Detecting clonemates in multicellular clonal species based on Shared Heterozygosity (SH) and technical replicates

Clonal reproduction, the formation of new individuals that are genetically nearly identical to the parent via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi, and animals. Current genetic marker based methods fail to detect clonal structure when all collected samples belong to one single clone, which seems to be more common than previously thought. Here we propose a new similarity index, "Shared Heterozygosity (SH)" based on the number of genetic markers (typically SNPs, single-nucleotide polymorphisms) that are identically heterozygous among two or more genomes (i.e., NSH). Ideally NSH should be on the order of approximately >=3,000, which can be easily achieved nowadays via Restriction-site Associated DNA (RAD) sequencing or whole-genome resequencing. One should be careful when NSH is small (roughly <1,000). We analyze two large seagrass clones (Posidonia australis, Zostera marina) along with two Z. marina clones of known age (17-yrs), and show that SH can potentially extend the detection of clonemates to any pair of samples with the aid of technical replicates. Another potential application of SH is to detect possible parent-descendant pairs under selfing, because the heterozygous loci in the selfing-produced descendants represent a subset of those in the parent. Our proposed workflow takes advantage of the availability of the larger number of genetic markers in the genomic era, and fills a gap in detecting clonemates in the growing number of cases where many or all samples at a location belong to one single clone.