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Open Access Research

Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome

Sean MacEachern12*, John McEwan3, Andrew Mather1, Alan McCulloch3, Paul Sunnucks2 and Mike Goddard14

Author Affiliations

1 Primary Industries Research Victoria, Animal Genetics and Genomics, Attwood VIC 3049, Australia

2 Latrobe University, Department of Genetics, Bundoora VIC 3086, Australia

3 AgResearch, Department of Genetics, Private Bag 50034, Mosgiel, New Zealand

4 Melbourne University, School of Agriculture and Food Systems, Melbourne VIC 3000, Australia

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Genetics Selection Evolution 2006, 38:321-341  doi:10.1186/1297-9686-38-3-321

The electronic version of this article is the complete one and can be found online at: http://www.gsejournal.org/content/38/3/321


Received:31 August 2005
Accepted:8 December 2005
Published:26 April 2006

© 2006 INRA, EDP Sciences

Abstract

Despite growing evidence of rapid evolution in protein coding genes, the contribution of positive selection to intra- and interspecific differences in protein coding regions of the genome is unclear. We attempted to see if genes coding for secreted proteins and genes with narrow expression, specifically those preferentially expressed in the mammary gland, have diverged at a faster rate between domestic cattle (Bos taurus) and humans (Homo sapiens) than other genes and whether positive selection is responsible. Using a large data set, we identified groups of genes based on secretion and expression patterns and compared them for the rate of nonsynonymous (dN) and synonymous (dS) substitutions per site and the number of radical (Dr) and conservative (Dc) amino acid substitutions. We found evidence of rapid evolution in genes with narrow expression, especially for those expressed in the liver and mammary gland and for genes coding for secreted proteins. We compared common human polymorphism data with human-cattle divergence and found that genes with high evolutionary rates in human-cattle divergence also had a large number of common human polymorphisms. This argues against positive selection causing rapid divergence in these groups of genes. In most cases dN/dS ratios were lower in human-cattle divergence than in common human polymorphism presumably due to differences in the effectiveness of purifying selection between long-term divergence and short-term polymorphism.

Keywords:
adaptive evolution; Bos taurus; Homo sapiens; mammary gland; tissue specific genes

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