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

dc.contributor.author

Borges, Rui

dc.contributor.author

Borges, Rui

dc.contributor.author

Khan, Imran

dc.contributor.author

Johnson, Warren E

dc.contributor.author

Gilbert, M Thomas P

dc.contributor.author

Zhang, Guojie

dc.contributor.author

Jarvis, Erich D

dc.contributor.author

O'Brien, Stephen J

dc.contributor.author

Antunes, Agostinho

dc.coverage.spatial

England

dc.date.accessioned

2015-12-08T03:43:59Z

dc.date.issued

2015-10-06

dc.description.abstract

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.

dc.identifier

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

dc.identifier

10.1186/s12864-015-1924-3

dc.identifier.eissn

1471-2164

dc.identifier.uri

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

dc.language

eng

dc.publisher

Springer Science and Business Media LLC

dc.relation.ispartof

BMC Genomics

dc.relation.isversionof

10.1186/s12864-015-1924-3

dc.subject

Adaptation, Biological

dc.subject

Animals

dc.subject

Biological Evolution

dc.subject

Birds

dc.subject

Evolution, Molecular

dc.subject

Genome

dc.subject

Genomics

dc.subject

Melanins

dc.subject

Opsins

dc.subject

Phenotype

dc.subject

Phylogeny

dc.subject

Selection, Genetic

dc.title

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

dc.type

Journal article

pubs.author-url

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

pubs.begin-page

751

pubs.organisational-group

Basic Science Departments

pubs.organisational-group

Duke

pubs.organisational-group

Duke Institute for Brain Sciences

pubs.organisational-group

Institutes and Provost's Academic Units

pubs.organisational-group

Neurobiology

pubs.organisational-group

School of Medicine

pubs.organisational-group

University Institutes and Centers

pubs.publication-status

Published online

pubs.volume

16

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
Gene loss, adaptive evolution and the co-evolution of plumage coloration genes with opsins in birds.pdf
Size:
1.28 MB
Format:
Adobe Portable Document Format