Data from: Origins and functional diversification of salinity-responsive Na+, K+ ATPase α1 paralogs in salmonids

We found that these paralogs arose during a small scale duplication event prior to the Salmoniform, but after the teleost, whole-genome duplication. The ‘freshwater paralog’ (α1a) is primarily expressed in the gills of Salmoniformes and an unduplicated freshwater sister-species (Esox lucius), and experienced positive selection in the fresh-water ancestor of Salmoniformes and Esociformes. Contrary to our predictions, the ‘saltwater paralog’ (α1b), which is more widely expressed than α1a, did not experience positive selection during the evolution of anadromy in the Coregoninae and Salmonine.

To determine if parallel mutations in Na+, K+ ATPase α1 may contribute to salinity tolerance in other fishes, we studied independently evolved salinity-responsive Na+, K+ ATPase α1 paralogs in Anabas testudineus and Oreochromis mossambicus. We found that a quarter of the mutations occurring between salmonid α1a and α1b in functionally important sites also evolved in parallel in at least one of these species. Together, these data argue that paralogs contributing to salinity tolerance evolved prior to the Salmoniform whole-genome duplication and that strong selection and/or functional constraints have led to parallel evolution in salinity-responsive Na+, K+ ATPase α1 paralogs in fishes.

Usage notes

Key for Figure 2 Accession numbers for all sequences used in Figure 2 and the short name used in sequence files for PAML and alignments (Appendix S1). Fig2_SequenceIDs_to_GenbankNumbers.txt Fig4- Pike real time data Gene expression of Na+, K+ ATPase paralogs and 18S in the Northern Pike (Esox lucius) Fig4_Pike real time datal.xls Supplementary Fig1 Teleost Na+, K+ ATPase α1 (ATP1A1) gene tree reconstructed using Bayesian inference (BI) with MrBayes version 3.2.1 (Ronquist et al. 2012) and the GTR+I+Γ model of nucleotide evolution.

SuppFig1_MrBayes_Jan_7_2013.rtf Supplementary Figure 2 Teleost Na+, K+ ATPase α1 (ATP1A1) gene tree reconstructed using the maximum likelihood (ML) method with RAxML software version 7.2.7 (Stamatakis 2006) and the GTR+Γ model of nucleotide evolution. SuppFig2_RAxML_Dec_30.rtf Tree file for PAML Tree file to be used with the one and free ratios models in PAML (Table 1, Test 1a). ATP1A1.trees Control file for PAML - Branch Model Control file for PAML branch model to test for selection along Branch D of Fig.2 (Table 1).

BranchModel_BranchD.ctl Tree file for PAML - 2 Tree file for PAML's Branch-Site Model A (testing for selection along Branch D of Fig.2. Table 3) BranchModel_BranchD.trees Control file for PAML - Branch Null Model Control file for the null PAML Branch Model testing for selection along Branch D in Figure 2 (Table 1). BranchModel_BranchDnull.ctl Control file for PAML - Branch-Sites Model Control file for PAML`to run Branch-sites Model A along branch D in Figure 2 (Table 3).

BranchSite_BranchD.ctl Tree file for PAML - 3 Tree file for PAML's Branch-Site Model A, testing for selection in sites along Branch D in Figure 2 (Table 3). BranchSite_BranchD.trees Control file for PAML Branch-Site Null Model Control file for PAML's null Branch-site Model A testing for selection along Branch D in Figure 2 (Table 3). BranchSite_BranchDnull.ctl PAML control file - Free Ratio Control file for PAML's Free-Ratios model (Table 1) FreeRatios.ctl PAML control file - Clade model C null (M2a_rel) Control file for the null model to PAML's Clade Model C (Table 2).

M2a_rel.ctl PAML control file - Clade model C Control file for PAML's Clade Model C model testing for divergent selection among all a1a and a1b paralogs (Table 2, Test 2a). ModelC_a1a_a1b.ctl Tree file for PAML- 4 Tree file for PAML's clade Model C, to run Test 2a (Table 2). ModelC_a1a_a1b.trees PAML Control file - One-Ratio Control file for PAML's One-Ratio model (Table 1) OneRatio.ctl PAML sequence file Sequence file to use during all PAML models.

All 36 species from Figure 2 are included. Seq_ATP1A1.txt