Complete species-level phylogeny of Madagascar’s tufted-tailed rats, Eliurus (Rodentia: Nesomyidae) reveals hidden diversity

Abstract Accurate species delimitation is essential for understanding diversification and setting conservation priorities, particularly in biodiversity hotspots such as Madagascar. The tufted-tailed rats of Madagascar (genera Eliurus and Voalavo) are a morphologically diverse group inhabiting a wide range of habitats, yet their species boundaries and evolutionary relationships remain poorly understood. This study provides the first comprehensive assessment of species limits and phylogenetic relationships in this clade using genetic data. Initially, we identify independent, species-level groups based on a new phylogeny of 468 cytochrome b sequences from all described species sampled across Madagascar. We then test these species limits using Bayesian multispecies coalescent analyses of four nuclear loci, along with a heuristic criterion (genealogical divergence index) that evaluates the evidence for these limits relative to the speciation continuum. We discover cryptic diversity in four known species and identify one new species-level lineage. We also clarify the phylogenetic positions of two previously unsampled species and address paraphyly in Eliurus by reassigning species to Voalavo. A time-calibrated phylogeny supports the role of glacial refugia in driving microendemism. These findings underscore the value of integrating multiple lines of evidence in species delimitation and highlight specific taxa that require further study to resolve their taxonomic and conservation status fully.