Genomic data suggest parallel dental vestigialization within the xenarthran radiation

Supplementary Material for:

Emerling C.A., Gibb G.C., Tilak M.-K., Hughes J., Kuch M., Duggan A.T., Poinar H.N., Nachman M.W. & Delsuc F. (2023). Genomic data suggest parallel dental vestigialization within the xenarthran radiation. Peer Community Journal 3: e75. Recommended by PCI Genomics.

SCRIPTS

Script S1: Commands used for running CoEvol analyses on the 11 dental genes.

DATASETS

Dataset S1. Set of 5,262 baits used in the exon capture experiments of the 11 dental genes considered in Xenarthra.

Dataset S2. ACP4 genomic alignment used for characterizing inactivating mutations.

Dataset S3. AMBN genomic alignment used for characterizing inactivating mutations.

Dataset S4. AMELX genomic alignment used for characterizing inactivating mutations.

Dataset S5. AMTN genomic alignment used for characterizing inactivating mutations.

Dataset S6. DMP1 genomic alignment used for characterizing inactivating mutations.

Dataset S7. DSPP genomic alignment used for characterizing inactivating mutations.

Dataset S8. ENAM genomic alignment used for characterizing inactivating mutations.

Dataset S9. MEPE genomic alignment used for characterizing inactivating mutations.

Dataset S10. MMP20 genomic alignments used for characterizing inactivating mutations.

Dataset S11. ODAM genomic alignments used for characterizing inactivating mutations.

Dataset S12. ODAPH genomic alignments used for characterizing inactivating mutations.

Dataset S13. ACP4 codon alignment used in Coevol and PAML analyses.

Dataset S14. AMBN codon alignment used in Coevol and PAML analyses.

Dataset S15. AMELX codon alignment used in Coevol and PAML analyses.

Dataset S16. AMTN codon alignment used in Coevol and PAML analyses.

Dataset S17. DMP1 codon alignment used in Coevol and PAML analyses.

Dataset S18. DSPP codon alignment used in Coevol and PAML analyses.

Dataset S19. ENAM codon alignment used in Coevol and PAML analyses.

Dataset S20. MEPE codon alignment used in Coevol and PAML analyses.

Dataset S21. MMP20 codon alignment used in Coevol and PAML analyses.

Dataset S22. ODAM codon alignment used in Coevol and PAML analyses.

Dataset S23. ODAPH codon alignment used in Coevol and PAML analyses.

SUPPLEMENTARY TABLES (Supplementary_Tables_S1-S26.xlsx)

Table S1. Specimen information for newly generated sequences.

Table S2. Sources for DNA sequences listed for each gene, indicating methodology used. In some cases, sequences were generated via two or three methodologies. Accession numbers are associated with NCBI-derived sequences.

Table S3. Primers used in PCR amplification experiments.

Table S4. Results from PAML analyses (one ratio models) to determine the best codon frequency model fits. CF = codon frequency model; K = free parameters.

Table S5. Inactivating mutations recorded in ACP4. The details in this caption also apply to Tables S6–S15. Taxa in bold are represented by whole genome assemblies. Exon colors code for the following: green = putatively functional; yellow = missing; pink = one or more inactivating mutations found. Abbreviations for mutations are as follows: del = deletion; ins = insertion; start = start codon mutation; stop = premature stop codon; ? = ambiguity whether the mutation is shared among all members of the clade; poly = polymorphism inferred by short reads. Abbreviations in brackets following an inactivating mutation indicate shared inactivating mutation. Key for each abbreviation follows: Bpyg = Bradypus pygmaeus; BRAD = Bradypus; Btri = Bradypus tridactylus; Bvar = Bradypus variegatus; CAB = Cabassous; Ccen = Cabassous centralis; Ccha = Cabassous chacoensis; CHAET = Chaetophractus; CHLAM = Chlamyphoridae; CHOL = Choloepus; Cnat = Chaetophractus nationi; Cuni = Cabassous unicinctus; Cvel = Chaetophractus vellerosus; Cvil = Chaetophractus villosus; DASY = Dasypodidae; Dkap = Dasypus kappleri; Dnov = Dasypus novemcinctus; Dpil = Dasypus pilosus; Dsab = Dasypus sabanicola; FOLI = Folivora; MYRM = Myrmecophagidae; PEUT = Tolypeutinae; PHOR = Chlamyphorinae; PHRAC = Euphractinae; PILO = Pilosa; Pmax = Priodontes maximus; TAM = Tamandua; TOLY = Tolypeutes; VERM = Vermilingua; XEN = Xenarthra; Zpic = Zaedyus pichiy.

Table S6. Inactivating mutations recorded in AMBN. See additional details in Table S5 caption.

Table S7. Inactivating mutations recorded in AMELX. See additional details in Table S5 caption.

Table S8. Inactivating mutations recorded in AMTN. See additional details in Table S5 caption.

Table S9. Inactivating mutations recorded in DMP1. See additional details in Table S5 caption.

Table S10. Inactivating mutations recorded in DSPP. See additional details in Table S5 caption.

Table S11. Inactivating mutations recorded in ENAM. See additional details in Table S5 caption.

Table S12. Inactivating mutations recorded in MEPE. See additional details in Table S5 caption.

Table S13. Inactivating mutations recorded in MMP20. See additional details in Table S5 caption.

Table S14. Inactivating mutations recorded in ODAM. See additional details in Table S5 caption.

Table S15. Inactivating mutations recorded in ODAPH. See additional details in Table S5 caption.

Table S16. PAML results for ACP4. Model: BG = branch(es) grouped with background; fixed 1 = branch(es) fixed at 1. p-value: specific p-value only shown if lower than 0.05. Model Comparison: if model comparison yields statistically significant differences (p < 0.05), model comparison bolded and given green background. For most models, w only shown for branch(es) of interest.

Table S17. PAML results for AMBN. See additional details in Table S16 caption.

Table S18. PAML results for AMELX. See additional details in Table S16 caption.

Table S19. PAML results for AMTN. See additional details in Table S16 caption.

Table S20. PAML results for DMP1. See additional details in Table S16 caption.

Table S21. PAML results for DSPP. See additional details in Table S16 caption.

Table S22. PAML results for ENAM. See additional details in Table S16 caption.

Table S23. PAML results for MEPE. See additional details in Table S16 caption.

Table S24. PAML results for MMP20. See additional details in Table S16 caption.

Table S25. PAML results for ODAM. See additional details in Table S16 caption.

Table S26. PAML results for ODAPH. See additional details in Table S16 caption.

SUPPLEMENTARY FIGURES

Figure S1. Figure summarizing the various methodologies used to construct the various genes. Compare with Supplementary Table S2, which summarizes the methods used in the finalized constructed genes.

Figure S2. Diagram showing the flow of models used in PAML dN/dS model analyses (Supplementary Tables S16–S26). This example uses real analysis results for the gene AMELX. Compare to Supplementary Table S18 and see manuscript for further details.

Figure S3. Summary of the relative completeness of ACP4 for each species included in this study, within their phylogenetic context. In this figure, branch lengths are proportional to time and exon symbols are proportional to length. Bold species indicate species for which we had sequence data for this gene, and bolded branches show the nodes and branches for which we can reconstruct the gene's functional history. For each gene, all coding exons are numbered and colored according to mutation status: green = no evidence of inactivating mutations; yellow = missing data (i.e., not amplified and/or assembled); red = one or more inactivating mutations present. Note that a green exon does not necessarily mean the entire exon was recovered. Black boxes around exons of multiple species indicate the earliest shared inactivating mutations (SIMs) for a particular clade. For example, ACP4 shows exons 5 and 6 in chlamyphorids surrounded by a black box. This is due to SIMs being recorded in both exons within species in this clade, whereas there are no SIMs in common between chlamyphorids and dasypodids. To summarize the earliest examples of SIMs within a clade, we recorded the branch on which the mutational events happened. For example, in ACP4, we recorded at least 13 SIMs across five exons between Dasypus novemcinctus and Dasypus kappleri. Given that their relationships represent the basal split for all dasypodids, this suggests that ACP4 was inactivated on prior to the last common ancestor of Dasypodidae. See Supplementary Tables S5–15 and Supplementary Datasets S2-S12 for more details.

Figure S4. Summary of the relative completeness of AMBN for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S5. Summary of the relative completeness of AMELX for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S6. Summary of the relative completeness of AMTN for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S7. Summary of the relative completeness of DMP1 for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S8. Summary of the relative completeness of DSPP for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S9. Summary of the relative completeness of ENAM for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S10. Summary of the relative completeness of MEPE for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S11. Summary of the relative completeness of MMP20 for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S12. Summary of the relative completeness of ODAM for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S13. Summary of the relative completeness of ODAPH for each species included in this study, within their phylogenetic context. See caption for Figure S3 for more details.

Figure S14. Visualization of PAML results for ACP4. Phylogram branch lengths optimized for substitutions per codon. Red bars represent minimum dates for pseudogenization based on shared or unique inactivating mutations. Blue branches = w statistically lower than 1; blue branches with asterisk = w statistically lower than 1 and background; purple branches = statistically higher than background and lower than 1; red branches = w statistically higher than background ; red branches with asterisk = w statistically higher than background and 1; black branches that pre-date inactivating mutations = not statistically distinguishable from background or 1; black branches that post-date inactivating mutations = no statistically analyses performed on these branches.

Figure S15. Visualization of PAML results for AMBN. See caption for Figure S2 for more details.

Figure S16. Visualization of PAML results for AMELX. See caption for Figure S2 for more details.

Figure S17. Visualization of PAML results for AMTN. See caption for Figure S2 for more details.

Figure S18. Visualization of PAML results for DMP1. See caption for Figure S2 for more details.

Figure S19. Visualization of PAML results for DSPP. See caption for Figure S2 for more details.

Figure S20. Visualization of PAML results for ENAM. See caption for Figure S2 for more details.

Figure S21. Visualization of PAML results for MEPE. See caption for Figure S2 for more details.

Figure S22. Visualization of PAML results for MMP20. See caption for Figure S2 for more details.

Figure S23. Visualization of PAML results for ODAM. See caption for Figure S2 for more details.

Figure S24. Visualization of PAML results for ODAPH. See caption for Figure S2 for more details.

Figure S25. Visualization of Coevol results for ACP4. The figure shows the Bayesian reconstruction of dN/dS across the placental phylogeny with focus on xenarthrans (armadillos, anteaters, and sloths). The variation of dN/dS was jointly reconstructed with divergence times while controlling the effect of three life-history traits (body mass, longevity, and sexual maturity). The tree is rooted with Afrotheria as the sister-group to all other placentals according to Emerling et al. (2015). Asterisks indicate non-functional sequences.

Figure S26. Visualization of Coevol results for AMBN. See caption for Figure S13 for more details.

Figure S27. Visualization of Coevol results for AMELX. See caption for Figure S13 for more details.

Figure S28. Visualization of Coevol results for AMTN. See caption for Figure S13 for more details.

Figure S29. Visualization of Coevol results for DMP1. See caption for Figure S13 for more details.

Figure S30. Visualization of Coevol results for DSPP. See caption for Figure S13 for more details.

Figure S31. Visualization of Coevol results for ENAM. See caption for Figure S13 for more details.

Figure S32. Visualization of Coevol results for MEPE. See caption for Figure S13 for more details.

Figure S33. Visualization of Coevol results for MMP20. See caption for Figure S13 for more details.

Figure S34. Visualization of Coevol results for ODAM. See caption for Figure S13 for more details.

Figure S35. Visualization of Coevol results for ODAPH. See caption for Figure S13 for more details.