Table 1.
Species included in the study.
Table 2.
Genes sequenced and aligned for phylogenetic analysis.
Figure 1.
Maximum clade credibility ultrametric phylogeny for the 16 Bodega Bay species.
Obtained from BEAST analyses using all genes (COI, 16S, 18S), branch lengths are in uncalibrated (relative) time units. Node labels are posterior probabilities. The isopods (Paracerceis cordata and Idotea resecata) are the outgroup.
Figure 2.
50% majority rule consensus cladogram for all 88 species based on the nuclear gene 18S.
Node labels give posterior probabilities. Branch lengths are not meaningful. As shown in the upper left diagram, the cladogram consists of the Isopoda outgroup, and two subsections: A) suborder Gammaridea, and B) suborder Corophiidea. Two species (*) are grouped with the Corophiidea (although with low support), but are classified as Gammaridean. Rounded brackets show families with monophyletic topologies, plus the monophyletic superfamily Lysianassoidea (**). Monophyly brackets are supported with probability >0.99 with the exception of two families marked with ***. Non-monophyletic families are marked with vertical lines; families with no marking are represented by 1 species. New sequences from Bodega Bay are marked with BB for the 14 amphipod species with trait data and bb for the 2 without.
Figure 3.
Comparison of phylogenies obtained for the 16 Bodega Bay species.
A) mitochondrial gene tree (COI and 16S), B) nuclear gene tree (18S), C) topology for Bodega Bay species extracted from the 88 species 18S tree shown in Figure 2. All trees are 50% majority rule consensus trees from MrBayes analyses, with the node labels giving posterior probabilities. For full species names see Figure 1 (note that multiple genera with the same initial letter are abbreviated here). The only conflict between these topologies is within the Talitroidea (Protohyale frequens, Parallorchestes cowani, and Allorchestes angusta). However, the alternate topology obtained in the 88 species analysis is not well supported; the posterior probability = 0.89, where strong support is typically >95% for posterior probabilities (rather than >70% for bootstrap probabilities [89], [90]).
Figure 4.
Relative phylogenetic signal in A) continuous, and B) discrete traits.
For continuous traits, signal was assessed using both Blomberg’s K and Pagel’s λ, with significance tests for each. For discrete traits, signal was assessed with Pagel’s λ. The dashed lines indicate the p = 0.05 significance threshold for each test. The distributions of K, λ, and their p-values result from testing for phylogenetic signal across 1000 trees sampled from the Bayesian posterior distribution of ultrametric trees. Within the continuous and discrete categories, traits are ordered top to bottom from most to least evidence for phylogenetic signal. Signal in continuous feeding rates for eelgrass, detritus, and epiphytes decreased when examined on a per-mg of grazer basis (eelgrass: mean K decreased [0.9 to 0.7], mean λ decreased [1.0 to 0.8]; detritus: K decreased [0.8 to 0.5], λ decreased [0.9 to 0.02]; epiphytes: K decreased [0.6 to 0.5], λ decreased [0.3 to 0.03]; p-values for all tests increased). Results were opposite for macroalgae (mean K increased [0.4 to 0.6], mean λ increased [0 to 0.3], and p-values decreased).
Figure 5.
Relationship between phylogeny and A) biomass and fecundity, B) temperature tolerance and tube building.
In A) larger circles represent higher biomass (dry weight) and fecundity (eggs per female) on log scales. In B) temperature tolerance is measured as the reduction in average survival time in the elevated temperature treatment (25°C) compared to controls. Larger circles indicate a larger effect of elevated temperature (i.e., lower tolerance). Species with non-significant effect of treatment (using survival analysis) have the effect set to 0 (this is indicated by a+sign). Additional figures with both means and standard errors for each trait are available as supplementary material (Figure S1).
Figure 6.
Relationship between phylogeny and A) feeding rates, B) stable isotope signatures.
In A) circle size indicates feeding rates (species with non-significant feeding rates on a particular food [compared to controls] have that rate set to 0; this is indicated by a+sign). Feeding rates for eelgrass, detritus, and macroalgae (Ulva spp.) were measured in mg wet weight consumed per individual per day, so circle size is comparable between those foods. Feeding rates on epiphytes were measured in µg chla per individual per day, and so are not on the same scale as the other 3 foods. In B), larger circles indicate higher δ13C or δ15N. The scale is comparable across seasons within a single isotope only (i.e., N or C). Note that the 3 species found on the outer coast have been trimmed from the phylogeny and excluded from the analysis of phylogenetic signal. The species with missing winter values is present only in the summer. Additional figures with both means and standard errors for each trait are available as supplementary material (Figure S1).
Figure 7.
Grazers are represented with error bars (±1 Standard Error [SE]) and primary producers with shaded boxes (±1SE). Panels show signatures in A) winter and B) summer.