BOEM 2017-066 Genomics of Arctic

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BOEM 2017-066 Genomics of Arctic OCS Study BOEM 2017 -066 Genomics of Arctic Cod US Department of the Interior Bureau of Ocean Energy Management Alaska OCS Region OCS Study BOEM 2017-066 Genomics of Arctic Cod 30 September 2017 Authors Robert E. Wilson, George K. Sage, Sarah A. Sonsthagen, Meg C. Gravley, Damian M. Menning and Sandra L. Talbot Prepared under BOEM Award M14PG00008 By U. S. Geological Survey, Alaska Science Center 4210 University Drive Anchorage, AK 99508 USA US Department of the Interior Bureau of Ocean Energy Management Alaska OCS Region DISCLAIMER This study was funded, in part, by the US Department of the Interior, Bureau of Ocean Energy Management (BOEM), Environmental Studies Program, Washington, DC, through Agreement Number M14PG00008 with the U.S. Geological Survey (USGS). The findings and conclusions in this article are those of the authors and do not necessarily represent the views of the Bureau of Oceans Energy and Management. REPORT AVAILABILITY To download a PDF file of this report, go to the U.S. Department of the Interior, Bureau of Ocean Energy Management Data and Information Systems webpage (https://marinecadastre.gov/espis/#) and search on 2017-066. CITATION Wilson, R.E, G.K. Sage, S.A. Sonsthagen, M.C. Gravley, D.M. Menning, and S.L. Talbot. 2017. Genomics of Arctic Cod. Anchorage, AK: US Dept. of the Interior, Bureau of Ocean Energy Management, Alaska OCS Region. OCS Study BOEM 2017-066. 92pp. ACKNOWLEDGEMENTS We thank the numerous staff at U.S. Geological Survey for providing samples and for laboratory and graphical assistance. The BOEM Alaska OCS Region contributed to this document. We thank Brenda Norcross (University of Alaska Fairbanks), Vanessa von Biela (USGS), Andrew Majewski (Fisheries and Ocean Canada), Tony Gharrett (University of Alaska Fairbanks), Noel Sme (University of Alaska Fairbanks), Lorena Edenfield (University of Alaska Fairbanks), and John Nelson (University of Victoria, Canada), University of Washington Burke Museum, Institute of Marine Science at the University of Alaska, Bureau of Ocean Energy Management, and Fisheries and Ocean Canada for providing samples. Gabriel DeGange (USGS) provided laboratory support. We also thank Han Ming Gan (Deakin University) for mitogenome assembly support. This report has been reviewed and approved for publication consistent with USGS Fundamental Science Practices. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Table of Contents List of Figures ................................................................................................................................................ iii List of Tables ................................................................................................................................................ iv List of Supplementary Tables....................................................................................................................... iv List of Abbrevations Acronyms and Symbols ............................................................................................... vi Executive Summary ...................................................................................................................................... 1 1 Introduction ............................................................................................................................................... 2 1.1 Objectives ........................................................................................................................................... 3 1.2 Notes on Terminology ......................................................................................................................... 3 1.3 Notes on Taxonomy ............................................................................................................................ 5 1.4 Study Chronology ................................................................................................................................ 5 1.5 References .......................................................................................................................................... 5 2 Population Genetic Structure and Diversity of Arctic Cod ........................................................................ 8 2.1 Introduction ......................................................................................................................................... 8 2.2 Methods: Population structure within Chukchi and Beaufort Sea ....................................................... 9 2.2.1 Sample Collection and DNA Extraction ....................................................................................... 9 2.2.2 Laboratory Techniques – DNA Sequencing and Microsatellite Genotyping ................................ 9 2.2.3 Genetic Diversity and Population Subdivision – Among Seas .................................................. 10 2.3 Methods: Comparative Phylogeography – Mitogenome ................................................................... 11 2.3.1 Sample Collection and DNA Extraction ..................................................................................... 11 2.3.2 Mitogenome Sequencing and Annotations ................................................................................ 11 2.3.3 Mitogenome Assembly and Verification ..................................................................................... 11 2.3.4 Genetic Diversity and Population Structure ............................................................................... 12 2.3.5 Demographic History, Tests of Neutrality and Analyses of Selection on Mitochondrial DNA ... 12 2.4 Methods: ddRAD Sequencing – Species Identification .................................................................... 14 2.4.1 Sample Collection and DNA Extraction ..................................................................................... 14 2.4.2 ddRAD-seq Library Preparation ................................................................................................. 14 2.4.3 Bioinformatics ............................................................................................................................. 14 2.4.4 Level of Divergence ................................................................................................................... 15 i 2.5 Results: Population Structure within Chukchi and Beaufort Seas .................................................... 15 2.5.1 Effects of Sampling Time Periods .............................................................................................. 15 2.5.3 Genetic Diversity and Population Subdivision – Among Seas .................................................. 15 2.6 Results: Comparative Phylogeography within Alaskan waters ......................................................... 16 2.6.1 Mitogenome Assembly and Mapping ......................................................................................... 16 2.6.2 Genetic Diversity and Population Divergence ........................................................................... 16 2.6.3 Neutrality Test ............................................................................................................................ 17 2.6.4 McDonald–Kreitman Tests ......................................................................................................... 17 2.6.5 Detecting Selection Using Codon Models.................................................................................. 17 2.6.6 Radical Changes in Physiological Properties ............................................................................ 17 2.7 Results: ddRAD sequencing – Species Identification ....................................................................... 18 2.7.1 Loci Recovered .......................................................................................................................... 18 2.7.2 Genetic divergence between species ........................................................................................ 18 2.8 Discussion ......................................................................................................................................... 18 2.8.1 Population Genetic (Stock) Structure and Diversity ................................................................... 18 2.8.2 Selection on the Mitogenome .................................................................................................... 19 2.8.3 Species Identification and Hybridization .................................................................................... 20 2.9 References ........................................................................................................................................ 21 3 A Transcriptome Resource for the Arctic Cod ........................................................................................ 52 3.1 Abstract ............................................................................................................................................. 52 3.2 Introduction ....................................................................................................................................... 52 3.3 Methods ............................................................................................................................................ 52 3.3.1 Sample Collection and Sequencing ..........................................................................................
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