A new set of Multilocus Intron Polymorphism Loci (MIPs) for identifying mammal species, subspecies and their first hybrid and backcross generations with their closely related taxa or domestic counterparts

Animal conservation efforts benefit from rapid, cost-effective genomic markers for species and hybrid identification across taxa. PCR-based protocols have dominated the study of gene flow and introgression in the last 30 years, allowing the molecular characterization of target DNA even from low-quality non-invasive samples. While whole genome sequencing remains beyond the budget of most conservation studies, the characterization of genome-wide single nucleotide polymorphisms (SNPs) has overcome the need for expensive development of marker sets yet provides thousands or tens of thousands of markers; however, SNP-chips or other SNP-based approaches like genotyping-by-sequencing (GBS), require large quantities of high-quality DNA from each sample. Marker sets that combine the advantages of a PCR step (requiring less good quality DNA) applicable to a wide range of species, remain elusive. Recently, Multilocus Intron Polymorphisms (MIPs) have been shown to be useful for defining species, hybrids, and population genomic structure in freshwater fish. Here, we propose a new panel of 187 MIPs for mammals, selected by aligning 121 genomes. Cross-amplification performance of the panel was tested across 15 species, subspecies and hybrids from six different mammalian families. To validate the capacity of this panel to distinguish different classes of hybrids and backcrosses, offspring from known laboratory crosses of Muridae, as well as from free-ranging and domestic taxa of Leporidae, Bovidae, Canidae, Felidae and Suidae were analysed. Results compared favourably with simulated genotypes representing different hybrid and backcross classes, generated from real parental genotypes. The main advantages and limitations of our proposed method are discussed, including its cross-amplification efficiency across different mammalian families and its limited ability to resolve complex patterns of historical introgression.