Conservation Genetics

, Volume 18, Issue 5, pp 1119–1130 | Cite as

Genetic and individual assignment of tetraploid green sturgeon with SNP assay data

  • Eric C. Anderson
  • Thomas C. Ng
  • Eric D. Crandall
  • John Carlos Garza
Research Article

Abstract

Polyploid organisms pose substantial obstacles to genetic analysis, as molecular assay data are usually difficult to evaluate in a Mendelian framework. Green sturgeon (Acipenser medirostris) is a tetraploid species and is facing significant conservation challenges, including bycatch in ocean fisheries. We present here novel molecular genetic assays and analytical methodology for green sturgeon that allow discrimination of fish from the two visually indistinguishable distinct population segments (DPSs), and also provide individual-specific genetic tags. We show how the relative fluorescence intensity data from a standard quantitative PCR assay, designed for a biallelic single nucleotide polymorphism, can be grouped into “genotype categories” using standard analytical software and post-processing manipulation. We then show how these genotype category data can be used to discriminate green sturgeon from the southern DPS, which is protected under the US Endangered Species Act, and the northern DPS, which is not. We also show how these data can be used to reliably identify individual green sturgeon, and can therefore be used in capture/recapture analyses. Both types of identification are extremely accurate even when fewer than half of the assays are successfully called. We then apply these new techniques to show that proportions of the two green sturgeon DPSs are extremely different in the two major fishery areas where they are encountered as bycatch. While these assays and methods do not provide data that can be used in pedigree-based analyses, they are an important advance in the application of genetic analysis to conservation and management of polyploid organisms.

Keywords

Polyploids Population assignment Bycatch 

Notes

Acknowledgements

We are grateful to Phaedra Doukakis, Melissa Neuman, and Susan Wang (NMFS West Coast Regional Office) for engaging us in this project with the goal of identifying green sturgeon bycatch, Toz Soto (Karuk Tribe) and Bill Poytress (US Fish and Wildlife Service) for providing samples of juvenile green sturgeon from the Klamath and Sacramento rivers, respectively, Vanessa Apkenas and Cassie Columbus (Southwest Fisheries Science Center) for assistance with laboratory analyses. Joshua Strange (Stillwater Sciences) and Stephen Kullman (Wiyot Tribe) provided samples from fish encountered in the Eel River, and observations regarding their reproductive status, and staff from the NMFS West Coast Fisheries Observer Program provided samples from fishery bycatch. Steven Lindley, Ethan Mora, and two anonymous referees provided helpful comments on the manuscript.

Supplementary material

10592_2017_963_MOESM1_ESM.pdf (4.5 mb)
Supplementary material 1 (Pdf 4628 kb)
10592_2017_963_MOESM2_ESM.csv (39 kb)
Supplementary material 2 csv (39 kb)
10592_2017_963_MOESM3_ESM.html (836 kb)
Supplementary material 3 (html 836 kb)

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Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2017

Authors and Affiliations

  1. 1.Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries Service and University of California, Santa CruzSanta CruzUSA
  2. 2.Department of Biomolecular EngineeringUniversity of California and Southwest Fisheries Science Center, National Marine Fisheries ServiceSanta CruzUSA
  3. 3.University of California and Southwest Fisheries Science Center, National Marine Fisheries ServiceSanta CruzUSA
  4. 4.Division of Science and Environmental PolicyCalifornia State UniversitySeasideUSA

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