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 https://github.com/jdalapicolla/SpeciesDelimitation
Permits: SISBIO[#14419-3] and SISGEN [#A58279D]

GENOMIC DATA:
VCF: proechimys.vcf.gz and proechimys.vcf.gz.tbi
Loci data: proechimys_184ind_ipyrad.7z
Nexus Alignments for SVDQuartets: proechimys_complete_svd_final_speciestrees.nex (complete dataset); proechimys_subset1_svd_indtree.nex (Subset 1); proechimys_subset2_svd_speciestree.nex (Subset 2);
Phylip alignments for IQTree: proechimys_MPE1_184.phylip (complete dataset); proechimys_subset1.phylip (Subset 1); proechimys_subset2.phylip (Subset 2).

SUPPLEMENTARY MATERIAL
Appendix A: A brief taxonomic history of the genus Proechimys.
Appendix B: Summary of mitochondrial DNA (mtDNA) data available for the genus Proechimys.
Appendix C: Details on SNPs calling and filtering steps used in genomic data.
Appendix D: Details on repeatability and filtering steps used in morphometric data.
Appendix E: Comments on the nomenclatural decisions regarding the species-group taxa of the genus Proechimys.
Table S1: Samples used in the genomics analyses.
Table S2: Morphometric data consisting of raw values for 22 morphometric variables.
Table S3: RAD processing results for 184 genomic samples.
Table S4: ICC test for cranial measurements with upper and lower values for the confidence interval.
Table S5: Posterior probabilities (PP) found in all demographic scenarios in the iBP&P analyses.
Table S6: Patterson’s D (ABBA-BABA), and related statistics.
Table S7: Divergence times in millions of years ago (Ma) for the species tree of Proechimys.
Table S8: Available cytogenetic, mtDNA, and nuDNA data in the literature for delimited species of Proechimys.
Figure S1: Geographical distribution of genomic samples.
Figure S2: Geographical distribution of morphometric samples.
Figure S3: The 29 cranial measurements with their respective acronyms.
Figure S4: Details of clade A in the individual phylogenetic tree.
Figure S5: Details of clade B in the individual phylogenetic tree.
Figure S6: Details of clade C, D, E, F and G in the individual phylogenetic tree.
Figure S7: Partitions used in iBP&P.
Figure S8: Species tree and IQTree2 using 17,162 unlinked SNPs subset 2.
Figure S9: The branch-specific statisticfb(F-branch).