The giant house bat Scotophilus nigrita, one of the largest vespertilioniform bat species in the world, is a poorly known taxon, especially with respect to its phylogenetic relationships to congeneric species. Its phylogenetic position was thus assessed by analysing DNA sequences of single mitochondrial and nuclear genes.
Based on the mitochondrial cytochrome b, S. nigrita was found to be paraphyletic with respect to continental African species S. colias, S. dinganii, S. nigritellus and S. viridis. Analysis of sequences of the nuclear zinc finger protein gene on the Y chromosome corroborated the general pattern of the cytochrome b phylogeny, although phylogenetic relationships were poorly resolved.
These results clearly contradict the published data on S. nigrita from Kenya for both markers, rendering the hypothesis of historical hybridization with S. colias implausible and questioning the taxonomic affiliation of the particular Kenyan sequence. A deep split in the cytochrome b phylogeny between S. nigrita from West and Southern Africa reached sequence divergence values of 7.6% to 8.1%, a finding that supports taxonomic elevation of the two currently recognized subspecies into separate species S. nigrita and S. alvenslebeni.