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Our MSS results under a codon model (divergence at 12.0 MY) may suggest that sufficient information exists in the data without this additional calibration point.
High FST and a lack of evidence for admixture in our cluster analyses also led us to model divergence in isolation.
In our DTLI model, divergence in a gene tree arises through one of four events: duplication, transfer, speciation and deep coalescence.
In support of the selection model, divergence, taken as a proxy for the rate of mutation, had either no effect or an unexpected minor negative effect.
The positive value derived for model divergence (0.66%/hour) indicates that the difference between predicted and actual Org25435 plasma concentrations increased over time.
Based on the coalescent model, divergence of the Mallorcan clade B -comprising localities from the central area of the island- can be traced back at 2.3-2.7 2.3-2.7reas that of clade E - occupying the N and NE of the island- seeMa to have occurred at 2.0-2.4 Ma.
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However, there is no guarantee this assumption is true, since those algorithms do not rely on any theoretical background to ensure that model divergences truly indicate data changes.
More details on the inter-model divergence are presented in the Discussion section.
Despite differences in performance among the three clock models, divergence time estimates among oomycetes were strikingly consistent (Table 3 and Additional file 2), and all models estimated a mid-Paleozoic origin for oomycetes.
Log-likelihood tests comparing models of divergence without gene flow (Model 0) and with gene flow (Models 1 & 2) in 3s supported divergence with gene flow for each of the five contacts (Additional file 2: Table S2).
Development of computational methods that properly model the divergence of expression breadth or specificity across species may be an important part of comprehensively assessing conservation of gene expression.
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