Median-joining networks for inferring intraspecific phylogenies.

Abstract:

:Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolutionary paths in the form of cycles. We present a method ("median joining" [MJ]) for constructing networks from recombination-free population data that combines features of Kruskal's algorithm for finding minimum spanning trees by favoring short connections, and Farris's maximum-parsimony (MP) heuristic algorithm, which sequentially adds new vertices called "median vectors", except that our MJ method does not resolve ties. The MJ method is hence closely related to the earlier approach of Foulds, Hendy, and Penny for estimating MP trees but can be adjusted to the level of homoplasy by setting a parameter epsilon. Unlike our earlier reduced median (RM) network method, MJ is applicable to multistate characters (e.g., amino acid sequences). An additional feature is the speed of the implemented algorithm: a sample of 800 worldwide mtDNA hypervariable segment I sequences requires less than 3 h on a Pentium 120 PC. The MJ method is demonstrated on a Tibetan mitochondrial DNA RFLP data set.

journal_name

Mol Biol Evol

authors

Bandelt HJ,Forster P,Röhl A

doi

10.1093/oxfordjournals.molbev.a026036

subject

Has Abstract

pub_date

1999-01-01 00:00:00

pages

37-48

issue

1

eissn

0737-4038

issn

1537-1719

journal_volume

16

pub_type

杂志文章
  • Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors.

    abstract::Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn148

    authors: Burgess R,Yang Z

    更新日期:2008-09-01 00:00:00

  • Statistical potentials for improved structurally constrained evolutionary models.

    abstract::Assessing the influence of three-dimensional protein structure on sequence evolution is a difficult task, mainly because of the assumption of independence between sites required by probabilistic phylogenetic methods. Recently, models that include an explicit treatment of protein structure and site interdependencies ha...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq047

    authors: Kleinman CL,Rodrigue N,Lartillot N,Philippe H

    更新日期:2010-07-01 00:00:00

  • Nineteenth century seeds reveal the population genetics of landrace barley (Hordeum vulgare).

    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

    authors: Leino MW,Hagenblad J

    更新日期:2010-04-01 00:00:00

  • Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom.

    abstract::Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu294

    authors: Reyes-Velasco J,Card DC,Andrew AL,Shaney KJ,Adams RH,Schield DR,Casewell NR,Mackessy SP,Castoe TA

    更新日期:2015-01-01 00:00:00

  • Translational selection on codon usage in Xenopus laevis.

    abstract::A correspondence analysis of codon usage in Xenopus laevis revealed that the first axis is strongly correlated with the base composition at third codon positions. The second axis discriminates between putatively highly expressed genes and the other coding sequences, with expression levels being confirmed by the analys...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a003958

    authors: Musto H,Cruveiller S,D'Onofrio G,Romero H,Bernardi G

    更新日期:2001-09-01 00:00:00

  • Intra- and interspecific variation of the CCR5 gene in higher primates.

    abstract::We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light o...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msg198

    authors: Zhang YW,Ryder OA,Zhang YP

    更新日期:2003-10-01 00:00:00

  • Divergence time of porcine reproductive and respiratory syndrome virus subtypes.

    abstract::Porcine reproductive and respiratory syndrome virus (PRRSV) recently emerged in domestic pigs of Western Europe and North America. Although time of emergence was identical on the two continents, genetic composition was markedly different with a clear geographical subtype structure, indicating that subtypes diverged in...

    journal_title:Molecular biology and evolution

    pub_type: 评论,信件

    doi:10.1093/molbev/msi208

    authors: Forsberg R

    更新日期:2005-11-01 00:00:00

  • Rapid R2 retrotransposition leads to the loss of previously inserted copies via large deletions of the rDNA locus.

    abstract::R2 non-long terminal repeat retrotransposable elements insert specifically into the 28S rRNA genes of a wide range of animals. These elements maintain long-term stable relationships with the host genome. By scoring the variation present at the 5' ends of individual R2 copies, lines of Drosophila simulans have been ide...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msm250

    authors: Zhang X,Zhou J,Eickbush TH

    更新日期:2008-01-01 00:00:00

  • Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.

    abstract::In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also exp...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa210

    authors: Ho AT,Hurst LD

    更新日期:2021-01-04 00:00:00

  • Changes in Rubisco kinetics during the evolution of C4 photosynthesis in Flaveria (Asteraceae) are associated with positive selection on genes encoding the enzyme.

    abstract::Rubisco, the primary photosynthetic carboxylase, evolved 3-4 billion years ago in an anaerobic, high CO(2) atmosphere. The combined effect of low CO(2) and high O(2) levels in the modern atmosphere, and the inability of Rubisco to distinguish completely between CO(2) and O(2), leads to the occurrence of an oxygenation...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq335

    authors: Kapralov MV,Kubien DS,Andersson I,Filatov DA

    更新日期:2011-04-01 00:00:00

  • MAFFT multiple sequence alignment software version 7: improvements in performance and usability.

    abstract::We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/mst010

    authors: Katoh K,Standley DM

    更新日期:2013-04-01 00:00:00

  • Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery.

    abstract::Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa221

    authors: Foflonker F,Blaby-Haas CE

    更新日期:2021-01-23 00:00:00

  • Characterization of the Cadherin-Catenin Complex of the Sea Anemone Nematostella vectensis and Implications for the Evolution of Metazoan Cell-Cell Adhesion.

    abstract::The cadherin-catenin complex (CCC) mediates cell-cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-bind...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msw084

    authors: Clarke DN,Miller PW,Lowe CJ,Weis WI,Nelson WJ

    更新日期:2016-08-01 00:00:00

  • Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication.

    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

    authors: Guo B,Zou M,Wagner A

    更新日期:2012-10-01 00:00:00

  • Nucleolar binding sequences of the ribosomal protein S6e family reside in evolutionary highly conserved peptide clusters.

    abstract::Proteomic analyses of the nucleolus have revealed almost 700 functionally diverse proteins implicated in ribosome biogenesis, nucleolar assembly, and regulation of vital cellular processes. However, this nucleolar inventory has not unveiled a specific consensus motif necessary for nucleolar binding. The ribosomal prot...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn002

    authors: Kundu-Michalik S,Bisotti MA,Lipsius E,Bauche A,Kruppa A,Klokow T,Kammler G,Kruppa J

    更新日期:2008-03-01 00:00:00

  • Molecular clocks do not support the Cambrian explosion.

    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

    authors: Blair JE,Hedges SB

    更新日期:2005-03-01 00:00:00

  • ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy.

    abstract::Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa139

    authors: Zhang C,Scornavacca C,Molloy EK,Mirarab S

    更新日期:2020-11-01 00:00:00

  • Partial genetic turnover in neandertals: continuity in the East and population replacement in the West.

    abstract::Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recen...

    journal_title:Molecular biology and evolution

    pub_type: 信件

    doi:10.1093/molbev/mss074

    authors: Dalén L,Orlando L,Shapiro B,Brandström-Durling M,Quam R,Gilbert MT,Díez Fernández-Lomana JC,Willerslev E,Arsuaga JL,Götherström A

    更新日期:2012-08-01 00:00:00

  • Evolution of nicotinic acetylcholine receptor subunits.

    abstract::A phylogenetic tree of a gene family of nicotinic acetylcholine receptor subunits was constructed using 84 nucleotide sequences of receptor subunits from 18 different species in order to elucidate the evolutionary origin of receptor subunits. The tree constructed showed that the common ancestor of all subunits may hav...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025951

    authors: Tsunoyama K,Gojobori T

    更新日期:1998-05-01 00:00:00

  • Efficient implementation of MrBayes on multi-GPU.

    abstract::MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)(3)), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)(3) Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-wor...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/mst043

    authors: Bao J,Xia H,Zhou J,Liu X,Wang G

    更新日期:2013-06-01 00:00:00

  • Human L1 Transposition Dynamics Unraveled with Functional Data Analysis.

    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

    authors: Chen D,Cremona MA,Qi Z,Mitra RD,Chiaromonte F,Makova KD

    更新日期:2020-12-16 00:00:00

  • A generalized mechanistic codon model.

    abstract::Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substit...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu196

    authors: Zaheri M,Dib L,Salamin N

    更新日期:2014-09-01 00:00:00

  • Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia.

    abstract::The genotypic signature of spatially varying selection is ubiquitous across the Drosophila melanogaster genome. Spatially structured adaptive phenotypic differences are also commonly found, particularly along New World and Australian latitudinal gradients. However, investigation of gene expression variation in one or ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq197

    authors: Levine MT,Eckert ML,Begun DJ

    更新日期:2011-01-01 00:00:00

  • Constraints on the evolution of plastid introns: the group II intron in the gene encoding tRNA-Val(UAC).

    abstract::The evolution of the group II intron in the plastid gene encoding tRNA(Val)UAC (trnV) from seven plant taxa was studied by aligning secondary and other structural features. Levels of evolutionary divergence between six angiosperms and a liverwort, Marchantia polymorpha, were compared for the six domains commonly demon...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040765

    authors: Learn GH Jr,Shore JS,Furnier GR,Zurawski G,Clegg MT

    更新日期:1992-09-01 00:00:00

  • SSU rRNA-based phylogenetic position of the genera Amoeba and Chaos (Lobosea, Gymnamoebia): the origin of gymnamoebae revisited.

    abstract::Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a003777

    authors: Bolivar I,Fahrni JF,Smirnov A,Pawlowski J

    更新日期:2001-12-01 00:00:00

  • Molecular evolution of the 5'-flanking regions of the duplicated Amy genes in Drosophila melanogaster species subgroup.

    abstract::The nucleotide sequences of the 5'-flanking regions of the duplicated Amy genes in eight sibling species belonging to the melanogaster species subgroup are analyzed. In Drosophila melanogaster, a region of about 450 bp immediately upstream of the translation initiation site of the two paralogous genes (the proximal an...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025617

    authors: Okuyama E,Shibata H,Tachida H,Yamazaki T

    更新日期:1996-04-01 00:00:00

  • An unexpectedly complex mitoribosome in Andalucia godoyi, a protist with the most bacteria-like mitochondrial genome.

    abstract::The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly a...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa223

    authors: Valach M,Alcazar JAG,Sarrasin M,Lang BF,Gray MW,Burger G

    更新日期:2020-09-04 00:00:00

  • Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans.

    abstract::Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we pr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025634

    authors: Rand DM,Kann LM

    更新日期:1996-07-01 00:00:00

  • Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate.

    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

    authors: Zeng K,Jackson BC,Barton HJ

    更新日期:2019-02-01 00:00:00

  • ERAD-derived preprotein transport across the second outermost plastid membrane of diatoms.

    abstract::The diatom Phaeodactylum tricornutum harbors a plastid that is surrounded by four membranes and evolved by way of secondary endosymbiosis. Like land plants, most of its plastid proteins are encoded as preproteins on the nuclear genome of the host cell and are resultantly redirected into the organelle. Because two more...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msp079

    authors: Hempel F,Bullmann L,Lau J,Zauner S,Maier UG

    更新日期:2009-08-01 00:00:00