Integrative taxonomic revision of the African thicket rats (Murinae: Grammomys): how genomics decreases the number of currently recognized species

Abstract

Abstract Thicket rats of the genus Grammomys are partly arboreal rodents distributed across a large part of sub-Saharan Africa. Previous work showed that their highest diversity is in forests and woodlands of Eastern Africa, that the evolutionary history of the genus roughly mirrors the evolution of African forests, and that the currently delimited species (names) do not correspond to major genetic clades. We used thousands of single nucleotide polymorphisms to perform phylogenomic analysis and to delimit genomic pools (i.e. candidate biological species). The resulting molecular operational taxonomic units were then compared with the most comprehensive sets of other available data (mitochondrial DNA variability, ecological requirements, morphology, karyotypes, sequences from the type material, etc.) and used for an integrative solution to the taxonomy of the genus. Our revision delimited seven species, which is less than the 12 recognized in the most recent literature on African rodents. We conclude that the African thicket rats represent a classic example of challenging problems in current integrative taxonomy. It is now relatively easy to obtain genomic data and to delimit candidate species, but it is much more complicated to give them species names using the valid rules of zoological nomenclature.