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Natural selection in protein-coding genes expressed in avian brain
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
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2008 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 17, no 12, 3008-3017 p.Article in journal (Refereed) Published
Abstract [en]

The evolution of birds from theropod dinosaurs took place approximately 150 million years ago, and was associated with a number of specific adaptations that are still evident among extant birds, including feathers, song and extravagant secondary sexual characteristics. Knowledge about the molecular evolutionary background to such adaptations is lacking. Here, we analyse the evolution of > 5000 protein-coding gene sequences expressed in zebra finch brain by comparison to orthologous sequences in chicken. Mean d(N)/d(S) is 0.085 and genes with their maximal expression in the eye and central nervous system have the lowest mean d(N)/d(S) value, while those expressed in digestive and reproductive tissues exhibit the highest. We find that fast-evolving genes (those which have higher than expected rate of nonsynonymous substitution, indicative of adaptive evolution) are enriched for biological functions such as fertilization, muscle contraction, defence response, response to stress, wounding and endogenous stimulus, and cell death. After alignment to mammalian orthologues, we identify a catalogue of 228 genes that show a significantly higher rate of protein evolution in the two bird lineages than in mammals. These accelerated bird genes, representing candidates for avian-specific adaptations, include genes implicated in vocal learning and other cognitive processes. Moreover, colouration genes evolve faster in birds than in mammals, which may have been driven by sexual selection for extravagant plumage characteristics.

Place, publisher, year, edition, pages
2008. Vol. 17, no 12, 3008-3017 p.
Keyword [en]
adaptive evolution, chicken, comparative genomics, positive selection, zebra finch
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-95331DOI: 10.1111/j.1365-294X.2008.03795.xISI: 000256494700018OAI: oai:DiVA.org:uu-95331DiVA: diva2:169502
Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2016-04-25Bibliographically approved
In thesis
1. Comparative Genomics in Birds
Open this publication in new window or tab >>Comparative Genomics in Birds
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

To shed light on forces that shape the molecular evolution of bird genomes, and in turn avian adaptations, comparative analyses of avian DNA sequences are important. Moreover, contrasting findings in birds to those of other organisms will lend a clearer view on general aspects of molecular evolution. However, few such analyses have been conducted in birds. Progress is presented in this thesis.

Theories predict a reduction in the mutation rate of the Z chromosome as the harmful effects of recessive mutations are exposed in female birds. We find no evidence for this. Instead, the substitution rates of sex chromosomes and autosomes are largely compatible with expectations from male-biased mutation. This suggests that a majority of mutations arise during DNA replication.

Substitution rates also vary across chicken autosomes. For instance, microchromosomes accumulate ~20% more substitutions than macrochromosomes. We show that a majority of the autosomal variation in substitution rate can be accounted for by GC content, mainly due to the incidence of mutable CpG-dinucleotides.

Sequence comparisons also show that the pattern of nucleotide substitution varies in the chicken genome and this reinforces regional differences in base composition.

The level of selective constraint in at least some avian lineages is higher than in mammalian lineages as indicated by low dN/dS – ratios. Larger historical population sizes of birds relative to mammals could explain this observation. Within the avian genome, the dN/dS is lower for genes on micro- than macrochromosomes, potentially owing to a higher incidence of house-keeping genes in the former category.

Contrasting data on non-synonymous and synonymous substitution for divergence and polymorphism shows that positive selection has contributed more to the evolution of Z-linked than autosomal genes. This is likely explained by the full exposure of beneficial recessive mutations on Z when in female birds.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 62 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 261
Molecular genetics, Birds, molecular evolution, macrochromosomes, microchromosomes, mutation rate, substitution rate, base composition, positive selection, genetic drift, population size, Genetik
urn:nbn:se:uu:diva-7432 (URN)978-91-554-6770-8 (ISBN)
Public defence
2007-02-02, Zootissalen, EBC, Villavägen 9, Uppsala, 13:00
Available from: 2007-01-11 Created: 2007-01-11Bibliographically approved

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