Detection of Gene Conversion

We used the program GENECONV to detect potential nonallelic gene conversion events between Na_v paralogs. We used a full codon alignment of all six Na_v paralogs from seven of the eight salamanders included in the study (excluding S. salamandra due to missing data), but targeted our search to include only genes Na_v1.1, Na_v1.2, and Na_v1.3 within each species under the assumption that gene conversion is more likely to occur between closely related sequences that reside on the same chromosome. This increased the power of detecting gene conversion from multiple pairwise comparisons. We also performed a separate search for gene conversion events between duplicate exons 26a and 26b of Na_v1.4. For this analysis, we used a codon alignment of Na_v1.4 exons 26a and 26b from ten salamander species. We assigned a mismatch penalty using gscale = 1 and used corrected P values from 10,000 permutations to determine significance.