Phylogenomic Insights into Rodent Diversification

Abstract

Rodentia is by far the most species-rich mammalian order -- approximately 2,600 described species constituting over 40% of all mammalian diversity -- yet the deep phylogenomic relationships among the major rodent lineages (the suprafamilial classification) remain incompletely resolved, with conflicting topologies among different molecular datasets and persistent uncertainty about the placement of Hystricomorpha, Castorimorpha, and Anomaluromorpha relative to the muroid crown. This study presents a genome-scale phylogenomic analysis of Rodentia using whole-genome shotgun sequencing for 84 species plus target-enrichment (UCE + exon capture) for 247 additional species, generating a matrix of 4,847 loci and mean 1.24 Mb of aligned sequence per species. The resulting time-calibrated phylogeny resolves several long-contested nodes with decisive support: the monophyly of Castorimorpha (bootstrap 99.7%; concordance factor 0.84) is confirmed; Anomaluromorpha is placed as sister to Myomorpha + Castorimorpha rather than to Hystricomorpha (bootstrap 97.4%; CF 0.74); and Ctenodactylidae (gundis) is confirmed as sister to Hystricomorpha. Diversification rate analysis identifies the Eocene-Oligocene boundary (33.7 Mya) as the primary diversification rate acceleration corresponding to the global rodent radiation into temperate grassland and woodland habitats, with three subsequent rate pulses in Muridae (12.4 Mya; Old World mice/rats), Cricetidae (14.7 Mya), and Sigmodontinae (8.4 Mya; South American expansion).