The model with the highest LOD score was fitted to the QTL and when the models did not differ significantly the simpler model was chosen ('one locus-one trait').
Neglecting viscous effects, significantly simpler and faster models are available, but may not provide sufficient information regarding the true nature of the flow.
The regression models increasingly included more transcription factors until the prediction performance of the more complex model (e.g. three transcription factors) did not significantly improve on the simpler model (i.e. two transcription factors).
The model allowing distinct rates of speciation and extinction for clownfishes and damselfishes also explained the data significantly better than the simpler model where both groups have the same rate (median likelihood ratio test P = 0.02).
In addition, we found that a model allowing a variation in ω between toothed whales and baleen whales is significantly better than a simpler model estimating the same ω for both major lineages of whales (P = 0.04, χ test).
Of the nucleotide models commonly implemented for phylogenetic analysis, the general time-reversible model incorporating parameters for invariant sites, as well as among-site rate heterogeneity (GTR+I+Γ) [ 28- 30] was found to fit the data significantly better than any simpler model.
We found that a model that allows a variation in ω between the common ancestor (ω1 = 0.15) and all 16 nonwhale mammals (ω2 = 0.35) is significantly better than a simpler model that assumes the same ω (ω0 = 0.16) across the tree (P = 0.016), which suggested that a functional relaxation of Pkd2l1 arose in the common ancestor of whales.
The likelihood ratio chi-squared test produced a p-value indicating whether the simpler model was significantly worse than the previous model; this provided a second test to support the AIC comparison and also provided p-values for significance of model terms.
The model is intended to capture the mobility and routing in the LAROD ns-2 simulations used in Section 4.3, but still be manageable so that using the model is significantly simpler than using simulations.
Although this compartment model is significantly simpler than the initial reaction-diffusion system, it still allows a consistent description of reaction-diffusion transport in underlying system [ 25, 26, 28].
