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1.  The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila 
Biology Letters  2015;11(4):20150117.
A faster rate of adaptive evolution of X-linked genes compared with autosomal genes may be caused by the fixation of new recessive or partially recessive advantageous mutations (the Faster-X effect). This effect is expected to be largest for mutations that affect only male fitness and absent for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using genes with different levels of sex-biased expression and by estimating the extent of adaptive evolution of non-synonymous mutations from polymorphism and divergence data. We detected both a Faster-X effect and an effect of male-biased gene expression. There was no evidence for a strong association between the two effects—modest levels of male-biased gene expression increased the rate of adaptive evolution on both the autosomes and the X chromosome, but a Faster-X effect occurred for both unbiased genes and female-biased genes. The rate of genetic recombination did not influence the magnitude of the Faster-X effect, ruling out the possibility that it reflects less Hill–Robertson interference for X-linked genes.
PMCID: PMC4424624  PMID: 25926696
Faster-X effect; sex-biased gene expression; Drosophila; sexual selection; recombination
2.  Selection on codon usage and base composition in Drosophila americana 
Biology Letters  2011;8(1):82-85.
We have used a polymorphism dataset on introns and coding sequences of X-linked loci in Drosophila americana to estimate the strength of selection on codon usage and/or biased gene conversion (BGC), taking into account a recent population expansion detected by a maximum-likelihood method. Drosophila americana was previously thought to have a stable demographic history, so that this evidence for a recent population expansion means that previous estimates of selection need revision. There was evidence for natural selection or BGC favouring GC over AT variants in introns, which is stronger for GC-rich than GC-poor introns. By comparing introns and coding sequences, we found evidence for selection on codon usage bias, which is much stronger than the forces acting on GC versus AT basepairs in introns.
PMCID: PMC3259966  PMID: 21849309
Drosophila americana; codon usage; biased gene conversion; population expansion
3.  Editorial 2012 
Biology Letters  2011;8(1):1-2.
PMCID: PMC3259987  PMID: 22171021
4.  Editorial 2011 
Biology Letters  2010;7(1):1.
PMCID: PMC3030907  PMID: 21123251
5.  Editorial 2010 
Biology Letters  2009;6(1):1-2.
PMCID: PMC2817274  PMID: 20015857
6.  Elevated levels of expression associated with regions of the Drosophila genome that lack crossing over 
Biology Letters  2008;4(6):758-761.
The recombinational environment influences patterns of molecular evolution through the effects of Hill–Robertson interference. Here, we examine genome-wide patterns of gene expression with respect to recombinational environment in Drosophila melanogaster. We find that regions of the genome lacking crossing over exhibit elevated levels of expression, and this is most pronounced for genes on the entirely non-crossing over fourth chromosome. We find no evidence for differences in the patterns of gene expression between regions of high, intermediate and low crossover frequencies. These results suggest that, in the absence of crossing over, selection to maintain control of expression may be compromised, perhaps due to the accumulation of deleterious mutations in regulatory regions. Alternatively, higher gene expression may be evolving to compensate for defective protein products or reduced translational efficiency.
PMCID: PMC2614156  PMID: 18782733
recombination; crossing over; Drosophila; gene expression
7.  Editorial 
Biology Letters  2007;4(1):1.
PMCID: PMC2412953
8.  Editorial 
Biology Letters  2008;5(1):1-2.
PMCID: PMC2657769
9.  Non-neutral processes drive the nucleotide composition of non-coding sequences in Drosophila 
Biology Letters  2008;4(4):438-441.
The nature of the forces affecting base composition is a key question in genome evolution. There is uncertainty as to whether differences in the GC contents of non-coding sequences reflect differences in mutational bias, or in the intensity of selection or biased gene conversion. We have used a polymorphism dataset for non-coding sequences on the X chromosome of Drosophila simulans to examine this question. The proportion of GC→AT versus AT→GC polymorphic mutations in a locus is correlated with its GC content. This implies the action of forces that favour GC over AT base pairs, which are apparently strongest in GC-rich sequences.
PMCID: PMC2515589  PMID: 18505714
GC content; biased gene conversion; selection; Drosophila
10.  Inferring the distribution of mutational effects on fitness in Drosophila 
Biology Letters  2006;2(3):426-430.
The properties of the distribution of deleterious mutational effects on fitness (DDME) are of fundamental importance for evolutionary genetics. Since it is extremely difficult to determine the nature of this distribution, several methods using various assumptions about the DDME have been developed, for the purpose of parameter estimation. We apply a newly developed method to DNA sequence polymorphism data from two Drosophila species and compare estimates of the parameters of the distribution of the heterozygous fitness effects of amino acid mutations for several different distribution functions. The results exclude normal and gamma distributions, since these predict too few effectively lethal mutations and power-law distributions as a result of predicting too many lethals. Only the lognormal distribution appears to fit both the diversity data and the frequency of lethals. This DDME arises naturally in complex systems when independent factors contribute multiplicatively to an increase in fitness-reducing damage. Several important parameters, such as the fraction of effectively neutral non-synonymous mutations and the harmonic mean of non-neutral selection coefficients, are robust to the form of the DDME. Our results suggest that the majority of non-synonymous mutations in Drosophila are under effective purifying selection.
PMCID: PMC1686194  PMID: 17148422
Drosophila; distribution of mutational effects; lethals; lognormal; gamma; power law
11.  Editorial 
Biology Letters  2005;1(1):1.
PMCID: PMC1629068

Results 1-11 (11)