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In all cases, the fraction of genes that have been inferred to evolve by positive selection is significantly higher in poorly covered genes.
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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.
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.
At first glance, it might seem surprising that the HKY85: π model "correctly" infers conservation in figure 2 A. Given that it uses the correct neutral substitution model one might expect that, similar to figure 1 A, constrained sites would be inferred to evolve faster than neutral sites.
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).
Several of these residues are inferred to be evolving adaptively in all three subspecies, including residues 186 in ESAG6 and 81 and 434 in ESAG2.
In particular, sites where selection and mutational biases oppose might actually be inferred to have evolved under positive selection.
The remaining codons 165V, 472Q and 485A are inferred to be evolving rapidly along the lineage separating the plant parasitic nematodes from the animal parasitic and free-living species studied (branch C, Figure 3).
Saccules type2, present in Scutovertex and Exochocepheus hungaricus, was inferred to have evolved twice from an ancestor lacking porose organs (Fig. 3D).
This is recorded as an annotation of a gene at an internal node in the phylogenetic tree and means that the function is inferred to have evolved along the branch leading to that gene.
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