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 replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Gascuel Odoi
10.1093/oxfordjournals.molbev.a025808subject
Has Abstractpub_date
1997-07-01 00:00:00pages
685-95issue
7eissn
0737-4038issn
1537-1719journal_volume
14pub_type
杂志文章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：: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：:Epigenetic information, which can be passed on independently of the DNA sequence, is stored in part in the form of histone posttranslational modifications and specific histone variants. Although complexes necessary for deposition have been identified for canonical and variant histones, information regarding the chroma...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msz039
更新日期：2019-05-01 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：:The Sm family of proteins is closely associated with RNA metabolism throughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Ar...
journal_title：Molecular biology and evolution
pub_type： 杂志文章,评审
doi：10.1093/molbev/msn175
更新日期：2008-11-01 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：:Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-geno...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msk013
更新日期：2006-06-01 00:00:00
abstract：:The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorous...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msl010
更新日期：2006-07-01 00:00:00
abstract：:The mitochondrial (mt) DNA control region (CR) of dogs and wolves contains an array of imperfect 10 bp tandem repeats. This region was studied for 14 domestic dogs representing the four major phylogenetic groups of nonrepetitive CR and for 5 wolves. Three repeat types were found among these individuals, distributed so...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026328
更新日期：2000-04-01 00:00:00
abstract：:Pseudogenes are nonfunctional relics of formerly functional genes and are thought to evolve neutrally. In some pseudogenes, however, the molecular evolutionary patterns are atypical of neutrally evolving sequences, exhibiting sequence conservation, codon-usage bias, and other features associated with functional genes....
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msh230
更新日期：2004-12-01 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：:The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the het...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mst067
更新日期：2013-07-01 00:00:00
abstract：:Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msr079
更新日期：2011-09-01 00:00:00
abstract：:We report the presence of four nuclear paralogs of a 380-bp segment of cytochrome b in callitrichine primates (marmosets and tamarins). The mitochondrial cytochrome b sequence and each nuclear paralog were obtained from several species, allowing multiple comparisons of rates and patterns of substitution both between m...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026388
更新日期：2000-07-01 00:00:00
abstract：:Current sequencing methods produce large amounts of data, but genome assemblies constructed from these data are often fragmented and incomplete. Incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. This means that methods attempting to estimate...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mst100
更新日期：2013-08-01 00:00:00
abstract：:The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelate...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msp120
更新日期：2009-09-01 00:00:00
abstract：:The robustness (sensitivity to violation of assumptions) of the maximum-likelihood and neighbor-joining methods was examined using simulation. Maximum likelihood and neighbor joining were implemented with Jukes-Cantor, Kimura, and gamma models of DNA substitution. Simulations were performed in which the assumptions of...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a040261
更新日期：1995-09-01 00:00:00
abstract：:Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolate...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msx178
更新日期：2017-10-01 00:00:00
abstract：:The cDNA of mouse pancreatic mRNA has been cloned. After the library was screened with a rat ribonuclease cDNA probe, the positive clones were isolated and sequenced. There were no differences from the previously determined protein sequence. The mRNA codes for a preribonuclease of 149 amino acid residues including a s...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a040585
更新日期：1990-01-01 00:00:00
abstract：:Phylogenetic relationships among the 5 groups of extant seed plants are presently unsettled. To reexamine this long-standing debate, we determine the complete chloroplast genome (cpDNA) of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium. The cpDNA of Cycas is a circular molecu...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msm059
更新日期：2007-06-01 00:00:00
abstract：:Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana en...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msv025
更新日期：2015-05-01 00:00:00
abstract：:Histone modification is an important mechanism of gene regulation in eukaryotes. Why many histone modifications can be stably maintained in the midst of genetic and environmental changes is a fundamental question in evolutionary biology. We obtained genome-wide profiles of three histone marks, H3 lysine 4 tri-methylat...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mss022
更新日期：2012-07-01 00:00:00
abstract：:Cytochrome c oxidase (COX) consists of 13 subunits, 3 encoded in the mitochondrial genome and 10 in the nucleus. Little is known of the role of the nuclear-encoded subunits, some of which exhibit tissue-specific isoforms. Subunit VIa is unique in having tissue-specific isoforms in all mammalian species examined. We ex...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a025798
更新日期：1997-06-01 00:00:00
abstract：:Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations....
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msp308
更新日期：2010-04-01 00:00:00
abstract：:It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variatio...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msy212
更新日期：2019-02-01 00:00:00
abstract：:Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid-bacteria coevolution is solely base...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msaa024
更新日期：2020-06-01 00:00:00
abstract：:Measuring natural selection on genomic elements involved in the cis-regulation of gene expression--such as transcriptional enhancers and promoters--is critical for understanding the evolution of genomes, yet it remains a major challenge. Many studies have attempted to detect positive or negative selection in these non...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/mst134
更新日期：2013-11-01 00:00:00
abstract：:Cyanobacteria contain up to three highly divergent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes: gap1, gap2, and gap3. Genes gap1 and gap2 are closely related at the sequence level to the nuclear genes encoding cytosolic and chloroplast GAPDH of higher plants and have recently been shown to play distinct key...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/oxfordjournals.molbev.a026125
更新日期：1999-04-01 00:00:00
abstract：:High-affinity antibodies arise within weeks of infection from the evolution of B-cell receptors under selection to improve antigen recognition. This rapid adaptation is enabled by the distribution of highly mutable "hotspot" motifs in B-cell receptor genes. High mutability in antigen-binding regions (complementarity d...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msy024
更新日期：2018-05-01 00:00:00
abstract：:Plasmodium vivax in southern Mexico exhibits different infectivities to 2 local mosquito vectors, Anopheles pseudopunctipennis and Anopheles albimanus. Previous work has tied these differences in mosquito infectivity to variation in the central repeat motif of the malaria parasite's circumsporozoite (csp) gene, but su...
journal_title：Molecular biology and evolution
pub_type： 杂志文章
doi：10.1093/molbev/msn073
更新日期：2008-06-01 00:00:00
