Molecular Phylogenetics and Evolution (Mol Phylogenet Evol)

Publisher: Elsevier

Journal description

Molecular Phylogenetics and Evolution is dedicated to bringing Darwin's dream - to "have fairly true genealogical trees of each great kingdom of Nature" - within grasp. The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution. This journal plays an important role by publishing the results of molecular studies that identify the actual clades to which different species and higher taxa belong. Such knowledge will further the development of phylogenetically more accurate taxonomic classifications and ultimately lead to a unified classification for all the ramifying lines of life.

Current impact factor: 3.92

Impact Factor Rankings

2015 Impact Factor Available summer 2016
2014 Impact Factor 3.916
2013 Impact Factor 4.018
2012 Impact Factor 4.066
2011 Impact Factor 3.609
2010 Impact Factor 3.889
2009 Impact Factor 3.556
2008 Impact Factor 3.871
2007 Impact Factor 3.994
2006 Impact Factor 3.528
2005 Impact Factor 3.431
2004 Impact Factor 4.213
2003 Impact Factor 2.826
2002 Impact Factor 2.59
2001 Impact Factor 2.979
2000 Impact Factor 3.345
1999 Impact Factor 3.127
1998 Impact Factor 3.753
1997 Impact Factor 3.25
1996 Impact Factor 3.08

Impact factor over time

Impact factor

Additional details

5-year impact 4.06
Cited half-life 6.80
Immediacy index 0.96
Eigenfactor 0.03
Article influence 1.32
Website Molecular Phylogenetics and Evolution website
Other titles Molecular phylogenetics and evolution (Online), Molecular phylogenetics and evolution
ISSN 1095-9513
OCLC 36950039
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details


  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Authors pre-print on any website, including arXiv and RePEC
    • Author's post-print on author's personal website immediately
    • Author's post-print on open access repository after an embargo period of between 12 months and 48 months
    • Permitted deposit due to Funding Body, Institutional and Governmental policy or mandate, may be required to comply with embargo periods of 12 months to 48 months
    • Author's post-print may be used to update arXiv and RepEC
    • Publisher's version/PDF cannot be used
    • Must link to publisher version with DOI
    • Author's post-print must be released with a Creative Commons Attribution Non-Commercial No Derivatives License
    • Publisher last reviewed on 03/06/2015
  • Classification
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: tRNA-guanine transglycosylases are found in all domains of life and mediate the base exchange of guanine with queuine in the anticodon loop of tRNAs. They can also regulate virulence in bacteria such as Shigella flexneri, which has prompted the development of drugs that inhibit the function of these enzymes. Here we report a group of tRNA-guanine transglycosylases in eukaryotic microbes (algae and protozoa) which are more similar to their bacterial counterparts than previously characterized eukaryotic tRNA-guanine transglycosylases. We provide evidence demonstrating that the genes encoding these enzymes were acquired by these eukaryotic lineages via horizontal gene transfer from the Chlamydiae group of bacteria. Given that the S. flexneri tRNA-guanine transglycosylase can be targeted by drugs, we propose that the bacterial-like tRNA-guanine transglycosylases could potentially be targeted in a similar fashion in pathogenic amoebae that possess these enzymes such as Acanthamoeba castellanii. This work also presents ancient prokaryote-to-eukaryote horizontal gene transfer events as an untapped resource of potential drug target identification in pathogenic eukaryotes.
    Molecular Phylogenetics and Evolution 10/2015; DOI:10.1016/j.ympev.2015.09.022
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    ABSTRACT: Of the 97 currently recognized genera of Celastraceae, 19 are native to Madagascar, including six endemics. In this study we conducted the most thorough phylogenetic analysis of Celastraceae yet completed with respect to both character and taxon sampling, and include representatives of five new endemic genera. Fifty-one new accessions, together with 328 previously used accessions of Celastrales, were sampled for morphological characters, two rDNA gene regions, and two plastid gene regions. The endemic Malagasy genera are resolved in two separate lineages-Xenodrys by itself and all other endemic genera in a clade that also includes four lineages inferred to have dispersed from Madagascar: Brexia madagascariensis (Mascarene Islands, coastal Africa), Elaeodendron (West Indies, Africa to New Caledonia), and Pleurostylia (Africa to New Caledonia). Of the 12 extant Malagasy Celastraceae lineages identified, eight are clearly of African origin. The origins of the remaining four lineages are less clear, but reasonable possibilities include America, Eurasia, Africa, southern India, Malesia, and Australia. Based on 95% credible age intervals from fossil-calibrated molecular dating, all 12 extant Malagasy Celastraceae lineages appear to have arisen following dispersal after the separation of Madagascar from other landmasses within the last 70 million years.
    Molecular Phylogenetics and Evolution 10/2015; DOI:10.1016/j.ympev.2015.09.013
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    ABSTRACT: Studies of caterpillar defense strategy evolution typically focus on aposematic coloration, gregarious behavior, and/or chemical defense. In the slug moth family Limacodidae, the evolution of chemical defense is coupled to the life history trait of first instar feeding behaviors. In nettle caterpillars, the first instars fast and molt into a second instar that feeds. In contrast, gelatines and monkey slug larval forms feed in the first instar. This study focused on whether the evolution of fasting associated with the nettle morphology was a derived trait of single or multiple origins. Twenty-nine species of Limacodidae (including one Chrysopolominae) representing 27 genera and four outgroup species with known first and final instar morphologies and behaviors were included. Four out-group species representing Megalopygidae (1 sp), Dalceridae (1 sp) and Aididae (2 sp) were included. These were sequenced for three molecular markers fragments for a total of 4073bp, mitochondrial COI (∼1500bp), 18S (∼1900bp) and the D2 region of 28S (approximately 670bp). Maximum likelihood and Bayesian analyses were conducted. The resulting phylogeny and comparative analysis of feeding strategy revealed that the nettle caterpillar morphology and behavior of larval fasting may have a single origin.
    Molecular Phylogenetics and Evolution 10/2015; DOI:10.1016/j.ympev.2015.09.017
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    ABSTRACT: The accumulation of DNA sequence data in public repositories allows for phylogenetic inference on unprecedented taxonomic scales using supermatrix approaches. Careful analysis of available data allows strategic augmentation with new sequences in order to maximize taxonomic sampling and coverage of informative loci. I inferred relationships among 179 species (76%) in the avian family Picidae (woodpeckers, piculets, and wrynecks), using publicly available sequence data supplemented with targeted sequencing to increase species-level and locus-level sampling and maximize resolution. Results of these analyses generally corroborate previous molecular studies, with consensus on the membership of most genera and tribes. However, several newly placed taxa show surprising affinities, and several genera as currently delineated appear to be paraphyletic. Relationships among major clades of Picidae remain poorly resolved, particularly among the three lineages of piculets, the unusual woodpecker genus Hemicircus, and the remaining woodpeckers, and among the major groups of true woodpeckers (Picinae). Phylogenomic approaches may be necessary to resolve these deep relationships.
    Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.08.025
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    ABSTRACT: Carnivorous sponges are characterized by their unique method of capturing mesoplanktonic prey coupled with the complete or partial reduction of the aquiferous system characteristic of the phylum Porifera. Current systematics place the vast majority of carnivorous sponges within Cladorhizidae, with certain species assigned to Guitarridae and Esperiopsidae. Morphological characters have not been able to show whether this classification is evolutionary accurate, and whether carnivory has evolved once or in several lineages. In the present paper we present the first comprehensive molecular phylogeny of the carnivorous sponges, interpret these results in conjunction with morphological characters, and propose a revised classification of the group. Molecular phylogenies were inferred using 18S rDNA and a combined dataset of partial 28S rDNA, COI and ALG11 sequences. The results recovered carnivorous sponges as a clade closely related to the families Mycalidae and Guitarridae, showing family Cladorhizidae to be monophyletic and also including carnivorous species currently placed in other families. The genus Lycopodina is resurrected for species currently placed in the paraphyletic subgenus Asbestopluma (Asbestopluma) featuring forceps spicules and lacking sigmas or sigmancistras. The genera Chondrocladia and Cladorhiza are found to be monophyletic. However, results indicate that the subgenus Chondrocladia is polyphyletic with respect to the subgenera Meliiderma and Symmetrocladia. Euchelipluma, formerly Guitarridae, is retained, but transferred to Cladorhizidae. The four known carnivorous species currently in Esperiopsis are transferred to Abyssocladia. Neocladia is a junior homonym and is here renamed Koltunicladia. Our results provide strong evidence in support of the hypothesis that carnivory in sponges has evolved only once. While spicule characters mostly reflect monophyletic groups at the generic level, differences between genera represent evolution within family Cladorhizidae rather than evolution of carnivory in separate lineages. Conflicting spicule characters can be reinterpreted to support the inclusion of all carnivorous sponges within Cladorhizidae, and a carnivorous habit should thus be considered the main diagnostic character in systematic classification.
    Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.08.022
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    ABSTRACT: The triggerfishes (family Balistidae) and filefishes (family Monacanthidae) comprise a charismatic superfamily (Balistoidea) within the diverse order Tetraodontiformes. This group of largely marine fishes occupies an impressive ecological range across the world's oceans, and is well known for its locomotor and feeding diversity, unusual body shapes, small genome size, and ecological and economic importance. In order to investigate the evolutionary history of these important fish families, we used multiple phylogenetic methods to analyze molecular data from 86 species spanning the extant biodiversity of Balistidae and Monacanthidae. In addition to three gene regions that have been used extensively in phylogenetic analyses, we include sequence data for two mitochondrial regions, two nuclear markers, and the growth factor gene bmp4, which is involved with cranial development. Phylogenetic analyses strongly support the monophyly of the superfamily Balistoidea, the sister-family relationship of Balistidae and Monacanthidae, as well as three triggerfish and four filefish clades that are well resolved. A new classification for the Balistidae is proposed based on phylogenetic groups. Bayesian topology, as well as the timing of major cladogenesis events, is largely congruent with previous hypotheses of balistid phylogeny. However, we present a novel topology for major clades in the filefish family that illustrate the genera Aluterus and Stephanolepis are more closely related than previously posited. Molecular rates suggest a Miocene and Oligocene origin for the families Balistidae and Monacanthidae, respectively, and significant divergence of species in both families within the past 5 million years. A second key finding of this study is that, relative to the other protein-coding gene regions in our DNA supermatrix, bmp4 shows a rapid accumulation of both synonymous and non-synonymous substitutions, especially within the family Monacanthidae. Overall substitution patterns in bmp4 support the hypothesis of stabilizing selection during the evolutionary history of regulatory genes, with a small number of isolated examples of accelerated non-synonymous changes detected in our phylogeny.
    Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.09.014
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    ABSTRACT: Thelypteridaceae is one of the largest fern families, having about 950 species and a cosmopolitan distribution but with most species occurring in tropical and subtropical regions. Its generic classification remains controversial, with different authors recognizing from one up to 32 genera. Phylogenetic relationships within the family have not been exhaustively studied, but previous studies have confirmed the monophyly of the lineage. Thus far, sampling has been inadequate for establishing a robust hypothesis of infrafamilial relationships within the family. In order to understand phylogenetic relationships within Thelypteridaceae and thus to improve generic reclassification, we expand the molecular sampling, including new samples of Old World taxa and, especially, many additional neotropical representatives. We also explore the monophyly of exclusively or mostly neotropical genera Amauropelta, Goniopteris, Meniscium, and Steiropteris. Our sampling includes 70 taxa and 121 newly generated sequences from two plastid genomic regions (rps4-trnS and trnL-trnF), plus 71 rps4 and 70 trnL-trnF sequences from GenBank. These data resulted in a concatenated matrix of 1980 molecular characters for 144 taxa. The combined data set was analyzed using maximum parsimony and bayesian inference of phylogeny. Our results are consistent with the general topological structure found in previous studies, including two main lineages within the family: phegopteroid and thelypteroid. The thelypteroid lineage comprises two clades; one of these included the segregates Metathelypteris, Coryphopteris, and Amauropelta (including part of Parathelypteris), whereas the other comprises all segregates of Cyclosorus s.l., such as Goniopteris, Meniscium, and Steiropteris (including Thelypteris polypodioides, previously incertae sedis). The three mainly neotropical segregates were found to be monophyletic but nested in a broadly defined Cyclosorus. The fourth mainly neotropical segregate, Amauropelta, was found to comprise species considered to be part of the Parathelypteris. In Old World thelypteroids, which correspond to nearly half the diversity in the family, an increase in sampling is still needed to resolve relationships and circumscription of genera, particularly in the christelloid clade (i.e., Amphineuron, Chingia, Christella, Pneumatopteris, Pronephrium, and Sphaerostephanos). Based on currently available knowledge, we propose the recognition of 16 genera in the family.
    Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.09.009
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    ABSTRACT: Sea anemones of the family Aiptasiidae sensu Grajales and Rodríguez (2014) are conspicuous members of shallow-water environments, including several species widely used as model systems for the study of cnidarian-dinoflagellate symbiosis and coral bleaching. Although previously published phylogenetic studies of sea anemones recovered Aiptasiidae as polyphyletic, they only included a sparse sample in terms of its taxonomic diversity and membership of the family had not been yet revised. This study explores the phylogenetic relationships of this family using five molecular markers and including newly collected material from the geographical distribution of most of the currently described genera and species. We find a monophyletic family Aiptasiidae. All the currently proposed genera were recovered as monophyletic units, a finding also supported by diagnostic morphological characters. Our results confirm Bellactis and Laviactis as members of Aiptasiidae, also in agreement with previous morphological studies. The monophyly of the group is congruent with the morphological homogeneity of the members of this family. The obtained results also allow discussing the evolution of morphological characters within the family. Furthermore, we find evidence for and describe a new cryptic species, Exaiptasia brasiliensis sp. nov., based on molecular data, geographical distribution, and the identity of its endosymbiotic dinoflagellate.
    Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.09.004
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    ABSTRACT: The quality of phylogenetic inference made from protein-coding genes depends, in part, on the realism with which the codon substitution process is modeled. Here we propose a new mechanistic model that combines the standard M0 substitution model of Yang (1997) with a simplified model from Gilchrist (2007) that includes selection on synonymous substitutions as a function of codon-specific nonsense error rates. We tested the newly proposed model by applying it to 104 protein-coding genes in brewer's yeast, and compared the fit of the new model to the standard M0 model and to the mutation-selection model of Yang and Nielsen (2008) using the AIC. Our new model provided significantly better fit in approximately 85% of the cases considered for the basic M0 model and in approximately 25% of the cases for the M0 model with estimated codon frequencies, but only in a few cases when the mutation-selection model was considered. However, our model includes a parameter that can be interpreted as a measure of the rate of protein production, and the estimates of this parameter were highly correlated with an independent measure of protein production for the yeast genes considered here. Finally, we found that in some cases the new model led to the preference of a different phylogeny for a subset of the genes considered, indicating that substitution model choice may have an impact on the estimated phylogeny.
    Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.08.026
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    ABSTRACT: Members of the phylum Chordata and the subphylum Vertebrata are presently distinguished solely on the basis of morphological characteristics. The relationship of the vertebrates to the two non-vertebrate chordate subphyla is also a subject of debate. Analyses of protein sequences have identified multiple conserved signature indels (CSIs) that are specific for Chordata or for Vertebrata. Five CSIs in 4 important proteins are specific for the Vertebrata, whereas two other CSIs are uniquely found in all sequenced chordate species including Ciona intestinalis and Oikapleura dioica (Tunicates) as well as Brachiostoma floridae (Cephalochordates). The shared presence of these molecular signatures by all vertebrates/chordate species, but in no other animal taxa, strongly indicates that the genetic changes represented by the identified CSIs diagnose monophyletic groups. Two other discovered CSIs are uniquely shared by different vertebrate species and by either one (Ciona intestinalis) or both tunicate (Ciona and Oikapleura) species, but they are not found in Branchiostoma or other animal species. Specific presence of these CSIs in different vertebrates and either one or both tunicate species provides strong independent evidence that the vertebrate species are more closely related to the urochordates (tunicates) than to the cephalochordates.
    Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.09.019
  • Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.09.016
  • Molecular Phylogenetics and Evolution 09/2015; DOI:10.1016/j.ympev.2015.09.020