Journal of Molecular Evolution (J Mol Evol )

Publisher: Springer Verlag


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.

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    Journal of Molecular Evolution website
  • Other titles
    Journal of molecular evolution (Online), Molecular evolution, J mol evol
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    Document, Periodical, Internet resource
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Springer Verlag

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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Across the tree of life, species vary dramatically in nuclear genome size. Mutations that add or remove sequences from genomes-insertions or deletions, or indels-are the ultimate source of this variation. Differences in the tempo and mode of insertion and deletion across taxa have been proposed to contribute to evolutionary diversity in genome size. Among vertebrates, most of the largest genomes are found within the salamanders, an amphibian clade with genome sizes ranging from ~14 to ~120 Gb. Salamander genomes have been shown to experience slower rates of DNA loss through small (i.e., <30 bp) deletions than do other vertebrate genomes. However, no studies have addressed DNA loss from salamander genomes resulting from larger deletions. Here, we focus on one type of large deletion-ectopic-recombination-mediated removal of LTR retrotransposon sequences. In ectopic recombination, double-strand breaks are repaired using a "wrong" (i.e., ectopic, or non-allelic) template sequence-typically another locus of similar sequence. When breaks occur within the LTR portions of LTR retrotransposons, ectopic-recombination-mediated repair can produce deletions that remove the internal transposon sequence and the equivalent of one of the two LTR sequences. These deletions leave a signature in the genome-a solo LTR sequence. We compared levels of solo LTRs in the genomes of four salamander species with levels present in five vertebrates with smaller genomes. Our results demonstrate that salamanders have low levels of solo LTRs, suggesting that ectopic-recombination-mediated deletion of LTR retrotransposons occurs more slowly than in other vertebrates with smaller genomes.
    Journal of Molecular Evolution 01/2015;
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    ABSTRACT: Abstract Nitrogen assimilation is a highly regulated process requiring metabolic coordination of enzymes and pathways in the cytosol, chloroplast, and mitochondria. Previous studies of prasinophyte genomes revealed that genes encoding nitrate and ammonium transporters have a complex evolutionary history involving both vertical and horizontal transmission. Here we examine the evolutionary history of well-conserved nitrogen-assimilating enzymes to determine if a similar complex history is observed. Phylogenetic analyses suggest that genes encoding glutamine synthetase (GS) III in the prasinophytes evolved by horizontal gene transfer from a member of the heterokonts. In contrast, genes encoding GSIIE, a canonical vascular plant and green algal enzyme, were found in the Micromonas genomes but have been lost from Ostreococcus. Phylogenetic analyses placed the Micromonas GSIIs in a larger chlorophyte/vascular plant clade; a similar topology was observed for ferredoxin-dependent nitrite reductase (Fd-NiR), indicating the genes encoding GSII and Fd-NiR in these prasinophytes evolved via vertical transmission. Our results show that genes encoding the nitrogen-assimilating enzymes in Micromonas and Ostreococcus have been differentially lost and as well as recruited from different evolutionary lineages, suggesting that the regulation of nitrogen assimilation in prasinophytes will differ from other green algae.
    Journal of Molecular Evolution 12/2014;
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    ABSTRACT: Stereochemical assignment of amino acids and corresponding codons or anticodons has not been successful so far. Here, we focused on proline and GGG (anticodon of tRNA(Pro)) and investigated their mutual interaction. Circular dichroism spectroscopy revealed that guanosine nucleotides (GG, GGG) formed G-quartet structures. The structures were destroyed by adding high concentrations of proline. We propose that the possibility of the reversible proline/G-quartet interaction could have contributed to the specific assignment of proline on GGG and that this coding could have been the first in the genetic code.
    Journal of Molecular Evolution 06/2014; 78(6):310-2.
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    ABSTRACT: Proteins are elaborate biopolymers balancing between contradicting intrinsic propensities to fold, aggregate, or remain disordered. Assessing their primary structural preferences observable without evolutionary optimization has been reinforced by the recent identification of de novo proteins that have emerged from previously non-coding sequences. In this paper we investigate structural preferences of hypothetical proteins translated from random DNA segments using the standard genetic code and three of its proposed evolutionarily predecessor models encoding 10, 6, and 4 amino acids, respectively. Our only main assumption is that the disorder, aggregation, and transmembrane helix predictions used are able to reflect the differences in the trends of the protein sets investigated. We found that the 10-residue code encodes proteins that resemble modern proteins in their predicted structural properties. All of the investigated early genetic codes give rise to proteins with enhanced disorder and diminished aggregation propensities. Our results suggest that an ancestral genetic code similar to the proposed 10-residue one is capable of encoding functionally diverse proteins but these might have existed under conditions different from today's common physiological ones. The existence of a protein functional repertoire for the investigated earlier stages which is quite distinct as it is today can be deduced from the presented results.
    Journal of Molecular Evolution 05/2014;
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    ABSTRACT: We previously reported that 5'-mononucleotides organized within a multilamellar lipid matrix can produce oligomers in the anhydrous phase of hydration-dehydration (HD) cycles. However, hydrolysis of oligomers can occur during hydration, and it is important to better understand the steady state in which ester bond synthesis is balanced by hydrolysis. In order to study condensation products of mononucleotides and hydrolysis of their polymers, we established a simulation of HD cycles that would occur on the early Earth when volcanic land masses emerged from the ocean over 4 billion years ago. At this stage on early Earth, precipitation produced hydrothermal fields characterized by small aqueous pools undergoing evaporation and refilling at elevated temperatures. Here, we confirm that under these conditions, the chemical potential made available by cycles of hydration and dehydration is sufficient to drive synthesis of ester bonds. If 5'-mononucleotides are in solution at millimolar concentrations, then oligomers resembling RNA are synthesized and exist in a steady state with their monomers. Furthermore, if the mononucleotides can form complementary base pairs, then some of the products have properties suggesting that secondary structures are present, including duplex species stabilized by hydrogen bonds.
    Journal of Molecular Evolution 05/2014;
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    ABSTRACT: We propose a genealogy-sampling algorithm, Sequential Markov Ancestral Recombination Tree (SMARTree), that provides an approach to estimation from SNP haplotype data of the patterns of coancestry across a genome segment among a set of homologous chromosomes. To enable analysis across longer segments of genome, the sequence of coalescent trees is modeled via the modified sequential Markov coalescent (Marjoram and Wall, Genetics 7:16, 2006). To assess performance in estimating these local trees, our SMARTree implementation is tested on simulated data. Our base data set is of the SNPs in 10 DNA sequences over 50 kb. We examine the effects of longer sequences and of more sequences, and of a recombination and/or mutational hotspot. The model underlying SMARTree is an approximation to the full recombinant-coalescent distribution. However, in a small trial on simulated data, recovery of local trees was similar to that of LAMARC (Kuhner et al. Genetics 156:1393-1401, 2000a), a sampler which uses the full model.
    Journal of Molecular Evolution 05/2014;
  • Journal of Molecular Evolution 05/2014;
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    ABSTRACT: The study of which life history traits primarily affect molecular evolutionary rates is often confounded by the covariance of these traits. Scombroid fishes (billfishes, tunas, barracudas, and their relatives) are unusual in that their mass-specific metabolic rate is positively associated with body size. This study exploits this atypical pattern of trait variation, which allows for direct tests of whether mass-specific metabolic rate or body size is the more important factor of molecular evolutionary rates. We inferred a phylogeny for scombroids from a supermatrix of molecular and morphological characters and used new phylogenetic comparative approaches to assess the associations of body size and mass-specific metabolic rate with substitution rate. As predicted by the body size hypothesis, there is a negative correlation between body size and substitution rate. However, unexpectedly, we also find a negative association between mass-specific metabolic and substitution rates. These relationships are supported by analyses of the total molecular data, separate mitochondrial and nuclear genes, and individual loci, and they are robust to phylogenetic uncertainty. The molecular evolutionary rates of scombroids are primarily tied to body size. This study demonstrates that groups with novel patterns of trait variation can be particularly informative for identifying which life history traits are the primary factors of molecular evolutionary rates.
    Journal of Molecular Evolution 05/2014;
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    ABSTRACT: The montmorillonite-catalyzed reactions of the 5'-phosphorimidazolide of adenosine in the presence of fluoride were investigated to complete our study on the effect of salts on this type of reaction. Both anions and cations have been found to influence the oligomerization reactions of the activated nucleotides, being used here as a model system for pre-biotic RNA synthesis. However, in total contrast to the behavior of the activated nucleotides in the presence of montmorillonite and other salts, alkali metal fluorides did not yield any detectable oligomerization products except in very dilute (<0.005 M) solutions of fluoride. Instead, 5'-phosphorofluoridates were formed. Their identity was confirmed by a combination of HPLC, mass spectrometry, synthesis, and NMR.
    Journal of Molecular Evolution 04/2014;
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    ABSTRACT: The major histocompatibility complex (MHC) class IIB genes show considerable sequence similarity between loci. The MHC class II DQB and DRB genes are known to exhibit a high level of polymorphism, most likely maintained by parasite-mediated selection. Studies of the MHC in wild rodents have focused on DRB, whilst DQB has been given much less attention. Here, we characterised DQB genes in Swedish bank voles Myodes glareolus, using full-length transcripts. We then designed primers that specifically amplify exon 2 from DRB (202 bp) and DQB (205 bp) and investigated molecular signatures of natural selection on DRB and DQB alleles. The presence of two separate gene clusters was confirmed using BLASTN and phylogenetic analysis, where our seven transcripts clustered according to either DQB or DRB homologues. These gene clusters were again confirmed on exon 2 data from 454-amplicon sequencing. Our DRB primers amplify a similar number of alleles per individual as previously published DRB primers, though our reads are longer. Traditional d N/d S analyses of DRB sequences in the bank vole have not found a conclusive signal of positive selection. Using a more advanced substitution model (the Kumar method) we found positive selection in the peptide binding region (PBR) of both DRB and DQB genes. Maximum likelihood models of codon substitutions detected positively selected sites located in the PBR of both DQB and DRB. Interestingly, these analyses detected at least twice as many positively selected sites in DQB than DRB, suggesting that DQB has been under stronger positive selection than DRB over evolutionary time.
    Journal of Molecular Evolution 04/2014;
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    ABSTRACT: Soon after the origin of RNA-based life, depletion of prebiotically synthesised ribonucleotides would have driven the evolution of a biosynthetic pathway to these key building blocks. Ribozyme-catalysed nucleosidation-the key biosynthetic step-requires that ribose and the nucleobases are produced by abiotic chemistry and are relatively stable to the conditions of their synthesis. The most plausible prebiotic synthesis of sugars involves photoreduction of cyanohydrins by hydrogen sulphide in the presence of copper(I) cyanide, and we therefore subjected ribose to these conditions whereupon it was partially converted to 2-deoxyribose. Furthermore, a derivative of uracil is reduced under similar conditions to thymine. Thus, DNA biosynthetic precursors can be formed abiotically from those of RNA allowing for an early evolutionary transition to life based on RNA and DNA.
    Journal of Molecular Evolution 04/2014;
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    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;