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Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, McGowen MR, Olsen MT, Van Cise AM. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. J Hered 2016; 107:481-95. [PMID: 27511190 DOI: 10.1093/jhered/esw044] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022] Open
Abstract
The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.
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Affiliation(s)
- Kristina M Cammen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise).
| | - Kimberly R Andrews
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emma L Carroll
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Andrew D Foote
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Emily Humble
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Jane I Khudyakov
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Marie Louis
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Michael R McGowen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Morten Tange Olsen
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
| | - Amy M Van Cise
- From the School of Marine Sciences, University of Maine, Orono, ME 04469 (Cammen); Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844-1136 (Andrews); Scottish Oceans Institute, University of St Andrews, East Sands, St Andrews, Fife KY16 8LB, UK (Carroll and Louis); Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, Bern CH-3012, Switzerland (Foote); Department of Animal Behaviour, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany (Humble); British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 OET, UK (Humble); Department of Biology, Sonoma State University, Rohnert Park, CA 94928 (Khudyakov); School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK (Mcgowen); Evolutionary Genomics Section, Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen K, Denmark (Olsen); and Scripps Institution of Oceanography, University of California San Diego, 8622 Kennel Way, La Jolla, CA 92037 (Van Cise)
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