Abstract
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Proceedings of the National Academy of Science of the United States of America |
| Vol/bind | 104 |
| Udgave nummer | 7 |
| Sider (fra-til) | 2271-6 |
| Antal sider | 5 |
| ISSN | 0027-8424 |
| DOI | |
| Status | Udgivet - 2007 |
Bibliografisk note
Keywords: Adaptation, Biological; Amino Acid Substitution; Animals; Drosophila melanogaster; Evolution, Molecular; Genome, Insect; Molecular Sequence Data; Polymorphism, Genetic; Recombination, GeneticAdgang til dokumentet
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I: Proceedings of the National Academy of Science of the United States of America, Bind 104, Nr. 7, 2007, s. 2271-6.
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review
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TY - JOUR
T1 - Adaptive genic evolution in the Drosophila genomes
AU - Shapiro, Joshua A
AU - Huang, Wei
AU - Zhang, Chenhui
AU - Hubisz, Melissa J
AU - Lu, Jian
AU - Turissini, David A
AU - Fang, Shu
AU - Wang, Hurng-Yi
AU - Hudson, Richard R
AU - Nielsen, Rasmus
AU - Chen, Zhu
AU - Wu, Chung-I
N1 - Keywords: Adaptation, Biological; Amino Acid Substitution; Animals; Drosophila melanogaster; Evolution, Molecular; Genome, Insect; Molecular Sequence Data; Polymorphism, Genetic; Recombination, Genetic
PY - 2007
Y1 - 2007
N2 - Determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. A suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and stable population. In this study, we sequenced 419 genes from 24 lines of Drosophila melanogaster and its close relatives. Together with data from Drosophila simulans, these data reveal the following. (i) Approximately 10% of the loci in regions of normal recombination are much less polymorphic at silent sites than expected, hinting at the action of selective sweeps. (ii) The level of polymorphism is negatively correlated with the rate of nonsynonymous divergence across loci. Thus, even under strict neutrality, the ratio of amino acid to silent nucleotide changes (A:S) between Drosophila species is expected to be 25-40% higher than the A:S ratio for polymorphism when data are pooled across the genome. (iii) The observed A/S ratio between species among the 419 loci is 28.9% higher than the (adjusted) neutral expectation. We estimate that nearly 30% of the amino acid substitutions between D. melanogaster and its close relatives were adaptive. (iv) This signature of adaptive evolution is observable only in regions of normal recombination. Hence, the low level of polymorphism observed in regions of reduced recombination may not be driven primarily by positive selection. Finally, we discuss the theories and data pertaining to the interpretation of adaptive evolution in genomic studies.
AB - Determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. A suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and stable population. In this study, we sequenced 419 genes from 24 lines of Drosophila melanogaster and its close relatives. Together with data from Drosophila simulans, these data reveal the following. (i) Approximately 10% of the loci in regions of normal recombination are much less polymorphic at silent sites than expected, hinting at the action of selective sweeps. (ii) The level of polymorphism is negatively correlated with the rate of nonsynonymous divergence across loci. Thus, even under strict neutrality, the ratio of amino acid to silent nucleotide changes (A:S) between Drosophila species is expected to be 25-40% higher than the A:S ratio for polymorphism when data are pooled across the genome. (iii) The observed A/S ratio between species among the 419 loci is 28.9% higher than the (adjusted) neutral expectation. We estimate that nearly 30% of the amino acid substitutions between D. melanogaster and its close relatives were adaptive. (iv) This signature of adaptive evolution is observable only in regions of normal recombination. Hence, the low level of polymorphism observed in regions of reduced recombination may not be driven primarily by positive selection. Finally, we discuss the theories and data pertaining to the interpretation of adaptive evolution in genomic studies.
U2 - 10.1073/pnas.0610385104
DO - 10.1073/pnas.0610385104
M3 - Journal article
C2 - 17284599
SN - 0027-8424
VL - 104
SP - 2271
EP - 2276
JO - Proceedings of the National Academy of Science of the United States of America
JF - Proceedings of the National Academy of Science of the United States of America
IS - 7
ER -