New mitogenomic data for Leporidae upholds the understanding of microevolution in the order

Lagomorpha comprises two living families, Ochotonidae (pikas) with one genus and Leporidae (hares and rabbits) with 11 genera (seven of them monospecific) and 106 species in total. The leporid Sylvilagus (the second most speciose genus after Lepus) and some monotypic genera (e.g. Brachylagus) lacked robust genomic data until now. We sampled 10 to100 years old muscle and skin tissues of museum collections (University of Washington Burke Museum, Seattle, WA, and Field Museum of Natural History, Chicago, IL, USA) to generate complete mitochondrial genomes with custom-designed mRNA probes. Extraction protocols for both modern and ancient DNA were used prior to enrichment and Illumina sequencing. We de novo assembled mitogenomes of Lepus alleni (Mexico), S. aquaticus, and Brachylagus idahoensis (USA). We found six misidentified Lepus, Ochotona, and Sylvilagus species acquired from the museums. Further, our study concerning an unidentified Lepus sp. from Iran and Xinjiang (China) indicated the occurrence of Lepus tibetanus in Iran and the unusual degree of hybridization within the genus respectively.