Supplementary Materials

Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammals

Wynn K. Meyer, Jerrica Jamison, Rebecca Richter, Stacy E. Woods, Raghavendran Partha, Amanda Kowalczyk, Charles Kronk, Maria Chikina, Robert K. Bonde, Daniel E. Crocker, Joseph Gaspard, Janet M. Lanyon, Judit Marsillach, Clement E. Furlong, Nathan L. Clark

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • ┬áMaterials and Methods
  • Figs. S1 to S6
  • Tables S2, S3, S6, S8, S11, and S12
  • Captions for Tables S1, S4, S5, S7, S9, S10, and S13
  • References
Table S1
Predicted presence/absence/excluded (NA) values for extant species and results of BayesTraits model comparison for gene loss (where applied) for all 9,950 genes included in the analysis, 3,904 genes excluded from analysis but whose loss rates were used for simulations, and 6,140 genes excluded from analysis and simulations due to missing data filters or all-0 or all-1 calls
Table S4
GOrilla gene ontology enrichment for top genes lost in marine lineages, with gene lists (see Table S2).
Table S5
Additional gene set enrichment for top genes lost in marine lineages, with gene lists (see Table S3).
Table S7
Gene ontology enrichment for top genes that co-evolve with PON1, with gene lists (see Table S6).
Table S9
Results from manual validation of pseudogene calls for 20 top genes, 5 genes representing known cases of pseudogenization, and 20 randomly selected genes, using manual checks of the sequences within the 100-way alignment.
Table S10
Results from manual validation of pseudogene calls for 20 top genes, 5 genes representing known cases of pseudogenization, and 20 randomly selected genes, using sequences from the reference genomes for all 58 species
Table S13
Values from triplicate assays of hydrolysis for four PON1 substrates and alkaline phosphatase control (means plotted in Figs. 2 and S2).