Figure 4.

Evolutionary rate analyses. (a) The Branch-site test models of Zhang et al.[42]. The schematic represents the alternative model that allows for positive selection. Under the null model, sites fall into site classes 0 or 1 only. The two models are compared using a likelihood ratio test. (b) The number of positively selected genes identified on G. magnirostris, T. guttata, passerine, G. gallus, M. gallopavo, galliform, and avian branches. (c) Average levels of dN/dS for the G. magnirostris or T. guttata lineages for G. magnirostris and T. guttata positively-selected genes (PSGs) and for non-PSGs inferred by parsimony. Alignment showing the candidate Geospiza positively selected codon sites (highlighted in red) in (d) POU1F1 and (e) IGF2R. Alignment visualised with the belvu software [90].