Journal of Molecular Evolution (J Mol Evol)

Publisher: Springer Verlag

Journal 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.

Current impact factor: 1.68

Impact Factor Rankings

2015 Impact Factor Available summer 2016
2014 Impact Factor 1.68
2013 Impact Factor 1.863
2012 Impact Factor 2.145
2011 Impact Factor 2.274
2010 Impact Factor 2.311
2009 Impact Factor 2.323
2008 Impact Factor 2.762
2007 Impact Factor 3.234
2006 Impact Factor 2.767
2005 Impact Factor 2.703
2004 Impact Factor 2.751
2003 Impact Factor 3.114
2002 Impact Factor 3.041
2001 Impact Factor 4.011
2000 Impact Factor 3.984
1999 Impact Factor 3.655
1998 Impact Factor 3.271
1997 Impact Factor 3.181
1996 Impact Factor 3.052
1995 Impact Factor 3.519
1994 Impact Factor 3.777
1993 Impact Factor 3.484
1992 Impact Factor 3.15

Impact factor over time

Impact factor

Additional details

5-year impact 1.95
Cited half-life >10.0
Immediacy index 0.37
Eigenfactor 0.00
Article influence 0.74
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
    • Author's pre-print on pre-print servers such as
    • Author's post-print on author's personal website immediately
    • Author's post-print on any open access repository after 12 months after publication
    • Publisher's version/PDF cannot be used
    • Published source must be acknowledged
    • Must link to publisher version
    • Set phrase to accompany link to published version (see policy)
    • 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: Deoxyribozymes (DNA enzymes) have been developed for a growing variety of chemical reactions, including with peptide substrates. We recently described the first tyrosine kinase deoxyribozymes, which lacked the ability to discriminate among peptide substrates on the basis of the amino acids surrounding the tyrosine residue. Those deoxyribozymes were identified by in vitro selection using a DNA-anchored peptide substrate in which the residues neighboring tyrosine were all alanine. Here, we performed in vitro selection for tyrosine kinase activity using three peptide substrates in which the neighboring residues included a variety of side chains. For one of these three peptides, we found numerous deoxyribozymes that discriminate strongly in favor of phosphorylating tyrosine when the surrounding residues are specifically those used in the selection process. Three different short peptide sequence motifs of 2-4 amino acids were required for catalysis by three unique deoxyribozymes. For a second peptide substrate, the selection process led to one deoxyribozyme which exhibits partial discrimination among peptide sequences. These findings establish the feasibility of identifying DNA enzymes that catalyze sequence-selective tyrosine phosphorylation, which suggests the downstream practical utility of such deoxyribozymes. More broadly, this outcome reinforces the conclusion that nucleic acid catalysts can discriminate among peptide substrates in the context of biochemically relevant reactions.
    Journal of Molecular Evolution 09/2015; DOI:10.1007/s00239-015-9699-3
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    ABSTRACT: Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported-high thermostability and high catalytic activity-compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network.
    Journal of Molecular Evolution 09/2015; DOI:10.1007/s00239-015-9697-5
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    ABSTRACT: tRNA with a terminal UCCA-3' forms a structure in which the 3'-sequence folds back. The adenine of glycyl-AMP can base-pair with the uridine of the UCCA-3' region, which places the glycine residue in close proximity to the 3'-terminal adenosine of tRNA, possibly enabling the transfer of glycine from glycyl-AMP to tRNA. Thus, the UCCA-3'-containing tRNA (as seen in eubacterial tRNA(Gly)s) would possess an intrinsic property of glycylation by glycyl-AMP. This model provides a new perspective on the origins of the glycine assignment in the genetic code, beyond the "frozen accident" hypothesis.
    Journal of Molecular Evolution 08/2015; DOI:10.1007/s00239-015-9694-8
  • Journal of Molecular Evolution 08/2015; DOI:10.1007/s00239-015-9695-7
  • Journal of Molecular Evolution 08/2015;
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    ABSTRACT: Chicken repeat 1 (CR1) retroposons are the most abundant superfamily of transposable elements in the genomes of birds, crocodilians, and turtles. However, CR1 mobilization remains poorly understood. In this article, I document that the diverse CR1 lineages of land vertebrates share a highly conserved hairpin structure and an octamer microsatellite motif at their very 3' ends. Together with the presence of these same motifs in the tails of CR1-mobilized short interspersed elements, this suggests that the minimum requirement for CR1 transcript recognition and retrotransposition is a complex >50-nt structure. Such a highly specific recognition sequence readily explains why CR1-dominated genomes generally contain very few retrogenes. Conversely, the mammalian richness in retrogenes results from CR1 extinction in their early evolution and subsequent establishment of L1 dominance.
    Journal of Molecular Evolution 07/2015; 81(1-2). DOI:10.1007/s00239-015-9692-x
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    ABSTRACT: I present a model for the evolution of the genetic code that seems to predict, in a totally natural way, the origin of the first mRNAs. In particular, the model-bestowing to peptidated-RNAs the major catalytic role in the phase that triggered the genetic code origin-suggests that interactions between peptidated-RNAs led to the synthesis of these ancestral catalysts. Within every group of these interactions, a pre-mRNA molecule evolved that was able to direct all interactions between peptidated-RNAs of that particular group. This represented an improvement in the coding of these interactions compared to the interaction groups that did not evolve these pre-mRNAs. This would represent a natural and intrinsic tendency. Therefore, these molecules of pre-mRNAs were positively selected because they improved the synthesis of the catalysts through this first form of coding of interactions among peptidated-RNAs. Thus, according to the model were the pairings-involving a base number greater than three (ennuplet code)-between peptidated-RNAs and pre-mRNAs that would represent the first form of the genetic code. The evolution of this ennuplet code to the triplet code might have been simply triggered by the natural tendency to make the reading module-that is the interactions between peptidated-RNAs and pre-mRNAs-of the different ennuplets to the triplet uniform, because in this way the heterogeneity existing in interactions between the aminoacylated or peptidated-RNAs and pre-mRNAs was eliminated. That is to say, there might have been the natural tendency toward the triplets because these would have made these interactions more efficient, given that the ennuplets were at least more cumbersome and therefore less economic and with an inferior adaptive value; and also because the triplets would represent the simpler choice among that available given that the doublets would have codified too few meanings and quartets instead too many. Therefore, the genetic code would result from a very long era of interactions among peptidated-RNAs under the continuous and fundamental selective pressure for improving catalysts' syntheses and thus catalysis. The model is strongly corroborated by the explanation that the tmRNA molecule (transfer-messenger RNA) would seem to be the very molecule of pre-mRNAs that the model predicts. In other words, the tmRNA would be the molecular fossil of the evolutionary stages that led to the appearance of the first mRNAs.
    Journal of Molecular Evolution 07/2015; 81(1-2). DOI:10.1007/s00239-015-9691-y
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    ABSTRACT: Processes exhibiting diversity and selection would have been necessary to promote chemical evolution on early Earth. In this work, a model process was developed using non-kinetic selection to synthesize and isolate small molecule imidazolium catalysts. These catalysts were purified by affinity chromatography and recycled back into the process, forming a product feedback loop. In dimethylformamide, the catalysts activated the coupling of formaldehyde to short chain sugars. This sugar mixture was reacted with aniline, acetic acid, and paraformaldehyde to generate new catalysts. Thus chemical diversity was produced through non-selective, multi-component synthesis. Applying sequential dilution-reaction-purification cycles it was demonstrated that this process can function independently of starting catalyst. Over three process cycles, the initiator catalyst is effectively diluted out as a new catalyst population emerges to take its place. This system offers an alternative viewpoint for chemical evolution via the generation of small molecule organocatalysts.
    Journal of Molecular Evolution 07/2015; 81(1-2). DOI:10.1007/s00239-015-9687-7
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    ABSTRACT: B-family DNA-directed DNA polymerases are DNA replication enzymes found in Eukaryota, Archaea, large DNA viruses, and in some, but not all, bacteria. Several polymerase domains are conserved among the B-family DNA polymerases from these organisms, suggesting that the B-family DNA polymerases evolved from a common ancestor. Eukaryotes retain at least three replicative B-family DNA polymerases, DNA polymerase α, δ, and ε, and one translesion B-family DNA polymerase, DNA polymerase ζ. Here, we present molecular evolutionary evidence that suggests DNA polymerase genes evolved through horizontal gene transfer between the viral and archaeal-eukaryotic lineages. Molecular phylogenetic analyses of the B-family DNA polymerases from nucleo-cytoplasmic large DNA viruses (NCLDVs), eukaryotes, and archaea suggest that different NCLDV lineages such as Poxviridae and Mimiviridae were involved in the evolution of different DNA polymerases (pol-α-, δ-, ε-, and ζ-like genes) in archaeal-eukaryotic cell lineages, putatively through horizontal gene transfer. These results support existing theories that link the evolution of NCLDVs and the origin of the eukaryotic nucleus.
    Journal of Molecular Evolution 07/2015; 81(1-2). DOI:10.1007/s00239-015-9690-z
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    ABSTRACT: DNA repair refers to a collection of processes by which a cell identifies and corrects damage to genomic DNA molecules. DNA repair processes significantly overcome DNA damage and restore the normal nucleotide sequence and DNA structure. This study focuses on the evolution of the endonuclease III gene/protein family, which plays a key role in the base excision repair pathway. We analyzed 463 homologs of the endonuclease III protein and compared them with the corresponding gene and 16S/18S rRNA sequences to understand the evolutionary processes of this protein family. The sequence analysis and comparison reveal consensus sequence motifs within the ENDO3c and iron-sulfur cluster loop domains that are functionally and structurally important. On the basis of phylogenetic analysis, we propose an evolutionary model of the endonuclease III protein family. Horizontal gene transfer was identified as the key event among bacteria, archaea, and eukaryotic organisms that occurred during the evolution of the endonuclease III gene family among bacteria, archaea, and eukaryotic organisms. This analysis may be exploited to achieve a better prediction of the endonuclease III family gene/protein in unannotated organisms or families of organisms that are completely sequenced as well as in those for which sequencing is ongoing.
    Journal of Molecular Evolution 07/2015; 81(1-2):57-64. DOI:10.1007/s00239-015-9689-5
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    ABSTRACT: There have been two distinct phases of evolution of the genetic code: an ancient phase-prior to the divergence of the three domains of life, during which the standard genetic code was established-and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly from the standard code. Here we discuss the factors that are most important in these two phases, and we argue that these are substantially different. In the modern phase, changes are driven by chance events such as tRNA gene deletions and codon disappearance events. Selection acts as a barrier to prevent changes in the code. In contrast, in the ancient phase, selection for increased diversity of amino acids in the code can be a driving force for addition of new amino acids. The pathway of code evolution is constrained by avoiding disruption of genes that are already encoded by earlier versions of the code. The current arrangement of the standard code suggests that it evolved from a four-column code in which Gly, Ala, Asp, and Val were the earliest encoded amino acids.
    Journal of Molecular Evolution 06/2015; 80(5-6). DOI:10.1007/s00239-015-9686-8
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    ABSTRACT: The wide spread and high rate of gene exchange and loss in the prokaryotic world translate into "network genomics". The rates of gene gain and loss are comparable with the rate of point mutations but are substantially greater than the duplication rate. Thus, evolution of prokaryotes is primarily shaped by gene gain and loss. These processes are essential to prevent mutational meltdown of microbial populations by stopping Muller's ratchet and appear to trigger emergence of major novel clades by opening up new ecological niches. At least some bacteria and archaea seem to have evolved dedicated devices for gene transfer. Despite the dominance of gene gain and loss, evolution of genes is intrinsically tree-like. The significant coherence between the topologies of numerous gene trees, particularly those for (nearly) universal genes, is compatible with the concept of a statistical tree of life, which forms the framework for reconstruction of the evolutionary processes in the prokaryotic world.
    Journal of Molecular Evolution 04/2015; 80(5-6). DOI:10.1007/s00239-015-9679-7
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    ABSTRACT: Phylogenetic reconstruction of ribosomal history suggests that the ribonucleoprotein complex originated in structures supporting RNA decoding and ribosomal mechanics. A recent study of accretion of ancestral expansion segments of rRNA, however, contends that the large subunit of the ribosome originated in its peptidyl transferase center (PTC). Here I re-analyze the rRNA insertion data that supports this claim. Analysis of a crucial three-way junction connecting the long-helical coaxial branch that supports the PTC to the L1 stalk and its translocation functions reveals an incorrect branch-to-trunk insertion assignment that is in conflict with the PTC-centered accretion model. Instead, the insertion supports the ancestral origin of translocation. Similarly, an insertion linking a terminal coaxial trunk that holds the L7-12 stalk and its GTPase center to a seven-way junction of the molecule again questions the early origin of the PTC. Unwarranted assumptions, dismissals of conflicting data, structural insertion ambiguities, and lack of phylogenetic information compromise the construction of an unequivocal insertion-based model of macromolecular accretion. Results prompt integration of phylogenetic and structure-based models to address RNA junction growth and evolutionary constraints acting on ribosomal structure.
    Journal of Molecular Evolution 04/2015; 80(3-4). DOI:10.1007/s00239-015-9677-9