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

Dalziel AC, Bittman J, Mandic M, Ou M, Schulte PM

Date Published: June 5, 2014

DOI: http://dx.doi.org/10.5061/dryad.5c6v7

 

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Title Key for Figure 2
Downloaded 9 times
Description Accession numbers for all sequences used in Figure 2 and the short name used in sequence files for PAML and alignments (Appendix S1).
Download Fig2_SequenceIDs_to_GenbankNumbers.txt (2.228 Kb)
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Title Fig4- Pike real time data
Downloaded 38 times
Description Gene expression of Na+, K+ ATPase paralogs and 18S in the Northern Pike (Esox lucius)
Download Fig4_Pike real time datal.xls (27.64 Kb)
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Title Supplementary Fig1
Downloaded 10 times
Description 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.
Download SuppFig1_MrBayes_Jan_7_2013.rtf (2.229 Kb)
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Title Supplementary Figure 2
Downloaded 7 times
Description 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.
Download SuppFig2_RAxML_Dec_30.rtf (2.316 Kb)
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Title Tree file for PAML
Downloaded 28 times
Description Tree file to be used with the one and free ratios models in PAML (Table 1, Test 1a).
Download ATP1A1.trees (1.95 Kb)
Download README.txt (3.217 Kb)
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Title Control file for PAML - Branch Model
Downloaded 37 times
Description Control file for PAML branch model to test for selection along Branch D of Fig.2 (Table 1).
Download BranchModel_BranchD.ctl (1.718 Kb)
Download README.txt (3.217 Kb)
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Title Tree file for PAML - 2
Downloaded 31 times
Description Tree file for PAML's Branch-Site Model A (testing for selection along Branch D of Fig.2. Table 3)
Download BranchModel_BranchD.trees (1.952 Kb)
Download README.txt (3.217 Kb)
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Title Control file for PAML - Branch Null Model
Downloaded 29 times
Description Control file for the null PAML Branch Model testing for selection along Branch D in Figure 2 (Table 1).
Download BranchModel_BranchDnull.ctl (1.756 Kb)
Download README.txt (3.217 Kb)
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Title Control file for PAML - Branch-Sites Model
Downloaded 26 times
Description Control file for PAML`to run Branch-sites Model A along branch D in Figure 2 (Table 3).
Download BranchSite_BranchD.ctl (2.469 Kb)
Download README.txt (3.217 Kb)
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Title Tree file for PAML - 3
Downloaded 18 times
Description Tree file for PAML's Branch-Site Model A, testing for selection in sites along Branch D in Figure 2 (Table 3).
Download BranchSite_BranchD.trees (1.952 Kb)
Download README.txt (3.217 Kb)
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Title Control file for PAML Branch-Site Null Model
Downloaded 15 times
Description Control file for PAML's null Branch-site Model A testing for selection along Branch D in Figure 2 (Table 3).
Download BranchSite_BranchDnull.ctl (2.461 Kb)
Download README.txt (3.217 Kb)
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Title PAML control file - Free Ratio
Downloaded 18 times
Description Control file for PAML's Free-Ratios model (Table 1)
Download FreeRatios.ctl (1.692 Kb)
Download README.txt (3.217 Kb)
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Title PAML control file - Clade model C null (M2a_rel)
Downloaded 79 times
Description Control file for the null model to PAML's Clade Model C (Table 2).
Download M2a_rel.ctl (1.528 Kb)
Download README.txt (3.217 Kb)
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Title PAML control file - Clade model C
Downloaded 104 times
Description Control file for PAML's Clade Model C model testing for divergent selection among all a1a and a1b paralogs (Table 2, Test 2a).
Download ModelC_a1a_a1b.ctl (1.599 Kb)
Download README.txt (3.217 Kb)
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Title Tree file for PAML- 4
Downloaded 23 times
Description Tree file for PAML's clade Model C, to run Test 2a (Table 2).
Download ModelC_a1a_a1b.trees (1.954 Kb)
Download README.txt (3.217 Kb)
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Title PAML Control file - One-Ratio
Downloaded 20 times
Description Control file for PAML's One-Ratio model (Table 1)
Download OneRatio.ctl (1.758 Kb)
Download README.txt (3.217 Kb)
Details View File Details
Title PAML sequence file
Downloaded 26 times
Description Sequence file to use during all PAML models. All 36 species from Figure 2 are included.
Download Seq_ATP1A1.txt (98.26 Kb)
Download README.txt (3.217 Kb)
Details View File Details

When using this data, please cite the original publication:

Dalziel AC, Bittman J, Mandic M, Ou M, Schulte PM (2014) Origins and functional diversification of salinity-responsive Na+, K+ ATPase α1 paralogs in salmonids. Molecular Ecology 23(14): 3483–3503. http://dx.doi.org/10.1111/mec.12828

Additionally, please cite the Dryad data package:

Dalziel AC, Bittman J, Mandic M, Ou M, Schulte PM (2014) Data from: Origins and functional diversification of salinity-responsive Na+, K+ ATPase α1 paralogs in salmonids. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.5c6v7
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