Abstract:
Background: The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number
of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species
limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor
sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys
in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer
a new basis for understanding its evolutionary history.
Results: We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of
Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and
informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals
on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the
widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree
phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees
revealed phylogenetic relationships and population structure of the Afrotropical species and species groups.
Conclusions: Multiple well-supported and deeply divergent lineages were resolved in each of the six African
Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include
several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new
undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently
recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses.
Validation of these cryptic lineages as species and formal relegation of current names to synonymy will
require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior.
The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology
and evolution.
Keywords: Afrotropical biodiversity, East Africa, Introgression, Introns, Phylogeny, Rhinolophus, Species tree,
Taxonomy