Abstract:
:Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurements of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters, such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations. Rapidly emerging next-generating sequencing technology has supplanted this phenotype-dependent approach, enabling direct empirical estimates of the mutation rate and a more nuanced understanding of the relative contributions of different classes of mutations to the standing genetic variation. Whole-genome sequencing of MA lines bears immense potential to provide a unified account of the evolutionary process at multiple levels-the genetic basis of variation, and the evolutionary dynamics of mutations under the forces of selection and drift. In this review, we have attempted to synthesize key insights into the spontaneous mutation process that are rapidly emerging from the partnering of classical MA experiments with high-throughput sequencing, with particular emphasis on the spontaneous rates and molecular properties of different mutational classes in nuclear and mitochondrial genomes of diverse taxa, the contribution of mutations to the evolution of gene expression, and the rate and stability of transgenerational epigenetic modifications. Future advances in sequencing technologies will enable greater species representation to further refine our understanding of mutational parameters and their functional consequences.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Katju V,Bergthorsson Udoi
10.1093/gbe/evy252subject
Has Abstractpub_date
2019-01-01 00:00:00pages
136-165issue
1issn
1759-6653pii
5209700journal_volume
11pub_type
杂志文章,评审abstract::Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trema...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evab010
更新日期:2021-01-23 00:00:00
abstract::Chemoreception is a widespread biological function that is essential for the survival, reproduction, and social communication of animals. Though the molecular mechanisms underlying chemoreception are relatively well known in insects, they are poorly studied in the other major arthropod lineages. Current availability o...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy081
更新日期:2018-04-01 00:00:00
abstract::Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male dete...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv128
更新日期:2015-07-02 00:00:00
abstract::Determining the rate of protein evolution and identifying the causes of its variation across the genome are powerful ways to understand forces that are important for genome evolution. By using a multitissue transcriptome data set from great tit (Parus major), we analyzed patterns of molecular evolution between two pas...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu157
更新日期:2014-08-01 00:00:00
abstract::Geosmithia morbida is an emerging fungal pathogen which serves as a model for examining the evolutionary processes behind pathogenicity because it is one of two known pathogens within a genus of mostly saprophytic, beetle-associated, fungi. This pathogen causes thousand cankers disease in black walnut trees and is vec...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx242
更新日期:2017-12-01 00:00:00
abstract::Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-in...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw014
更新日期:2016-03-09 00:00:00
abstract::By comparing the patterns of evolution in the coding and upstream noncoding regions of yeast ribosomal protein (RP) genes duplicated in a genome duplication, we find that although nonsynonymous sites in the coding sequences show strong evidence for the fixation of recent gene conversion events, similar patterns are le...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evq067
更新日期:2010-01-01 00:00:00
abstract::The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt091
更新日期:2013-01-01 00:00:00
abstract::Taeniid cestodes (including the human parasites Echinococcus spp. and Taenia solium) have very few mobile genetic elements (MGEs) in their genome, despite lacking a canonical PIWI pathway. The MGEs of these parasites are virtually unexplored, and nothing is known about their expression and silencing. In this work, we ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv126
更新日期:2015-07-01 00:00:00
abstract::Bartonella is a genetically diverse group of vector-borne bacteria. Over 40 species have been characterized to date, mainly from mammalian reservoirs and arthropod vectors. Rodent reservoirs harbor one of the largest Bartonella diversity described to date, and novel species and genetic variants are continuously identi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy236
更新日期:2018-11-01 00:00:00
abstract::A major mode of gene expression evolution is based on changes in cis-regulatory elements (CREs) whose function critically depends on the presence of transcription factor-binding sites (TFBS). Because CREs experience extensive TFBS turnover even with conserved function, alignment-based studies of CRE sequence evolution...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evp010
更新日期:2009-05-25 00:00:00
abstract::Tandem repeats (TRs) are highly dynamic regions of the genome. Mutations at these loci represent a significant source of genetic variation and can facilitate rapid adaptation. Bumblebees are important pollinating insects occupying a wide range of habitats. However, to date, molecular mechanisms underlying the potentia...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy244
更新日期:2018-12-01 00:00:00
abstract::Chaperonins promote protein folding and are known to play a role in the maintenance of cellular stability under stress conditions. The group I bacterial chaperonin complex comprises GroEL, that forms a barrel-like oligomer, and GroES that forms the lid. In most eubacteria the GroES/GroEL chaperonin is encoded by a sin...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw287
更新日期:2017-01-01 00:00:00
abstract::Selection modulates gene sequence evolution in different ways by constraining potential changes of amino acid sequences (purifying selection) or by favoring new and adaptive genetic variants (positive selection). The number of nonsynonymous differences in a pair of protein-coding sequences can be used to quantify the ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evp030
更新日期:2009-08-13 00:00:00
abstract::The evolution of a mechanically resilient epidermis was a key adaptation in the transition of amniotes to a fully terrestrial lifestyle. Skin appendages usually form via a specialized type of programmed cell death known as cornification which is characterized by the formation of an insoluble cornified envelope (CE). M...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz054
更新日期:2019-03-01 00:00:00
abstract::The loss of Y-linked genes during sex chromosome evolution creates a potentially deleterious low gene dosage in males. Recent studies have reported different strategies of dosage compensation. Unfortunately, most of these studies investigated taxa with comparatively old sex chromosome systems, which may limit insights...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv013
更新日期:2015-01-23 00:00:00
abstract::Ubiquinone (Q) is an isoprenoid quinone that functions as membrane electron carrier in mitochondria and bacterial organisms belonging to the alpha, beta, and gamma class of proteobacteria. The biosynthesis of Q follows various biochemical steps catalyzed by diverse proteins that are, in general, homologous in mitochon...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx225
更新日期:2017-11-01 00:00:00
abstract::Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv076
更新日期:2015-04-29 00:00:00
abstract::Chlorarachniophytes are unicellular marine algae with plastids (chloroplasts) of secondary endosymbiotic origin. Chlorarachniophyte cells retain the remnant nucleus (nucleomorph) and cytoplasm (periplastidial compartment, PPC) of the green algal endosymbiont from which their plastid was derived. To characterize the di...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs115
更新日期:2012-01-01 00:00:00
abstract::Lycopodiophyta-consisting of three orders, Lycopodiales, Isoetales and Selaginellales, with different types of shoot apical meristems (SAMs)-form the earliest branch among the extant vascular plants. They represent a sister group to all other vascular plants, from which they differ in that their leaves are microphylls...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx169
更新日期:2017-09-01 00:00:00
abstract::Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics, and proteomics to ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa159
更新日期:2020-09-01 00:00:00
abstract::Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. Although hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we d...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx268
更新日期:2018-01-01 00:00:00
abstract::Recent whole-genome approaches to microbial phylogeny have emphasized partitioning genes into functional classes, often focusing on differences between a stable core of genes and a variable shell. To rigorously address the effects of partitioning and combining genes in genome-level analyses, we developed a novel techn...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr121
更新日期:2012-01-01 00:00:00
abstract::RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx046
更新日期:2017-04-01 00:00:00
abstract::Fish use olfaction to sense a variety of nonvolatile chemical signals in water. However, the evolutionary importance of olfaction in species-rich cichlids is controversial. Here, we determined an almost complete sequence of the vomeronasal type 2 receptor-like (OlfC: putative amino acids receptor in teleosts) gene clu...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt041
更新日期:2013-01-01 00:00:00
abstract::In clonal systems, interpreting driver genes in terms of molecular networks helps understanding how these drivers elicit an adaptive phenotype. Obtaining such a network-based understanding depends on the correct identification of driver genes. In clonal systems, independent evolved lines can acquire a similar adaptive...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw010
更新日期:2016-01-23 00:00:00
abstract::In the experimental evolution of microbes such as Escherichia coli, many replicate populations are evolved from a common ancestor. Freezing a population sample supplemented with the cryoprotectant glycerol permits later analysis or restarting of an evolution experiment. Typically, each evolving population, and thus ea...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evw054
更新日期:2016-05-09 00:00:00
abstract::Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy042
更新日期:2018-04-01 00:00:00
abstract::Bacteria of the genus Xenorhabdus are symbionts of soil entomopathogenic nematodes of the genus Steinernema. This symbiotic association constitutes an insecticidal complex active against a wide range of insect pests. Unlike other Xenorhabdus species, Xenorhabdus poinarii is avirulent when injected into insects in the ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu119
更新日期:2014-06-05 00:00:00
abstract::Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insert...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw302
更新日期:2017-02-01 00:00:00