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

  • Sean MacEachern1, 2Email author,

    Affiliated with

    • John McEwan3,

      Affiliated with

      • Andrew Mather1,

        Affiliated with

        • Alan McCulloch3,

          Affiliated with

          • Paul Sunnucks2 and

            Affiliated with

            • Mike Goddard1, 4

              Affiliated with

              Genetics Selection Evolution200638:321

              DOI: 10.1186/1297-9686-38-3-321

              Received: 31 August 2005

              Accepted: 8 December 2005

              Published: 26 April 2006

              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.

              adaptive evolution Bos taurus Homo sapiens mammary gland tissue specific genes

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              Authors’ Affiliations

              (1)
              Animal Genetics and Genomics, Primary Industries Research Victoria
              (2)
              Department of Genetics, Latrobe University
              (3)
              AgResearch, Department of Genetics, Private Bag
              (4)
              Melbourne University, School of Agriculture and Food Systems

              Copyright

              © INRA, EDP Sciences 2006

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