Data from: Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield

The nine-banded armadillo (Dasypus novemcinctus) is the most widespread
xenarthran species across the Americas. Recent studies have suggested it
is composed of four morphologically and genetically distinct lineages of
uncertain taxonomic status. To address this issue, we used a museomic
approach to sequence 80 complete mitogenomes and capture 997 nuclear loci
for 71 Dasypus individuals sampled across the entire distribution. We
carefully cleaned up potential genotyping errors and cross contaminations
that could blur species boundaries by mimicking gene flow. Our results
unambiguously support four distinct lineages within the D. novemcinctus
complex. We found cases of mito-nuclear phylogenetic discordance but only
limited contemporary gene flow confined to the margins of the lineage
distributions. All available evidence including the restricted gene flow,
phylogenetic reconstructions based on both mitogenomes and nuclear loci,
and phylogenetic delimitation methods consistently supported the four
lineages within D. novemcinctus as four distinct species. Comparable
genetic differentiation values to other recognized Dasypus species further
reinforced their status as valid species. Considering congruent
morphological results from previous studies, we provide an integrative
taxonomic view to recognise four species within the D. novemcinctus
complex: D. novemcinctus, D. fenestratus, D. mexicanus, and D. guianensis
sp. nov., a new species endemic of the Guiana Shield that we describe
here. The two available individuals of D. mazzai and D. sabanicola were
consistently nested within D. novemcinctus lineage and their status
remains to be assessed. The present work offers a case study illustrating
the power of museomics to reveal cryptic species diversity within a widely
distributed and emblematic species of mammals.