Protein sequence data for mitogenome analyses

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)

Data files for salmonid nuclear gene paralogs

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

Data files related to CO1 diversification analyses

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

Nucleotide alignment for the 508-sequence 16S rRNA tree

Nucleotide alignment for the 508-sequence 16S rRNA tree, derived from merging non-redundant sequences available from the Silva database with non-redundant 454 dataset

613_sequence amoA tree

Bayesian 613-sequence phylogenetic amoA tree derived from merging non-redundant sequences available from GenBank database with non-redundant 454 dataset

Nucleotide alignment for the 370-sequence amoA tree

Nucleotide alignment (codon positions 1 and 2) for the 370-sequence amoA tre

Nucleotide alignment for the 613-sequence amoA tree

Nucleotide alignment for the 613-sequence amoA tree (codon positions 1 and 2), derived from merging non-redundant sequences available from GenBank database with non-redundant 454 dataset

508-sequence 16S rRNA tree

Bayesian 508-sequence phylogenetic 16S rRNA tree derived from merging non-redundant sequences available from the Silva database with non-redundant 454 dataset