Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Abstract

Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

Genome‐wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes

“…We considered that the occurrence of different backcross classes in wild dingo populations may inform conservation and management policy directions, with some previous studies considering animals with >93% dingo ancestry as pure (Allen et al, 2017). Therefore, we categorised backcrosses as being either: (1) historical backcrosses (>93% parental ancestry) that were likely to be third generation or higher or (2) recent backcrosses (55%–93% parental ancestry) which described animals that were likely to have had a dingo × dog hybrid ancestor in the last one to three generations (Dziech, 2021; Harmoinen et al, 2021; McFarlane & Pemberton, 2019). A map depicting the FastStructure ancestry assignment of each wild origin sample was created using the QGIS v3.12 (QGIS, 2020).…”

“…(1) historical backcrosses (>93% parental ancestry) that were likely to be third generation or higher or (2) recent backcrosses (55%-93% parental ancestry) which described animals that were likely to have had a dingo × dog hybrid ancestor in the last one to three generations (Dziech, 2021;Harmoinen et al, 2021;McFarlane & Pemberton, 2019).…”

How to Choose? Comparing Different Methods to Count Wolf Packs in a Protected Area of the Northern Apennines

“…Therefore, these results should be implemented in additional future studies, applying this survey design for several reproductive years and replicating it in different areas. Furthermore, other future perspectives in wolf pack detection should be considered, such as the support of telemetry [ 69 ], drones [ 70 ] or improved molecular tools, such as specific panels of single nucleotide polymorphisms, highly performing in genotyping non-invasively collected samples (SNPs) [ 71 , 72 ] and innovative environmental DNA techniques [ 73 ].…”

“Guess Who’s Coming to Dinner”: Molecular Tools to Reconstruct multilocus Genetic Profiles from Wild Canid Consumption Remains

“…Our methodological procedures could be further improved by using highly performing markers to genotype non-invasively collected samples such as metabarcoding or highly informative and easily inter-lab comparable SNP panels, in cases of canid or felid predation on wildlife or other domestic pets to establish the real taxonomic status of the predators through a finer scale admixture identification and to provide a more reliable assessment of their potential impact on other threatened species [ 20 , 47 , 48 , 49 ].…”