Abstract:
:The rate at which genomes adapt to environmental changes and the prevalence of adaptive processes in molecular evolution are two controversial issues in current evolutionary genetics. Previous attempts to quantify the genome-wide rate of adaptation through amino-acid substitution have revealed a surprising diversity of patterns, with some species (e.g. Drosophila) experiencing a very high adaptive rate, while other (e.g. humans) are dominated by nearly-neutral processes. It has been suggested that this discrepancy reflects between-species differences in effective population size. Published studies, however, were mainly focused on model organisms, and relied on disparate data sets and methodologies, so that an overview of the prevalence of adaptive protein evolution in nature is currently lacking. Here we extend existing estimators of the amino-acid adaptive rate by explicitly modelling the effect of favourable mutations on non-synonymous polymorphism patterns, and we apply these methods to a newly-built, homogeneous data set of 44 non-model animal species pairs. Data analysis uncovers a major contribution of adaptive evolution to the amino-acid substitution process across all major metazoan phyla-with the notable exception of humans and primates. The proportion of adaptive amino-acid substitution is found to be positively correlated to species effective population size. This relationship, however, appears to be primarily driven by a decreased rate of nearly-neutral amino-acid substitution because of more efficient purifying selection in large populations. Our results reveal that adaptive processes dominate the evolution of proteins in most animal species, but do not corroborate the hypothesis that adaptive substitutions accumulate at a faster rate in large populations. Implications regarding the factors influencing the rate of adaptive evolution and positive selection detection in humans vs. other organisms are discussed.
journal_name
PLoS Genetjournal_title
PLoS geneticsauthors
Galtier Ndoi
10.1371/journal.pgen.1005774subject
Has Abstractpub_date
2016-01-11 00:00:00pages
e1005774issue
1eissn
1553-7390issn
1553-7404pii
PGENETICS-D-15-01679journal_volume
12pub_type
杂志文章相关文献
PLoS Genetics文献大全abstract::Neural stem cell self-renewal, neurogenesis, and cell fate determination are processes that control the generation of specific classes of neurons at the correct place and time. The transcription factor Pax6 is essential for neural stem cell proliferation, multipotency, and neurogenesis in many regions of the central n...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000511
更新日期:2009-06-01 00:00:00
abstract::RNA silencing is a defense system against "genomic parasites" such as transposable elements (TE), which are potentially harmful to host genomes. In plants, transcripts from TEs induce production of double-stranded RNAs (dsRNAs) and are processed into small RNAs (small interfering RNAs, siRNAs) that suppress TEs by RNA...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002953
更新日期:2012-09-01 00:00:00
abstract::ATM and ATR are two redundant checkpoint kinases essential for the stable maintenance of telomeres in eukaryotes. Previous studies have established that MRN (Mre11-Rad50-Nbs1) and ATRIP (ATR Interacting Protein) interact with ATM and ATR, respectively, and recruit their partner kinases to sites of DNA damage. Here, we...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000839
更新日期:2010-02-05 00:00:00
abstract::We have taken an engineering approach to extending the lifespan of Caenorhabditis elegans. Aging stands out as a complex trait, because events that occur in old animals are not under strong natural selection. As a result, lifespan can be lengthened rationally using bioengineering to modulate gene expression or to add ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002780
更新日期:2012-01-01 00:00:00
abstract::Although DNA methylation is the best characterized epigenetic mark, the mechanism by which it is targeted to specific regions in the genome remains unclear. Recent studies have revealed that local DNA methylation profiles might be dictated by cis-regulatory DNA sequences that mainly operate via DNA-binding factors. Co...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1009189
更新日期:2020-11-20 00:00:00
abstract::Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. Thes...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005268
更新日期:2015-05-28 00:00:00
abstract::During development of the cerebral cortex, neural stem cells (NSCs) divide symmetrically to proliferate and asymmetrically to generate neurons. Although faithful segregation of mitotic chromosomes is critical for NSC divisions, its fundamental mechanism remains unclear. A class of evolutionarily conserved protein comp...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004847
更新日期:2014-12-04 00:00:00
abstract::Cellular toxicity introduced by protein misfolding threatens cell fitness and viability. Failure to eliminate these polypeptides is associated with various aggregation diseases. In eukaryotes, the ubiquitin proteasome system (UPS) plays a vital role in protein quality control (PQC), by selectively targeting misfolded ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005178
更新日期:2015-04-28 00:00:00
abstract::We recently reported that centrosomal protein 164 (CEP164) regulates both cilia and the DNA damage response in the autosomal recessive polycystic kidney disease nephronophthisis. Here we examine the functional role of CEP164 in nephronophthisis-related ciliopathies and concomitant fibrosis. Live cell imaging of RPE-FU...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004594
更新日期:2014-10-23 00:00:00
abstract::The circadian clocks in chlorophyte algae have been studied in two model organisms, Chlamydomonas reinhardtii and Ostreococcus tauri. These studies revealed that the chlorophyte clocks include some genes that are homologous to those of the angiosperm circadian clock. However, the genetic network architectures of the c...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1008814
更新日期:2020-06-17 00:00:00
abstract::The combination of large-scale population genomic analyses and trait-based mapping approaches has the potential to provide novel insights into the evolutionary history and genome organization of crop plants. Here, we describe the detailed genotypic and phenotypic analysis of a sunflower (Helianthus annuus L.) associat...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1003378
更新日期:2013-03-01 00:00:00
abstract::Detailed information about stage-specific changes in gene expression is crucial for the understanding of the gene regulatory networks underlying development. Here, we describe the global gene expression dynamics during early flower development, a key process in the life cycle of a plant, during which floral patterning...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.0020117.eor
更新日期:2006-07-01 00:00:00
abstract::Bromodomain proteins are key regulators of gene expression. How the levels of these factors are regulated in specific environmental conditions is unknown. Previous work has established that expression of yeast Bromodomain factor 2 (BDF2) is limited by spliceosome-mediated decay (SMD). Here we show that BDF2 is subject...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1004661
更新日期:2014-09-18 00:00:00
abstract::There is growing evidence that gene expression profiling of peripheral blood cells is a valuable tool for assessing gene signatures related to exposure, drug-response, or disease. However, the true promise of this approach can not be estimated until the scientific community has robust baseline data describing variatio...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000873
更新日期:2010-03-12 00:00:00
abstract::Genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants associated with various phenotypes, but together they explain only a fraction of heritability, suggesting many variants have yet to be discovered. Recently it has been recognized that incorporating functional info...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1008947
更新日期:2020-08-24 00:00:00
abstract::The human genome encodes thousands of long noncoding RNA (lncRNA) genes; the function of majority of them is poorly understood. Aberrant expression of a significant number of lncRNAs is observed in various diseases, including cancer. To gain insights into the role of lncRNAs in breast cancer progression, we performed ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1007802
更新日期:2018-11-29 00:00:00
abstract::Sexual development is a key evolutionary innovation of eukaryotes. In many species, mating involves interaction between compatible mating partners that can undergo cell and nuclear fusion and subsequent steps of development including meiosis. Mating compatibility in fungi is governed by the mating type (MAT) loci. In ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1008365
更新日期:2019-09-06 00:00:00
abstract::NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005969
更新日期:2016-04-05 00:00:00
abstract::Rhizobial infection of legume root hairs requires a rearrangement of the actin cytoskeleton to enable the establishment of plant-made infection structures called infection threads. In the SCAR/WAVE (Suppressor of cAMP receptor defect/WASP family verpolin homologous protein) actin regulatory complex, the conserved N-te...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005623
更新日期:2015-10-30 00:00:00
abstract::One of the striking findings of comparative developmental genetics was that expression patterns of core transcription factors are extraordinarily conserved in bilaterians. However, it remains unclear whether cis-regulatory elements of their target genes also exhibit common signatures associated with conserved embryoni...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000912
更新日期:2010-04-15 00:00:00
abstract::Long interspersed nuclear element-1s (LINE-1s, or L1s) are an active family of retrotransposable elements that continue to mutate mammalian genomes. Despite the large contribution of L1 to mammalian genome evolution, we do not know where active L1 particles (particles in the process of retrotransposition) are located ...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1006837
更新日期:2017-06-06 00:00:00
abstract::A role for variant histone H2A.Z in gene expression is now well established but little is known about the mechanisms by which it operates. Using a combination of ChIP-chip, knockdown and expression profiling experiments, we show that upon gene induction, human H2A.Z associates with gene promoters and helps in recruiti...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000687
更新日期:2009-10-01 00:00:00
abstract::Mutational fitness effects can be measured with relatively high accuracy in viruses due to their small genome size, which facilitates full-length sequencing and genetic manipulation. Previous work has shown that animal and plant RNA viruses are very sensitive to mutation. Here, we characterize mutational fitness effec...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000742
更新日期:2009-11-01 00:00:00
abstract::Aging in Caenorhabditis elegans is characterized by widespread physiological and molecular changes, but the mechanisms that determine the rate at which these changes occur are not well understood. In this study, we identify a novel link between reproductive aging and somatic aging in C. elegans. By measuring global ag...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005725
更新日期:2015-12-11 00:00:00
abstract::Intragenomic conflicts arise when a genetic element favours its own transmission to the detriment of others. Conflicts over sex chromosome transmission are expected to have influenced genome structure, gene regulation, and speciation. In the mouse, the existence of an intragenomic conflict between X- and Y-linked mult...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002900
更新日期:2012-09-01 00:00:00
abstract::During neurogenesis, transcription factors combinatorially specify neuronal fates and then differentiate subtype identities by inducing subtype-specific gene expression profiles. But how is neuronal subtype identity maintained in mature neurons? Modeling this question in two Drosophila neuronal subtypes (Tv1 and Tv4),...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1002501
更新日期:2012-01-01 00:00:00
abstract::Genetical genomics is a strategy for mapping gene expression variation to expression quantitative trait loci (eQTLs). We performed a genetical genomics experiment in four functionally distinct but developmentally closely related hematopoietic cell populations isolated from the BXD panel of recombinant inbred mouse str...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000692
更新日期:2009-10-01 00:00:00
abstract::Filamentous fungi produce diverse secondary metabolites (SMs) essential to their ecology and adaptation. Although each SM is typically produced by only a handful of species, global SM production is governed by widely conserved transcriptional regulators in conjunction with other cellular processes, such as development...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1005096
更新日期:2015-03-18 00:00:00
abstract::Mating and gametogenesis are two essential components of animal reproduction. Gametogenesis must be modulated by the need for gametes, yet little is known of how mating, a process that utilizes gametes, may modulate the process of gametogenesis. Here, we report that mating stimulates female germline stem cell (GSC) pr...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1006123
更新日期:2016-06-16 00:00:00
abstract::Resection of DNA double-strand break (DSB) ends is generally considered a critical determinant in pathways of DSB repair and genome stability. Unlike for enzymatically induced site-specific DSBs, little is known about processing of random "dirty-ended" DSBs created by DNA damaging agents such as ionizing radiation. He...
journal_title:PLoS genetics
pub_type: 杂志文章
doi:10.1371/journal.pgen.1000656
更新日期:2009-09-01 00:00:00