A comprehensive phylogenomic view of the living xenarthran radiation
Résumé
Xenarthrans (armadillos, anteaters, and sloths) represent one of the four main clades of placental mammals but remain underrepresented in genomic studies. Recent molecular evidence revealed hidden species diversity which suggests that additional species remain to be discovered. To address this knowledge gap, we generated 72 new xenarthran genomes constituting the most comprehensive genomic dataset for the group to date. By first analyzing 261 mitochondrial genomes, including several new museum specimens of three-toed sloths (Bradypus spp.) and pygmy anteaters (Cyclopes spp.), we confirmed divergent lineages and revealed potentially overlooked species diversity. Genome-wide comparisons of 92 individuals largely validated these mitogenomic findings, uncovering distinct species within the broadly distributed brown-throated three-toed sloth (B. variegatus), now restricted to the Amazon Basin, with B. ephippiger west of the Andes and B. griseus in Central America. Similarly, we corroborated recently described pygmy anteater species and suggested two distinct lineages within C. didactylus. In armadillos, genome-scale data affirmed the four recently described Dasypus species and supported reclassifying all Euphractinae members under the genus Euphractus. Our phylogenomic analyses detected signals of incomplete lineage sorting and gene flow pointing to a few remaining phylogenetic uncertainties. Demographic reconstructions revealed a general decline in effective population sizes, with four species showing critically low genomic diversity, raising potential conservation concerns. Our study provides the first exhaustive assessment of the evolutionary history of xenarthrans at the genome level and identifies directions for future taxonomic investigations and conservation status assessments in this major placental clade.