Conservation Genetics

, Volume 19, Issue 4, pp 865–878 | Cite as

Cooperative research sheds light on population structure and listing status of threatened and endangered rockfish species

  • Kelly S. Andrews
  • Krista M. Nichols
  • Anna Elz
  • Nick Tolimieri
  • Chris J. Harvey
  • Robert Pacunski
  • Dayv Lowry
  • K. Lynne Yamanaka
  • Daniel M. Tonnes
Research Article


Population genetics has increasingly become an important tool for determining appropriate taxonomic units for managing species of conservation interest. Yelloweye rockfish (Sebastes ruberrimus), canary rockfish (S. pinniger) and bocaccio (S. paucispinis) in the inland waterways of Puget Sound (PS), WA, USA were listed under the U.S. Endangered Species Act (ESA) in 2010. These listings relied heavily on evidence from other species that these populations were ‘discrete’ taxonomic units because little information was available for these species in PS. To fill this data gap, we collaborated with recreational fishing communities in PS to collect tissue samples and used population genetics analyses to determine whether samples from PS were genetically differentiated from samples collected from the outer coasts of the U.S. and Canada. Multiple analyses using restriction-site associated DNA sequencing data showed that yelloweye rockfish in PS and British Columbia, Canada were genetically different from coastal populations, while canary rockfish showed no genetic differentiation. These results support hypotheses that the genetic connectivity of rockfish populations is based on interactions between life-history characteristics and oceanographic conditions. These data also support the ESA designation status and the expansion of protected geographical boundaries for yelloweye rockfish but also suggest canary rockfish in PS are not a ‘discrete’ population and may not meet the first criterion of the ESA, as initially assumed. Collaboration among agencies and fishing communities, and cost-efficient genetic analyses provided a framework for collecting and analyzing data essential to the conservation and management of threatened and endangered species.


Endangered Species Act Population connectivity Fishing Local ecological knowledge Population genetics RAD-seq 



We thank captains J. Field, S. Kesling, M. Jamboretz, G. Krein, R. Jones, B. Rosson, C. Long, N. Kester, and T. Burlingame for their expertise in putting us on these rare fish; Puget Sound Anglers and the Kitsap Poggie Club for helping coordinate anglers for these trips, and the nearly 100 local anglers who helped collect these fish. We thank A. Hennings & J. Blaine for providing GPS coordinates of sightings of listed species from ROV surveys, K. Cooke, R. Withler and C. Gummer for logistical support in getting samples from the Department of Fisheries and Oceans, Canada, J. Harms from the Northwest Fisheries Science Center for sharing fin clip samples from coastal populations and M. Craig, J. Hyde and R. Vetter from the Southwest Fisheries Science Center for sharing fin clip samples from coastal bocaccio. Thanks to C. Do, G. Goetz, and T. Gosselin for assistance with analysis tools. We also thank the members of NOAA’s Biological Review Team who reviewed preliminary analyses of this work, and peer reviewers that provided comments previously on the five-year status review and the science presented in the proposal for the ESA delisting of canary rockfish. We also thank external reviewers and the editor for their comments. Samples were collected under ESA Section 10a permit #17062-3M. The National Oceanic & Atmospheric Administration’s National Cooperative Research Program provided funding for this research in 2014. The scientific results and conclusions, as well as any views or opinions expressed herein, are those of the authors and do not necessarily reflect the views of NOAA or the Department of Commerce.

Supplementary material

10592_2018_1060_MOESM1_ESM.xlsx (73 kb)
Supplementary material 1 (XLSX 73 KB)
10592_2018_1060_MOESM2_ESM.docx (4.9 mb)
Supplementary material 2 (DOCX 4980 KB)


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Copyright information

© The Author(s) 2018

Authors and Affiliations

  1. 1.Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationSeattleUSA
  2. 2.Washington Department of Fish and WildlifeMill CreekUSA
  3. 3.Washington Department of Fish and WildlifeOlympiaUSA
  4. 4.Fisheries and Oceans CanadaNanaimoCanada
  5. 5.Protected Resources DivisionNOAA Fisheries West Coast Regional OfficeSeattleUSA

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