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Why it might have greater influence at higher levels of rate variation will be explored in future work.
These analyses also suggest that a strict clock may be suitable at slightly higher levels of rate variation when multiple independent loci are available.
Unlike the independent rates analyses, the correlated rates model did not perform well at higher levels of rate heterogeneity (σ = 0.2-2).
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These models are expected to be able to accommodate high levels of rate heterogeneity, and therefore to perform better.
Both the UCLD and random local clock models indicated moderate to high levels of rate variation among lineages (as shown by the coefficient of variation parameter, Table 4), suggesting that a strict clock model was not appropriate for our dataset regardless of performance of the MCMC.
Similarly, our simulation study showed that the high level of rate variation can not be explained solely by the fast turn-over rates of recently transferred genes (Additional file 11).
Of the 25 phylogenetic groups, 20 groups showed a fairly high level of rate variation for gene insertions/deletions among genes, and the confidence interval falls into a small range for each α value (Table 4).
At the highest level of rate variation (σ = 2), all internal node ages were recovered by 67% of analyses under the relaxed clock, compared with none under the strict clock.
Worse still would be a combination of a return to higher levels of interest rates combined with a decline in crop prices.
These higher levels of transcription rates were consistent throughout the whole time of the experiment.
We achieved higher levels of retention rates compared with our previous results in the same target population.
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