DOI: 10.5281/zenodo.17759845
title: Pseudogenes document protracted parallel regression of oral anatomy in myrmecophagous mammals

description: Supplementary Data for: Pseudogenes Document Protracted Parallel Regression of Oral Anatomy in Myrmecophagous Mammals 

Christopher A. Emerling*, Sophie Teullet, Rémi Allio, John Gatesy, Mark S. Springer and Frédéric Delsuc*

*Correspondence to christopher.emerling@reedleycollege.edu and frederic.delsuc@umontpellier.fr

 

Description of available files:

Supplementary Dataset S1: Complete DNA sequence alignments for all focal genes and taxa.

Supplementary Dataset S2: Reference phylogeny and DNA sequence alignments for PAML analyses.

Supplementary Dataset S3. Logistic PCA dataset to be used with Supplementary Code S1. 1 = gene loss; 0 = gene functional. See Supplementary Table S18.

 

Supplementary Dataset S4. Phylogeny to be used in PGLS analyses, implemented with Supplementary Code S2.

 

Supplementary Dataset S5. PGLS and OLS dataset to be used with Supplementary Code S2. Myrmecophagy = Myrmecophagy score from Redford (1987); Pseudogenes = Total gene losses for candidate gene set. See Supplementary Table S18.

Supplementary Figure S1: RAxML gene trees based on alignments after cleaning in preparation for PAML analyses. 

Supplementary Figure S2: DNA sequence alignments for ostentorian (Carnivora + Pholidota) genes ACP4, AMBN, AMELX, and AMTN.

Supplementary Figure S3: DNA sequence alignments for ostentorian (Carnivora + Pholidota) genes DSPP, ENAM, KLK4, and MMP20. 

Supplementary Figure S4: DNA sequence alignments for ostentorian (Carnivora + Pholidota) genes ODAM, ODAPH, TAS1R3, MYH16, and PKD2L1.

Supplementary Figure S5: DNA sequence alignments for ostentorian (Carnivora + Pholidota) TAS1R1.

Supplementary Figure S6: DNA sequence alignments for ostentorian (Carnivora + Pholidota) TAS1R2.

Supplementary Figure S7: DNA sequence alignments for xenarthran TAS1R genes.

Supplementary Figure S8: DNA sequence alignments for xenarthran MYH16 and PKD2L1. 

Supplementary Figure S9: DNA sequence alignments for aardvark genes. 

Supplementary Figure S10: DNA sequence alignments for numbat ACP4 and TAS1R2. 

Supplementary Figure S11: DNA sequence alignments for numbat TAS1R1. 

Supplementary Figure S12: DNA sequence alignments for monotreme genes. 

Supplementary Figure S13. Logistic PCA Plot assuming k = 10 and m = 7.

 

Supplementary Figure S14. Scatter plot of myrmecophagy score versus number of oral pseudogenes, with point sizes by count. Fitted OLS and PGLS regression lines are both shown.

Supplementary Table S1: Information on genome assemblies used in this study.

Supplementary Table S2: Species used as outgroups for PAML analyses.

Supplementary Table S3: PAML and pseudogene dating analysis results for ACP4.

Supplementary Table S4: PAML and pseudogene dating analysis results for AMBN.

Supplementary Table S5: PAML and pseudogene dating analysis results for AMELX.

Supplementary Table S6: PAML and pseudogene dating analysis results for AMTN.

Supplementary Table S7: PAML and pseudogene dating analysis results for DSPP.

Supplementary Table S8: PAML and pseudogene dating analysis results for ENAM.

Supplementary Table S9: PAML and pseudogene dating analysis results for KLK4.

Supplementary Table S10: PAML and pseudogene dating analysis results for MMP20.

Supplementary Table S11: PAML and pseudogene dating analysis results for MYH16.

Supplementary Table S12: PAML and pseudogene dating analysis results for ODAM.

Supplementary Table S13: PAML and pseudogene dating analysis results for ODAPH.

Supplementary Table S14: PAML and pseudogene dating analysis results for PKD2L1.

Supplementary Table S15: PAML and pseudogene dating analysis results for TAS1R1.

Supplementary Table S16: PAML and pseudogene dating analysis results for TAS1R2.

Supplementary Table S17: PAML and pseudogene dating analysis results for TAS1R3.



Supplementary Table S18. Candidate gene categorizations for focal taxa and outgroup species for use in logistic PCA and PGLS analyses. Included are functional designations as determined by manual curation of genes in this study or previous studies (reference details in manuscript), as well as through NCBI's eukaryotic genome annotation pipeline. Green cells = gene determined to be functional; Yellow cells = gene determined to be lost. "Pseudogene" may indicate a pseudogene or, in rare cases, a whole gene deletion. Agree and disagree counts are listed at the bottom of each gene, with totals shown at the bottom towards the far right. 

 

Supplementary Table S19. Control gene dataset, including functional status of each. Gene losses indicated by yellow cells and "Low quality" or "No BLAST results" designations. Candidate genes functional / total counts can be found in Figure 1 of the manuscript. See manuscript for details on Manis pentadactyla RefSeq assembly gaps. 

 
Supplementary Code S1. R code for executing logistic PCA analysis, using Supplementary Dataset S3 as input.

 

Supplementary Code S2. R code for executing PGLS and OLS analyses, using Supplementary Datasets S4 and S5 as inputs.