Complete mitochondrial genomes of Pipistrellus pipistrellus and Pipistrellus nathusii, along with the resolution of the taxonomic positions of Pipistrellus and Nyctalus

Vespertilionidae is the bat family with the highest number of species and has been studied for years using various methods such as morphology, mitochondrial, and nuclear DNA. However, the taxonomy and systematics of several groups within this family remain controversial, and many relationships are still unresolved. In this study, complete mitochondrial data (15.797-16.719 base pairs) of Pipistrellus pipistrellus and Pipistrellus nathusii were presented with the gene characteristics, and it was also aimed to reveal the phylogenetic relationship between Pipistrellus and Nyctalus. In this context, Eastern Pipistrellus species (P. coromandra, P. abramus, together with Glischropus bucephalus) were located distantly from Western Pipistrellus (P. pipistrellus, P. pygmaeus, P. kuhlii, and P. nathusii) and Nyctalus (N. noctula, N. aviator, and N. plancyi) species, with the mean genetic distance (d) values of 15.9-17.0% between these three lineages. On the other hand, P. nathusii showed a closer relationship with Nyctalus than with Pipistrellus. The genetic distances indicate that Nyctalus, Western Pipistrellus, and the Eastern Pipistrellus lineage (e.g., Alionoctula) may represent three distinct genus-level lineages suggesting that the genus Pipistrellus in its current definition may be paraphyletic. Moreover, the d value of 0.03% between N. noctula and N. plancyi supports the subspecies status of N. plancyi.