TY - JOUR
T1 - Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura
AU - Fuller, Zachary L.
AU - Haynes, Gwilym D.
AU - Zhu, Dianhui
AU - Batterton, Matthew
AU - Chao, Hsu
AU - Dugan, Shannon
AU - Javaid, Mehwish
AU - Jayaseelan, Joy C.
AU - Lee, Sandra
AU - Li, Mingmei
AU - Ongeri, Fiona
AU - Qi, Sulan
AU - Han, Yi
AU - Doddapaneni, Harshavardhan
AU - Richards, Stephen
AU - Schaeffer, Stephen W.
N1 - Publisher Copyright:
© 2014 Fuller et al.
PY - 2014
Y1 - 2014
N2 - There has been a renewed interest in investigating the role of stabilizing selection acting on genomewide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standardmodels.Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.
AB - There has been a renewed interest in investigating the role of stabilizing selection acting on genomewide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standardmodels.Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura.
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U2 - 10.1534/g3.114.014860
DO - 10.1534/g3.114.014860
M3 - Article
C2 - 25326424
AN - SCOPUS:84916890014
SN - 2160-1836
VL - 4
SP - 2433
EP - 2449
JO - G3: Genes, Genomes, Genetics
JF - G3: Genes, Genomes, Genetics
IS - 12
ER -