Molecular Biology and Evolution (MOL BIOL EVOL )

Publisher: Molecular Biology and Evolution Society; American Society of Naturalists; Society for the Study of Evolution, Oxford University Press


Molecular Biology and Evolution (MBE) is devoted to the interdisciplinary science between molecular biology and evolutionary biology. MBE emphasizes experimental papers, but theoretical papers are also published if they have a solid biological basis. Although this journal is primarily for original papers, review articles and book reviews are also published. MBE is an appropriate outlet for the examination of molecular evolutionary processes and patterns, and the testing of evolutionary hypotheses with molecular data. MBE is not an appropriate outlet for purely taxonomic treatments and the detailing of systematic issues. Published by the Society for Molecular Biology and Evolution.

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    Molecular Biology and Evolution website
  • Other titles
    Molecular biology and evolution, MBE
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    Periodical, Internet resource
  • Document type
    Journal / Magazine / Newspaper, Internet Resource

Publisher details

Oxford University Press

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    • 12 month embargo on science, technology, medicine articles
    • 24 month embargo on arts and humanities articles
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Publications in this journal

  • Molecular Biology and Evolution 01/2013;
  • Molecular Biology and Evolution 03/2012;
  • [show abstract] [hide abstract]
    ABSTRACT: Nitric oxide (NO) is essential to many physiological functions and operates in several well-known signaling pathways. Yet, it is not fully understood how and when nitric oxide synthase (NOS), the enzyme responsible for NO production, evolved across metazoan phylogeny. This study investigates the number and structure of eukaryotic NOS enzymes by genome data mining and direct cloning of Nos genes from the lamprey. In total, 181 NOS proteins are analyzed from 33 invertebrate and 63 vertebrate species. Comparisons among protein and gene structures, combined with phylogenetic and syntenic studies, provide novel insights into how NOS isoforms arose and diverged. Protein domains and gene organization – i.e., intron positions and phases – of animal NOS are remarkably conserved across all lineages, even in fast-evolving species. Phylogenetic and syntenic analyses support the view that a proto-NOS isoform was recurrently duplicated in different lineages, acquiring new structural configurations through gains and losses of protein motifs. We propose that in vertebrates a first duplication took place after the agnathan-gnathostome split, followed by a paralog loss. A second duplication occurred during early tetrapod evolution, giving rise to the three isoforms – I, II and III – in current mammals. Overall, NOS family evolution was the result of multiple gene and genome duplication events together with changes in protein architecture.
    Molecular Biology and Evolution 01/2011;
  • Molecular Biology and Evolution 01/2011; 28(9-28):2603.
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    ABSTRACT: Cytochrome P450 family 1 (CYP1) proteins are important in a large number of toxicological processes. CYP1A and CYP1B genes are well known in mammals, but the evolutionary history of the CYP1 family as a whole is obscure; that history may provide insight into endogenous functions of CYP1 enzymes. Here, we identify CYP1-like genes in early deuterostomes (tunicates and echinoderms), and several new CYP1 genes in vertebrates (chicken, Gallus gallus and frog, Xenopus tropicalis). Profile hidden Markov models (HMMs) generated from vertebrate CYP1A and CYP1B protein sequences were used to identify 5 potential CYP1 homologs in the tunicate Ciona intestinalis genome. The C. intestinalis genes were cloned and sequenced, confirming the predicted sequences. Orthologs of 4 of these genes were found in the Ciona savignyi genome. Bayesian phylogenetic analyses group the tunicate genes in the CYP1 family, provisionally in 2 new subfamilies, CYP1E and CYP1F, which fall in the CYP1A and CYP1B/1C clades. Bayesian and maximum likelihood analyses predict functional divergence between the tunicate and vertebrate CYP1s, and regions within CYP substrate recognition sites were found to differ significantly in position-specific substitution rates between tunicates and vertebrates. Subsequently, 10 CYP1-like genes were found in the echinoderm Strongylocentrotus purpuratus (sea urchin) genome. Several of the tunicate and echinoderm CYP1-like genes are expressed during development. Canonical xenobiotic response elements are present in the upstream genomic sequences of most tunicate and sea urchin CYP1s, and both groups are predicted to possess an aryl hydrocarbon receptor (AHR), suggesting possible regulatory linkage of AHR and these CYPs. The CYP1 family has undergone multiple rounds of gene duplication followed by functional divergence, with at least one gene lost in mammals. This study provides new insight into the origin and evolution of CYP1 genes.
    Molecular Biology and Evolution 01/2008; 24(12):2619-31.
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    ABSTRACT: We develop an approximate maximum likelihood method to estimate flanking nucleotide context-dependent mutation rates and amino acid exchange-dependent selection in orthologous protein-coding sequences and use it to analyze genome-wide coding sequence alignments from mammals and yeast. Allowing context-dependent mutation provides a better fit to coding sequence data than simpler (context-independent or CpG "hotspot") models and significantly affects selection parameter estimates. Allowing asymmetric (nonreciprocal) selection on amino acid exchanges gives a better fit than simple dN/dS or symmetric selection models. Relative selection strength estimates from our models show good agreement with independent estimates derived from human disease-causing and engineered mutations. Selection strengths depend on local protein structure, showing expected biophysical trends in helical versus nonhelical regions and increased asymmetry on polar-hydrophobic exchanges with increased burial. The more stringent selection that has previously been observed for highly expressed proteins is primarily concentrated in buried regions, supporting the notion that such proteins are under stronger than average selection for stability. Our analyses indicate that a highly parameterized model of mutation and selection is computationally tractable and is a useful tool for exploring a variety of biological questions concerning protein and coding sequence evolution.
    Molecular Biology and Evolution 01/2008; 24(12):2632-47.
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    ABSTRACT: A new family, termed TxpB, of DNA transposons belonging to the piggyBac superfamily was found in 3 Xenopus species (Xenopus tropicalis, Xenopus laevis, and Xenopus borealis). Two TxpB subfamilies of Kobuta and Uribo1 were found in all the 3 species, and another subfamily termed Uribo2 was found in X. tropicalis. Molecular phylogenetic analyses of their open reading frames (ORFs) revealed that TxpB transposons have been maintained for over 100 Myr. Both the Uribo1 and the Uribo2 ORFs were present as multiple copies in each genome, and some of them were framed by terminal inverted repeat sequences. In contrast, all the Kobuta ORFs were present as a single copy in each genome and exhibited high evolutionary conservation, suggesting domestication of Kobuta genes by the host. Genomic insertion polymorphisms of the Uribo1 and Uribo2 transposons (nonautonomous type) were observed in a single species of X. tropicalis, indicating recent transposition events. Transfection experiments in cell culture revealed that an expression vector construct for the intact Uribo2 ORF caused precise excision of a nonautonomous Uribo2 element from the target vector construct but that for the Kobuta ORF did not. The present results support our viewpoint that some Uribo2 members are naturally active autonomous transposons, whereas Kobuta members may be domesticated by hosts.
    Molecular Biology and Evolution 01/2008; 24(12):2648-56.
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    ABSTRACT: In Drosophila melanogaster, synonymous codons corresponding to the most abundant cognate tRNAs are used more frequently, especially in highly expressed genes. Increased use of such "optimal" codons is considered an adaptation for translational efficiency. Need it always be the case that selection should favor the use of a translationally optimal codon? Here, we investigate one possible confounding factor, namely, the need to specify information in exons necessary to enable correct splicing. As expected from such a model, in Drosophila many codons show different usage near intron-exon boundaries versus exon core regions. However, this finding is in principle also consistent with Hill-Robertson effects modulating usage of translationally optimal codons. However, several results support the splice model over the translational selection model: 1) the trends in codon usage are strikingly similar to those in mammals in which codon usage near boundaries correlates with abundance in exonic splice enhancers (ESEs), 2) codons preferred near boundaries tend to be enriched for A and avoid C (conversely those avoided near boundaries prefer C rather than A), as expected were ESEs involved, and 3) codons preferred near boundaries are typically not translationally optimal. We conclude that usage of translationally optimal codons usage is compromised in the vicinity of splice junctions in intron-containing genes, to the effect that we observe higher levels of usage of translationally optimal codons at the center of exons. On the gene level, however, controlling for known correlates of codon bias, the impact on codon usage patterns is quantitatively small. These results have implications for inferring aspects of the mechanism of splicing given nothing more than a well-annotated genome.
    Molecular Biology and Evolution 01/2008; 24(12):2755-62.
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    ABSTRACT: We evaluate the performance of maximum likelihood (ML) analysis of allele frequency data in a linear array of populations. The parameters are a mutation rate and either the dispersal rate in a stepping stone model or a dispersal rate and a scale parameter in a geometric dispersal model. An approximate procedure known as maximum product of approximate conditional (PAC) likelihood is found to perform as well as ML. Mis-specification biases may occur because the importance sampling algorithm is formally defined in term of mutation and migration rates scaled by the total size of the population, and this size may differ widely in the statistical model and in reality. As could be expected, ML generally performs well when the statistical model is correctly specified. Otherwise, mutation rate estimates are much closer to mutation probability scaled by number of demes in the statistical model than scaled by number of demes in reality when mutation probability is high and dispersal is most limited. This mis-specification bias actually has practical benefits. However, opposite results are found in opposite conditions. Migration rate estimates show roughly similar trends, but they may not always be easily interpreted as low-bias estimates of dispersal rate under any scaling. Estimation of the dispersal scale parameter is also affected by mis-specification of the number of demes, and the different biases compensate each other in such a way that good estimation of the so-called neighborhood size (or more precisely the product of population density and mean-squared parent-offspring dispersal distance) is achieved. Results congruent with these findings are found in an application to a damselfly data set.
    Molecular Biology and Evolution 01/2008; 24(12):2730-45.

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