Dataset: Diversification and Biogeographic History of African Dormice (Graphiurus)

Dataset: Diversification and Biogeographic History of African Dormice (Graphiurus) This repository contains sequence data, phylogenomic alignments, supplementary materials, and the accepted manuscript associated with: Onditi, K. O., Demos, T. C., Kerbis Peterhans, J. C., Nicolas, V., Mikula, O., Bryjová, A., Hounmavo, A., Monadjem, A., & Bryja, J. (2026).Diversification and biogeographic history of African dormice (genus Graphiurus) revealed by ultraconserved elements and mitochondrial data.Molecular Phylogenetics and Evolution, 217, 108549.https://doi.org/10.1016/j.ympev.2026.108549 Manuscript 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 an Upper Guinean origin followed by jump dispersal across the Afrotropics, with most subsequent divergences occurring in East Africa. Many MOTUs appear range restricted, underscoring vulnerability to ongoing habitat loss within montane refugia. Contents 1. Accepted Manuscript Journal pre-proof version of the accepted article. 2. CYTB Alignments Full nucleotide alignment (341 sequences) Redundancy-filtered alignment (130 sequences) 3. UCE Data SPAdes-assembled contigs (59 samples) 4,452 aligned and trimmed UCE loci with standardized sequence names 4. Supplementary Materials Supplementary tables (.xlsx) Supplementary figures (.docx) Data Characteristics Marker types: Ultraconserved elements (UCEs) and mitochondrial CYTB UCE loci: 4,452 UCE samples: 59 CYTB sequences: 341 (full), 130 (thinned) Geographic scope: Sub-Saharan Africa Taxonomic scope: Genus Graphiurus (Gliridae) Reuse All alignments are provided in FASTA format and are compatible with standard phylogenetic and phylogenomic software (e.g., IQ-TREE, BEAST, MrBayes, ASTRAL). UCE loci are provided as individual aligned files suitable for supermatrix or species-tree inference approaches. Citation If you use these data, please cite the associated publication: Onditi et al. (2026), Molecular Phylogenetics and Evolution, 217, 108549.https://doi.org/10.1016/j.ympev.2026.108549