DOI: 10.5061/dryad.2m3v4
title: Data from: A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

description: Whole genome duplication (WGD) is often considered to be mechanistically
 associated with species diversification. Such ideas have been anecdotally
 attached to a WGD at the stem of the salmonid fish family, but remain
 untested. Here, we characterized an extensive set of gene paralogues
 retained from the salmonid WGD, in species covering the major lineages
 (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the
 data in calibrated relaxed molecular clock analyses, we provide the first
 well-constrained and direct estimate for the timing of the salmonid WGD.
 Our results suggest that the event occurred no later in time than 88 Ma
 and that 40–50 Myr passed subsequently until the subfamilies diverged. We
 also recovered a Thymallinae–Coregoninae sister relationship with maximal
 support. Comparative phylogenetic tests demonstrated that salmonid
 diversification patterns are closely allied in time with the continuous
 climatic cooling that followed the Eocene–Oligocene transition, with the
 highest diversification rates coinciding with recent ice ages. Further
 tests revealed considerably higher speciation rates in lineages that
 evolved anadromy—the physiological capacity to migrate between fresh and
 seawater—than in sister groups that retained the ancestral state of
 freshwater residency. Anadromy, which probably evolved in response to
 climatic cooling, is an established catalyst of genetic isolation,
 particularly during environmental perturbations (for example, glaciation
 cycles). We thus conclude that climate-linked ecophysiological factors,
 rather than WGD, were the primary drivers of salmonid diversification.
description: Data files related to
 CO1 diversification analysesThis 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.CO1
 data.7zData files for salmonid
 nuclear gene paralogsThis 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.WGD paralog
 alignments.7zNucleotide sequence data
 used for mitogenome analysesThis 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).Nuc sequences for mitogenome
 analyses.7zProtein sequence data
 for mitogenome analysesThis 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).Prot sequenes for mitogenome
 analyses.7z