Abstract:
:Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether and how this occurs is limited. Here, we present an analysis of the great tit (Parus major) genome, aiming to detect signals of faster-Z evolution. We find mixed evidence of faster divergence on the Z chromosome than autosomes, with significantly higher divergence being found in ancestral repeats, but not at 4- or 0-fold degenerate sites. Interestingly, some 4-fold sites appear to be selectively constrained, which may mislead analyses that use these sites as the neutral reference (e.g., dN/dS). Consistent with other studies in birds, the mutation rate is significantly higher in males than females, and the long-term Z-to-autosome effective population size ratio is only 0.5, significantly lower than the expected value of 0.75. These are indicative of male-driven evolution and high variance in male reproductive success, respectively. We find no evidence for an increased efficacy of positive selection on the Z chromosome. In contrast, the Z chromosome in great tits appears to be affected by increased genetic drift, which has led to detectable signals of weakened intensity of purifying selection. These results provide further evidence that the Z chromosome often has a low effective population size, and that this has important consequences for its evolution. They also highlight the importance of considering multiple factors that can affect the rate of evolution and effective population sizes of sex chromosomes.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Hayes K,Barton HJ,Zeng Kdoi
10.1093/gbe/evaa044subject
Has Abstractpub_date
2020-03-01 00:00:00pages
210-222issue
3issn
1759-6653pii
5771331journal_volume
12pub_type
杂志文章abstract::The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu288
更新日期:2015-01-09 00:00:00
abstract::It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of gene...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt178
更新日期:2013-01-01 00:00:00
abstract::Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abioti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy087
更新日期:2018-04-01 00:00:00
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 mut...
journal_title:Genome biology and evolution
pub_type: 杂志文章,评审
doi:10.1093/gbe/evy252
更新日期:2019-01-01 00:00:00
abstract::Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw185
更新日期:2016-09-19 00:00:00
abstract::Genome reduction is a hallmark of symbiotic genomes, and the rate and patterns of gene loss associated with this process have been investigated in several different symbiotic systems. However, in long-term host-associated coevolving symbiont clades, the genome size differences between strains are normally quite small ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv108
更新日期:2015-05-28 00:00:00
abstract::DNA methylation and chromatin states play key roles in development and disease. However, the extent of recent evolutionary divergence in the human epigenome and the influential factors that have shaped it are poorly understood. To determine the links between genome sequence and human epigenome evolution, we examined t...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu142
更新日期:2014-06-24 00:00:00
abstract::The genus Claviceps has been known for centuries as an economically important fungal genera for pharmacology and agricultural research. Only recently have researchers begun to unravel the evolutionary history of the genus, with origins in South America and classification of four distinct sections through ecological, m...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa267
更新日期:2021-01-29 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::Dosage compensation--equalizing gene expression levels in response to differences in gene dose or copy number--is classically considered to play a critical role in the evolution of heteromorphic sex chromosomes. As the X and Y diverge through degradation and gene loss on the Y (or the W in female-heterogametic ZW taxa...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr036
更新日期:2011-01-01 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::Campylobacter sputorum is a nonthermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase neg...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx112
更新日期:2017-06-01 00:00:00
abstract::In this study, the full genome sequence of Bacillus velezensis strain UFLA258, a biological control agent of plant pathogens was obtained, assembled, and annotated. With a comparative genomics approach, in silico analyses of all complete genomes of B. velezensis and closely related species available in the database we...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz208
更新日期:2019-10-01 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::The predominantly aquatic order Alismatales, which includes approximately 4,500 species within Araceae, Tofieldiaceae, and the core alismatid families, is a key group in investigating the origin and early diversification of monocots. Despite their importance, phylogenetic ambiguity regarding the root of the Alismatale...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv260
更新日期:2016-04-06 00:00:00
abstract::Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evs056
更新日期:2012-01-01 00:00:00
abstract::Organelle DNA is no stranger to palindromic repeats. But never has a mitochondrial or plastid genome been described in which every coding region is part of a distinct palindromic unit. While sequencing the mitochondrial DNA of the nonphotosynthetic green alga Polytomella magna, we uncovered precisely this type of geni...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt122
更新日期:2013-01-01 00:00:00
abstract::Isochores are large regions of relatively homogeneous nucleotide composition and are present in the genomes of all mammals and birds that have been sequenced to date. The newly sequenced genome of Anolis carolinensis provides the first opportunity to quantify isochore structure in a nonavian reptile. We find Anolis to...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr072
更新日期:2011-01-01 00:00:00
abstract::Explaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct time-scales on potentially interdependent traits, can benefit from ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz182
更新日期:2019-09-01 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 evolution of heterogametic sex chromosomes is often-but not always-accompanied by the evolution of dosage compensating mechanisms that mitigate the impact of sex-specific gene dosage on levels of gene expression. One emerging view of this process is that such mechanisms may only evolve in male-heterogametic (XY) s...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv156
更新日期:2015-09-02 00:00:00
abstract::Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic an...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt195
更新日期:2013-01-01 00:00:00
abstract::Cytoplasmic male sterility (MS) in plants is caused by MS-inducing mitochondria, which have emerged frequently during plant evolution. Nuclear restorer-of-fertility (Rf)genes can suppress their cognate MS-inducing mitochondria. Whereas many Rfs encode a class of RNA-binding protein, the sugar beet (Caryophyllales) Rf ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa186
更新日期:2020-12-06 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::Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustai...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv002
更新日期:2015-01-07 00:00:00
abstract::Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meni...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu094
更新日期:2014-05-06 00:00:00
abstract::The contribution of the transposons' promoter in the horizontal transfer process is quite overlooked in the scientific literature. To shed light on this aspect we have mimicked the horizontal transfer process in laboratory and assayed in a wide range of hosts (fly, human, yeast and bacteria) the promoter activity of t...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx122
更新日期:2017-06-01 00:00:00
abstract::Gene duplication is the primary source of new genes, but the mechanisms underlying the functional divergence and retention of duplicate genes are not well understood. Because eukaryotic proteins are localized to subcellular structures and localization can be altered by a single amino acid replacement, it was recently ...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evp021
更新日期:2009-07-22 00:00:00
abstract::In 1957, an invasive and highly defensive honey bee began to spread across Brazil. In the previous year, Brazilian researchers hoped to produce a subtropical-adapted honey bee by crossing local commercial honey bees (of European origin) with a South African honey bee subspecies (Apis mellifera scutellata; an A-lineage...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa128
更新日期:2020-08-01 00:00:00
abstract::We previously discovered that lagging strand genes evolve faster in Bacillus subtilis (and potentially other bacteria). Lagging strand genes are transcribed in the head-on orientation with respect to DNA replication, leading to collisions between the two machineries that stall replication and can destabilize genomes. ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw274
更新日期:2016-12-01 00:00:00