# Gene conversion facilitates the adaptive evolution of self-resistance in highly toxic newts Investigation of the evolution of tetrodotoxin autoresistance in newts and related salamanders. This repository includes datasets used in the analyses conducted for Gendreau et al. (2021) (link to paper). See manuscript for methods. ![Taricha torosa](Taricha_torosa.jpeg) ### 1. Phylogenetic trees Multiple sequence alignments of all Nav paralogs from amphibians and *Danio rerio* can be downloaded here: [All Navs amino acid alignment](SCNA_protein_alignment_RAxML_Tree.fasta) (**Fig. 1** in Gendreau et al. (2021)) and here: [All Navs full coding sequence alignment](SCN_CDS_alignment_RAxML_Tree.fasta) (**Fig. S2** in Gendreau et al. (2021)). Alignment of coding sequences for only exon 26 from all Nav paralogs (**Fig. S3** in Gendreau et al. (2021)) can be found here: [All Navs exon 26 alignment](Exon_26_all_SCNAs.fasta). Alignment of amino acid translations of exon 26 from all Nav paralogs can be found here: [All Navs exon 26 amino acid alignment](Exon26_all_SCNAs_amino_acid.fasta). Coding sequence alignment for exon 26 of only Nav1.4 (**Fig. 2** in Gendreau et al. (2021)) can be downloaded here: [*SCN4A* exon 26 CDS alignment](SCN4A_exon26_RAxML_Tree.fasta) Code for trimming species phylogeny and estimating ultrametric trees for visualization in **Figs. 3, 5, and S10 ** can be found here: [Code for trimming phylogeny](amphibian_time_tree.R) ### 2. Evolutionary rates and selection with PAML Alignment files used for PAML analyses: * [Nav1.1](SCN1A_CDS_alignment.fasta) * [Nav1.2](SCN2A_CDS_alignment.fasta) * [Nav1.3](SCN3A_CDS_alignment.fasta) * [Nav1.4](SCN4A_CDS_alignment.fasta) * [Nav1.5](SCN5A_CDS_alignment.fasta) * [Nav1.6](SCN8A_CDS_alignment.fasta) ### 3. Gene conversion * [Alignment file](SCNA_amphibian_CDS_alignment_geneconv.fasta) and [configuration file](Geneconv_config_SCN1A-2A-3A.cfg) used to search for gene conversion in Nav1.1, Nav1.2, and Nav1.3. Output files: [SCNA_amphibian_CDS_alignment_PAL2NAL.frags](SCNA_amphibian_CDS_alignment_PAL2NAL.frags) and [SCNA_amphibian_CDS_alignment_PAL2NAL.sum](SCNA_amphibian_CDS_alignment_PAL2NAL.sum). * [Alignment file](SCN4A_exon_26_alignment_geneconv.fasta) and [configuration file](Geneconv_config_SCN4A.cfg) used to search for gene conversion in Nav1.4 exons 26a and 26b. Output files: [SCN4ADIVa_2.frags](SCN4ADIVa_2.frags) and [SCN4ADIVa_2.sum](SCN4ADIVa_2.sum) ### 3. Probe sequences * [Probe sequences used for targeted sequencing of amphibian Nav genes](Amphibian_SCN_probes.txt)