Molecular evolution of genes in avian genomes.
BACKGROUND
Obtaining a draft genome sequence of the zebra finch (Taeniopygia guttata), the second bird genome to be sequenced, provides the necessary resource for whole-genome comparative analysis of gene sequence evolution in a non-mammalian vertebrate lineage. To analyze basic molecular evolutionary processes during avian evolution, and to contrast these with the situation in mammals, we aligned the protein-coding sequences of 8,384 1:1 orthologs of chicken, zebra finch, a lizard and three mammalian species.


RESULTS
We found clear differences in the substitution rate at fourfold degenerate sites, being lowest in the ancestral bird lineage, intermediate in the chicken lineage and highest in the zebra finch lineage, possibly reflecting differences in generation time. We identified positively selected and/or rapidly evolving genes in avian lineages and found an over-representation of several functional classes, including anion transporter activity, calcium ion binding, cell adhesion and microtubule cytoskeleton.


CONCLUSIONS
Focusing specifically on genes of neurological interest and genes differentially expressed in the unique vocal control nuclei of the songbird brain, we find a number of positively selected genes, including synaptic receptors. We found no evidence that selection for beneficial alleles is more efficient in regions of high recombination; in fact, there was a weak yet significant negative correlation between omega and recombination rate, which is in the direction predicted by the Hill-Robertson effect if slightly deleterious mutations contribute to protein evolution. These findings set the stage for studies of functional genetics of avian genes.
Nam
Kiwoong
K
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, S-752 36, Sweden.
Mugal
Carina
C
Nabholz
Benoit
B
Schielzeth
Holger
H
Wolf
Jochen B W
JB
Backström
Niclas
N
Künstner
Axel
A
Balakrishnan
Christopher N
CN
Heger
Andreas
A
Ponting
Chris P
CP
Clayton
David F
DF
Ellegren
Hans
H
D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D001482:Base Composition / Q000235:genetics; D002645:Chickens / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D019143:Evolution, Molecular; D046369:Finches / Q000235:genetics*; D016678:Genome / Q000235:genetics*; D009420:Nervous System / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic; D012641:Selection, Genetic; D012689:Sequence Homology, Nucleic Acid