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To define the conservation of orthology and synteny of Enterobacteriales genomes in comparison with the Rhizobiales, we compared the S. meliloti and E. coli chromosomes.
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We define the conservation value of old-growth forest by the percentage of species that do not occur in the surrounding modified land-uses: put simply, the more species that are unique to old-growth forests, the greater their importance for conservation.
We use two different metrics to define the conservation value of primary forest in our samples: The proportion of the entire species pool that is unique to primary forest in our samples, and the proportion of primary forest species that are unique to primary forest (herafter, primary forest species are defined as those that were sampled at least once in any of the primary forest sites).
Third, we define the conservation score of the m-kb long human region as the best score obtained at the second step.
To define the conservation score, C R), of a human region R of m-kb long, we implemented the three-step procedure below.
We define the conservation coherency score as the percentage of the pattern's occurrences with coherent conservation, (i.e. occurrences with all genes in an occurrence having the same conservation level; Methods).
The DEX model produced uniform results and defined the conservation status of all three FHTs as least favorable.
We defined
We defined the "conservation ratio", a degree of evolutionary constraint, as the value of the conservation fraction stated above divided by the same value but computed after the random assignment of the orthology data to the proteins (see Methods).
Instead of a fixed threshold level, we defined the conservation ratios for a set of household proteins that do not exhibit an AM-related bias in conservation.
In order to obtain a direct quantitative measure for the degree of AM-related conservation, we defined the conservation ratio, which represents the ratio of the averaged E-values from psiblast (as log10) between the non-mycorrhizal species, and the AM-competent species (dicots or monocots, respectively) (Additional file 14: Table S6a).
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