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: 4.02

Impact Factor Rankings

2015 Impact Factor Available summer 2015
2013 / 2014 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

Impact factor over time

Impact factor
Year

Additional details

5-year impact 4.11
Cited half-life 5.90
Immediacy index 0.89
Eigenfactor 0.04
Article influence 1.29
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

Elsevier

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
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    • Pre-print allowed on any website or open access repository
    • Voluntary deposit by author of authors post-print allowed on authors' personal website, arXiv.org or institutions open scholarly website including Institutional Repository, without embargo, where there is not a policy or mandate
    • Deposit due to Funding Body, Institutional and Governmental policy or mandate only allowed where separate agreement between repository and the publisher exists.
    • 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 .
    • Set statement to accompany deposit
    • Published source must be acknowledged
    • Must link to journal home page or articles' DOI
    • Publisher's version/PDF cannot be used
    • Articles in some journals can be made Open Access on payment of additional charge
    • NIH Authors articles will be submitted to PubMed Central after 12 months
    • Publisher last contacted on 18/10/2013
  • Classification
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Panorpidae are the largest family in Mecoptera, covering approximately 70% species of the order. However, the phylogenetic relationship within Panorpidae has not been adequately explored. Here we analyzed the phylogenetic relationships among 70 species of five genera in Panorpidae using maximum likelihood and Bayesian inference based on two mitochondrial (cox1 and cox2) and one nuclear (28S rRNA) gene fragments with Panorpodes kuandianensis and Brachypanorpa carolinensis in Panorpodidae as outgroups. The results show that the genera Neopanorpa, Sinopanorpa and Dicerapanorpa are monophyletic, while the widespread genus Panorpa is reconfirmed to be a paraphyletic group. The P. centralis group is monophyletic and may merit a generic status, while the P. davidi and P. amurensis groups are paraphyletic. The divergence time estimated from BEAST analysis indicates that the Panorpidae may originate in the period from early Paleogene (63.6 mya) to middle Eocene (41.2 mya), and most diversification within Panorpidae occurred in the Cenozoic. The phylogeny and biogeography of Panorpidae are briefly discussed.
    Molecular Phylogenetics and Evolution 04/2015; 85.
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    ABSTRACT: Stag beetles (family Lucanidae Latreille, 1804) are one of the earliest branching lineages of scarab beetles that are characterized by the striking development of the male mandibles. Despite stag beetles’ popularity among traditional taxonomists and amateur collectors, there has been almost no study of lucanid relationships and evolution. Entomologists, including Jeannel (1942), have long recognized resemblance between the austral stag beetles of the tribes Chiasognathini, Colophonini, Lamprimini, Pholidotini, Rhyssonotini, and Streptocerini, but this hypothesis of their close relationship across the continents has never been tested. To gain further insight into lucanid phylogeny and biogeography, we reconstructed the first molecular phylogeny of world stag beetles using DNA sequences from mitochondrial 16S rDNA, nuclear 18S and 28S rDNA, and the nuclear protein-coding (NPC) gene wingless for 93 lucanid species representing all extant subfamilies and 24 out of the 27 tribes, together with 14 representative samples of other early branching scarabaeoid families and two staphyliniform beetle families as outgroups. Both Bayesian inference (BI) and maximum likelihood inference (MLI) strongly supported the monophyly of Lucanidae sensu lato that includes Diphyllostomatidae. Within Lucanidae sensu stricto, the subfamilies Lucaninae and Lampriminae appeared monophyletic under both methods of phylogenetic inferences; however, Aesalinae and Syndesinae were found to be polyphyletic. A time-calibrated phylogeny based on five fossil data estimated the origin of crown group Lucanidae as circa 160 million years ago (MYA). Divergence between the Neotropical and Australasian groups of the Chiasognathini was estimated to be circa 47 MYA, with the South African Colophonini branching off from the ancient Chiasognathini lineage around 87 MYA. Another Gondwanan relationship was recovered between the Australasian Eucarteria and the Neotropical Casignetus, which diverged circa 58 MYA. Lastly, as Jeannel’s hypothesis predicted, divergence within Lampriminae between the Australasian Lamprima and the Neotropical Streptocerus was estimated to be circa 37 MYA. The split of these lineages were generally concordant with the pattern of continental break-up of the super-continent Gondwana, and our biogeographic reconstructions based on the dispersal-extinction-cladogenesis model (DEC) corroborate our view that the divergences in these austral lineages were caused by vicariance events following the Gondwanan break-up. In addition, the phylogenetic position and geographic origin of the Hawaiian genus Apterocyclus was revealed for the first time. Overall, our results provide the framework toward studying lucanid relationships and divergence time estimates, which allowed for more accurate biogeographic explanations and discussions on ancestral lucanids and the evolutionary origin of the enlarged male mandibles.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: The subtribe Aeridinae, which contains approximately 90 genera, is one of the most diverse and taxonomically puzzling groups in Orchidaceae. In the present study, the phylogenetic relationships of Aeridinae were reconstructed utilizing five DNA sequences (ITS, atpI-H, matK, psbA-trnH, and trnL-F) from 211 taxa in 74 genera. The results of the phylogenetic analyses indicate that Aeridinae is monophyletic and that the subtribe can primarily be grouped into 10 clades: (1) Saccolabium clade, (2) Chiloschista clade, (3) Phalaenopsis clade, (4) Thrixspermum clade, (5) Vanda clade, (6) Aerides clade, (7) Trichoglottis clade, (8) Abdominea clade, (9) Gastrochilus clade, and (10) Cleisostoma clade. In our examination, most genera of Aeridinae were well-supported as monophyletic, and several genera, namely, Pteroceras, Cleisostoma, Vandopsis, Diploprora, Malleola, and Robiquetia, were found to be polyphyletic as currently circumscribed. In addition, several classifications of intra-genera, such as the subgenus Codonosepalum of Taeniophyllum and the section Gastrochilus of Gastrochilus, were also revealed to be paraphyletic. Due to the many questions raised by our phylogenies, the present study may serve as a reference for future taxonomic studies of Aeridinae. Copyright © 2015. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: The understanding of the diversity of species in the Palearctic and the processes that have generated it is still weak for large parts of the arid areas of North Africa and Arabia. Reptiles are among their most remarkable representatives, with numerous groups well adapted to the diverse environments. The Ptyodactylus geckos are a strictly rock-dwelling genus with homogeneous morphology distributed across mountain formations and rocky plateaus from the western African ranges in Mauritania and the Maghreb to the eastern tip of the Arabian Peninsula, with an isolated species in southern Pakistan. Here, we use a broad sampling of 378 specimens, two mitochondrial (12S and cytb) and four nuclear (c-mos, MC1R, ACM4, RAG2) markers in order to obtain the first time-calibrated molecular phylogeny of the genus and place its diversification in a temporal framework. The results reveal high levels of intraspecific variability, indicative of undescribed diversity, and they do not support the monophyly of one species (P. ragazzii). Ptyodactylus species are allopatric across most of their range, which may relate to their high preference for the same type of structural habitat. The onset of their diversification is estimated to have occurred in the Late Oligocene, while that of several deep clades in the phylogeny took place during the Late Miocene, a period when an increase in aridification in North Africa and Arabia initiated. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: The current classifications of arcoids are based on phenetic similarity, which display considerable convergence in several shell and anatomical characters, challenging phylogenetic analysis. Independent molecular analysis of DNA sequences is often necessary for accurate taxonomic assignments of arcoids, especially when morphological characters are equivocal. Here we present molecular evidence of the phylogenetic relationships among arcoid species based on Bayesian inference and Maximum Likelihood analyses of three nuclear genes (18S rRNA, 28S rRNA, and histone H3) and two mitochondrial genes (COI and 12S). Tree topologies are discussed by considering traditional arrangements of taxonomic units and previous molecular studies. The results confirm the monophyly of the order Arcoida, the family Noetiidae, and the subfamilies Anadarinae and Striarcinae, with support for the inclusion of the Glycymerididae in the Arcoidea. The subfamily Arcinae and the genera Arca, Barbatia, Scapharca, Anadara, and Glycymeris are non-monophyletic, suggesting that taxonomic issues still remain. The families Noetiidae, Cucullaeidae, and Glycymerididae appear as subgroups within, rather than sister groups to, the Arcidae. This study strongly suggests the need to carry out a taxonomic revision of the Arcoidea, especially the Arcidae, through combined analysis of morphological, paleontological, and molecular data. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: The increased rate at which complete mitogenomes are being sequenced and their increasing use for phylogenetic studies have resulted in a bioinformatic bottleneck in preparing and utilising such data for phylogenetic analysis. Hence, we present MitoPhAST, an automated tool that 1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, 2) generates a maximum likelihood phylogenetic tree using optimised protein models and 3) reports various mitochondrial genes and sequence information in a table format. To demonstrate the capacity of MitoPhAST in handling a large dataset, we used 81 publicly available decapod mitogenomes, together with eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus, to undertake an updated test of the monophyly of the major groups of the order Decapoda and their phylogenetic relationships. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting there is value in utilising more fully mitogenomic data. Additionally, the simple table output from MitoPhAST provides an efficient summary and statistical overview of the mitogenomes under study at the gene level, allowing the identification of missing or duplicated genes and gene rearrangements. The finding of new mtDNA gene rearrangements in several genera of Australian freshwater crayfishes indicates that this group has undergone an unusually high rate of evolutionary change for this organelle compared to other major families of decapod crustaceans. As a result, freshwater crayfishes are likely to be a useful model for studies designed to understand the evolution of mtDNA rearrangements. We anticipate that our bioinformatics pipeline will substantially help mitogenome-based studies increase the speed, accuracy and efficiency of phylogenetic studies utilising mitogenome information. MitoPhAST is available for download at https://github.com/mht85/MitoPhAST. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: Cytogenetic data has indicated the presence of St and Y genome in Elymus longearistatus (Boiss.) Tzvelev. However, a random amplified polymorphic DNA (RAPD) based sequence tagged site (STS) study suggested one accession of Pseudoroegneria spicata (Pursh) Á Löve (St genome) as a potential Y genome donor candidate in tetraploid E. longearistatus. To examine the origin of Y genome in and the phylogeny of tetraploid E. longearistatus, sequences of cpDNA (RPS16 and TrnD/T intergenic spacer) and single copy nuclear genes (EF-G and HTL) from eight accessions of E. longearistatus, six StY genomic Elymus species and 62 accessions of diploid in Triticeae were analyzed. The cpDNA data suggested that P. stipifolia (St) is the most likely maternal donor of these six Iranian accessions of E. longearistatus, although P. strigosa could not be excluded. Two nuclear gene data convincingly showed that tetraploid E. longearistatus contains two distinct genomes, St and Y genome. The phylogenetic analyses from both the EF-G and HTL rejected the previous suggestion that accession PI 232134 of Pseudoroegneria spicata (Pursh) Á Löve (St genome) was potential Y genome donor to E. longearistatus. Phylogenetic analyses revealed a separation of the Y genome sequences in Iranian accessions of E. longearistatus from the sequences in the Pakistan accession, indicating that geographic isolation might influence the evolution of the Y genome in E. longearistatus. Copyright © 2015. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: Data from molecular phylogenetics were used to assess aspects of diversity and relationships in Brickellia, a large and widespread genus of Eupatorieae. The dataset included sequence data from nuclear ribosomal ITS, ETS, and plastid psbA-trnH regions. An initial question was to assess the monophyly of the genus and whether Barroetea, Phanerostylis, and Kuhnia should be recognized as separate from or included in Brickellia. The results supported the hypothesis that Brickellia is monophyletic, with the small (2-3 species) Pleurocoronis as the sister group and showed Barroetea, Phanerostylis, and Kuhnia all embedded within the genus. Results of a time calibrated phylogeny from a BEAST analysis gave an estimated origination time for Brickellia at about 9 million years ago (Ma), with the oldest split within the genus dated at about 7.5 Ma. A BAMM analysis based on the time calibrated tree showed that Brickellia has one rate shift in diversification associated with its origin in the late Miocene. Some lineages within the genus have had an increase in the rate of diversification over the past 5 Ma, whereas other lineages have had a decrease in net diversification during this period. The results also elucidated nine clades within Brickellia which are accepted as taxonomic sections, and that will form logical units for future detailed studies. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: A phylogenetic hypothesis for the lepidopteran superfamily Noctuoidea was inferred based on the complete mitochondrial (mt) genomes of 12 species (six newly sequenced). The monophyly of each noctuoid family in the latest classification was well supported. Novel and robust relationships were recovered at the family level, in contrast to previous analyses using nuclear genes. Erebidae was recovered as sister to (Nolidae + (Euteliidae + Noctuidae)), while Notodontidae was sister to the remaining Noctuoidea (the putatively basalmost lineage Oenosandridae was not included). In order to improve phylogenetic resolution using mt genomes, various analytical approaches were tested: Bayesian inference (BI) vs. maximum likelihood (ML), excluding vs. including RNA genes (rRNA or tRNA), and Gblocks treatment. The evolutionary signal within mt genomes had low sensitivity to analytical changes. Inference methods had the most significant influence. Inclusion of tRNAs positively increased the congruence of topologies, while inclusion of rRNAs resulted in a range of phylogenetic relationships varying depending on other analytical factors. The two Gblocks parameter settings had opposite effects on nodal support between the two inference methods. The relaxed parameter (GBRA) resulted in higher support values in BI analyses, while the strict parameter (GBDH) resulted in higher support values in ML analyses. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 02/2015;
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    ABSTRACT: The genus Xiphorhynchus is a species rich avian group widely distributed in Neotropical forests of Central and South America. Although recent molecular studies have improved our understanding of the spatial patterns of genetic diversity in some species of this genus, most are still poorly known, including their taxonomy. Here, we address the historical diversification and phylogenetic relationships of the X. guttatus/susurrans complex, using data from two mitochondrial (cyt b and ND2) and one nuclear (β-fibint7) genes. Phylogenetic relationships were inferred with both gene trees and a Bayesian-based species tree under a coalescent framework (∗BEAST). With exception of the nuclear β-fibint7 gene that produced an unresolved tree, both mtDNA and the species tree showed a similar topology and were congruent in recovering five main clades with high statistical support. These clades, however, are not fully concordant with traditional delimitation of some X. guttatus subspecies, since X. g. polystictus, X. g. guttatus, and X. connectens are not supported as distinct clades. Interestingly, these three taxa are more closely related to the mostly trans-Andean X. susurrans than the other southern and western Amazonian subspecies of X. guttatus, which constitutes a paraphyletic species. Timing estimates based on the species tree indicated that diversification in X. guttatus occurred between the end of the Pliocene and early Pleistocene, likely associated with the formation of the modern Amazon River and its main southern tributaries (Xingu, Tocantins, and Madeira), in addition to climate-induced changes in the distribution of rainforest biomes. Our study supports with an enlarged dataset a previous proposal for recognizing at least three species level taxa in the X. guttatus/susurrans complex: X. susurrans, X. guttatus, and X. guttatoides.
    Molecular Phylogenetics and Evolution 02/2015;