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Finally, sites inferred to evolve under a Ka/Ks ratio not significantly different from 1 are regarded as free from selection at the protein level [ 6].
In all cases, the fraction of genes that have been inferred to evolve by positive selection is significantly higher in poorly covered genes.
The effect was quantitatively stronger in the Drosophila clade than in the Tephritidae (Additional File 6, Table S3); 16 sites were inferred to evolve neutrally in Drosophila, but only 1 in the Tephritidae.
They are particularly detrimental to molecular evolution studies, since they can seriously inflate the number of sites inferred to evolve under positive selection or the number of insertion and deletion events.
In fact, given that the expected divergence at the constrained sites can be higher than that at the neutral sites, such sites might even be inferred to evolve under positive selection.
In accordance with this observation, under the CAT model, most sites are indeed inferred to evolve under highly peaked amino-acid profiles (figure 3 in [ 31]), that give a significant probability to only a few amino-acids.
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Based on the topologies of the MPTs, the derived state is inferred to have evolved independently in Sphenisciformes and Plotopteridae.
Syncarpy was inferred to have evolved once with no losses or c. four times with four losses within Annonaceae (Table 1).
In particular, sites where selection and mutational biases oppose might actually be inferred to have evolved under positive selection.
We found that two of the codons inferred to be evolving under positive Darwian selection, B4 and C49, had changed in parallel (fig. 4).
Saccules type2, present in Scutovertex and Exochocepheus hungaricus, was inferred to have evolved twice from an ancestor lacking porose organs (Fig. 3D).
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