Datasets for Dalapicolla et al., 2024. Phylogenomics and species delimitation of an abundant and little-studied Amazonian forest spiny rat. Molecular Phylogenetics and Evolution, 107992.

All scripts are available at <b>https://github.com/jdalapicolla/SpeciesDelimitation</b><b>Permits:</b> SISBIO[#14419-3] and SISGEN [#A58279D]<br><b>GENOMIC DATA:</b><b>VCF:</b> proechimys.vcf.gz and proechimys.vcf.gz.tbi<b>Loci data:</b> proechimys_184ind_ipyrad.7z<b>Nexus A</b><b>lignments for SVDQuartets:</b> proechimys_complete_svd_final_speciestrees.nex (complete dataset); proechimys_subset1_svd_indtree.nex (Subset 1); proechimys_subset2_svd_speciestree.nex (Subset 2);<b>Phylip alignments for IQTree:</b> proechimys_MPE1_184.phylip (complete dataset); proechimys_subset1.phylip (Subset 1); proechimys_subset2.phylip (Subset 2).<br><b>SUPPLEMENTARY MATERIAL</b><b>Appendix A: </b>A brief taxonomic history of the genus <i>Proechimys</i>.<b>Appendix B: </b>Summary of mitochondrial DNA (mtDNA) data available for the genus <i>Proechimys</i>.<b>Appendix C: </b>Details on SNPs calling and filtering steps used in genomic data.<b>Appendix D: </b>Details on repeatability and filtering steps used in morphometric data.<b>Appendix E: </b>Comments on the nomenclatural decisions regarding the species-group taxa of the genus <i>Proechimys</i>.<b>Table S1: </b>Samples used in the genomics analyses.<b>Table S2: </b>Morphometric data consisting of raw values for 22 morphometric variables.<b>Table S3: </b>RAD processing results for 184 genomic samples.<b>Table S4: </b>ICC test for cranial measurements with upper and lower values for the confidence interval.<b>Table S5: </b>Posterior probabilities (PP) found in all demographic scenarios in the iBP&amp;P analyses.<b>Table S6: </b>Patterson’s D (ABBA-BABA), and related statistics.<b>Table S7: </b>Divergence times in millions of years ago (Ma) for the species tree of <i>Proechimys.</i><b>Table S8: </b>Available cytogenetic, mtDNA, and nuDNA data in the literature for delimited species of <i>Proechimys.</i><b>Figure S1: </b>Geographical distribution of genomic samples.<b>Figure S2: </b>Geographical distribution of morphometric samples.<b>Figure S3: </b>The 29 cranial measurements with their respective acronyms.<b>Figure S4: </b>Details of clade A in the individual phylogenetic tree.<b>Figure S5: </b>Details of clade B in the individual phylogenetic tree.<b>Figure S6: </b>Details of clade C, D, E, F and G in the individual phylogenetic tree.<b>Figure S7: </b>Partitions used in iBP&amp;P.<b>Figure S8: </b>Species tree and IQTree2 using 17,162 unlinked SNPs subset 2.<b>Figure S9: </b>The branch-specific statistic<i>f</i>_b(F-branch).