Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

To gain insights into the evolution and ecology of visually acute animals such as birds, biologists often need to understand how these animals perceive colors. This poses a problem, since the human eye is of a different design than that of most other animals. The standard solution is to examine the spectral sensitivity properties of animal retinas through microspectophotometry-a procedure that is rather complicated and therefore only has allowed examinations of a limited number of species to date. We have developed a faster and simpler molecular method, which can be used to estimate the color sensitivities of a bird by sequencing a part of the gene coding for the ultraviolet or violet absorbing opsin in the avian retina. With our method, there is no need to sacrifice the animal, and it thereby facilitates large screenings, including rare and endangered species beyond the reach of microspectrophotometry. Color vision in birds may be categorized into two classes: one with a short-wavelength sensitivity biased toward violet (VS) and the other biased toward ultraviolet (UVS). Using our method on 45 species from 35 families, we demonstrate that the distribution of avian color vision is more complex than has previously been shown. Our data support VS as the ancestral state in birds and show that UVS has evolved independently at least four times. We found species with the UVS type of color vision in the orders Psittaciformes and Passeriformes, in agreement with previous findings. However, species within the families Corvidae and Tyrannidae did not share this character with other passeriforms. We also found UVS type species within the Laridae and Struthionidae families. Raptors (Accipitridae and Falconidae) are of the violet type, giving them a vision system different from their passeriform prey. Intriguing effects on the evolution of color signals can be expected from interactions between predators and prey. Such interactions may explain the presence of UVS in Laridae and Passeriformes.

Sexual selection often favors brighter and exaggerated traits, which also increase the risk of detection by predators. Signals that are preferentially conspicuous to conspecifics would reduce the predation cost of signaling and, therefore, might facilitate the evolution of stronger sexual and social signals. This selective signaling is possible if predators and prey have differently tuned sensory systems. By using a retinal model to compare reflectance from the plumages of Swedish songbirds to the reflectance of their natural backgrounds, we found their color badges to be significantly more conspicuous to other songbirds (which have a UVtuned visual system) than to raptors and corvids (which have a violet-tuned system) in both coniferous and deciduous forests, consistent with an adaptive private communication system. plumage reflectance ͉ predation ͉ sexual selection ͉ UV vision

BackgroundColour vision in birds can be categorized into two classes, the ultraviolet (UVS) and violet sensitive (VS). Their phylogenetic distributions have traditionally been regarded as highly conserved. However, the complicated nature of acquiring spectral sensitivities from cone photoreceptors meant that until recently, only a few species had actually been studied. Whether birds are UVS or VS can nowadays be inferred from a wide range of species via genomic sequencing of the UV/violet SWS1 cone opsin gene.ResultsWe present genomic sequencing results of the SWS1 gene from 21 avian orders. Amino acid residues signifying UV sensitivity are found in the two most important spectral tuning sites 86 and 90 of Pteroclidiformes and Coraciiformes, in addition to the major clades, Palaeognathae, Charadriiformes, Trogoniformes, Psittaciformes and Passeriformes, where they where previously known to occur. We confirm that the presumed UVS-conferring amino acid combination F86, C90 and M93 is common to Palaeognathae and unique to this clade, despite available spectrometric evidence showing the ostrich retina to be VS.ConclusionsBy mapping our results together with data from previous studies on a molecular phylogeny we show that avian colour vision shifted between VS and UVS at least 14 times. Single nucleotide substitutions can explain all these shifts. The common ancestor of birds most likely had a VS phenotype. However, the ancestral state of the avian SWS1 opsin’s spectral tuning sites cannot be resolved, since the Palaeognathae are F86, C90 while the Neognathae are ancestrally S86, S90. The phylogenetic distribution of UVS and VS colour vision in birds is so complex that inferences of spectral sensitivities from closely related taxa should be used with caution.