Supplementary Material
1. Calculating Evolutionary Distinctiveness (ED)
5 We calculated the evolutionary distinctiveness (ED) scores following Isaac et al. (2007).
Each branch of an additive phylogenetic tree (i.e. one with branch lengths assigned) is assigned a value that is simply its length divided by the number of species subtending the branch (i.e. the size of the group that a particular branch defines). So, the branch leading to a species is unchanged (it is fully non-redundant), while an interior branch leading to a
10 clade of two species would be halved, such that each species represents the unique evolution represented by that branch equally. Summing these modified branch lengths across all branches that lie on the path from a species to the root of the tree gives the ED score for that species.
A sample phylogenetic tree is given in Figure 1, accompanied by the ED score for
15 each species. For species A, we have indicated what portion of the branch lengths contribute to its ED scores using red highlighting. Species A and B each have ED = 2 +
1/2 + 1/4 +1/5 = 2.95 million years (my). The ED scores for species C and D = 1 + 2/2 +
1/4 + 1/5 = 2.45my; species E = 4 + 1/5 = 4.20my; species F and G = 1 + 1/2 + 3/3 =
2.50my; and species H = 2 + 3/3 = 3.00my.
20

2. The Phylogeny
25
2.1. Methods
Hyde and Vetter (2007) produced the most complete phylogeny of the Sebastes genus to date, including 97 of the 110 recognized species plus two new cryptic species ( Sebastes miniatus Type 1 [Hyde et al., 2008] and S. saxicola Type N). Eight of the missing 13 species were excluded because they are part of species complexes that are still
30 undergoing lineage sorting (Y. Kai, pers. comm. in Hyde and Vetter 2007). We repeated the Bayesian analysis using the same molecular sequence data (5581 sites from cytochrome b , cytochrome c oxidase subunit 1, 12S rRNA, 16S rRNA, tRNA proline, tRNA threonine and the control region, recombination activating gene 2 and internal transcribed spacer 1) and evolutionary models as Hyde and Vetter (2007) to
35 accommodate 10 of the 13 omitted species and to produce a full posterior distribution of trees.
In order to have all species included in our final set of trees, we assigned molecular sequence data to all the species found in the species complexes by copying the sequence data from those species that Hyde and Vetter (2007) had used to represent the
40 complexes. As the mitochondrial DNA of the Sebastes species within species complexes are not reciprocally monophyletic (Y. Kai, pers. comm. in Hyde and Vetter, 2007), we can assume that using the same sequence data for each species within a species complex will not produce significantly different results than if we used molecular sequence data that had been obtained for each species within the species complex – i.e. we assumed

45 each complex was monophyletic. Because species complexes will contain non-distinctive species almost by definition, the actual (very short) branch lengths leading to these species is less important. The following are the four complexes where the first species of each complex has original molecular data sequenced by Hyde and Vetter (2007): S. hubbsi -- S. longispinis ; S. inermis -- S. cheni -- S. ventricosus ; S. pachycephalus -- S.
50 chalcogrammus -- S. nigricans -- S. nudus ; and S. vulpes -- S. ijimae -- S. zonatus . The species within a given complex were then constrained during the Bayesian analysis to ensure they remained as a monophyletic clade. Two of the five remaining missing species were included in the analysis in the same way, constraining S. itinus , and S. wakiyai to form a monophyletic clade with their putative close relative S. steindachneri
55 (Barsukov, 1981; Y. Kai, pers. comm. in Hyde and Vetter, 2007). Since there is no genetic sequence data available for S. varispinis, S. koreanus and S. nivosus and we were unable to identify sister species from which genetic sequence data could be “borrowed”, we were prevented from including these three species in the Bayesian analysis. We added
60 the three remaining species to the phylogeny after the Bayesian analysis by hand.
We included the closely related sebastid species Sebastiscus marmoratus ,
Hozukius emblemarius and Helicolenus avius as outgroups, for a total of 112 species.
Using MrModeltest v2.2 (Nylander, 2004), we confirmed that all genes but RAG2 were best fit with a Generalized Time Reversal model with invariant sites and among-site variation (modeled as a gamma function) and estimated (or, for tRNAthreonine and
65 tRNAproline, equal) base frequencies. RAG2 was best fit with the simpler Kimura twoparameter model. We followed Hyde and Vetter (2007), partitioning genes into unlinked sets except for tRNA threonine and tRNA proline, which were analysed together. We ran

Metropolis-Coupled Markov Chain Monte Carlo analyses (2 runs for 5 million generations, 4 chains each, default heating and priors, rates=invgamma, nst=6 or nst=2
70 for RAG2) in MrBayes v3.1.2 (Huelsenbeck and Ronquist, 2001; Ronquist and
Huelsenbeck, 2003). We sampled every 5000th tree to obtain 1000 trees from each run and discarded the first 25% (burnin = 250), leaving a total of 1502 trees to comprise the posterior distribution of trees from which one 50% majority-rule consensus tree was formed. To convert the additive trees that were produced in the Bayesian analysis to
75 ultrametric trees, we used the program r8s (version 1.70, Sanderson 2003). We scaled all rates and times for each tree to have unit depth (i.e. the root of the tree was set to be 1.0 units from the tips for every tree) because there is currently uncertainty as to the absolute age of the genus (C. Brock and M. Alfaro, pers. comm.). We completed this conversion for the consensus tree as well as for each of the 1502 trees in the posterior distribution.
80 The final three species were then added to the phylogeny. S. varispinis was placed at the base of the clade containing S. peduncularis , S. cortezi , S. sinensis , S. melanosema and S. diploproa as a polytomy. S. peduncularis , S. cortezi and S. sinensis coexist in Gulf of California and S. varispinis is most likely related to the sinensisdiploproa-cortezi complex (Chen, 1975). Genetic lineage sorting between these species
85 is also still taking place (J. Hyde, unpub. data in Hyde and Vetter, 2007). There is little data available for both S. koreanus and S. nivosus besides the understanding that they are both related to the S. pachycephalus complex, the S. hubbsi complex and S. oblongus , as suggested by cytochrome b data (Y. Kai, pers. comm. in Hyde and Vetter, 2007).
Therefore, S. koreanus and S. nivosus were placed at the base of this clade, bringing the
90 total number of Sebastes species to 112. By placing these few species at the base of

different clades, we created two soft polytomies in the tree that represent phylogenetic uncertainty (as distinct from hard polytomies that represent a species radiation). This is an important distinction because when evolutionary distinctiveness (ED) is calculated, soft polytomies lead to over-inflated ED scores for those species that descend from the
95 multi-furcating node (Isaac et al., 2007). Their actual isolation is less, as these species could branch farther up in the clade. We therefore followed Isaac et al. (2007), shortening the branch lengths leading to the species descending from these two nodes by a simple factor based on a pure-birth model of evolution.
100 2.2. Results
The Bayesian analysis produced a well-supported phylogeny (Fig. 1), containing only four nodes in the consensus tree with <50% consensus support. After five million generations the average standard deviation of split frequencies was 0.009, indicating
105 convergence of the two runs (Ronquist et al., 2005). Aside from the species we added, there are only three very minor differences between the consensus tree that we produced and that of Hyde and Vetter (2007). The nodes at which these changes took place have low posterior probabilities, as expected. The consensus tree has a negative score (-1.00) for Pybus’ gamma (Pybus and Harvey, 2000), and has a score greater than 0.5 (0.645) for
110 Purvis et al.’s (2002) Iw, meaning that interior edges are shorter, and there is more variation in clade sizes through the tree, relative to random diversification. Such aspects of the tree increase the variation in ED across species (Redding et al., 2008). The ED scores of the additive and ultrametric consensus tree are well correlated (r = 0.809, p <

0.0001, n = 112), indicating that the process of transforming branch lengths from the
115 number of nucleotide substitutions to a measure of relative time using auto-correlated rate variation did not overly distort the branch lengths.

120 3. Principal Components Analysis
Supplementary Table 1. Summary of principal component analysis used to quantify morphological distinctiveness of rockfish species.
Traits are species means, log-transformed in all cases except gill raker number.
Percent Variance
Explained
Cumulative Variance
Explained
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16 PC17 PC18
87.36 8.19 1.49 0.99 0.55 0.40 0.35 0.26 0.11 0.09 0.05 0.05 0.04 0.03 0.02 0.01 0.01 0.00
87.36 95.54 97.03 98.03 98.58 98.97 99.32 99.58 99.70 99.79 99.84 99.89 99.93 99.96 99.98 99.99 100.0 100.0
Factor Loadings
Total Length
Head Length
Snout Length
Pre-Pectoral Length
-0.25 0.04 -0.19 0.05 -0.11 0.07 -0.19 0.01 -0.26 0.07 -0.23 0.22 0.15 -0.72 0.05 0.25 -0.25 0.03
-0.25 -0.06 0.04 0.16 0.00 -0.03 0.00 0.04 -0.10 0.02 -0.12 -0.24 0.00 -0.26 0.23 -0.40 0.67 0.31
-0.25 -0.07 0.02 0.35 -0.04 0.14 -0.30 -0.36 0.09 0.12 -0.24 -0.26 0.52 0.35 -0.06 0.15 -0.05 0.04
-0.25 -0.04 0.06 0.18 -0.06 -0.07 -0.16 -0.16 0.13 -0.04 -0.04 0.13 -0.16 -0.08 0.02 -0.38 0.02 -0.79
Pre-Pelvic Length
Interopercular Width
-0.25 0.00 -0.03 0.15 -0.09 -0.16 -0.29 -0.33 0.12 -0.15 0.11 0.49 -0.42 0.18 0.08 0.02 -0.03 0.42
-0.25 -0.12 -0.05 0.02 0.08 -0.29 0.26 -0.02 -0.09 -0.83 0.00 -0.11 0.19 -0.02 -0.13 0.08 -0.05 -0.01
Interorbital Width -0.23 0.22 -0.28 -0.09 -0.62 0.05 -0.14 0.49 0.26 -0.10 0.14 -0.05 0.12 0.17 0.13 -0.02 0.01 0.00
Eye Size (horizontal) -0.24 0.08 0.53 -0.06 0.12 -0.21 -0.11 0.16 -0.16 0.05 0.17 -0.13 -0.03 0.08 0.57 0.37 -0.05 -0.12
Eye Size (vertical)
Upper Jaw Length
Lower Jaw Length
-0.24 0.08 0.50 -0.14 0.13 -0.20 -0.13 0.32 0.19 0.12 -0.09 0.23 0.21 -0.05 -0.52 -0.18 -0.03 0.15
-0.25 -0.13 0.02 0.27 0.07 0.12 0.38 0.06 0.06 0.16 0.28 -0.10 0.04 -0.04 0.18 -0.41 -0.57 0.21
-0.25 -0.07 0.00 0.28 -0.03 0.19 0.28 -0.01 0.02 0.16 0.55 0.11 0.00 -0.08 -0.32 0.40 0.35 -0.12
Gill Arch Length
(lower)
Gill Raker Number
-0.25
0.07
0.00
0.77
0.02
-0.23
0.22
0.37
-0.07
0.38
0.07
-0.21
0.27
-0.06
0.23
0.08
-0.06
0.03
0.09
0.00
-0.56
0.06
-0.19
-0.09
-0.53
-0.01
0.17
-0.02
-0.18
-0.03
0.22
-0.02
-0.07
-0.01
-0.01
-0.01

Gill Raker Length
(longest)
Pectoral Fin Length
Pectoral Fin Width
Pelvic Spine Length
Pelvic Fin Length
-0.18 0.54 0.23 -0.36 -0.27 0.23 0.37 -0.47 -0.09 -0.02 -0.08 0.02 0.04 0.00 -0.01 -0.08 0.01 0.01
-0.25 -0.01 -0.21 -0.23 0.02 -0.09 -0.24 0.01 -0.71 0.13 0.23 -0.16 -0.10 0.25 -0.26 -0.18 -0.06 -0.03
-0.24 -0.09 -0.32 -0.36 0.08 -0.54 0.15 -0.22 0.37 0.35 0.00 -0.22 -0.03 -0.09 0.00 0.12 0.00 -0.01
-0.24 0.02 -0.06 -0.31 0.41 0.54 -0.30 0.02 0.30 -0.21 0.10 -0.27 -0.22 -0.12 -0.04 0.04 -0.04 0.02
-0.25 -0.03 -0.28 -0.16 0.38 0.16 0.23 0.17 -0.06 0.07 -0.22 0.52 0.24 0.30 0.26 -0.02 0.15 -0.09

125

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