Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome
<p>Abstract</p> <p>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 g...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | deu |
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BMC
2006-04-01
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| Series: | Genetics Selection Evolution |
| Subjects: | |
| Online Access: | http://www.gsejournal.org/content/38/3/321 |
| _version_ | 1819087268444372992 |
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| author | McCulloch Alan Mather Andrew McEwan John MacEachern Sean Sunnucks Paul Goddard Mike |
| author_facet | McCulloch Alan Mather Andrew McEwan John MacEachern Sean Sunnucks Paul Goddard Mike |
| author_sort | McCulloch Alan |
| collection | DOAJ |
| description | <p>Abstract</p> <p>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 (<it>Bos taurus</it>) and humans (<it>Homo sapiens</it>) 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 (<it>dN</it>) and synonymous (<it>dS) </it>substitutions per site and the number of radical (<it>Dr</it>) and conservative (<it>Dc</it>) 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 <it>dN</it>/<it>dS </it>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.</p> |
| first_indexed | 2024-12-21T21:33:27Z |
| format | Article |
| id | doaj.art-c5dde6910126408f9e917a7f9b2b840c |
| institution | Directory Open Access Journal |
| issn | 0999-193X 1297-9686 |
| language | deu |
| last_indexed | 2024-12-21T21:33:27Z |
| publishDate | 2006-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-c5dde6910126408f9e917a7f9b2b840c2022-12-21T18:49:33ZdeuBMCGenetics Selection Evolution0999-193X1297-96862006-04-0138332134110.1186/1297-9686-38-3-321Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptomeMcCulloch AlanMather AndrewMcEwan JohnMacEachern SeanSunnucks PaulGoddard Mike<p>Abstract</p> <p>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 (<it>Bos taurus</it>) and humans (<it>Homo sapiens</it>) 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 (<it>dN</it>) and synonymous (<it>dS) </it>substitutions per site and the number of radical (<it>Dr</it>) and conservative (<it>Dc</it>) 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 <it>dN</it>/<it>dS </it>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.</p>http://www.gsejournal.org/content/38/3/321adaptive evolution<it>Bos taurus</it><it>Homo sapiens</it>mammary glandtissue specific genes |
| spellingShingle | McCulloch Alan Mather Andrew McEwan John MacEachern Sean Sunnucks Paul Goddard Mike Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome Genetics Selection Evolution adaptive evolution <it>Bos taurus</it> <it>Homo sapiens</it> mammary gland tissue specific genes |
| title | Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome |
| title_full | Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome |
| title_fullStr | Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome |
| title_full_unstemmed | Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome |
| title_short | Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome |
| title_sort | testing the neutral theory of molecular evolution using genomic data a comparison of the human and bovine transcriptome |
| topic | adaptive evolution <it>Bos taurus</it> <it>Homo sapiens</it> mammary gland tissue specific genes |
| url | http://www.gsejournal.org/content/38/3/321 |
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