Species limits and phylogeographic structure in two genera of solitary African mole-rats Georychus and Heliophobius

African mole-rats (Bathyergidae) are an intensively studied family of subterranean rodents including three highly social and three solitary genera. Although their phylogenetic interrelations are clear, genetic diversity and the number of species within each genus is much less certain. Among the solitary genera, Heliophobius and Georychus were for a long time considered as monotypic, but molecular studies demonstrated strong phylogeographic structure within each genus and proposed that they represent complexes of cryptic species. The present study re-evaluates their internal genetic/phylogenetic structure using a combination of methodological approaches. We generated datasets of one mitochondrial and six specifically selected nuclear markers as well as of a large number of double digest restriction site associated (ddRAD) loci and then applied species delimitation analyses based on the multispecies coalescent model or clustering on co-ancestry matrices. The population structure was largely congruent across all analyses, but the methods differed in their resolution scale when determining distinct gene pools. While the multispecies coalescent model distinguished five Georychus and between eleven to thirteen Heliophobius gene pools in both Sanger sequenced and ddRAD loci, two clustering algorithms revealed significantly finer or coarser structure in ddRAD based co-ancestry matrices. Tens of clusters were distinguished by fineRADstructure and one (in Georychus) or two clusters (in Heliophobius) by Infomap. The divergence dating of the bathyergid phylogeny estimated that diversification within both genera coincided with the onset of the Pleistocene and was likely driven by repeated large-scale climatic changes. Based on this updated genetic evidence, we suggest recognizing one species of Georychus and two species of Heliophobius, corresponding to a northern and southern major lineage, separated by the Eastern Arc Mountains. Yet, the final taxonomic revision should await integrated evidence stemming from e.g.. morphological, ecological, or behavioral datasets.

Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion

Murid rodents of the genus Aethomys are one of the most common rodents in drier habitats in sub-Saharan Africa. Among them, the red veld rat Aethomys chrysophilus is the most widespread species with the core distribution located in the Zambezian bioregion. In this study, we describe phylogeographic structure of the species and estimate its age from a time-calibrated phylogeny of the genus. Seven parapatric clades were identified in the mitochondrial cytochrome b phylogeny, where some of the distributions of these clades have been separated by previously described biogeographical divides (Zambezi-Kafue river system, Rukwa Rift and the Eastern Arc Mountains). One internal clade corresponded to populations previously described as a distinct species, Aethomys ineptus. The whole A. chrysophilus complex was estimated to be 1.3 (0.5–2.4) Mya old, with A. ineptus originating 0.7 (0.1–1.4) Mya before present. The internal position of A. ineptus was also recovered in phylogenetic reconstruction based on two nuclear genes and thus it is not a consequence of mitochondrial introgression. In addition, we analyzed skull form variation across the species’ distributional range and found no significant difference between A. ineptus and the rest of A. chrysophilus complex.