Systematics and Phylogeography of The Non-Ethiopian Speckled-Pelage Brush-Furred Rats (Lophuromys Flavopunctatus Group) Inferred From Integrative Genetics and Morphometry

Abstract

Background: The speckled-pelage brush-furred rats (Lophuromys flavopunctatus group) has been difficult to define given conflicting genetic, morphological, and distributional records that combine to obscure meaningful accounts of its taxonomic diversity. In this study, we inferred the systematics, phylogeography, and evolutionary history of the L. flavopunctatus group using maximum likelihood and Bayesian phylogenetic inference, divergence times, historical biogeographic reconstruction, and morphometric discriminant tests. We compiled comprehensive datasets of three loci (two mitochondrial [mtDNA] and one nuclear) and two morphometric datasets (linear and geometric) from across the known range of the genus Lophuromys.Results: The mtDNA phylogeny supported the division of the genus Lophuromys into three primary groups with nearly equidistant pairwise differentiation: one group corresponding to the subgenus Kivumys (Kivumys group) and two groups corresponding to the subgenus Lophuromys (L. sikapusi group and L. flavopunctatus group). The L. flavopunctatus group comprised the speckled-pelage brush-furred Lophuromys endemic to Ethiopia (Ethiopian L. flavopunctatus members [ETHFLAVO]) and the non-Ethiopian ones (non-Ethiopian L. flavopunctatus members [NONETHFLAVO]) in deeply nested relationships. There were distinctly geographically structured mtDNA clades among the NONETHFLAVO, which were incongruous with the nuclear tree where several clades were unresolved. The morphometric datasets did not systematically assign samples to meaningful taxonomic units or agreed with the mtDNA clades. The divergence dating and ancestral range reconstructions showed the NONETHFLAVO colonized the current ranges over two independent dispersal events out of Ethiopia in the early Pleistocene.Conclusion: The phylogenetic associations and divergence times of the L. flavopunctatus group conform to demonstrated hypotheses surrounding the paleoclimatic and ecosystem refugium impacts on the evolutionary radiation of rodents dependent on stably humid conditions in the East Africa region. The overlap in craniodental variation between distinct mtDNA clades among the NONETHFLAVO suggests unraveling underlying ecomorphological drivers is key to reconciling taxonomically informative morphological characters. The genus Lophuromys requires a taxonomic reassessment based on extensive genomic evidence to elucidate the patterns and impacts of genetic isolation at clade contact zones.

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

“…To date, relatively little is known about the behavioural ecology of the four closely related Lophuromys species that harboured co-infections. These belong to the so-called L. flavopunctatus complex ( Verheyen et al 2002 , 2007 ) and they diverged in Pleistocene in different forest fragments ( Onditi et al 2021 ). Most of the species from this complex are endemic in central and east Africa ( Sabuni et al 2018 ; Van de Perre et al 2019a ).…”