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Fast-X on the Z: Rapid evolution of sex-linked genes in birds
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
2007 (English)In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 17, no 5, 618-624 p.Article in journal (Refereed) Published
Abstract [en]

Theoretical work predicts natural selection to be more efficient in the fixation of beneficial mutations in X-linked genes than in autosomal genes. This “fast-X effect” should be evident by an increased ratio of nonsynonymous to synonymous substitutions (dN/dS) for sex-linked genes; however, recent studies have produced mixed support for this expectation. To make an independent test of the idea of fast-X evolution, we focused on birds, which have female heterogamety (males ZZ, females ZW), where analogous arguments would predict a fast-Z effect. We aligned 2.8 Mb of orthologous protein-coding sequence of zebra finch and chicken from 172 Z-linked and 4848 autosomal genes. Zebra finch data were in the form of EST sequences from brain cDNA libraries, while chicken genes were from the draft genome sequence. The dN/dS ratio was significantly higher for Z-linked (0.110) than for all autosomal genes (0.085; P = 0.002), as well as for genes linked to similarly sized autosomes 1–10 (0.0948; P = 0.04). This pattern of fast-Z was evident even after we accounted for the nonrandom distribution of male-biased genes. We also examined the nature of standing variation in the chicken protein-coding regions. The ratio of nonsynonymous to synonymous polymorphism (pN/pS) did not differ significantly between genes on the Z chromosome (0.104) and on the autosomes (0.0908). In conjunction, these results suggest that evolution proceeds more quickly on the Z chromosome, where hemizygous exposure of beneficial nondominant mutations increases the rate of fixation.

Place, publisher, year, edition, pages
2007. Vol. 17, no 5, 618-624 p.
National Category
Biological Sciences
URN: urn:nbn:se:uu:diva-95330DOI: 10.1101/gr.6031907ISI: 000246297900009PubMedID: 17416747OAI: oai:DiVA.org:uu-95330DiVA: diva2:169501
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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