acoRn: A Forest Adventure in Search of Oak Parents

Parentage assignment is a technique that can be used in several biological applications, including biodiversity conservation and animal and plant breeding. It compares different sets of multi-locus genotype data for parents and offspring, deriving from codominant gene markers (microsatellites, SNPs). Parentage assignment is very useful for studying mating patterns, gene flow and hybridization. Here, we present acoRn, an exclusion-based parentage assignment tool that uses the Mendelian segregation principle of alleles to assign possible parents from a given dataset to each offspring within a different given dataset, after dealing with genotyping errors, missing values and duplicate genotypes. acoRn is a workflow composed by a collection of R (v4.3.0) scripts. The user provides two abundance matrices for parents and offspring as input. The output produced is a table with the estimated matches. We tested acoRn in a real use case, a natural forest where three different oak species occur sympatrically and possibly interbreed. Two datasets with multi-locus genotypes at 17 nuclear microsatellites were compared; one containing the genotypes of all 59 adult trees within a specific forest stand and the other with the genotypes of 110 juvenile trees in the same stand. acoRn was used to assign all possible (not-excluded) parents for each progeny. After identifying and clearing duplicate genotypes and cases with missing values, the results were presented in comprehensive plots and tables. acoRn has revealed that most juvenile trees derive from just a small number of parents in the forest, while many of the juvenile trees had no parent of either sex located in the specific area. Possible hybridization events were identified. acoRn depends on the assignment power of the gene marker used and for this reason we expect that it will be even more useful with large SNP datasets, for parentage assignment in any organism.