Diversification and biogeographic history of African dormice (genus Graphiurus) revealed by ultraconserved elements and mitochondrial data

Abstract

The sub-Saharan Africa endemic dormouse genus Graphiurus is a morphologically diverse group of rodents that has lacked a genus-wide genetic framework, hindering inference of their evolution and biogeography. Here, we assembled the first comprehensive, range-wide genomic dataset for Graphiurus, including ultraconserved elements and the cytochrome b gene. We used phylogenetic reconstruction, divergence-time estimation, and ancestral area reconstruction to clarify biogeographic histories and evaluate how historical range dynamics may have influenced lineage diversification. Graphiurus is the earliest-diverging lineage within Gliridae sister to all other extant genera. Within Graphiurus, we recovered 24 molecular operational taxonomic units (MOTUs) forming two reciprocally monophyletic, deeply divergent clades: a West African lineage comprising three MOTUs and a pan-sub-Saharan Africa lineage comprising 21 MOTUs. Genetic distances between these clades are equal to or greater than those used to distinguish genera. Diversification within Graphiurus started in the middle Miocene, peaking in a rapid radiation during the Plio-Pleistocene. These diversification events coincided with increased climatic instability that fragmented forests into isolated refugia. Ancestral-area reconstructions suggest a Graphiurus origin in the Upper Guinean rainforest, followed by jump dispersal across the Afrotropics, with most subsequent divergences occurring in East Africa. As the first comprehensive phylogenetic analysis of Graphiurus, our study underscores the urgent need for an integrated taxonomic revision of the genus that couples genomic data with detailed morphology and critical re-examination of type material to resolve species limits and formally describe the recovered MOTUs. Many MOTUs appear range restricted, underscoring vulnerability to ongoing habitat loss within montane refugia.

HIGHLIGHTS • The first phylogenomic dataset clarifies evolutionary relationships and highlights diversity within Graphiurus. • 24 highly supported genetic lineages in two deeply divergent, reciprocally monophyletic clades at genera level identified. • Divergence started in early Miocene, but major diversification aligned with Pliocene–Pleistocene climatic fluctuations. • Long-term habitat refugia in the Eastern African highlands were critical for lineage persistence. • An integrative taxonomic revision of the genus is needed.