scholarly journals Codon Usage Bias and Effective Population Sizes on the X Chromosome versus the Autosomes in Drosophila melanogaster

2012 ◽  
Vol 30 (4) ◽  
pp. 811-823 ◽  
Author(s):  
Jose L. Campos ◽  
Kai Zeng ◽  
Darren J. Parker ◽  
Brian Charlesworth ◽  
Penelope R. Haddrill
Keyword(s):  
Drosophila Melanogaster ◽  
Codon Usage ◽  
X Chromosome ◽  
Codon Usage Bias ◽  
Chromosome Versus ◽  
Effective Population ◽  
Population Sizes

scholarly journals Evolution of Codon Usage Bias in Diatoms

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 894 ◽  
Author(s):  
Marc Krasovec ◽  
Dmitry A. Filatov
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Codon Bias ◽  
Diatom Species ◽  
Effective Population ◽  
Weak Selection ◽  
Optimal Codons ◽  
Wide Range ◽  
Population Sizes ◽  
Selection For

Codon usage bias (CUB)—preferential use of one of the synonymous codons, has been described in a wide range of organisms from bacteria to mammals, but it has not yet been studied in marine phytoplankton. CUB is thought to be caused by weak selection for translational accuracy and efficiency. Weak selection can overpower genetic drift only in species with large effective population sizes, such as Drosophila that has relatively strong CUB, while organisms with smaller population sizes (e.g., mammals) have weak CUB. Marine plankton species tend to have extremely large populations, suggesting that CUB should be very strong. Here we test this prediction and describe the patterns of codon usage in a wide range of diatom species belonging to 35 genera from 4 classes. We report that most of the diatom species studied have surprisingly modest CUB (mean Effective Number of Codons, ENC = 56), with some exceptions showing stronger codon bias (ENC = 44). Modest codon bias in most studied diatom species may reflect extreme disparity between astronomically large census and modest effective population size (Ne), with fluctuations in population size and linked selection limiting long-term Ne and rendering selection for optimal codons less efficient. For example, genetic diversity (pi ~0.02 at silent sites) in Skeletonema marinoi corresponds to Ne of about 10 million individuals, which is likely many orders of magnitude lower than its census size. Still, Ne ~107 should be large enough to make selection for optimal codons efficient. Thus, we propose that an alternative process—frequent changes of preferred codons, may be a more plausible reason for low CUB despite highly efficient selection for preferred codons in diatom populations. The shifts in the set of optimal codons should result in the changes of the direction of selection for codon usage, so the actual codon usage never catches up with the moving target of the optimal set of codons and the species never develop strong CUB. Indeed, we detected strong shifts in preferential codon usage within some diatom genera, with switches between preferentially GC-rich and AT-rich 3rd codon positions (GC3). For example, GC3 ranges from 0.6 to 1 in most Chaetoceros species, while for Chaetoceros dichaeta GC3 = 0.1. Both variation in selection intensity and mutation spectrum may drive such shifts in codon usage and limit the observed CUB. Our study represents the first genome-wide analysis of CUB in diatoms and the first such analysis for a major phytoplankton group.

scholarly journals Linkage disequilibrium in natural and experimental populations of Drosophila melanogaster.

Genetics ◽  
1988 ◽  
Vol 120 (4) ◽  
pp. 1043-1051
Author(s):  
Z Smit-McBride ◽  
A Moya ◽  
F J Ayala
Keyword(s):  
Drosophila Melanogaster ◽  
Linkage Disequilibrium ◽  
Assay Method ◽  
Effective Population ◽  
Population Mixing ◽  
Locus Pair ◽  
Two Samples ◽  
In The Wild ◽  
Population Sizes ◽  
Experimental Populations

Abstract We have studied linkage disequilibrium in Drosophila melanogaster in two samples from a wild population and in four large laboratory populations derived from the wild samples. We have assayed four polymorphic enzyme loci, fairly closely linked in the third chromosome: Sod Est-6, Pgm, and Odh. The assay method used allows us to identify the allele associations separately in each of the two homologous chromosomes from each male sampled. We have detected significant linkage disequilibrium between two loci in 16.7% of the cases in the wild samples and in 27.8% of the cases in the experimental populations, considerably more than would be expected by chance alone. We have also found three-locus disequilibria in more instances than would be expected by chance. Some disequilibria present in the wild samples disappear in the experimental populations derived from them, but new ones appear over the generations. The effective population sizes required to generate the observed disequilibria by randomness range from 40 to more than 60,000 individuals in the natural population, depending on which locus pair is considered, and from 100 to more than 60,000 in the experimental populations. These population sizes are unrealistic; the fact that different locus-pairs yield disparate estimates within the same population argues against the likelihood that the disequilibria may have arisen as a consequence of population bottlenecks. Migration, or population mixing, cannot be excluded as the process generating the disequilibria in the wild samples, but can in the experimental populations. We conclude that linkage disequilibrium in these populations is most likely due to natural selection acting on the allozymes, or on loci very tightly linked to them.

scholarly journals Pervasive Strong Selection at the Level of Codon Usage Bias in Drosophila melanogaster

Genetics ◽  
2019 ◽  
Vol 214 (2) ◽  
pp. 511-528 ◽  
Author(s):  
Heather E. Machado ◽  
David S. Lawrie ◽  
Dmitri A. Petrov
Keyword(s):  
Drosophila Melanogaster ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Purifying Selection ◽  
Weak Selection ◽  
Strong Selection ◽  
Genome Wide ◽  
Synonymous Sites ◽  
Alternatively Spliced ◽  
Splice Junctions

Codon usage bias (CUB), where certain codons are used more frequently than expected by chance, is a ubiquitous phenomenon and occurs across the tree of life. The dominant paradigm is that the proportion of preferred codons is set by weak selection. While experimental changes in codon usage have at times shown large phenotypic effects in contrast to this paradigm, genome-wide population genetic estimates have supported the weak selection model. Here we use deep genomic population sequencing of two Drosophila melanogaster populations to measure selection on synonymous sites in a way that allowed us to estimate the prevalence of both weak and strong purifying selection. We find that selection in favor of preferred codons ranges from weak (|Nes| ∼ 1) to strong (|Nes| > 10), with strong selection acting on 10–20% of synonymous sites in preferred codons. While previous studies indicated that selection at synonymous sites could be strong, this is the first study to detect and quantify strong selection specifically at the level of CUB. Further, we find that CUB-associated polymorphism accounts for the majority of strong selection on synonymous sites, with secondary contributions of splicing (selection on alternatively spliced genes, splice junctions, and spliceosome-bound sites) and transcription factor binding. Our findings support a new model of CUB and indicate that the functional importance of CUB, as well as synonymous sites in general, have been underestimated.

scholarly journals The response to artificial selection from new mutations in Drosophila melanogaster.

Genetics ◽  
1991 ◽  
Vol 128 (1) ◽  
pp. 89-102 ◽  
Author(s):  
A Caballero ◽  
M A Toro ◽  
C López-Fanjul
Keyword(s):  
Drosophila Melanogaster ◽  
Single Mutation ◽  
Effective Population ◽  
Environmental Variance ◽  
Epistatic Interactions ◽  
Bristle Number ◽  
Population Sizes ◽  
Selection For ◽  
Mutational Variance ◽  
New Mutations

Abstract Twenty generations of divergent selection for abdominal bristle number were carried out starting from a completely homozygous population of Drosophila melanogaster. All lines were selected with the same proportion (20%) but at two different numbers of selected parents of each sex (5 or 25). A significant response to selection was detected in eight lines (out of 40) and, in most cases, it could be wholly attributed to a single mutation of relatively large effect (0.5-2 phenotypic standard deviations). The ratio of new mutational variance to environmental variance was estimated to be (0.33 +/- 0.11) X 10(-3). The distribution of mutant effects was asymmetrical, both with respect to bristle number (85% of it was negative) and to fitness (most detected bristle mutations were lethal or semilethal). Moreover, this distribution was leptokurtic, due to the presence of major genes. Gene action on bristles ranged from additive to completely recessive, no epistatic interactions being found. In agreement with theory, larger responses in each direction were achieved by those lines selected at greater effective population sizes. Furthermore, the observed divergence between lines selected in opposite directions was proportional to their effective size, as predicted for mutations of large effect.

scholarly journals Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

2018 ◽  
Vol 35 (5) ◽  
pp. 1092-1103 ◽  
Author(s):  
Nicolas Galtier ◽  
Camille Roux ◽  
Marjolaine Rousselle ◽  
Jonathan Romiguier ◽  
Emeric Figuet ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Population Size ◽  
Gene Conversion ◽  
Effective Population Size ◽  
Codon Usage Bias ◽  
Effective Population ◽  
Biased Gene Conversion

scholarly journals Comparative losses of quantitative and molecular genetic variation in finite populations of Drosophila melanogaster

2005 ◽  
Vol 85 (1) ◽  
pp. 47-55 ◽  
Author(s):  
DEAN M. GILLIGAN ◽  
DAVID A. BRISCOE ◽  
RICHARD FRANKHAM
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variation ◽  
Molecular Genetic ◽  
Neutral Theory ◽  
Similar Rate ◽  
Sampling Errors ◽  
Effective Population ◽  
Quantitative Genetic ◽  
Population Sizes ◽  
Molecular Genetic Variation

Quantitative genetic variation, the main determinant of the ability to evolve, is expected to be lost in small populations, but there are limited data on the effect, and controversy as to whether it is similar to that for near neutral molecular variation. Genetic variation for abdominal and sternopleural bristle numbers and allozyme heterozygosity were estimated in 23 populations of Drosophila melanogaster maintained at effective population sizes of 25, 50, 100, 250 or 500 for 50 generations, as well as in 19 highly inbred populations and the wild outbred base population. Highly significant negative regressions of proportion of initial genetic variation retained on inbreeding due to finite population size were observed for both quantitative characters (b=−0·67±0·14 and −0·58±0·11) and allozyme heterozygosity (b=−0·79±0·10), and the regression coefficients did not differ significantly. Thus, quantitative genetic variation is being lost at a similar rate to molecular genetic variation. However, genetic variation for all traits was lost at rates significantly slower than predicted by neutral theory, most likely due to associative overdominance. Positive, but relatively low correlations were found among the different measures of genetic variation, but their low magnitudes were attributed to large sampling errors, rather than differences in the underlying processes of loss.

scholarly journals Spontaneous mutation for a quantitative trait in Drosophila melanogaster. I. Response to artificial selection

1993 ◽  
Vol 61 (2) ◽  
pp. 107-116 ◽  
Author(s):  
María A. López ◽  
Carlos López-Fanjul
Keyword(s):  
Drosophila Melanogaster ◽  
Large Fraction ◽  
Spontaneous Mutation ◽  
Single Mutation ◽  
Effective Population ◽  
Environmental Variance ◽  
Bristle Number ◽  
Population Sizes ◽  
Selection For ◽  
Mutational Variance

SummaryDivergent selection for abdominal bristle number was carried out for 47 generations, starting from a completely homozygous population of Drosophila melanogaster. All lines were selected with the same proportion (20%) but at two different numbers of selected parents of each sex (5 or 25). A significant response to selection was obtained in 25 lines (out of 40). In most cases, it could be wholly attributed to a single mutation of relatively large effect (> 0·3 phenotypic standard deviations). A total number of 30 mutations were detected. In agreement with theory, larger responses in each direction were achieved by those lines selected at greater effective population sizes. A large fraction of mutations were lethals (10/30). Thus, the observed divergence between lines of the same effective size selected in opposite directions was smaller than expected under neutrality. The ratio of new mutational variance to environmental variance was estimated to be(0·52±0·09)×10−3.

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