Framing the Salmonidae family phylogenetic portrait: a more complete picture from increased taxon sampling

Abstract

Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63) to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY) old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ~0.31%/MY (CI: 0.27-0.36%/MY). Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our findings represent an important contribution to the systematics of Salmonidae, and provide a useful tool for addressing questions related to fundamental and applied evolutionary issues.

Figure 1. Unrooted ML phylogram based on the cytochromes data set.

A: Nodes with bootstrap values less than 75% are indicated with open circles (n = 29). For some deep nodes, ML bootstrap support/BAY posterior probabilities/MP bootstrap supports are shown above the node. B: Radial view of the same tree. Abbreviations: B = Brachymystax, C = Coregonus, H = Hucho, O = Oncorhynchus, Pa = Parahucho perryi, P = Prosopium, Sm = Salmo, Sv = Salvelinus, Svth = Salvethymus svetovidovi, St = Stenodus leucichthys and T = Thymallus. Numbers beside each sample correspond to identification numbers in Table S1.

Figure 2. Strict consensus of 48 MP trees inferred using MitoNuc-NT showing the distribution of sequences across taxa.

Bootstrap support values are indicated above branches; Bremer support indices are shown below branches. Underlined Bremer support indices indicate nodes that support significant clades. Nodes with bootstrap values less than 75% are indicated with open circles, as are nodes where conflicts between mitochondrial and nuclear genes were detected (n = 5; Bremer supports partitioned by genomic compartment are annotated in the following order: Mitochondrial/Nuclear).

Figure 3. ML tree inferred by the MitoNuc-NT data set with 1 model of molecular evolution.

A: Nodes with less than 75% bootstrap support are indicated by open circles (n = 24). Bootstrap values less than 100% are denoted above branches and posterior probabilities less than 100% for BAY analyses are shown under branches. B: Radial view of the same tree.

Figure 4. Phylogenetic analyses for MitoNuc25-NT and MitoNuc25-RY.

For MP trees (A and C), bootstrap values are indicated above branches and Bremer support values are below branches. Underlined Bremer support indices indicate significant clades. Bremer support indices are partitioned by genomic compartment (Mitochondrial/Nuclear) at nodes where conflicts occur. For ML trees (B and D), bootstrap values are indicated above branches and BAY posterior probabilities are shown below branches.

Figure 5. Alternative rooting for Salmonidae based on posterior probabilities of 10,000 MC³ trees.

Boxes on radial phylograms indicated the location of the magnified areas to the left of each tree. The width of the branches indicates posterior probabilities for the position of the outgroup and the length of the branches represents the average of the posterior distributions. Trees in the left column show inferences for NT matrices; trees in the right column show inferences for RY matrices. A: Esociformes: NT 99.1% RY 57.9% (Thymallinae); NT 0.9% RY 35.2% (Salmoninae); RY 6.9% (Coregoninae); B: Alepocephaloidea: NT 3.5% RY 11.8% (Thymallinae); NT 61.6% RY 4.8% (Salmoninae); NT 34.8% RY 42.6% (Coregoninae); C: Argentinoidea: NT 22.5% RY 67.8% (Thymallinae); NT 41.4% RY 13.9% (Salmoninae); NT 33.1% RY 7.3% (Coregoninae); D: Osmeroidei: RY 0.3% (Thymallinae); RY 0.1% (Salmoninae); NET 2.2% RY 2.2% (Coregoninae).

Figure 6. Chronogram of Salmonidae inferred on the MitoNuc-NT ML tree with a constrained fixed age of 50MY for †Eosalmo driftwoodensis (node 1, identified by a star).

Other fossil calibration points employed as a constrained minimum age are identified by numbers in circles to the left of the appropriate nodes: †Paleolox larsoni (node 2); †Oncorhynchus lacustris (node 3); †O. rastrotus (node 4); †O. keptosis (node 5). Confidence intervals for principal divergence dates (family, subfamilies, genera and calibration points) are indicated by rectangles superimposed on the nodes indicating these divergences.