Journal of Molecular Evolution (J Mol Evol )

Publisher: Springer Verlag

Description

The Journal covers experimental and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features from the initial formation of macromolecular systems onward. Topics addressed in the Journal include the evolution of informational macromolecules and their relation to more complex levels of biological organization up to populations and taxa. This coverage accommodates well such subfields as comparative structural and functional genomics population genetics the molecular evolution of development the evolution of gene regulation and gene interaction networks and in vitro evolution of DNA and RNA.

  • Impact factor
    2.15
  • 5-year impact
    2.38
  • Cited half-life
    0.00
  • Immediacy index
    0.31
  • Eigenfactor
    0.01
  • Article influence
    0.88
  • Website
    Journal of Molecular Evolution website
  • Other titles
    Journal of molecular evolution (Online), Molecular evolution, J mol evol
  • ISSN
    1432-1432
  • OCLC
    39983975
  • Material type
    Document, Periodical, Internet resource
  • Document type
    Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Springer Verlag

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Authors own final version only can be archived
    • Publisher's version/PDF cannot be used
    • On author's website or institutional repository
    • On funders designated website/repository after 12 months at the funders request or as a result of legal obligation
    • Published source must be acknowledged
    • Must link to publisher version
    • Set phrase to accompany link to published version (The original publication is available at www.springerlink.com)
    • Articles in some journals can be made Open Access on payment of additional charge
  • Classification
    ​ green

Publications in this journal

  • [show abstract] [hide abstract]
    ABSTRACT: Prediction of the thermodynamic behaviors of biomolecules at high temperature and pressure is fundamental to understanding the role of hydrothermal systems in the origin and evolution of life on the primitive Earth. However, available thermodynamic dataset for amino acids, essential components for life, cannot represent experimentally observed polymerization behaviors of amino acids accurately under hydrothermal conditions. This report presents the thermodynamic data and the revised HKF parameters for the simplest amino acid "Gly" and its polymers (GlyGly, GlyGlyGly and DKP) based on experimental thermodynamic data from the literature. Values for the ionization states of Gly (Gly(+) and Gly(-)) and Gly peptides (GlyGly(+), GlyGly(-), GlyGlyGly(+), and GlyGlyGly(-)) were also retrieved from reported experimental data by combining group additivity algorithms. The obtained dataset enables prediction of the polymerization behavior of Gly as a function of temperature and pH, consistent with experimentally obtained results in the literature. The revised thermodynamic data for zwitterionic Gly, GlyGly, and DKP were also used to estimate the energetics of amino acid polymerization into proteins. Results show that the Gibbs energy necessary to synthesize a mole of peptide bond is more than 10 kJ mol(-1) less than previously estimated over widely various temperatures (e.g., 28.3 kJ mol(-1) → 17.1 kJ mol(-1) at 25 °C and 1 bar). Protein synthesis under abiotic conditions might therefore be more feasible than earlier studies have shown.
    Journal of Molecular Evolution 03/2014;
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    ABSTRACT: In the vertebrate central nervous system, glycinergic neurotransmission is regulated by the action of the glycine transporters 1 and 2 (GlyT1 and GlyT2)-members of the solute carrier family 6 (SLC6). Several invertebrate deuterostomes have two paralogous glycine carrier genes, with one gene in the pair having greater sequence identity and higher alignment scores with respect to GlyT1 and the other paralog showing greater similarity to GlyT2. In phylogenetic trees, GlyT2-like sequences from invertebrate deuterostomes form a monophyletic subclade with vertebrate GlyT2, while invertebrate GlyT1-like proteins constitute an outgroup to both the GlyT2-like proteins and to vertebrate GlyT1 sequences. These results are consistent with the hypothesis that vertebrate GlyT1 and GlyT2 are, respectively, derived from GlyT1- and GlyT2-like genes in invertebrate deuterostomes. This implies that the gene duplication which gave rise to these paralogs occurred prior to the origin of vertebrates. GlyT2 subsequently diverged significantly from its invertebrate orthologs (i.e., through the acquisition of a unique N-terminus) as a consequence of functional specialization, being expressed principally in the lower CNS; while GlyT1 has activity in both the lower CNS and several regions of the forebrain.
    Journal of Molecular Evolution 03/2014;
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    ABSTRACT: NLRP proteins are important components of inflammasomes with a major role in innate immunity. A subset of NLRP genes, with unknown functions, are expressed in oocytes and early embryos. Mutations of Nlrp5 in mice are associated with maternal-effect embryonic lethality and mutations of NLRP7 in women are associated with conception of biparental complete hydatidiform moles (biCHMs), suggesting perturbed processes of genomic imprinting. Recessive mutations on NLRP2/7 in humans are associated with reproductive disorders and appear to be induced by a demethylation of the maternal pronucleus. In this study, we find that radiation of NLRP genes occurred before the common ancestor of Afrotheria and Boreoeutheria, with the clade of oocyte-expressed genes originating before the divergence of marsupial and eutherian mammals. There have been multiple independent duplications of NLRP2 genes one of which produced the NLRP7 gene associated with biCHMs.
    Journal of Molecular Evolution 03/2014;
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    ABSTRACT: The structural and biosynthetic features of archaeal phospholipids provide clues to the membrane lipid composition in the last universal common ancestor (LUCA) membranes. The evident similarity of the phospholipid biosynthetic pathways in Archaea and Bacteria suggests that one set of these biosynthetic enzymes would have worked on a wide range of lipids composed of enantiomeric glycerophosphate backbones linked with a variety of hydrocarbon chains. This notion was supported by the discovery of a wide range reactivity of enzymes belonging to the CDP-alcohol phosphatidyltransferase family. It is hypothesized that lipid promiscuity is generated from the prebiotic surface metabolism on pyrite proposed by Wächtershäuser. The significance of the phosphate groups on the intermediates of phospholipid biosynthesis and the extra anionic groups of a polar head group suggested the likely involvement of surface metabolism. Anionic groups are essential for surface metabolism. Since the early chemical evolution reactions are presumed to be non-specific, every combination of the available lipid component parts would be expected to be formed. The mixed lipid membranes present in LUCA were segregated and this led to the differentiation of Archaea and Bacteria, as described previously. The proper arrangement of membrane lipids was generated by the physicochemical drive arising from the promiscuity of the primordial membrane lipids.
    Journal of Molecular Evolution 02/2014;
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    ABSTRACT: A gene for membrane-integral inorganic pyrophosphatase (miPPase) was found in the composite genome of the extremophile archaeon Candidatus Korarchaeum cryptofilum (CKc). This korarchaeal genome shows unusual partial similarity to both major archaeal phyla Crenarchaeota and Euryarchaeota. Thus this Korarchaeote might have retained features that represent an ancestral archaeal form, existing before the occurrence of the evolutionary bifurcation into Crenarchaeota and Euryarchaeota. In addition, CKc lacks five genes that are common to early genomes at the LUCA border. These two properties independently suggest a pre-LUCA evolutionary position of this extremophile. Our finding of the miPPase gene in the CKc genome points to a role for the enzyme in the energy conversion of this very early archaeon. The structural features of its miPPase indicate that it can pump protons through membranes. An miPPase from the extremophile bacterium Caldicellulosiruptor saccharolyticus also has a sequence indicating a proton pump. Recent analysis of the three-dimensional structure of the miPPase from Vigna radiata has resulted in the recognition of a strongly acidic substrate (orthophosphate: Pi, pyrophosphate: PPi) binding pocket, containing 11 Asp and one Glu residues. Asp (aspartic acid) is an evolutionarily very early proteinaceous amino acid as compared to the later appearing Glu (glutamic acid). All the Asp residues are conserved in the miPPase of CKc, V. radiata and other miPPases. The high proportion of Asp, as compared to Glu, seems to strengthen our argument that biological energy conversion with binding and activities of orthophosphate (Pi) and energy-rich pyrophosphate (PPi) in connection with the origin and early evolution of life may have started with similar or even more primitive acidic peptide funnels and/or pockets.
    Journal of Molecular Evolution 01/2014;
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    ABSTRACT: We report a route to synthesize a wide range of organophosphates of biological significance in a deep eutectic solvent (2:1 urea and choline chloride), utilizing various orthophosphate sources. Heating an organic alcohol in the solvent along with a soluble phosphorus source yields phosphorus esters of choline as well as that of the added organic in yields between 15 to 99 %. In addition, phosphite analogs of biological phosphates and peptides were also formed by the simple mixing of reagents and heating at 60-70 °C in the deep eutectic solvent. The presented dehydration reactions are relevant to prebiotic and green chemistry in alternative solvents.
    Journal of Molecular Evolution 12/2013;
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    ABSTRACT: Proteins are regarded as being robust to the deleterious effects of mutations. Here, the neutral emergence of mutational robustness in a population of single domain proteins is explored using computer simulations. A pairwise contact model was used to calculate the ΔG of folding (ΔG folding) using the three dimensional protein structure of leech eglin C. A random amino acid sequence with low mutational robustness, defined as the average ΔΔG resulting from a point mutation (ΔΔG average), was threaded onto the structure. A population of 1,000 threaded sequences was evolved under selection for stability, using an upper and lower energy threshold. Under these conditions, mutational robustness increased over time in the most common sequence in the population. In contrast, when the wild type sequence was used it did not show an increase in robustness. This implies that the emergence of mutational robustness is sequence specific and that wild type sequences may be close to maximal robustness. In addition, an inverse relationship between ∆∆G average and protein stability is shown, resulting partly from a larger average effect of point mutations in more stable proteins. The emergence of mutational robustness was also observed in the Escherichia coli colE1 Rop and human CD59 proteins, implying that the property may be common in single domain proteins under certain simulation conditions. The results indicate that at least a portion of mutational robustness in small globular proteins might have arisen by a process of neutral emergence, and could be an example of a beneficial trait that has not been directly selected for, termed a "pseudaptation."
    Journal of Molecular Evolution 12/2013;
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    ABSTRACT: Horizontal gene transfers (HGT) between four Crenarchaeota species (Metallosphaera cuprina Ar-4(T), Acidianus hospitalis W1(T), Vulcanisaeta moutnovskia 768-28(T), and Pyrobaculum islandicum DSM 4184(T)) were investigated with quartet analysis. Strong support was found for individual genes that disagree with the phylogeny of the majority, implying genomic mosaicism. One such gene, a ferredoxin-related gene, was investigated further and incorporated into a larger phylogeny, which provided evidence for HGT of this gene from the Vulcanisaeta lineage to the Acidianus lineage. This is the first application of quartet analysis of HGT for the phylum Crenarchaeota. The results have shown that quartet analysis is a powerful technique to screen homologous sequences for putative HGTs and is useful in visually describing genomic mosaicism and HGT within four taxa.
    Journal of Molecular Evolution 12/2013;
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    ABSTRACT: Vaccine design for rapidly changing viruses is based on empirical surveillance of strains circulating in a given season to assess those that will most likely spread during the next season. The choice of which strains to include in the vaccine is critical, as an erroneous decision can lead to a nonimmunized human population that will then be at risk in the face of an epidemic or, worse, a pandemic. Here, we present the first steps toward a very general phylogenetic approach to predict the emergence of novel viruses. Our genomic model builds upon natural features of viral evolution such as selection and recombination / reassortment, and incorporates episodic bursts of evolution and or of recombination. As a proof-of-concept, we assess the performance of this model in a retrospective study, focusing: (i) on the emergence of an unexpected H3N2 influenza strain in 2007, and (ii) on a longitudinal design. Based on the analysis of hemagglutinin (HA) and neuraminidase (NA) genes, our results show a lack of predictive power in both experimental designs, but shed light on the mode of evolution of these two antigens: (i) supporting the lack of significance of recombination in the evolution of this influenza virus, and (ii) showing that HA evolves episodically while NA changes gradually.
    Journal of Molecular Evolution 12/2013;
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    ABSTRACT: The distribution of variation in a quantitative trait and its underlying distribution of genotypic diversity can both be shaped by stabilizing and directional selection. Understanding either distribution is important, because it determines a population's response to natural selection. Unfortunately, existing theory makes conflicting predictions about how selection shapes these distributions, and very little pertinent experimental evidence exists. Here we study a simple genetic system, an evolving RNA enzyme (ribozyme) in which a combination of high throughput genotyping and measurement of a biochemical phenotype allow us to address this question. We show that directional selection, compared to stabilizing selection, increases the genotypic diversity of an evolving ribozyme population. In contrast, it leaves the variance in the phenotypic trait unchanged.
    Journal of Molecular Evolution 12/2013;
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    ABSTRACT: In species where females mate with multiple males during a single ovulatory cycle, sperm competition is hypothesized to increase the rate of adaptive evolution of proteins expressed in male reproductive tissues through recurrent selective sweeps (positive selection). The hominoids, comprising apes and humans, are a group of closely related primates with extensive variation in mating behaviors and predicted levels of sperm competition. Since previous studies of individual male reproductive genes have shown evidence of positive selection, we estimated rates of evolution of a comprehensive set of proteins expressed in ejaculated semen. Our results show that these proteins in hominoids do not have elevated rates of nonsynonymous substitutions (Ka) compared with a control dataset of nonreproductive genes. Species with greater sperm competition do not have faster rates of seminal protein evolution. Although at these broad levels our hypotheses were not confirmed, further analyses indicate specific patterns of molecular evolution. Namely, the Ka of seminal genes is more strongly correlated with measures of tissue specificity than nonreproductive genes, suggesting that the former may more readily adapt to tissue-specific functions. Proteins expressed from the seminal vesicles evolve more rapidly than those from other male reproductive tissues. Also, several gene ontology categories show elevated rates of protein evolution, not seen in the control data set. While the generalization that male reproductive genes evolve rapidly in hominoids is an oversimplification, a subset of proteins can be identified that are likely targets for adaptive evolution driven by sexual selection.
    Journal of Molecular Evolution 11/2013;
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    ABSTRACT: Sex-lethal (Sxl) functions as the switch gene for sex-determination in Drosophila melanogaster by engaging a regulatory cascade. Thus far the origin and evolution of both the regulatory system and SXL protein's sex-determination function have remained largely unknown. In this study, we explore systematically the Sxl homologs in a wide range of insects, including the 12 sequenced Drosophila species, medfly, blowflies, housefly, Megaselia scalaris, mosquitoes, butterfly, beetle, honeybee, ant, and aphid. We find that both the male-specific and embryo-specific exons exist in all Drosophila species. The homologous male-specific exon is also present in Scaptodrosophila lebanonensis, but it does not have in-frame stop codons, suggesting the exon's functional divergence between Drosophila and Scaptodrosophila after acquiring it in their common ancestor. Two motifs closely related to the exons' functions, the SXL binding site poly(U) and the transcription-activating motif TAGteam, surprisingly exhibit broader phylogenetic distributions than the exons. Some previously unknown motifs that are restricted to or more abundant in Drosophila and S. lebanonensis than in other insects are also identified. Finally, phylogenetic analysis suggests that the SXL's novel sex-determination function in Drosophila is more likely attributed to the changes in the N- and C-termini rather than in the RNA-binding region. Thus, our results provide a clearer picture of the phylogeny of the Sxl's cis-regulatory elements and protein sequence changes, and so lead to a better understanding of the origin of sex-determination in Drosophila and also raise some new questions regarding the evolution of Sxl.
    Journal of Molecular Evolution 11/2013;
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    ABSTRACT: Allopolyploidization, where two species come together to form a new species, plays a major role in speciation and genome evolution. Transfer RNAs (abbreviated tRNA) are typically 73-94 nucleotides in length, and are indispensable in protein synthesis, transferring amino acids to the cell protein synthesis machinery (ribosome). To date, the regularity and function of tRNA gene sequence variation during the process of allopolyploidization have not been well understood. In this study, the inter-tRNA gene corresponding to tRNA amplification polymorphism method was used to detect changes in tRNA gene sequences in the progeny of interspecific hybrids between Brassica rapa and B. oleracea, mimicking the original B. napus (canola) species formation event. Cluster analysis showed that tRNA gene variation during allopolyploidization did not appear to have a genotypic basis. Significant variation occurred in the early generations of synthetic B. napus (F1 and F2 generations), but fewer alterations were observed in the later generation (F3). The variation-prone tRNA genes tended to be located in AT-rich regions. BlastN analysis of novel tRNA gene variants against a Brassica genome sequence database showed that the variation of these tRNA-gene-associated sequences in allopolyploidization might result in variation of gene structure and function, e.g., metabolic process and transport.
    Journal of Molecular Evolution 11/2013;
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    ABSTRACT: Flightin is a thick filament protein that in Drosophila melanogaster is uniquely expressed in the asynchronous, indirect flight muscles (IFM). Flightin is required for the structure and function of the IFM and is indispensable for flight in Drosophila. Given the importance of flight acquisition in the evolutionary history of insects, here we study the phylogeny and distribution of flightin. Flightin was identified in 69 species of hexapods in classes Collembola (springtails), Protura, Diplura, and insect orders Thysanura (silverfish), Dictyoptera (roaches), Orthoptera (grasshoppers), Pthiraptera (lice), Hemiptera (true bugs), Coleoptera (beetles), Neuroptera (green lacewing), Hymenoptera (bees, ants, and wasps), Lepidoptera (moths), and Diptera (flies and mosquitoes). Flightin was also found in 14 species of crustaceans in orders Anostraca (water flea), Cladocera (brine shrimp), Isopoda (pill bugs), Amphipoda (scuds, sideswimmers), and Decapoda (lobsters, crabs, and shrimps). Flightin was not identified in representatives of chelicerates, myriapods, or any species outside Pancrustacea (Tetraconata, sensu Dohle). Alignment of amino acid sequences revealed a conserved region of 52 amino acids, referred herein as WYR, that is bound by strictly conserved tryptophan (W) and arginine (R) and an intervening sequence with a high content of tyrosines (Y). This motif has no homologs in GenBank or PROSITE and is unique to flightin and paraflightin, a putative flightin paralog identified in decapods. A third motif of unclear affinities to pancrustacean WYR was observed in chelicerates. Phylogenetic analysis of amino acid sequences of the conserved motif suggests that paraflightin originated before the divergence of amphipods, isopods, and decapods. We conclude that flightin originated de novo in the ancestor of Pancrustacea > 500 MYA, well before the divergence of insects (~400 MYA) and the origin of flight (~325 MYA), and that its IFM-specific function in Drosophila is a more recent adaptation. Furthermore, we propose that WYR represents a novel myosin coiled-coil binding motif.
    Journal of Molecular Evolution 11/2013;
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    ABSTRACT: The fourfold degenerate site (FDS) in coding sequences is important for studying the effect of any selection pressure on codon usage bias (CUB) because nucleotide substitution per se is not under any such pressure at the site due to the unaltered amino acid sequence in a protein. We estimated the frequency variation of nucleotides at the FDS across the eight family boxes (FBs) defined as Um(g), the unevenness measure of a gene g. The study was made in 545 species of bacteria. In many bacteria, the Um(g) correlated strongly with Nc'-a measure of the CUB. Analysis of the strongly correlated bacteria revealed that the U-ending codons (GGU, CGU) were preferred to the G-ending codons (GGG, CGG) in Gly and Arg FBs even in the genomes with G+C % higher than 65.0. Further evidence suggested that these codons can be used as a good indicator of selection pressure on CUB in genomes with higher G+C %.
    Journal of Molecular Evolution 11/2013;

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