Abstract:
:A major theoretical consequence of selection at a locus is the genetic hitchhiking of linked sites (selective sweep). The extent of hitchhiking around a gene is related to the strength of selection and the rate of recombination, with its impact diminishing with distance from the selected site. At the Rop-1 locus of the sheep blowfly, Lucilia cuprina, polymorphisms at two different sites within the LcαE7 gene encode forms of the protein that confer organophosphorus insecticide resistance. To assess the impact of selection at these two sites on variation around LcαE7, we sequenced regions within six other genes along chromosome IV across isogenic (IV) strains of L. cuprina. High levels of linkage disequilibrium, characterized by low haplotype number (K) and diversity (H), and significant R(2) values were observed for two genes, LcαE1 and LcαE10, both members of the same α-esterase gene cluster as LcαE7. A significant R(2) value was also observed for a gene predicted to be the next closest to LcαE7, AL03, but not for any of the other genes, LcRpL13a, Lcdsx, or LcAce. Skews in the site frequency spectra toward high-frequency variants were significant for LcαE1 (Fay and Wu's H = -2.91), LcαE10 (H = -1.85), and Lcdsx (H = -2.00). Since the selective sweeps, two forms of likely returning variation were observed, including variation in microsatellites in an intron of LcαE10 and a recombination event between LcαE7 and LcαE10. These data suggest that two incomplete soft sweeps have occurred at LcαE7 that have significantly affected variation across, and beyond, the α-esterase gene cluster of L. cuprina. The speed and impact of these selective sweeps on surrounding genomic variation and the ability of L. cuprina to respond to future environmental challenges are discussed.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Rose CJ,Chapman JR,Marshall SD,Lee SF,Batterham P,Ross HA,Newcomb RDdoi
10.1093/molbev/msr006subject
Has Abstractpub_date
2011-06-01 00:00:00pages
1835-46issue
6eissn
0737-4038issn
1537-1719pii
msr006journal_volume
28pub_type
杂志文章abstract::Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly acco...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp149
更新日期:2009-10-01 00:00:00
abstract::Sequence variation among 10 alleles of the alcohol dehydrogenase (Adh) gene of the Hawaiian drosophilid D. mimica was analyzed with reference to the evolutionary history of the Hawaiian subgroup as well as to levels and patterns of polymorphism of the Adh gene in continental drosophilid species. The Adh gene of D. mim...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025582
更新日期:1996-12-01 00:00:00
abstract::Gene expression changes contribute to complex trait variations in both individuals and populations. However, the evolution of gene expression underlying complex traits over macroevolutionary timescales remains poorly understood. Snake venoms are proteinaceous cocktails where the expression of each toxin can be quantif...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz125
更新日期:2019-09-01 00:00:00
abstract::Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst271
更新日期:2014-04-01 00:00:00
abstract::The spacer between the 16S and 23S rRNA genes of the chloroplast DNA has been implicated as an origin of replication in several species of plants. In the evening primrose, Oenothera, this site was found to vary greatly in size, with plastid genomes (plastomes) being readily distinguished. To determine whether plastome...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025645
更新日期:1996-07-01 00:00:00
abstract::Heterotachy is a general term to describe positions that evolve at different rates in different lineages. Heterotachy also can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq346
更新日期:2011-05-01 00:00:00
abstract::Selenocysteine (Sec) is the 21st amino acid in the genetic code, inserted in response to UGA codons with the help of RNA structures, the SEC Insertion Sequence (SECIS) elements. The three domains of life feature distinct strategies for Sec insertion in proteins and its utilization. While bacteria and archaea possess s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw122
更新日期:2016-09-01 00:00:00
abstract::Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss108
更新日期:2012-10-01 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::The evolutionary expansion of CAG repeats in human triplet expansion disease genes is intriguing because of their deleterious phenotype. In the past, this expansion has been suggested to reflect a broad genomewide expansion of repeats, which would imply that mutational and evolutionary processes acting on repeats diff...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003873
更新日期:2001-06-01 00:00:00
abstract::Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change-an "evolutionary fingerprint" of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp260
更新日期:2010-03-01 00:00:00
abstract::Drosophila melanogaster, unlike mammals, has seven insulin-like peptides (DILPS). In Drosophila, all seven genes (dilp1-7) are single copy in the 12 species studied, except for D. grimshawi with two tandem copies of dilp2. Our comparative analysis revealed that genes dilp1-dilp7 exhibit differential functional constra...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq353
更新日期:2011-05-01 00:00:00
abstract::Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy053
更新日期:2018-06-01 00:00:00
abstract::As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic vari...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg092
更新日期:2003-06-01 00:00:00
abstract::The mitochondrial genome has undergone radical changes in both the Chlorophyta and Streptophyta, yet little is known about the dynamics of mtDNA evolution in either of these lineages. In the Chlorophyta, which comprises four of the five recognized classes of green algae (Prasinophyceae, Trebouxiophyceae, Ulvophyceae, ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh099
更新日期:2004-05-01 00:00:00
abstract::The spontaneous deamination of cytosine produces uracil mispaired with guanine in DNA, which will produce a mutation, unless repaired. In all domains of life, uracil-DNA glycosylases (UDGs) are responsible for the elimination of uracil from DNA. Thus, UDGs contribute to the integrity of the genetic information and the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq318
更新日期:2011-03-01 00:00:00
abstract::Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the ava...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040071
更新日期:1993-11-01 00:00:00
abstract::The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (approximately 800 to 1,200 MYA), with and without the assump...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msi039
更新日期:2005-03-01 00:00:00
abstract::We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by repl...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025808
更新日期:1997-07-01 00:00:00
abstract::Empirical codon models (ECMs) estimated from a large number of globular protein families outperformed mechanistic codon models in their description of the general process of protein evolution. Among other factors, ECMs implicitly model the influence of amino acid properties and multiple nucleotide substitutions (MNS)....
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss266
更新日期:2013-03-01 00:00:00
abstract::zeta-Crystallin is a novel nicotinamide adenine dinucleotide phosphate:quinone reductase, present at enzymatic levels in various tissues of different species, which is highly expressed in the lens of some hystricomorph rodents and camelids. We report here the complementary DNA (cDNA) cloning of zeta-crystallin from li...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040111
更新日期:1994-03-01 00:00:00
abstract::This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the ori...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040081
更新日期:1993-11-01 00:00:00
abstract::How is adaptability generated in a system composed of interacting cellular machineries, each with a separate and functionally critical job to perform? The machinery for organelle inheritance is precisely one such system, requiring coordination between robust and ancient cellular modules, including the cell cycle, cyto...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr264
更新日期:2012-03-01 00:00:00
abstract::Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubis...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr008
更新日期:2011-06-01 00:00:00
abstract::Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) muta...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv055
更新日期:2015-07-01 00:00:00
abstract::Transposable elements are widespread mobile DNA sequences able to integrate into new locations within genomes. Through transposition and recombination, they significantly contribute to genome plasticity and evolution. They can also regulate gene expression and provide regulatory and coding sequences (CDSs) for the evo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr208
更新日期:2012-02-01 00:00:00
abstract::Bacterial populations have been shown to accumulate deleterious mutations during spatial expansions that overall decrease their fitness and ability to grow. However, it is unclear if and how they can respond to selection in face of this mutation load. We examine here if artificial selection can counteract the negative...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz148
更新日期:2019-10-01 00:00:00
abstract::Based on previous observations that newly inserted LINEs and SINEs have particularly long 3' A-tails, which shorten rapidly during evolutionary time, we have analyzed the rat and mouse genomes for evidence of recently inserted SINEs and LINEs. We find that the youngest predicted subfamilies of rodent identifier (ID) e...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh225
更新日期:2004-11-01 00:00:00
abstract::In primates, the craniofacial skeleton and the dentition are marked by high levels of interspecific variation. Despite this, there are few comparative species studies conducted at the molecular level to investigate this functional diversity. We have determined nucleotide sequences of MSX1 and PAX9, two developmental g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj072
更新日期:2006-03-01 00:00:00
abstract::Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is r...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw197
更新日期:2016-12-01 00:00:00