Abstract:
:The ParaHox and Hox gene clusters control aspects of animal anterior-posterior development and are related as paralogous evolutionary sisters. Despite this relationship, it is not clear if the clusters operate in similar ways, with similar constraints. To compare clusters, we examined the transposable-element (TE) content of amphioxus and mammalian ParaHox and Hox clusters. Chordate Hox clusters are known to be largely devoid of TEs, possibly due to gene regulation and constraints on clustering in these animals. Here, we describe several novel amphioxus TEs and show that the amphioxus ParaHox cluster is a hotspot for TE insertion. TE contents of mammalian ParaHox loci are at background levels, in stark contrast to chordate Hox clusters. This marks a significant difference between Hox and ParaHox clusters. The presence of so many potentially disruptive elements implies selection constrains these ParaHox clusters as they have not dispersed despite 500 My of evolution for each lineage.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Osborne PW,Ferrier DEdoi
10.1093/molbev/msp235subject
Has Abstractpub_date
2010-02-01 00:00:00pages
217-20issue
2eissn
0737-4038issn
1537-1719pii
msp235journal_volume
27pub_type
信件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
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp094
更新日期:2009-08-01 00:00:00
abstract::Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040244
更新日期:1995-07-01 00:00:00
abstract::DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040086
更新日期:1994-01-01 00:00:00
abstract::Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 lo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx050
更新日期:2017-04-01 00:00:00
abstract::Recently, Lee et al. (Lee JH, Silhavy JL, Lee JE, et al. (30 co-authors). 2012. Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science (335:966-969.) demonstrated that mutation in either of the transmembrane protein encoding genes, TMEM138 or TMEM216, causes phenotypically indistinguishabl...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss215
更新日期:2013-01-01 00:00:00
abstract::The phylogeny of Anisoptera, dragonflies in the strict sense, has proven to be notoriously difficult to resolve. Based on morphological characters, several recent publications dealing with the phylogeny of dragonflies proposed contradicting inter- and intrafamily relationships. We explored phylogenetic information con...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003717
更新日期:2001-01-01 00:00:00
abstract::We have used analysis of variance to partition the variation in synonymous and amino acid substitution rates between three effects (gene, lineage, and a gene-by-lineage interaction) in mammalian nuclear and mitochondrial genes. We find that gene effects are stronger for amino acid substitution rates than for synonymou...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004231
更新日期:2003-01-01 00:00:00
abstract::Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the n...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy106
更新日期:2018-08-01 00:00:00
abstract::The phylogenies for each of the protein-coding genes from the Methanococcus jannaschii genome were surveyed to determine the history of the major groups of life. For each gene, homologous sequences from other archaea, eucarya, and Gram-positive and Gram-negative bacteria were collected and aligned, and a phylogeny was...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025983
更新日期:1998-07-01 00:00:00
abstract::Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (R. Desper and O. Gascuel, J. Comp. Biol. 9:687-705, 2002), we introduced a new "balanced" minimum evolution (BME) principle, based on a branch length estimation scheme of Y. Pauplin (J. Mol. Evo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh049
更新日期:2004-03-01 00:00:00
abstract::The adaptive significance of enzyme variation has been of central interest in population genetics. Yet, how natural selection operates on enzymes in the larger context of biochemical pathways has not been broadly explored. A basic expectation is that natural selection on metabolic phenotypes will target enzymes that c...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm057
更新日期:2007-06-01 00:00:00
abstract::The selective pressure at the protein level is usually measured by the nonsynonymous/synonymous rate ratio (omega = dN/dS), with omega < 1, omega = 1, and omega > 1 indicating purifying (or negative) selection, neutral evolution, and diversifying (or positive) selection, respectively. The omega ratio is commonly calcu...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003945
更新日期:2001-08-01 00:00:00
abstract::Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz235
更新日期:2020-02-01 00:00:00
abstract::A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025892
更新日期:1998-12-01 00:00:00
abstract::Inactivation of the X chromosome in the male germ line has been suggested to contribute to the excess of gene movement off the X chromosome and the paucity of X-linked male-biased genes that have been observed in Drosophila species. Recent experimental work has demonstrated the transcriptional inactivation of the X ch...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq355
更新日期:2011-05-01 00:00:00
abstract::During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj036
更新日期:2006-02-01 00:00:00
abstract::That natural selection affects molecular evolution at synonymous sites in protein-coding sequences is well established and is thought to predominantly reflect selection for translational efficiency/accuracy mediated through codon bias. However, a recently developed maximum likelihood framework, when applied to 18 codi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm196
更新日期:2007-12-01 00:00:00
abstract::The complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the gene...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026417
更新日期:2000-09-01 00:00:00
abstract::Dogs exhibit more phenotypic variation than any other mammal and are affected by a wide variety of genetic diseases. However, the origin and genetic basis of this variation is still poorly understood. We examined the effect of domestication on the dog genome by comparison with its wild ancestor, the gray wolf. We comp...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn177
更新日期:2008-11-01 00:00:00
abstract::This study establishes a phylogenetic framework for the natural geographic isolates of the widely studied nematode species Caenorhabditis elegans. Virtually complete mitochondrial genomes are sequenced from 27 C. elegans natural isolates to characterize mitochondrial divergence patterns and to investigate the evolutio...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg044
更新日期:2003-03-01 00:00:00
abstract::Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication ev...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx234
更新日期:2017-12-01 00:00:00
abstract::Hepcidin is a small bioactive peptide with dual roles as an antimicrobial peptide and as the principal hormonal regulator of iron homeostasis in human and mouse. Hepcidin homologs of very similar structures are found in lower vertebrates, all comprise approximately 20-25 amino acids with 8 highly conserved cysteines f...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn056
更新日期:2008-06-01 00:00:00
abstract::One challenge of analyzing samples of DNA sequences is to account for the nonnegligible polymorphisms produced by error when the sequencing error rate is high or the sample size is large. Specifically, those artificial sequence variations will bias the observed single nucleotide polymorphism (SNP) frequency spectrum, ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp059
更新日期:2009-07-01 00:00:00
abstract::Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a G...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss265
更新日期:2013-03-01 00:00:00
abstract::Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn043
更新日期:2008-05-01 00:00:00
abstract::Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anse...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh065
更新日期:2004-06-01 00:00:00
abstract::Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa194
更新日期:2020-12-16 00:00:00
abstract::Unlike mammals, fish are able to regenerate axons in their central nervous system. This difference has been partly attributed to the loss/acquisition of inhibitory proteins during evolution. Nogo-A--the longest isoform of the reticulon4 (rtn4) gene product--is commonly found in mammalian myelin where it acts as a pote...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq313
更新日期:2011-04-01 00:00:00
abstract::The acquisition of photosynthesis by eukaryotic cells through enslavement of a cyanobacterium represents one of the most remarkable turning points in the history of life on Earth. In addition to endosymbiotic gene transfer, the acquisition of a protein import apparatus and the coordination of gene expression between h...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq158
更新日期:2010-12-01 00:00:00