Yu Lei, Stachowicz John J, DuBois Katie, Reusch Thorsten B H
Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany.
Center for Population Biology, University of California, Davis, California, USA.
Mol Ecol Resour. 2023 Apr;23(3):592-600. doi: 10.1111/1755-0998.13736. Epub 2022 Nov 23.
Clonal reproduction, the formation of nearly identical individuals via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi and animals. To detect clonal genetic structure, genetic similarity indices based on shared alleles are widely used, such as the Jaccard index, or identity by state. Here we propose a new pairwise genetic similarity index, the SH index, based on segregating genetic marker loci (typically single nucleotide polymorphisms) that are identically heterozygous for pairs of samples (N ). To test our method, we analyse two old seagrass clones (Posidonia australis, estimated to be around 8500 years old; Zostera marina, >750 years old) along with two young Z. marina clones of known age (17 years old). We show that focusing on shared heterozygosity amplifies the power to distinguish sample pairs belonging to different clones compared to methods focusing on all shared alleles. Our proposed workflow can successfully detect clonemates at a location dominated by a single clone. When the collected samples involve two or more clones, the SH index shows a clear gap between clonemate pairs and interclone sample pairs. Ideally N should be on the order of approximately ≥3000, a number easily achievable via restriction-site associated DNA (RAD) sequencing or whole-genome resequencing. Another potential application of the SH index is to detect possible parent-descendant pairs under selfing. Our proposed workflow takes advantage of the availability of the larger number of genetic markers in the genomic era, and improves the ability to distinguish clonemates from nonclonemates in multicellular diploid clonal species.
克隆繁殖是指在没有基因重组的情况下通过有丝分裂形成几乎相同个体的过程，这是植物、真菌和动物中非常常见的繁殖方式。为了检测克隆遗传结构，基于共享等位基因的遗传相似性指数被广泛使用，如杰卡德指数或状态一致性。在此，我们基于成对样本（N）中相同杂合的分离遗传标记位点（通常是单核苷酸多态性），提出了一种新的成对遗传相似性指数——SH指数。为了测试我们的方法，我们分析了两个古老的海草克隆体（澳大利亚波喜荡草，估计约有8500年历史；大叶藻，超过750年历史）以及两个已知年龄（17年）的年轻大叶藻克隆体。我们表明，与关注所有共享等位基因的方法相比，关注共享杂合性增强了区分属于不同克隆的样本对的能力。我们提出的工作流程能够在由单个克隆主导的位置成功检测出克隆配对。当收集的样本涉及两个或更多克隆时，SH指数在克隆配对和克隆间样本对之间显示出明显差距。理想情况下，N应该约为≥3000，通过限制性位点关联DNA（RAD）测序或全基因组重测序很容易达到这个数字。SH指数的另一个潜在应用是检测自交情况下可能的亲子对。我们提出的工作流程利用了基因组时代大量遗传标记的可用性，并提高了在多细胞二倍体克隆物种中区分克隆配对和非克隆配对的能力。
