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. Genomic data suggest parallel dental vestigialization within the xenarthran radiation. Submitted to PCI Genomics.

 

DATASETS

Dataset S1. Set of baits used in the exon capture experiments of the 11 tooth genes considered in Xenarthra. 

Dataset S2. ACPT 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. ACPT 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.

Dataset S24. Draft DISCOVAR de novo genome assembly of the southern naked-tailed armadillo (Cabassous unicinctus) specimen MVZ 155190 from the Museum of Vertebrate Zoology (University of California Berkeley, USA).

 

 

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 ACPT. 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 ACPT. 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. Portion of ACPT exon 7 alignment showing two alternative alignments for a putative shared 2-bp inactivating mutation. See manuscript for details.

Figure S2. Visualization of PAML results for ACPT. 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 S3. Visualization of PAML results for AMBN. See caption for Figure S2 for more details.

Figure S4. Visualization of PAML results for AMELX. See caption for Figure S2 for more details.

Figure S5. Visualization of PAML results for AMTN. See caption for Figure S2 for more details.

Figure S6. Visualization of PAML results for DMP1. See caption for Figure S2 for more details.

Figure S7. Visualization of PAML results for DSPP. See caption for Figure S2 for more details.

Figure S8. Visualization of PAML results for ENAM. See caption for Figure S2 for more details.

Figure S9. Visualization of PAML results for MEPE. See caption for Figure S2 for more details.

Figure S10. Visualization of PAML results for MMP20. See caption for Figure S2 for more details.

Figure S11. Visualization of PAML results for ODAM. See caption for Figure S2 for more details.

Figure S12. Visualization of PAML results for ODAPH. See caption for Figure S2 for more details.

Figure S13. Visualization of Coevol results for ACPT. 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. Asterisks indicate non-functional sequences.

Figure S14. Visualization of Coevol results for AMBN. See caption for Figure S13 for more details.

Figure S15. Visualization of Coevol results for AMELX. See caption for Figure S13 for more details.

Figure S16. Visualization of Coevol results for AMTN. See caption for Figure S13 for more details.

Figure S17. Visualization of Coevol results for DMP1. See caption for Figure S13 for more details.

Figure S18. Visualization of Coevol results for DSPP. See caption for Figure S13 for more details.

Figure S19. Visualization of Coevol results for ENAM. See caption for Figure S13 for more details.

Figure S20. Visualization of Coevol results for MEPE. See caption for Figure S13 for more details.

Figure S21. Visualization of Coevol results for MMP20. See caption for Figure S13 for more details.

Figure S22. Visualization of Coevol results for ODAM. See caption for Figure S13 for more details.

Figure S23. Visualization of Coevol results for ODAPH. See caption for Figure S13 for more details.