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

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.

多倍体生物给遗传分析带来了显著阻碍，因其分子检测数据通常难以在孟德尔遗传框架下开展评估解读。绿鲟（Acipenser medirostris）是一种四倍体物种，正面临诸多严峻的保护挑战，其中包括海洋渔业的兼捕问题。本研究针对绿鲟开发了全新的分子遗传检测方法与分析流程，可区分两种外观无法分辨的显著种群单元（distinct population segments, DPSs），同时还能提供个体专属的遗传标记。本研究证实，针对双等位单核苷酸多态性设计的标准化定量PCR检测所产出的相对荧光强度数据，可借助标准分析软件与后续处理操作被归类为若干“基因型类别”。随后我们证实，此类基因型类别数据可用于区分绿鲟的南部种群单元与北部种群单元：前者受《美国濒危物种法案》保护，后者则未获该法案保护。此外，此类数据还可用于精准识别个体绿鲟，因此可应用于标记重捕分析。即便仅成功完成不足半数的检测时，两类识别仍具备极强的准确性。本研究将此类新技术应用于实际样本后发现，在两处主要的兼捕渔业区域中，绿鲟两个种群单元的占比存在极大差异。尽管此类检测方法无法提供可用于谱系分析的遗传数据，但它们为多倍体生物的遗传分析应用于保护与管理领域带来了重要进展。