Using the MPE approach to infer the ancestral states of diel activity patterns [8,9,10,11], we analyzed the adaptive evolution of 33 phototransduction genes (Additional file 1) among diverse lineages of birds in the sauropsid phylogeny (Fig. 1) using the branch model, the branch-site model and clade model C implemented in PAML software [26]. Positively selected genes (PSGs) were identified using the branch-site model and clade model C, and inferences of positive selection remained robust in terms of the initial variation in kappa and ω values.

Many internal branches of the bird clade exhibited no signals of positive selection, and only partial branches were found to be under positive selection (Fig. 1, Table 1). In Ratitae, we found one rod-expressed gene, GRK1, to be under positive selection along the common ancestor branch of the ostrich (Struthio camelus) and the emu (Dromaius novaehollandiae). GRK1 is a photoresponse recovery gene involved in the inactivation of activated rhodopsin. As photoresponse recovery is associated with motion detection [27], the positive selection on the photoresponse recovery gene suggests an increased capacity for motion detection in dim-light conditions. For Carinatae, we initially examined the positive selection along the ancestral branch (branch A in Fig. 1) and found two PSGs (GRK1 and RCVRN) (Fig. 2). Both genes are involved in photoresponse recovery, and evidence of positive selection on these genes, which was also supported by a branch-site unrestricted statistical test for episodic diversification (BUSTED), which provides a gene-wide robust test for evidence of selection (Additional file 2), suggests that ancestral Carinatae may have evolved a particularly enhanced capacity for motion detection in at least dim-light conditions. Moreover, the red-sensitive cone opsin gene LWS and the ultraviolet/violet-sensitive cone opsin gene SWS1 were also found to be under positive selection along the Gallus gallus and Columba livia branches, respectively, suggesting an enhanced ability for bright-light vision in these lineages. One positively selected photoresponse recovery gene, GUCY2D, was identified along the branches leading to Cuculus canorus and the common ancestor branches of Upupa epops and Picus canus, respectively. GUCY2D encodes guanylyl cyclases, which are involved in the resynthesis of cGMP, promoting photoresponse recovery. We also detected signals of positive selection on the red-sensitive cone opsin gene LWS and two photoresponse recovery genes, RCVRN and GUCY2F, in two closely related groups, Passeriformes and Psittaciformes, suggesting their increased capacities for motion detection in bright-light conditions.

Table 1 Positively selected genes detected based on the PAML branch-site model. For convenience, only the ω values of foreground branches are shown. Only the positively selected sites with a high posterior probability support (> 0.900) are shown Full size table

Among the groups examined in Carinatae, owls and falcons showed relatively strong positive selection relative to the other groups in the clade. For falcons (branch H in Fig. 1), we found three positively selected photoresponse recovery genes (GRK1, SLC24A1 and GUCY2D), two of which (GRK1 and SLC24A1) were rod-expressed genes (Table 1, Fig. 2). In particular, SLC24A1 encodes the Na+/Ca2+-K+ ion exchanger, extruding free calcium in the outer segment of rods for the restoration of cGMP concentration. The finding of positive selection on these genes suggests that falcons have evolved an enhanced capability to detect motion in dim-light conditions, consistent with the findings of previous studies [7, 28,29,30,31]. For owls (branch G in Fig. 1), which are most active at night and during crepuscular periods, we found a marginally significant signal of positive selection on one rod-expressed gene, CNGB1 (LRT P-value = 0.050). CNGB1 encodes the β subunit of CNG channels and is involved in phototransduction activation. Moreover, two cone opsin genes, the red-sensitive opsin gene LWS and the blue-sensitive opsin gene SWS2, showed strong signals of positive selection (LRT P-value < 0.001) (Table 1, Fig. 2). Positive selection on these two cone opsin genes is associated with spectral tuning to maximize light abortion under crepuscular conditions [7]. When the evidence for positive selection on the PSGs found by PAML in falcons and owls was examined using BUSTED, positive selection on the gene GRK1 in falcons and the two cone opsin genes LWS and SWS2 in owls was retained (Additional file 2). In addition to the nocturnal owls, we also looked for evidence of positive selection in lineages that contain true nocturnal taxa, including Apterygiformes, Caprimulgiformes and Charadriiformes [1], for which only partial gene sequences were available, but found no evidence of positive selection in these groups. Future studies using retinal transcriptome sequencing would allow us to obtain full-length phototransduction gene sequences and perform detailed analyses of the genes underlying night-vision adaptation in these nocturnal lineages.

In addition to the branch model and branch-site model, we also used clade model C to look for evidence of positive selection on phototransduction genes in birds (Table 2). When the entire clade of birds was analyzed as a foreground clade, we detected relatively strong positive selection signals for both rod-expressed genes (CNGA1, PDE6B, SAG and SLC24A1) and cone-expressed genes (CNGB3, PDE6C and SLC24A2), suggesting that both the dim-light vision and bright-light vision of birds were subject to divergent selection compared to those of the reptiles included in the study. This finding is likely a result of the differential adaptation of different bird lineages to their specific light environments [1].