Abstract
Xenarthrans (armadillos, anteaters, and sloths) are the least diverse of the four major clades of placental mammals, with only 39 currently described species. However, this emblematic Neotropical clade includes species complexes with genetically distinct lineages of uncertain taxonomic status. To address this issue, we conducted a comprehensive genomic analysis, encompassing 261 individual mitogenomes, an exon capture dataset for 71 individuals, and 94 whole genomes, representing 34 distinct xenarthran species. As we included numerous museum samples, we carefully cleaned up potential genotyping errors and cross contaminations that could blur species boundaries by mimicking gene flow. This nearly exhaustive genome-wide dataset allowed us to revise Xenarthra taxonomy employing multiple lines of evidence (species delimitation methods, estimation of gene flow, genomic differentiation, morphology, demography) raising the number of xenarthran species to 44. This revised taxonomic framework enabled the reconstruction of the most comprehensive time-calibrated phylogeny of Xenarthra based on whole genomes, shedding new light on their evolutionary history. By disentangling incomplete lineage sorting and gene flow in discordant parts of the xenarthran phylogeny, we identified multiple events of gene flow suggesting the maintenance of contact zones during speciation events. Further exploring factors promoting speciation within xenarthrans pointed to the potential influence of Colombian and Venezuelan Andes in their diversification. Overall, this work contributes to a deeper understanding of xenarthran evolution but also provides insights into future directions for taxonomic investigations and conservation status assessment within this fascinating mammalian group.