Using “identity by heterozygosity (IBH)” to detect clonemates under prevalent clonal reproduction in multicellular diploids

Clonal reproduction, the production of asexual modular units with the ability to live independently under multicellularity, is a very common life history. Genetic markers have been widely used to detect clonemates tracing back to a single sexual event. However, the currently available methods cannot work in cases where all collected samples belong to a few or even one single clone. Here we propose the concept of identity by heterozygosity (IBH), meaning that two diploid genomes are identically heterozygous at some genetic markers such as SNPs (single-nucleotide polymorphisms). Based on IBH, we develop IBH similarity (IBHs), a novel measure of genetic similarity between two diploid genomes. The core of our IBH method for detecting clonemates is to use IBHs in combination with the cutoff of 0.95. Two samples with IBHs >0.95 are considered members of the same clone, while two samples with IBHs <=0.95 are considered to represent different clones. The method requires a relatively large number of marker loci where the two target samples are identically heterozygous (i.e., NIBH, on the order of >=3,000). Another potential application of IBH is to detect possible parent-descendant pairs under selfing because this reproductive mode leads to a predictable loss of heterozygosity. Our IBH method extends the detection of clonemates to any pair of samples, and will allow the detection of clonemates in extreme cases where all collected samples belong to one single clone. ### Competing Interest Statement The authors have declared no competing interest.