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Strong regional biases in nucleotide substitution in the chicken genome
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
2006 In: Mol. Biol. Evol., ISSN 0737-4038, Vol. 23, no 6, 1203-1216 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2006. Vol. 23, no 6, 1203-1216 p.
URN: urn:nbn:se:uu:diva-95329OAI: oai:DiVA.org:uu-95329DiVA: diva2:169500
Available from: 2007-01-11 Created: 2007-01-11 Last updated: 2016-04-08Bibliographically 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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Axelsson, Erik
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