Genetic and individual assignment of tetraploid green sturgeon with SNP assay data
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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.
KeywordsPolyploids Population assignment Bycatch
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.
- Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm (with discussion). J R Stat Soc Series B 39:1–38Google Scholar
- Havelka M, Kaspar V, Hulák M, Flajshans M (2011) Sturgeon genetics and cytogenetics: a review related to ploidy levels and interspecific hybridization. Folia Zoologica 60:93–103Google Scholar
- NMFS (2015) Southern distinct population segment of the North American green sturgeon (Acipenser medirostris) 5-year review: summary and evaluation. Tech. rep., National Marine Fisheries Service, West Coast Region, Long Beach, CA, https://swfsc.noaa.gov/publications/FED/00630.pdf
- Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7(e37):135Google Scholar
- R Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, http://www.R-project.org/