Molecular Biology & Evolution



Molecular Biology and Evolution (MBE) publishes research at the interface of molecular and evolutionary biology. The journal publishes molecular evolutionary patterns, processes, and predictions at all levels of taxonomic, functional, genomic, and phenotypic organization. It also publishes new and improved methods, resources, and theories that are critical for advancing the molecular evolutionary research. MBE publishes Articles, Letters, Brief Communications, Perspectives, Protocols, and Reviews.

MBE is entirely owned by The Society for Molecular Biology and Evolution. The Council of the Society appoints the Editor-in-Chief and approves the Board of Editors. The Journal is published by Oxford University Press in conjunction with HighWire Press.

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Molecular Biology and Evolution

2017-04-18

2017-04-18

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2017-04-18

2017-02-25

The History of Proteins

2017-02-15

2017-02-15

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2017-02-13

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2017-02-13

genes that neighbor a greater number of CNSs have a higher probability of differential expression and a higher probability of neighboring a CNS with lineage-specific acceleration. Thus, neighboring an accelerated element from any species signals that a gene likely neighbors many CNSs. We extend the analyses beyond the prenatal time points considered in previous studies to demonstrate that this association persists across developmental and adult periods. Examining differential expression between non-neural tissues suggests that the relationship between the number of CNSs a gene neighbors and its differential expression status may be particularly strong for expression differences among brain regions. In addition, by considering this relationship, we highlight a recently defined set of putative human-specific gain-of-function sequences that, even after adjusting for the number of CNSs neighbored by genes, shows a positive relationship with upregulation in the brain compared with other tissues examined.</span>

2017-02-13

2017-02-11

2017-02-11

A Genetic Window onto an Island's Past

2017-02-08

2017-01-31

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2017-01-19

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2017-01-12

GBE | Most Read

Genome Biology & Evolution

RNA Editing During Sexual Development Occurs in Distantly Related Filamentous Ascomycetes

2017-04-01

<span class="paragraphSection">RNA editing is a post-transcriptional process that modifies RNA molecules leading to transcript sequences that differ from their template DNA. A-to-I editing was found to be widely distributed in nuclear transcripts of metazoa, but was detected in fungi only recently in a study of the filamentous ascomycete <span style="font-style:italic;">Fusarium graminearum</span> that revealed extensive A-to-I editing of mRNAs in sexual structures (fruiting bodies). Here, we searched for putative RNA editing events in RNA-seq data from <span style="font-style:italic;">Sordaria macrospora</span> and <span style="font-style:italic;">Pyronema confluens</span>, two distantly related filamentous ascomycetes, and in data from the Taphrinomycete <span style="font-style:italic;">Schizosaccharomyces pombe</span>. Like <span style="font-style:italic;">F. graminearum</span>, <span style="font-style:italic;">S. macrospora</span> is a member of the Sordariomycetes, whereas <span style="font-style:italic;">P. confluens</span> belongs to the early-diverging group of Pezizomycetes. We found extensive A-to-I editing in RNA-seq data from sexual mycelium from both filamentous ascomycetes, but not in vegetative structures. A-to-I editing was not detected in different stages of meiosis of <span style="font-style:italic;">S. pombe</span>. A comparison of A-to-I editing in <span style="font-style:italic;">S. macrospora</span> with <span style="font-style:italic;">F. graminearum</span> and <span style="font-style:italic;">P. confluens</span>, respectively, revealed little conservation of individual editing sites. An analysis of RNA-seq data from two sterile developmental mutants of <span style="font-style:italic;">S. macrospora</span> showed that A-to-I editing is strongly reduced in these strains. Sequencing of cDNA fragments containing more than one editing site from <span style="font-style:italic;">P. confluens</span> showed that at the beginning of sexual development, transcripts were incompletely edited or unedited, whereas in later stages transcripts were more extensively edited. Taken together, these data suggest that A-to-I RNA editing is an evolutionary conserved feature during fruiting body development in filamentous ascomycetes.</span>

Recombination-Mediated Host Adaptation by Avian Staphylococcus aureus

2017-04-01

<span class="paragraphSection"><span style="font-style:italic;">Staphylococcus aureus</span> are globally disseminated among farmed chickens causing skeletal muscle infections, dermatitis, and septicaemia. The emergence of poultry-associated lineages has involved zoonotic transmission from humans to chickens but questions remain about the specific adaptations that promote proliferation of chicken pathogens. We characterized genetic variation in a population of genome-sequenced <span style="font-style:italic;">S. aureus</span> isolates of poultry and human origin. Genealogical analysis identified a dominant poultry-associated sequence cluster within the CC5 clonal complex. Poultry and human CC5 isolates were significantly distinct from each other and more recombination events were detected in the poultry isolates. We identified 44 recombination events in 33 genes along the branch extending to the poultry-specific CC5 cluster, and 47 genes were found more often in CC5 poultry isolates compared with those from humans. Many of these gene sequences were common in chicken isolates from other clonal complexes suggesting horizontal gene transfer among poultry associated lineages. Consistent with functional predictions for putative poultry-associated genes, poultry isolates showed enhanced growth at 42 °C and greater erythrocyte lysis on chicken blood agar in comparison with human isolates. By combining phenotype information with evolutionary analyses of staphylococcal genomes, we provide evidence of adaptation, following a human-to-poultry host transition. This has important implications for the emergence and dissemination of new pathogenic clones associated with modern agriculture.</span>

A Nonsynonymous SNP Catalog of Mycobacterium tuberculosis Virulence Genes and Its Use for Detecting New Potentially Virulent Sublineages

2017-04-01

<span class="paragraphSection"><span style="font-style:italic;">Mycobacterium tuberculosis</span> is divided into several distinct lineages, and various genetic markers such as IS-elements, VNTR, and SNPs are used for lineage identification. We propose an <span style="font-style:italic;">M. tuberculosis</span> classification approach based on functional polymorphisms in virulence genes. An <span style="font-style:italic;">M. tuberculosis</span> virulence genes catalog has been established, including 319 genes from various protein groups, such as proteases, cell wall proteins, fatty acid and lipid metabolism proteins, sigma factors, toxin–antitoxin systems. Another catalog of 1,573 <span style="font-style:italic;">M. tuberculosis</span> isolates of different lineages has been developed. The developed SNP-calling program has identified 3,563 nonsynonymous SNPs. The constructed SNP-based phylogeny reflected the evolutionary relationship between lineages and detected new sublineages. SNP analysis of sublineage F15/LAM4/KZN revealed four lineage-specific mutations in <span style="font-style:italic;">cyp125, mce3B, vapC25</span>, and <span style="font-style:italic;">vapB34</span>. The Ural lineage has been divided into two geographical clusters based on different SNPs in virulence genes. A new sublineage, B0/N-90, was detected inside the Beijing-B0/W-148 by SNPs in <span style="font-style:italic;">irtB, mce3F</span> and <span style="font-style:italic;">vapC46</span>. We have found 27 members of B0/N-90 among the 227 available genomes of the Beijing-B0/W-148 sublineage. Whole-genome sequencing of strain B9741, isolated from an HIV-positive patient, was demonstrated to belong to the new B0/N-90 group. A primer set for PCR detection of B0/N-90 lineage-specific mutations has been developed. The prospective use of <span style="font-style:italic;">mce3</span> mutant genes as genetically engineered vaccine is discussed.</span>

Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species

2017-04-01

<span class="paragraphSection">Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in <span style="font-style:italic;">cis-</span>regulatory elements and <span style="font-style:italic;">trans</span>-regulatory factors. Although previous work has suggested that <span style="font-style:italic;">cis</span>-regulatory differences preferentially accumulate with time, technical restrictions to closely related species and limited comparisons have made this observation difficult to test. To address this problem, we used allele-specific RNA-seq data from <span style="font-style:italic;">Saccharomyces</span> species and hybrids to expand both the evolutionary timescale and number of species in which the evolution of regulatory divergence has been investigated. We find that as sequence divergence increases, <span style="font-style:italic;">cis</span>-regulatory differences do indeed become the dominant type of regulatory difference between species, ultimately becoming a better predictor of expression divergence than <span style="font-style:italic;">trans</span>-regulatory divergence. When both <span style="font-style:italic;">cis</span>- and <span style="font-style:italic;">trans</span>-regulatory differences accumulate for the same gene, they more often have effects in opposite directions than in the same direction, indicating widespread compensatory changes underlying the evolution of gene expression. The frequency of compensatory changes within and between species and the magnitude of effect for the underlying <span style="font-style:italic;">cis-</span> and <span style="font-style:italic;">trans</span>-regulatory differences suggests that compensatory changes accumulate primarily due to selection against divergence in gene expression as a result of weak stabilizing selection on gene expression levels. These results show that <span style="font-style:italic;">cis</span>-regulatory differences and compensatory changes in regulation play increasingly important roles in the evolution of gene expression as time increases.</span>

Nonreplicative RNA Recombination of an Animal Plus-Strand RNA Virus in the Absence of Efficient Translation of Viral Proteins

2017-04-01

<span class="paragraphSection">RNA recombination is a major driving force for the evolution of RNA viruses and is significantly implicated in the adaptation of viruses to new hosts, changes of virulence, as well as in the emergence of new viruses including drug-resistant and escape mutants. However, the molecular details of recombination in animal RNA viruses are only poorly understood. In order to determine whether viral RNA recombination depends on translation of viral proteins, a nonreplicative recombination system was established which is based on cotransfection of cells with synthetic bovine viral diarrhea virus (family <span style="font-style:italic;">Flaviviridae</span>) RNA genome fragments either lacking the internal ribosome entry site required for cap-independent translation or lacking almost the complete polyprotein coding region. The emergence of a number of recombinant viruses demonstrated that IRES-mediated translation of viral proteins is dispensable for efficient recombination and suggests that RNA recombination can occur in the absence of viral proteins. Analyses of 58 independently emerged viruses led to the detection of recombinant genomes with duplications, deletions and insertions in the 5′ terminal region of the open reading frame, leading to enlarged core fusion proteins detectable by Western blot analysis. This demonstrates a remarkable flexibility of the pestivirus core protein. Further experiments with capped and uncapped genome fragments containing a luciferase gene for monitoring the level of protein translation revealed that even a ∼1,000-fold enhancement of translation of viral proteins did not increase the frequency of RNA recombination. Taken together, this study highlights that nonreplicative RNA recombination does not require translation of viral proteins.</span>

Phylogenetics of Lophotrochozoan bHLH Genes and the Evolution of Lineage-Specific Gene Duplicates

2017-04-01

<span class="paragraphSection">The gain and loss of genes encoding transcription factors is of importance to understanding the evolution of gene regulatory complexity. The basic helix–loop–helix (bHLH) genes encode a large superfamily of transcription factors. We systematically classify the bHLH genes from five mollusc, two annelid and one brachiopod genomes, tracing the pattern of bHLH gene evolution across these poorly studied Phyla. In total, 56–88 bHLH genes were identified in each genome, with most identifiable as members of previously described bilaterian families, or of new families we define. Of such families only one, <span style="font-style:italic;">Mesp</span>, appears lost by all these species. Additional duplications have also played a role in the evolution of the bHLH gene repertoire, with many new lophotrochozoan-, mollusc-, bivalve-, or gastropod-specific genes defined. Using a combination of transcriptome mining, RT-PCR, and in situ hybridization we compared the expression of several of these novel genes in tissues and embryos of the molluscs <span style="font-style:italic;">Crassostrea gigas</span> and <span style="font-style:italic;">Patella vulgata</span>, finding both conserved expression and evidence for neofunctionalization. We also map the positions of the genes across these genomes, identifying numerous gene linkages. Some reflect recent paralog divergence by tandem duplication, others are remnants of ancient tandem duplications dating to the lophotrochozoan or bilaterian common ancestors. These data are built into a model of the evolution of bHLH genes in molluscs, showing formidable evolutionary stasis at the family level but considerable within-family diversification by tandem gene duplication.</span>