Open Access Research article

Rates of evolution in stress-related genes are associated with habitat preference in two Cardamine lineages

Lino Ometto, Mingai Li, Luisa Bresadola and Claudio Varotto*

Author Affiliations

Department of Biodiversity and Molecular Ecology, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy

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BMC Evolutionary Biology 2012, 12:7  doi:10.1186/1471-2148-12-7

Published: 18 January 2012

Additional files

Additional file 1:

Genes in functional classes. Venn-diagrams showing the numbers of genes in the functional classes considered in this study.

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Additional file 2:

Correlation between substitution rate and gene length. Plot showing the correlation between the length of the A. thaliana orthogous gene and the substitution rate in C. impatiens and C. resedifolia genes.

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Additional file 3:

Rate of synonymous and non-synonymous substitution in Cardamine genes. I. Mean substitution rate in C. resedifolia and C. impatiens genes included in the four functional classes considered in this study. Statistical comparisons within and between lineages are also reported, including those calculated for values corrected for gene length.

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Additional file 4:

Number of genes identified by likelihood ratio tests that compared branch, site and branch-site codon substitution models. Number of genes identified (at decreasing probabilities thresholds) as putative targets of positive selection by likelihood ratio tests based on branch models (B tests, Table S4.1), site models (S tests, Table S4.2), and branch-site models (BS tests, Table S4.3).

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Additional file 5:

Description of the top ten genes identified by likelihood ratio tests that compared various codon substitution models. Top ten genes identified as putative targets of positive selection by likelihood ratio tests based on branch models (B tests, Tables S5.1-S5.3), site models (S tests, Tables S5.4-S5.5), and branch-site models (BS tests, Tables S5.6-S5.7).

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Additional file 6:

Phylogenetic trees of candidate genes. Phylogenetic trees for the five genes that were putative targets for positive selection (at FDR < 0.20) according to likelihood ratio tests based on the site and branch-site codon substitution models implemented in PAML.

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Additional file 7:

Correlation between the temporal breadth of expression and levels of selection. Spearman's correlations between levels of selection and both the spatial and temporal breadth of expression.

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Additional file 8:

Correlation between rate of molecular evolution and level of gene expression. Mean and maximum expression levels, and Spearman's correlations between such expression levels and levels of selection for the genes included in the four functional classes considered in this study.

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Additional file 9:

Rate of synonymous and non-synonymous substitution in Cardamine genes. II. Mean substitution rate in C. resedifolia and C. impatiens genes included in the four functional classes considered in this study. Comparisons of the values corrected for expression levels.

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Additional file 10:

Optimal codons in Cardamine. Putative optimal codons identified in C. resedifolia and C. impatiens.

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Additional file 11:

Codon usage bias in Cardamine genes. Mean codon usage bias, measured as Fop, in the four functional classes considered in this study. Statistical results of the comparisons between functional classes and species are also reported.

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Additional file 12:

Definition of the Gene Ontology (GO) terms associated with the functional classes analyzed in this study. GO terms and associated function used to identify genes in our dataset that were putatively involved in cold response, photosynthesis, and general stress response.

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Additional file 13:

Cold responsive genes. List of genes identified as involved in cold response in previous studies.

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