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

# 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 Figures and Tables ● Supplementary Data * Concatenated_mitochondrial_genes.fasta: Concatenated nucleotide sequences of 15 mitochondrial genes (13 protein-coding + 2 rRNAs). Sites with more than 50% missing data were excluded resulting in a total of 13,924 sites. * Concatenated_mitochondrial_genes_partition.txt: Partition file of concatenated sequences of the 15 mitochondrial genes (13 protein-coding + 2 rRNAs). * Concatenated_mitochondrial_genes_TESTNEW.treefile : Maximum likelihood phylogenetic tree inferred from the concatenated sequences of the 15 mitochondrial genes using IQ-TREE under a partitioned model applying ModelFinder on each partition. * Dloop_alignment.fasta: Alignment of the D-loop sequences obtained in this study with those from Arteaga et al. (2020). * Dloop_alignment.treefile: Maximum likelihood phylogenetic tree inferred from the D-loop alignment using IQ-TREE (GTR+G model). * Abba_shotgun.fasta: Alignment of the 16S rRNA of individuals from this study and those from Abba et al. (2018). * Abba_shotgun.fasta.treefile: Maximum likelihood phylogenetic tree inferred from the 16S rRNA alignment using IQ-TREE (GTR+G model). * TATU_1000exons4baits.fasta: Reference sequences of 1,000 exons and flanking regions used to define the probes for exon capture extracted from the Dasypus novemcinctus genome. * Diploid_837_nuclear_loci.fasta: Diploid sequences of the 837 nuclear loci for the 62 individuals in PopPhyl format (Locus|lineage|individual|Allele). * Location_loci_targeted.bed : list of the loci targeted by exon capture, with their genomic locations on the chromosome scale assembly of Dasypus novemcinctus (mDasNov1.hap2) * Concatenated_nuclear_loci.fasta: Concatenated sequences of the 837 nuclear loci representing a total of 506,355 sites. * Concatenated_nuclear_loci_partition.txt: Partition file for the 837 nuclear loci concatenation. * Concatenated_nuclear_loci_TESTNEW.treefile: Maximum likelihood phylogenetic tree inferred from the 837 nuclear loci concatenation using IQ-TREE under a partitioned model applying ModelFinder on each partition. * Ultrametric_tree_concatenated_nuclear_loci.treefile: Ultrametric tree inferred from the 837 nuclear loci concatenation (Concatenated_nuclear_loci.fasta in Phylogram_Tree folder) using a partitioned model applying ModelFinder on each partition (Concatenated_nuclear_loci_partition.txt in Phylogram_Tree folder). The ML phylogram (Concatenated_nuclear_loci_TESTNEW.treefile in Phylogram_Tree folder) was used as a guide tree. The root was dated at 6 Mya. * Concatenate_gene_tree.treefile: File containing all gene trees reconstructed using IQ-TREE applying ModelFinder to each gene. * Astral_consensus_tree.txt: Summary species tree reconstructed with Astral using Concatenate_gene_tree_TESTNEW.treefile * input_for_bpp.phy: Sequence alignments of the 837 nuclear loci in phylip format. * lineage_for_BPP: Correspondence file between individuals and lineages. * PTPh_Support_Partition.txt: Details of the most supported species partition. * PTPh_tree_partition.png: Tree illustrating the most supported species partition. * Input_for_PCA.fasta: Diploid sequences of the 57 individuals (DNO-MC21 and DPI-L29 excluded) in PopPhyl format (Locus|species|individual|allele). * PCA_Output: Output of the PopPhyl2PCA analysis using the Input_for_PCA.fasta file. ## 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/1200/4a65cc83); [https://morphomuseum.com/specimenfiles/send-file-specimenfile/1201/7ed725a9](https://morphomuseum.com/specimenfiles/send-file-specimenfile/1201/7ed725a9)).