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Students received a score for accuracy (0 or 1) and for explanation quality (0, 0.5, or 1) for each evolutionary relatedness question.
For each evolutionary distance, we did 100 replicates.
For each evolutionary history, ten independent replicates were performed.
A single representative probe was used for each evolutionary lineage.
Gene networks for each evolutionary phase (Supplementary Figs S13 S15) also show significant over-representations of the inflammatory and apoptosis-related pathways.
Finally, we calculated an average AICc weight and lower (2.5 %) and upper (97.5 %) quantiles of the distributions of AICc weights for each evolutionary niche model.
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The technical reason is that reliable SDM may not be possible for each separate evolutionary unit at higher resolution clades, because they may not be sampled sufficiently often (~30 sites per evolutionary unit [ 38]).
Using a single sequence for each OTU, evolutionary distances were calculated with the Jukes-Cantor (tree-Markov) model and phlyogenetic trees determined by the Neighbour-Joining method, with 1000 trees generated.
(DOCX 79 kb) Additional file 3: Average AICc weights for each niche evolutionary model.
For each transcript, evolutionary rate was adjusted for the first two principal components and residuals were used as an estimate of population structure-adjusted evolutionary rate.
To perform the tests, we used a reduced dataset, which consisted of one sequence for each major evolutionary lineage that was mutually represented in the plastid and nuclear gene trees (Additional file 7: Figure S7).
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