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 ..., Biological sampling
A total of 80 armadillo tissue samples were obtained over the years for this study through multiple sources (Table S1). Our sampling notably includes 46 individuals sampled in the form of dried skin pieces. Among these, 38 were obtained from museum specimens collected between 1894 and 2000 and stored in 12 different collections. The other eight were received in the form of dried ear biopsies not associated with museum vouchers. The remaining samples were fresh tissue biopsies stored in 95% ethanol. In accordance with the policy of sharing benefits and advantages (APA TREL1916196S/224), biological material from French Guiana has been deposited in the JAGUARS collection supported by the Collectivité Territoriale de Guyane and the Direction Générale des Territoires et de la Mer de la Guyane.
DNA extractions and sequencing
Total genomic DNA extractions from fresh tissue biopsies preserved in 95% ethanol were performed using the DNeasy Blood & Tissue Kit (QIAGEN) acco..., , # Supplementary Material for: Exon capture museomics deciphers the nine-banded armadillo species complex and identifies a new species endemic to the Guiana Shield

[https://doi.org/10.5061/dryad.95x69p8sz](https://doi.org/10.5061/dryad.95x69p8sz)

## Description of the data and file structure

● Supplementary Material

* Barthe_et_al_SystBiol_Supplementary.pdf: Supplementary Text, Figures and Tables

● Supplementary Data

* Final_bait_set.fasta: Sequences of the 16,146 probes used to capture the 997 nuclear loci (exons and flanking regions).

## Sharing/Access information

Links to other publicly accessible locations of the data:
● Zenodo public online repository ([https://zenodo.org/records/11283950](https://zenodo.org/records/11283950)).
● Digital 3D models of the Dasypus guianensis holotype specimen are freely available through MorphoMuseuM ([https://morphomuseum.com/specimenfiles/send-file-specimenfile/1200/4a65cc83](https://morphomuseum.com/specimenfiles/send-file-specimenfile/1200...