.1111/mec.13647. Epub 2016 May 18.

Authors

Affiliations

¹ Departement de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6, Canada.
² Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, 83844, USA.
³ Flathead Lake Biological Station, Fish and Wildlife Genomic Group, Division of Biological Science, University of Montana, Missoula, MT, 59812, USA.
⁴ Wildlife Program, Fish and Wildlife Genomic Group, College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA.
⁵ Hollings Marine Lab, College of Charleston and Medical, University of South Carolina, 331 Fort Johnson Rd., Charleston, SC, 29412, USA.
⁶ Department of Biology, Pennsylvania State University, 208 Mueller Lab, University Park, PA, 1680, USA.
⁷ USDA Forest Service, National Genomics Center for Wildlife and Fish Conservation, 800 E. Beckwith Ave., Missoula, MT, 59801, USA.
⁸ School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA.

PMID: 27086132
DOI: 10.1111/mec.13647

Abstract

The boom of massive parallel sequencing (MPS) technology and its applications in conservation of natural and managed populations brings new opportunities and challenges to meet the scientific questions that can be addressed. Genomic conservation offers a wide range of approaches and analytical techniques, with their respective strengths and weaknesses that rely on several implicit assumptions. However, finding the most suitable approaches and analysis regarding our scientific question are often difficult and time-consuming. To address this gap, a recent workshop entitled 'ConGen 2015' was held at Montana University in order to bring together the knowledge accumulated in this field and to provide training in conceptual and practical aspects of data analysis applied to the field of conservation and evolutionary genomics. Here, we summarize the expertise yield by each instructor that has led us to consider the importance of keeping in mind the scientific question from sampling to management practices along with the selection of appropriate genomics tools and bioinformatics challenges.

Keywords: SNPs discovery and filtering; conservation genomics; effective population size; genetic population structure; local adaptation; massively parallel sequencing.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Biological Evolution
Congresses as Topic
Conservation of Natural Resources*
Genetics, Population / methods*
Genomics / methods*
High-Throughput Nucleotide Sequencing
Research Design
Sequence Analysis, DNA