This work presents the first genetic species identification and phylogenetic analyses of all six bat species known to inhabit the Maltese archipelago. The results provide a DNA-based reference library of 12S rRNA, 16S rRNA, COI, Cytb and ND1 mitochondrial sequences for Maltese bat species. Phylogenetic analyses revealed that the Maltese bat populations do not harbour cryptic diversity. Analyses of genetic diversity for Maltese bat species showed contrasting matrilineal diversity between species, Hypsugo savii exhibited the highest haplotype diversity (Hd = 0.802), while Rhinolophus hipposideros showed no haplotype diversity and Plecotus gaisleri exhibited low values for haplotype diversity (Hd = 0.091). Comparative phylogeographical analyses of mtDNA gene datasets from this study with sequences of conspecific bat populations outside of Malta indicate that mitochondrial haplotypes of Pipistrellus pipistrellus and Rhinolophus hipposideros are unique to the Maltese Islands. Hypsugo savii, Pipistrellus kuhlii, Myotis punicus and Plecotus gaisleri shared the most common mitochondrial haplotype with surrounding geographical areas, including the Ibero-Maghreb region, the Apennine Peninsula and Sicily. The observed genetic diversity and phylogenetic relationships are discussed in the context of the species’ biology and long-term conservation planning of Maltese bat populations.
Mitochondrial DNA, Genetic diversity, DNA barcoding, Bat conservation, Insular populations