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

Abstract

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.

Keywords: anadromy; climate change; evolution; salmonid fish; species diversification; whole genome duplication.

Figure 1.

The importance of considering diploidization outcomes when studying salmonid WGD paralogues. (a) Phylogenetic relationships of hypothetical species derived from the same WGD event (asterisk). (b) Expected phylogenetic tree when diploidization resolution (DR) occurred before speciation events in the WGD lineage. Ancestral paralogue divergence has occurred owing to the disomic inheritance of two physically separate loci. This should be reflected in two sister clades containing paralogues (P) P1 and P2 in each species, ideally recapturing true species relationships. (c) Expected tree when DR had not occurred by the point of speciation, and occurred separately in species 1 and the ancestor to species 2/3. (d) Under a similar scenario to (c), but when DR never occurred in species 1, up to four sequence variants are expected to cluster together, owing to a history of tetrasomic inheritance [14] with concerted evolution owing to gene conversion. Under many feasible scenarios other than that in (a), it will be difficult or impossible to recover the WGD or species relationships using phylogenetic analysis, while the molecular clock hypothesis is grossly negated [22]. Datasets that did not conform to the scenario in (b) were discarded.

Figure 2.

Phylogenetic analyses combining extensive and truly orthologous nuclear sequences across salmonid subfamily species provide compelling statistical support for a sister relationship between Thymallinae (graylings) and Coregoninae (whitefish and ciscos). The presented topology was recovered in phylogenetic analyses concatenating 36 salmonid nuclear gene orthologues representing WGD paralogue pairs. Statistical support did not fall below 0.99 at any studied node across 12 different analyses, including ML/BY/NJ/MP methods employing protein (7222 AA) and nucleotide data (21 666 bp). This included the root of the tree according to a BY method incorporating a relaxed molecular clock model [18]. Phylogenetic analyses contributing to this figure are presented in the electronic supplementary material, figure S20.

Figure 3.

Temporal decoupling of WGD from salmonid species diversification is correlated with historic climate change and the evolution of anadromy. (a) LTT plot (yellow line) showing the accumulation of salmonid lineages through time (right y-axis) based on the CO1 tree (see electronic supplementary material, figure S29). A supporting LTT plot is also shown (black dotted line) based on a similar salmonid tree, taken from an independent study [16]. The red line (left y-axis) shows published oxygen isotopic-based estimates of sea-levels [19], spanning 1 Myr mean intervals (error bars show s.d.). The gradated blue shading indicates the increased propensity towards glaciation episodes in the Northern Hemisphere from the Late Miocene, reflected in rapidly falling sea levels. (b) Temporal evolution of salmonid lineages (scaled as for (a)) based on the mitogenome tree. Major salmonid clades are compressed, with vertical height reflecting the number of recognised species. A and F, respectively, show lineages considered to be ancestrally anadromous or to have retained the ancestral state of pure freshwater residency (after [21,27]). 95% BY credibility intervals for divergence time estimates are shown as red bars. Blue bars show 95% BY credibility intervals from the WGD paralogue analysis. (c) Posterior probability distributions obtained from BiSSE for speciation rates comparing two salmonid groups—species that retained the ancestral state of pure freshwater residency (F) versus lineages whose common ancestor evolved anadromy (A). The shaded areas/bars show 95% credibility intervals.