Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

Borges, Rui

Borges, Rui

Khan, Imran

Johnson, Warren E

Gilbert, M Thomas P

Zhang, Guojie

Jarvis, Erich D

O'Brien, Stephen J

Antunes, Agostinho

England

2015-12-08T03:43:59Z

2015-10-06

BACKGROUND: The wide range of complex photic systems observed in birds exemplifies one of their key evolutionary adaptions, a well-developed visual system. However, genomic approaches have yet to be used to disentangle the evolutionary mechanisms that govern evolution of avian visual systems. RESULTS: We performed comparative genomic analyses across 48 avian genomes that span extant bird phylogenetic diversity to assess evolutionary changes in the 17 representatives of the opsin gene family and five plumage coloration genes. Our analyses suggest modern birds have maintained a repertoire of up to 15 opsins. Synteny analyses indicate that PARA and PARIE pineal opsins were lost, probably in conjunction with the degeneration of the parietal organ. Eleven of the 15 avian opsins evolved in a non-neutral pattern, confirming the adaptive importance of vision in birds. Visual conopsins sw1, sw2 and lw evolved under negative selection, while the dim-light RH1 photopigment diversified. The evolutionary patterns of sw1 and of violet/ultraviolet sensitivity in birds suggest that avian ancestors had violet-sensitive vision. Additionally, we demonstrate an adaptive association between the RH2 opsin and the MC1R plumage color gene, suggesting that plumage coloration has been photic mediated. At the intra-avian level we observed some unique adaptive patterns. For example, barn owl showed early signs of pseudogenization in RH2, perhaps in response to nocturnal behavior, and penguins had amino acid deletions in RH2 sites responsible for the red shift and retinal binding. These patterns in the barn owl and penguins were convergent with adaptive strategies in nocturnal and aquatic mammals, respectively. CONCLUSIONS: We conclude that birds have evolved diverse opsin adaptations through gene loss, adaptive selection and coevolution with plumage coloration, and that differentiated selective patterns at the species level suggest novel photic pressures to influence evolutionary patterns of more-recent lineages.

http://www.ncbi.nlm.nih.gov/pubmed/26438339

10.1186/s12864-015-1924-3

1471-2164

https://hdl.handle.net/10161/11120

eng

Springer Science and Business Media LLC

BMC Genomics

10.1186/s12864-015-1924-3

Adaptation, Biological

Animals

Biological Evolution

Birds

Evolution, Molecular

Genome

Genomics

Melanins

Opsins

Phenotype

Phylogeny

Selection, Genetic

Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.

Journal article

http://www.ncbi.nlm.nih.gov/pubmed/26438339

751

Basic Science Departments

Duke

Duke Institute for Brain Sciences

Institutes and Provost's Academic Units

Neurobiology

School of Medicine

University Institutes and Centers

Published online

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