Abstract:
:A recent genomewide screen identified 13 transposable elements that are likely to have been adaptive during or after the spread of Drosophila melanogaster out of Africa. One of these insertions, Bari-Juvenile hormone epoxy hydrolase (Bari-Jheh), was associated with the selective sweep of its flanking neutral variation and with reduction of expression of one of its neighboring genes: Jheh3. Here, we provide further evidence that Bari-Jheh insertion is adaptive. We delimit the extent of the selective sweep and show that Bari-Jheh is the only mutation linked to the sweep. Bari-Jheh also lowers the expression of its other flanking gene, Jheh2. Subtle consequences of Bari-Jheh insertion on life-history traits are consistent with the effects of reduced expression of the Jheh genes. Finally, we analyze molecular evolution of Jheh genes in both the long- and the short-term and conclude that Bari-Jheh appears to be a very rare adaptive event in the history of these genes. We discuss the implications of these findings for the detection and understanding of adaptation.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
González J,Macpherson JM,Petrov DAdoi
10.1093/molbev/msp107subject
Has Abstractpub_date
2009-09-01 00:00:00pages
1949-61issue
9eissn
0737-4038issn
1537-1719pii
msp107journal_volume
26pub_type
杂志文章abstract::Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa283
更新日期:2020-11-03 00:00:00
abstract::Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw048
更新日期:2016-07-01 00:00:00
abstract::With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi051
更新日期:2005-03-01 00:00:00
abstract::The organization of the mitochondrial genome is generally very conserved among vertebrates. Because of this, examination of the rare rearrangements which do occur has been suggested as offering a powerful alternative to phylogenetic analyses of mitochondrial DNA sequences. Here, we report on an avian mitochondrial rea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026223
更新日期:2000-01-01 00:00:00
abstract::Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to det...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp054
更新日期:2009-06-01 00:00:00
abstract::Much of evolutionary change is mediated at the level of gene expression, yet our understanding of regulatory evolution remains unsatisfying. In light of recent data indicating that transcription factor binding sites undergo substantial turnover between species, we attempt to quantify the process of binding site turnov...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg077
更新日期:2003-05-01 00:00:00
abstract::The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy237
更新日期:2019-05-01 00:00:00
abstract::Most of the well-characterized mitochondrial genomes from diverse green algal lineages are circular mapping DNA molecules; however, Chlamydomonas reinhardtii has a linear 15.8 kb unit mitochondrial genome with 580 or 581 bp inverted repeat ends. In mitochondrial-enriched fractions prepared from Polytomella parva (=P. ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004180
更新日期:2002-07-01 00:00:00
abstract::Two longstanding issues on the molecular clock hypothesis are studied in this article. First, is there a global molecular clock in mammals? Although many authors have observed unequal rates of nucleotide substitution among mammalian lineages, some authors have proposed a global clock for all eutherians, i.e., a single...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004043
更新日期:2002-12-01 00:00:00
abstract::Identifying mechanisms that underlie variation in adult survivorship provide insight into the evolution of life history strategies and phenotypic variation in longevity. There is accumulating evidence that shortening telomeres, the protective caps at the ends of chromosomes, play an important role in individual variat...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm244
更新日期:2008-01-01 00:00:00
abstract::There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv147
更新日期:2015-10-01 00:00:00
abstract::Amastin is a transmembrane glycoprotein found on the cell surfaces of trypanosomatid parasites. Encoded by a large, diverse gene family, amastin was initially described from the intracellular, amastigote stage of Trypanosoma cruzi and Leishmania donovani. Genome sequences have subsequently shown that the amastin reper...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp214
更新日期:2010-01-01 00:00:00
abstract::Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to crea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz185
更新日期:2019-12-01 00:00:00
abstract::Wolbachia bacteria infect about half of all arthropods, with diverse and extreme consequences ranging from sex-ratio distortion and mating incompatibilities to protection against viruses. These phenotypic effects, combined with efficient vertical transmission from mothers to offspring, satisfactorily explain the invas...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx073
更新日期:2017-05-01 00:00:00
abstract::The human major histocompatibility complex (Mhc) is a chromosomal segment approximately 4 million bp long that contains > or = 84 genes. Some of these genes code for the class I and class II molecules, while the remaining genes code for complement components, cytochrome P450, tumor necrosis factor, and many other, unr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a039999
更新日期:1993-01-01 00:00:00
abstract::The cosmopolitan dinoflagellate genus Alexandrium, and especially the A. tamarense species complex, contain both toxic and nontoxic strains. An understanding of their evolution and paleogeography is a necessary precursor to unraveling the development and spread of toxic forms. The inclusion of more strains into the ex...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg105
更新日期:2003-07-01 00:00:00
abstract::The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq305
更新日期:2011-05-01 00:00:00
abstract::The plant genus Lycium (Solanaceae) originated in the Americas and includes approximately 85 species that are distributed worldwide. The vast majority of Old World species occur in southern Africa and eastern Asia. In this study, we examine biogeographic relationships among Old World species using a phylogenetic appro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq253
更新日期:2011-01-01 00:00:00
abstract::Microbial species play important roles in different environments and the production of high-quality genomes from metagenome data sets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz237
更新日期:2020-02-01 00:00:00
abstract::We describe a method to establish chronologies of ancient ribosomal evolution. The method uses structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp163
更新日期:2009-11-01 00:00:00
abstract::Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu185
更新日期:2014-09-01 00:00:00
abstract::Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv206
更新日期:2016-01-01 00:00:00
abstract::Many methods exist for detecting introgression between nonsister species, but the most commonly used require either a single sequence from four or more taxa or multiple sequences from each of three taxa. Here, we present a test for introgression that uses only a single sequence from three taxa. This test, denoted D3, ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz178
更新日期:2019-12-01 00:00:00
abstract::Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv349
更新日期:2016-04-01 00:00:00
abstract::Forty-six strains derived from American and French natural populations of Drosophila melanogaster were tested for the presence and activity of hobo elements by using Southern blotting and a gonadal dysgenesis assay. The oldest available strains exhibited weak detectable hybridization to the hobo-element probe and reve...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040649
更新日期:1991-05-01 00:00:00
abstract::Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg149
更新日期:2003-08-01 00:00:00
abstract::The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonpar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004094
更新日期:2002-04-01 00:00:00
abstract::Sponges (Porifera) are among the simplest living and the earliest branching metazoans. They hold a pivotal role for studying genome evolution of the entire metazoan branch, both as an outgroup to Eumetazoa and as the closest branching phylum to the common ancestor of all multicellular animals (Urmetazoa). In order to ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq174
更新日期:2010-12-01 00:00:00
abstract::We have followed, in glucose-limited chemostats, the evolution of natural isolates of Escherichia coli possessing maximal growth rates of 0.48-1.43 doublings/h. Under these conditions a rapid-growth phenotype similar to that of standard laboratory wild-type strains was selected so that after 280 generations all of the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040731
更新日期:1992-05-01 00:00:00
abstract::A phylogenetic analysis of sex-chromosomal zinc-finger genes (Zfx and Zfy) indicates that the genes have not evolved completely independently since their initial separation. The sequence similarities suggest gene conversion in the last exon between the duplicated Y-chromosomal genes Zfy-1 and Zfy-2 in the mouse. There...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040003
更新日期:1993-03-01 00:00:00