Integrative Phylogeography of African Striped Grass Mice (Lemniscomys): Cryptic Diversity and Habitat Resilience

Small mammals serve as important model organisms for studying how climate and human activities influence biodiversity and human–animal interactions. However, their ecological and phylogeographic histories, and how these relate to rapid climate and land-use changes, remain poorly understood. The pan-African open-habitat murine genus <i>Lemniscomys </i>(striped grass mice) illustrates this pattern. Using the most comprehensive genetic data for this genus, we combined integrative phylogenetics, divergence dating, and ancestral-range reconstruction to connect lineage history with spatiotemporal habitat dynamics. We identified 15 molecular operational taxonomic units (MOTUs) corresponding to nine named species, along with cryptic diversity in three species. The genus diverged from its sister lineage (genus <i>Arvicanthis</i>) about 2.8 million years ago in the Sudanian Savanna belt, with internal diversification peaking during the early to mid-Pleistocene. Despite ongoing habitat contraction, <i>Lemniscomys </i>MOTUs maintained suitable habitats across past and future climate scenarios (from the late Pliocene to the end of the 21st century). Our results expand and clarify the genus’s phylogeography and emphasize the need for a formal reassessment of several traditional lineages using genomic evidence to clarify MOTUs-morphospecies relationships across different sampling depths.