Theoretical foundation of the minimum-evolution method of phylogenetic inference.

abstract：:The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such except...

journal_title：Molecular biology and evolution

authors： Svardal H,Quah FX,Malinsky M,Ngatunga BP,Miska EA,Salzburger W,Genner MJ,Turner GF,Durbin R

更新日期：2020-04-01 00:00:00

abstract：:Analysis of mitochondrial DNA restriction fragment length polymorphism in European anchovy (Engraulis encrasicolus) revealed a large number of mitotypes that form two distinct clusters (phylads). Phylad A consists of one common mitotype and many rare secondary mitotypes that are one mutational step removed from the ma...

journal_title：Molecular biology and evolution

authors： Magoulas A,Tsimenides N,Zouros E

更新日期：1996-01-01 00:00:00

abstract：:Among mammals, several lineages have independently adapted to a subterranean niche and possess similar phenotypic traits for burrowing (e.g., cylindrical bodies, short limbs, and absent pinnae). Previous research on mole-rats has revealed molecular adaptations for coping with reduced oxygen, elevated carbon dioxide, a...

journal_title：Molecular biology and evolution

authors： Davies KTJ,Bennett NC,Faulkes CG,Rossiter SJ

更新日期：2018-10-01 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

authors： Stern DB,Crandall KA

更新日期：2018-08-01 00:00:00

abstract：:Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic chang...

journal_title：Molecular biology and evolution

authors： de Mendoza A,Ruiz-Trillo I

更新日期：2011-11-01 00:00:00

abstract：:For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load ...

journal_title：Molecular biology and evolution

authors： Renaut S,Rieseberg LH

更新日期：2015-09-01 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

authors： Smukowski Heil CS,DeSevo CG,Pai DA,Tucker CM,Hoang ML,Dunham MJ

更新日期：2017-07-01 00:00:00

abstract：:About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for t...

journal_title：Molecular biology and evolution

authors： Churakov G,Smit AF,Brosius J,Schmitz J

更新日期：2005-04-01 00:00:00

abstract：:Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion sequences IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments of the same apparent length are identical by descent, parsimony analysis of these ch...

journal_title：Molecular biology and evolution

authors： Lawrence JG,Dykhuizen DE,DuBose RF,Hartl DL

更新日期：1989-01-01 00:00:00

abstract：:Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern in Caenorhabditis nematodes-...

journal_title：Molecular biology and evolution

authors： Irimia M,Rukov JL,Penny D,Garcia-Fernandez J,Vinther J,Roy SW

更新日期：2008-02-01 00:00:00

abstract：:Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrop...

journal_title：Molecular biology and evolution

authors： Nei M,Stephens JC,Saitou N

更新日期：1985-01-01 00:00:00

abstract：:The noncoding-DNA content of organelle and nuclear genomes can vary immensely. Both adaptive and nonadaptive explanations for this variation have been proposed. This study addresses a nonadaptive explanation called the mutational-hazard hypothesis and applies it to the mitochondrial, plastid, and nuclear genomes of th...

journal_title：Molecular biology and evolution

authors： Smith DR,Lee RW

更新日期：2010-10-01 00:00:00

abstract：:The roles of selection and horizontal transfer in the evolution of the canonical subfamily of P: elements were studied in the saltans and willistoni species groups of the genus Drosophila (subgenus Sophophora). We estimate that the common ancestor of the canonical P: subfamily dates back 2-3 Myr at the most, despite t...

journal_title：Molecular biology and evolution

authors： Silva JC,Kidwell MG

更新日期：2000-10-01 00:00:00

abstract：:An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several researchers (the initial idea due to Lake [1987] and Cavender and Felsenstein [1987]). However, the efficiency of methods based on invariants is still in doubt (Huelsenbeck 1995; Jin...

journal_title：Molecular biology and evolution

authors： Casanellas M,Fernández-Sánchez J

更新日期：2007-01-01 00:00:00

abstract：:Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For ea...

journal_title：Molecular biology and evolution

authors： Parkin EJ,Butlin RK

更新日期：2004-08-01 00:00:00

abstract：:The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonpar...

journal_title：Molecular biology and evolution

authors： Buckley TR,Cunningham CW

更新日期：2002-04-01 00:00:00

abstract：:A recent investigation found evidence that the transition of Arabidopsis thaliana from ancestral self-incompatibility (SI) to full self-compatibility occurred very recently and suggested that this occurred through a selective fixation of a nonfunctional allele (PsiSCR1) at the SCR gene, which determines pollen specifi...

journal_title：Molecular biology and evolution

authors： Bechsgaard JS,Castric V,Charlesworth D,Vekemans X,Schierup MH

更新日期：2006-09-01 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

authors： Flowers JM,Sezgin E,Kumagai S,Duvernell DD,Matzkin LM,Schmidt PS,Eanes WF

更新日期：2007-06-01 00:00:00

abstract：:To test whether gaps resulting from sequence alignment contain phylogenetic signal concordant with those of base substitutions, we analyzed the occurrence of indel mutations upon a well-resolved, substitution-based tree for three nuclear genes in bumble bees (Bombus, Apidae: Bombini). The regions analyzed were exon an...

journal_title：Molecular biology and evolution

authors： Kawakita A,Sota T,Ascher JS,Ito M,Tanaka H,Kato M

更新日期：2003-01-01 00:00:00

abstract：:Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sit...

journal_title：Molecular biology and evolution

authors： Zhang J,Kumar S

更新日期：1997-05-01 00:00:00

abstract：:The DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis in bacteria. It interacts both with nascent polypeptides and with proteins that have become unfolded, either funneling its clients toward the native state or ushering misfolded proteins into degradation. In line with its key role...

journal_title：Molecular biology and evolution

authors： Warnecke T

更新日期：2012-11-01 00:00:00

abstract：:It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can qu...

journal_title：Molecular biology and evolution

authors： White WT,Hills SF,Gaddam R,Holland BR,Penny D

更新日期：2007-09-01 00:00:00

abstract：:Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results ind...

journal_title：Molecular biology and evolution

authors： Forni D,Pontremoli C,Clerici M,Pozzoli U,Cagliani R,Sironi M

更新日期：2020-05-01 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

authors： Yang Y,Yan W,Hall AB,Jiang X

更新日期：2020-11-04 00:00:00

abstract：:The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, wi...

journal_title：Molecular biology and evolution

authors： Strasburg JL,Kane NC,Raduski AR,Bonin A,Michelmore R,Rieseberg LH

更新日期：2011-05-01 00:00:00

abstract：:Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprin...

journal_title：Molecular biology and evolution

authors： Broughton RE,Dowling TE

更新日期：1997-12-01 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

authors： Vieira MC,Zinder D,Cobey S

更新日期：2018-05-01 00:00:00

abstract：:We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction-enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per...

journal_title：Molecular biology and evolution

authors： Ford MJ,Yoon CK,Aquadro CF

更新日期：1994-03-01 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

authors： Pombert JF,Otis C,Lemieux C,Turmel M

更新日期：2004-05-01 00:00:00

abstract：:Nonsense-mediated decay (NMD) pathways for detection and degradation of transcripts containing premature termination (stop) codons (PTCs) are ubiquitous among the eukaryotes. NMD uses the presence of a second signal downstream of a termination codon to distinguish a PTC from a true stop codon. In mammals and perhaps o...

journal_title：Molecular biology and evolution

authors： Scofield DG,Hong X,Lynch M

更新日期：2007-04-01 00:00:00