Open Access Research article

Specialization-generalization trade-off in a Bradyrhizobium symbiosis with wild legume hosts

Martine Ehinger1, Toni J Mohr1, Juliana B Starcevich1, Joel L Sachs23, Stephanie S Porter1 and Ellen L Simms1*

Author Affiliations

1 Department of Integrative Biology, University of California, Berkeley, CA, USA

2 Department of Biology, University of California, Riverside, CA, USA

3 Institute of Integrative Genomic Biology, University of California, Riverside, CA, USA

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BMC Ecology 2014, 14:8  doi:10.1186/1472-6785-14-8

Published: 19 March 2014

Additional files

Additional file 1: Table S1:

Title of data: Field-sampled nodules, their source host, identifying symbols, and accession numbers for NifD and ITS sequences submitted to GenBank. Description of data: * host = host species, pln = plant within species, nod = nodule on plant, strain = strain identifier, T-type = inoculation type in greenhouse experiment (blank cells indicate strains not used in that experiment), g’type NifD and g’type ITS identify the NifD and ITS genotypes, respectively, included on Figure  1. Respective NifD and ITS GenBank sequence IDs and accession number are indicated as seq nifD, seq ITS, accession # NifD, and accession # ITS. Blank cells in these columns indicate isolates that did not amplify.

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Additional file 2: Table S2:

Title of data: Separate ANOVA for each host species of plant and bacterial fitness-components. Description of data: Significance: ns, not significant; **, p<0.01; ***, p<0.001. 1 Degrees of freedom for F-test of random block effect: numerator = 9; denominator for (a) = 271, for (b) = 256. 2 Degrees of freedom for F-test of random genotype effect: numerator = 30, denominator for (a) = 271, for (b) = 256. 3 Tests of contrast between Bradyrhizobium groups A (isolated from Acmispon) and L (isolated from Lupinus); degrees of freedom: numerator = 1, denominator for (a) = 271, for (b) = 256.

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Additional file 3: Table S3:

Title of data: Tukey-Kramer honestly significant differences in trait values between Bradyrhizobium genotypes inoculated on two host species, (a) A. strigosus, (b) L. bicolor. Description of data: Genotypes sharing the same capital letter are not statistically significantly different at p < 0.05. * shoot dry weight.

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Additional file 4: Table S4:

Title of data: Generalized linear mixed models fitted to variance in host shoot dry weight. Description of data:+ estimated G-matrix not positive definite. Host = test host species, block = spatial block, strain = Bradyrhizobium genotype, sp_orig = host species from which Bradyrhizobium genotypes were isolated, ge_orig = host genus from which Bradyrhizobium genotypes were isolated. All models assumed a gamma distribution with a logit link function. Model 16 (bold face) provided the best fit (i.e., minimized AICc). Adding the block by host species interaction improved the fit (e(AICmin-AICi)/2 = 5.21 x 10–13) but the proportion of variance explained by this component (4.91% + 2.42%, Additional file 7: Table S7) was only marginally significant. The next best fitting model (model 1) included the fixed effect of host and the random effects of block and Bradyrhizobium genotype, with interactions of host with strain and with block. Residuals plots suggested that this model did not perform much worse than the best model, but nesting Bradyrhizobium genotype into host species from which it was isolated greatly improved the relative likelihood that the model fit the data (model 16 versus model 1; e(AICmin-AICi)/2 = 1.28 × 10–12)). Examination of Q-Q plots revealed that all other models provided much poorer fits to the data.

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Additional file 5: Table S5:

Title of data: ANOVA table of Type III tests of fixed effects on test host shoot dry weight. Description of data: From model 16 of Additional file 4: Table S4.

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Additional file 6: Table S6:

Title of data: Differences of least square means (logits) of shoot dry weight of test hosts by host of origin. Description of data: From model 16 in Additional file 4: Table S4. Test host species: ACST = A.strigosus; LUBI = L. bicolor. Origin host species: ache = A. heermannii; acst = A.strigosus; luar = L. arboreus; lubi = L. bicolor.

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Additional file 7: Table S7:

Title of data: Covariance parameter estimates for random factors associated with test host shoot dry weight. Description of data: From model 16 of Additional file 4: Table S4.

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Additional file 8: Table S8:

Title of data: Least squares means (logits) of shoot dry weight of test plants inoculated with genotypes isolated from the four hosts. Description of data: From model 16 of Table  3.

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