Data from: A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

 

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Title Data files related to CO1 diversification analyses
Downloaded 23 times
Description This zip file contains data related to the diversification analyses. This includes the cytochrome c oxidase 1 DNA alignment in fasta format, the time-calibrated phylogenetic tree in newick format and nexus format (with FigTree annotations including node posterior probabilities and 95% credibility intervals) as well as the state file used in BiSSE as csv.
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Title Data files for salmonid nuclear gene paralogs
Downloaded 14 times
Description This zip file contains 18 nucleotide sequence alignment files in fasta format that were combined in the BEAST analyses that led to the dating of the salmonid whole genome duplication (WGD) event and in a range of other phylogenetic analyses described in the paper (see Figure 2, and Figure S20 and Figure S27 in the electronic supplementary material). Each alignment is in frame, so can be translated into coded protein data easily. These files have names that can be attached to individual phylogenetic tree data provided in the electronic supplementary material of the paper (Figures S1-S18). Note: the nomenclature for species is identical across alignments as follows: Osmerus = Osmerus mordax; Esox = Esox Lucius; Ss1 = Salmo salar WGD paralog 1; Ss2 = S. salar WGD paralog 2; Om1 = Oncorhynchus mykiss WGD paralog 1; Om2 = O. mykiss WGD paralog 2; Cl1 = Coregonus lavaretus WGD paralog 1; Cl2 = C. lavaretus WGD paralog 2; Tt1 = Thymallus thymallus WGD paralog 1; Tt2 = T. thymallus WGD paralog 2.
Download WGD paralog alignments.7z (9.201 Kb)
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Title Nucleotide sequence data used for mitogenome analyses
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Description This zip file contains 26 nucleotide sequence alignment files in fasta format, representing protein-coding genes spanning the mitogenome of 24 salmonid species and 3 related outgroup species. Each of 13 clearly named protein-coding genes is represented by two files, representing codon position 1 and 2, which are stated as P1 and P2. This data was combined in a time calibrated BEAST analysis, dating major divergence times in salmonid evolution and in a range of other phylogenetic analyses described in the paper (see Figures S21-S26 and Figure S28 in the electronic supplementary material).
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Title Protein sequence data for mitogenome analyses
Downloaded 11 times
Description This zip file contains 13 protein sequence alignment files in fasta format, representing 13 proteins coded in the mitogenomes of 24 salmonid species and 3 related outgroup species. This data was used in a range of other phylogenetic analyses described in the paper (see Figures S21-S26 and Figure S28 in the electronic supplementary material).
Download Prot sequenes for mitogenome analyses.7z (8.343 Kb)
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When using this data, please cite the original publication:

Macqueen DJ, Johnston IA (2014) A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proceedings of the Royal Society B 281(17780): 20132881. http://dx.doi.org/10.1098/rspb.2013.2881

Additionally, please cite the Dryad data package:

Macqueen DJ, Johnston IA (2014) Data from: A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.2m3v4
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