scholarly journals The Effects of Sex-Biased Gene Expression and X-Linkage on Rates of Sequence Evolution in Drosophila

2017 ◽  
Vol 35 (3) ◽  
pp. 655-665 ◽  
Author(s):  
José Luis Campos ◽  
Keira J A Johnston ◽  
Brian Charlesworth
Keyword(s):  
Gene Expression ◽  
Sequence Evolution ◽  
X Linkage

scholarly journals The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila

2015 ◽  
Vol 11 (4) ◽  
pp. 20150117 ◽  
Author(s):  
Victoria Ávila ◽  
José L. Campos ◽  
Brian Charlesworth
Keyword(s):  
Gene Expression ◽  
Adaptive Evolution ◽  
Genetic Recombination ◽  
Strong Association ◽  
Sequence Evolution ◽  
Female Fitness ◽  
Synonymous Mutations ◽  
X Linkage ◽  
Different Levels ◽  
Protein Sequence Evolution

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.

scholarly journals Modeling gene expression evolution with EvoGeneX uncovers differences in evolution of species, organs and sexes

2020 ◽  
Author(s):  
Soumitra Pal ◽  
Brian Oliver ◽  
Teresa M. Przytycka
Keyword(s):  
Gene Expression ◽  
Evolutionary Dynamics ◽  
Computational Method ◽  
Specific Gene ◽  
Species Variation ◽  
Evolutionary Divergence ◽  
Sequence Evolution ◽  
Study Gene Expression ◽  
Expression Evolution ◽  
Gene Expression Evolution

AbstractWhile DNA sequence evolution has been well studied, the expression of genes is also subject to evolution. Yet the evolution of gene expression is currently not well understood. In recent years, new tissue/organ specific gene expression datasets spanning several organisms across the tree of life, have become available providing the opportunity to study gene expression evolution in more detail. However, while a theoretical model to study evolution of continuous traits exist, in practice computational methods often cannot distinguish, with confidence, between alternative evolutionary scenarios. This lack of power has been attributed to the modest number of species with available expression data.To solve this challenge, we introduce EvoGeneX, a computationally efficient method to uncover the mode of gene expression evolution based on the Ornstein-Uhlenbeck process. Importantly, EvoGeneX in addition to modelling expression variations between species, models within species variation. To estimate the within species variation, EvoGeneX formally incorporates the data from biological replicates as a part of the mathematical model. We show that by modelling the within species diversity EvoGeneX significantly outperforms the currently available computational method. In addition, to facilitate comparative analysis of gene expression evolution, we introduce a new approach to measure the dynamics of evolutionary divergence of a group of genes.We used EvoGeneX to analyse the evolution of expression across different organs, species and sexes of the Drosophila genus. Our analysis revealed differences in the evolutionary dynamics of male and female gonads, and uncovered examples of adaptive evolution of genes expressed in the head and in the thorax.

scholarly journals An Overexpression Experiment Does Not Support the Hypothesis That Avoidance of Toxicity Determines the Rate of Protein Evolution

2020 ◽  
Vol 12 (5) ◽  
pp. 589-596
Author(s):  
Magdalena K Biesiadecka ◽  
Piotr Sliwa ◽  
Katarzyna Tomala ◽  
Ryszard Korona
Keyword(s):  
Gene Expression ◽  
Protein Evolution ◽  
Present Experiment ◽  
Structural Instability ◽  
Its Sequence ◽  
Sequence Evolution ◽  
Relative Toxicity ◽  
Considerable Decrease ◽  
Conserved Sequence ◽  
Yeast Genes

Abstract The misfolding avoidance hypothesis postulates that sequence mutations render proteins cytotoxic and therefore the higher the gene expression, the stronger the operation of selection against substitutions. This translates into prediction that relative toxicity of extant proteins is higher for those evolving faster. In the present experiment, we selected pairs of yeast genes which were paralogous but evolving at different rates. We expressed them artificially to high levels. We expected that toxicity would be higher for ones bearing more mutations, especially that overcrowding should rather exacerbate than reverse the already existing differences in misfolding rates. We did find that the applied mode of overexpression caused a considerable decrease in fitness and that the decrease was proportional to the amount of excessive protein. However, it was not higher for proteins which are normally expressed at lower levels (and have less conserved sequence). This result was obtained consistently, regardless whether the rate of growth or ability to compete in common cultures was used as a proxy for fitness. In additional experiments, we applied factors that reduce accuracy of translation or enhance structural instability of proteins. It did not change a consistent pattern of independence between the fitness cost caused by overexpression of a protein and the rate of its sequence evolution.

scholarly journals Effects of X-Linkage and Sex-Biased Gene Expression on the Rate of Adaptive Protein Evolution in Drosophila

2008 ◽  
Vol 25 (8) ◽  
pp. 1639-1650 ◽  
Author(s):  
J. F. Baines ◽  
S. A. Sawyer ◽  
D. L. Hartl ◽  
J. Parsch
Keyword(s):  
Gene Expression ◽  
Protein Evolution ◽  
X Linkage

scholarly journals Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes

2018 ◽  
Vol 115 (11) ◽  
pp. 2794-2799 ◽  
Author(s):  
Dan Sun ◽  
Iksoo Huh ◽  
Wendy M. Zinzow-Kramer ◽  
Donna L. Maney ◽  
Soojin V. Yi
Keyword(s):  
Gene Expression ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Large Scale ◽  
Parental Behavior ◽  
Phenotypic Traits ◽  
Sequence Evolution ◽  
Expression Divergence ◽  
Evolutionary Mechanisms ◽  
Behavioral Phenotypes

In the white-throated sparrow (Zonotrichia albicollis), the second chromosome bears a striking resemblance to sex chromosomes. First, within each breeding pair of birds, one bird is homozygous for the standard arrangement of the chromosome (ZAL2/ZAL2) and its mate is heterozygous for a different version (ZAL2/ZAL2m). Second, recombination is profoundly suppressed between the two versions, leading to genetic differentiation between them. Third, the ZAL2mversion is linked with phenotypic traits, such as bright plumage, high aggression, and low parental behavior, which are usually associated with males. These similarities to sex chromosomes suggest that the evolutionary mechanisms that shape sex chromosomes, in particular genetic degeneration of the heterogametic version due to the suppression of recombination, are likely important in this system as well. Here, we investigated patterns of protein sequence evolution and gene expression evolution between the ZAL2 and ZAL2mchromosomes by whole-genome sequencing and transcriptome analyses. Patterns of protein evolution exhibited only weak signals of genetic degeneration, and few genes harbored signatures of positive selection. We found substantial evidence of transcriptome evolution, such as significant expression divergence between ZAL2 and ZAL2malleles and signatures of dosage compensation for highly expressed genes. These results suggest that, early in the evolution of heteromorphic chromosomes, gene expression divergence and dosage compensation can prevail before large-scale genetic degeneration. Our results show further that suppression of recombination between heteromorphic chromosomes can lead to the evolution of alternative (sex-like) behavioral phenotypes before substantial genetic degeneration.

scholarly journals Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads

2018 ◽  
Author(s):  
Marylaure De La Harpe ◽  
Margot Paris ◽  
Jaqueline Hess ◽  
Michael H. J. Barfuss ◽  
Martha L. Serrano-Serrano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Carbohydrate Metabolism ◽  
Adaptive Radiation ◽  
Sequence Evolution ◽  
Protein Coding ◽  
Gene Duplication And Loss ◽  
Repeated Evolution ◽  
Differential Gene ◽  
Pleiotropic Regulators ◽  
Cam Photosynthesis

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by several ‘key innovations’ including the transition from C3 to CAM photosynthesis. We used a phylogenomic approach complemented by differential gene expression (RNA-seq) and targeted metabolite profiling to address the patterns and mechanisms of C3/CAM evolution in the extremely species-rich bromeliad genus Tillandsia and related taxa. Evolutionary analyses at a range of different levels (selection on protein-coding genes, gene duplication and loss, regulatory evolution) revealed three common themes driving the evolution of CAM: response to heat and drought, alterations to basic carbohydrate metabolism, and regulation of organic acid storage. At the level of genes and their products, CAM/C3 shifts were accompanied by gene expansion of a circadian regulator, re-programming of ABA-related gene expression, and adaptive sequence evolution of an enolase, effectively linking carbohydrate metabolism to ABA-mediated stress response. These changes include several pleiotropic regulators, which facilitated the evolution of correlated adaptive traits during a textbook adaptive radiation.

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