A reduced SNP panel to trace gene flow across southern European wolf populations and detect hybridization with other Canis taxa

• Published in: Scientific reports Vol. 12; no. 1; p. 4195
• Main Authors: Stronen, Astrid Vik, Mattucci, Federica, Fabbri, Elena, Galaverni, Marco, Cocchiararo, Berardino, Nowak, Carsten, Godinho, Raquel, Ruiz-González, Aritz, Kusak, Josip, Skrbinšek, Tomaž, Randi, Ettore, Vlasseva, Albena, Mucci, Nadia, Caniglia, Romolo
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09-03-2022; Nature Publishing Group; Nature Portfolio
• Subjects: 631/208; 631/208/182; 631/208/212; 631/208/721; Animal populations; Canidae; Canis lupus; Conservation; Divergence; Domestic animals; Gene flow; Genetic markers; Humanities and Social Sciences; Hybridization; Hybrids; multidisciplinary; Recolonization; Science; Science (multidisciplinary); Single-nucleotide polymorphism
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-022-08132-0

Intra- and inter-specific gene flow are natural evolutionary processes. However, human-induced hybridization is a global conservation concern across taxa, and the development of discriminant genetic markers to differentiate among gene flow processes is essential. Wolves (
Canis lupus
) are affected by hybridization, particularly in southern Europe, where ongoing recolonization of historic ranges is augmenting gene flow among divergent populations. Our aim was to provide diagnostic canid markers focused on the long-divergent Iberian, Italian and Dinaric wolf populations, based on existing genomic resources. We used 158 canid samples to select a panel of highly informative single nucleotide polymorphisms (SNPs) to (
i
) distinguish wolves in the three regions from domestic dogs (
C. l. familiaris
) and golden jackals (
C. aureus
), and (ii) identify their first two hybrid generations. The resulting 192 SNPs correctly identified the five canid groups, all simulated first-generation (F1) hybrids (0.482 ≤ 
Q
i
 ≤ 0.512 between their respective parental groups) and all first backcross (BC1) individuals (0.723 ≤ 
Q
i
 ≤ 0.827 to parental groups). An assay design and test with invasive and non-invasive canid samples performed successfully for 178 SNPs. By separating natural population admixture from inter-specific hybridization, our reduced panel can help advance evolutionary research, monitoring, and timely conservation management.