Abstract:
:Spatial distribution and clustering of repetitive elements are extensively studied during the last years, as well as their colocalization with other genomic components. Here we investigate the large-scale features of Alu and LINE1 spatial arrangement in the human genome by studying the size distribution of interrepeat distances. In most cases, we have found power-law size distributions extending in several orders of magnitude. We have also studied the correlations of the extent of the power law (linear region in double-logarithmic scale) and of the corresponding exponent (slope) with other genomic properties. A model has been formulated to explain the formation of the observed power laws. According to the model, 2 kinds of events occur repetitively in evolutionary time: random insertion of several types of intruding sequences and occasional loss of repeats belonging to the initial population due to "elimination" events. This simple mechanism is shown to reproduce the observed power-law size distributions and is compatible with our present knowledge on the dynamics of repeat proliferation in the genome.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Sellis D,Provata A,Almirantis Ydoi
10.1093/molbev/msm181subject
Has Abstractpub_date
2007-11-01 00:00:00pages
2385-99issue
11eissn
0737-4038issn
1537-1719pii
msm181journal_volume
24pub_type
杂志文章abstract::Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026215
更新日期:1999-09-01 00:00:00
abstract::In a series of highly influential publications, Cavalli-Sforza and colleagues used principal component (PC) analysis to produce maps depicting how human genetic diversity varies across geographic space. Within Europe, the first axis of variation (PC1) was interpreted as evidence for the demic diffusion model of agricu...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq010
更新日期:2010-06-01 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::Endogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa180
更新日期:2020-11-01 00:00:00
abstract::Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025995
更新日期:1998-07-01 00:00:00
abstract::With whole-genome sequences being completed at an increasing rate, it is important to develop and assess tools to analyze them. Following annotation of the protein content of a genome, one can compare sequences with previously characterized homologous genes to detect novel functions within specific proteins in the evo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003745
更新日期:2001-11-01 00:00:00
abstract::The most frequent measure of phylogenetic uncertainty for splits is bootstrap support. Although large bootstrap support intuitively suggests that a split in a tree is well supported, it has not been clear how large bootstrap support needs to be to conclude that there is significant evidence that a hypothesized split i...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq048
更新日期:2010-07-01 00:00:00
abstract::Novel coronaviruses, including SARS-CoV-2, SARS, and MERS, often originate from recombination events. The mechanism of recombination in RNA viruses is template switching. Coronavirus transcription also involves template switching at specific regions, called transcriptional regulatory sequences (TRS). It is hypothesize...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa281
更新日期:2020-11-04 00:00:00
abstract::We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that ar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025817
更新日期:1997-07-01 00:00:00
abstract::Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we exam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx098
更新日期:2017-07-01 00:00:00
abstract::Pathogen recognition is the first step of immune reactions. In animals and plants, direct or indirect pathogen recognition is often mediated by a wealth of fast-evolving receptors, many of which contain ligand-binding and signal transduction domains, such as leucine-rich or tetratricopeptide repeat (LRR/TPR) and NB-AR...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr296
更新日期:2012-04-01 00:00:00
abstract::While it is widely accepted that most animals (Metazoa) do not have endogenous cellulases, relying instead on intestinal symbionts for cellulose digestion, the glycosyl hydrolase family 9 (GHF9) cellulases found in the genomes of termites, abalone, and sea squirts could be an exception. Using information from expresse...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi107
更新日期:2005-05-01 00:00:00
abstract::The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of sta...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw046
更新日期:2016-06-01 00:00:00
abstract::We examined microsatellite variation in two diploid, outcrossing relatives of Arabidopsis thaliana, Arabis petraea and Arabis lyrata. The primer sequences were derived from A. thaliana. About 50% (14 loci) of the A. thaliana primers could successfully amplify microsatellites in the related species. Analysis of microsa...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025758
更新日期:1997-03-01 00:00:00
abstract::With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy228
更新日期:2019-03-01 00:00:00
abstract::We describe here a case of homologous introns containing homologous open reading frames (ORFs) that are inserted at the same site in the large subunit (LSU) rRNA gene of different organelles in distantly related organisms. We show that the chloroplast LSU rRNA gene of the green alga Chlamydomonas pallidostigmatica con...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040234
更新日期:1995-07-01 00:00:00
abstract::The ability to counter periods of low humidity is an important determinant of distribution range in Drosophila. Climate specialists with low physiological tolerance to desiccation stress are restricted to the tropics and may lack the ability to further increase resistance through evolution. Although the physiological ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr294
更新日期:2012-05-01 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::The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm012
更新日期:2007-04-01 00:00:00
abstract::Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy248
更新日期:2019-03-01 00:00:00
abstract::This report describes a lysozyme expressed at high levels in the stomach of the hoatzin, the only known foregut-fermenting bird. Evolutionary comparison places it among the calcium-binding lysozymes rather than among the conventional types. Conventional lysozymes were recruited as digestive enzymes twice in the evolut...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040173
更新日期:1994-11-01 00:00:00
abstract::Human histatins are a family of low-M(r), neutral to very basic, histidine-rich salivary polypeptides. They probably function as part of the nonimmune host defense system in the oral cavity. A 39-kb region of DNA containing the HIS1 and HIS2 genes was isolated from two human genomic phage libraries as a series of over...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040022
更新日期:1993-05-01 00:00:00
abstract::A 32-kb region including the Adh structural gene was analyzed with six restriction endonucleases in 20 lines of Drosophila pseudoobscura, one line of D. persimilis, and one line of D. miranda. Nineteen lines of D. pseudoobscura from a single population were estimated to be polymorphic at one in every 15 nucleotides (p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040438
更新日期:1987-05-01 00:00:00
abstract::Significance levels obtained from a chi 2 contingency test are suspect when sample sizes are small. Traditionally this has meant that data must be combined. However, such an approach may obscure heterogeneity and hence potentially reduce the power of the statistical test. In this paper, we present a Monte Carlo soluti...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040568
更新日期:1989-09-01 00:00:00
abstract::The origin and maintenance of sex remains one of the most debated topics in evolutionary biology. Investigations of the molecular genetic consequences of asexuality, such as direct estimation of mutation and recombination rates in asexual lineages, are critical for explaining the prevalence of sex in nature. In this s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq199
更新日期:2011-01-01 00:00:00
abstract::Directional evolution in microsatellites is the tendency for microsatellites either to increase or to decrease in size over time between populations. We analyzed 99 microsatellite loci in a sample of 193 maize plants representing the entire pre-Columbian range of this crop for evidence of directional evolution. We too...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg156
更新日期:2003-09-01 00:00:00
abstract::The acrosomal protein bindin attaches sperm to eggs during sea urchin fertilization. Complementary to ongoing functional biochemical studies, I take a comparative approach to explore the molecular evolution of bindin in a group of closely related free-spawning echinoid species. Two alleles of the mature bindin gene we...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025902
更新日期:1998-12-01 00:00:00
abstract::This study aims to unravel the biogeography of a model symbiont/host system by exploiting the prediction that a symbiont will leave a signature of infection on the host. Specifically, a global sample of 1,442 Drosophila simulans from 33 countries and 64 sampling localities was employed to infer the phylogeography of t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh028
更新日期:2004-03-01 00:00:00
abstract::Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between des...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr228
更新日期:2012-02-01 00:00:00
abstract::Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Drosophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addition, while conserva...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003805
更新日期:2001-03-01 00:00:00