Ratios of replacement to silent polymorphism () in , and substitutions () between and

<p><b>Copyright information:</b></p><p>Taken from "Recombination rate and protein evolution in yeast"</p><p>http://www.biomedcentral.com/1471-2148/7/235</p><p>BMC Evolutionary Biology 2007;7():235-235.</p><p>Published online 27 Nov 2007</p><p>PMCID:PMC2211315.</p><p></p> Results were obtained by pooling polymorphism and divergence data for multiple genes within each expression category (see Fig. S1 for similar results using a different approach). /ratios are lower in highly expressed genes: upper vs. lower 50% with singletons, = 0.172; upper vs. lower 25% with singletons, = 0.026; upper vs. lower 50% without singletons, = 0.203; upper vs. lower 25% without singletons, = 0.023. /ratios are lower for highly expressed genes for all comparisons (< 0.0001)

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/SpeciesDelimitationPermits: SISBIO[#14419-3] and SISGEN [#A58279D]GENOMIC DATA:VCF: proechimys.vcf.gz and proechimys.vcf.gz.tbiLoci data: proechimys_184ind_ipyrad.7zNexus 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 MATERIALAppendix 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).</p

SpeciesTreeAphelocomawithinstructions.xml

The XML file used to add fossil calibration to the species tree with some instructions for how the file should be hand-edited

SimulationCode.tar

Code for conducting coalescent simulations with a readme file