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
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 4.11
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


  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Pre-print allowed on any website or open access repository
    • Voluntary deposit by author of authors post-print allowed on authors' personal website, 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
    ​ green

Publications in this journal

  • Samuel D Martin, Ronald M Bonett
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    ABSTRACT: Body size is one of the most important traits influencing an organism's ecology and a major axis of evolutionary change. We examined body size disparification in the highly speciose North American minnows (Cyprinidae), which exhibit diverse body sizes and ecologies, including the giant piscivorous pikeminnows. We estimated a novel phylogeny for 285 species based on a supermatrix alignment of seven mitochondrial and ten nuclear genes, and used this to reconstruct ancestral body sizes (log-total length) and ancestral area. Additionally, given that fishes inhabiting Pacific drainages have historically been subjected to frequent local extinctions due to periodic flooding, droughts, and low drainage connectivity, we also compared body size disparification between the highly speciose Atlantic drainages and comparatively depauperate Pacific drainages. We found that dispersal between Atlantic and Pacific drainages has been infrequent and generally occurred in minnows with southerly distributions, where drainage systems are younger and less stable. The long isolation between Atlantic and Pacific drainages has allowed for divergent patterns of morphological disparification; we found higher rates of body size disparification in minnows from the environmentally harsher Pacific drainages. We propose several possible explanations for the observed patterns of size disparification in the context of habitat stability, niche space, and species diversification. Copyright © 2015. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 07/2015; DOI:10.1016/j.ympev.2015.07.006
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    ABSTRACT: Pong-like elements are members of the PIF/Harbinger superfamily of DNA transposons that has been described in many plants, animals, and fungi. Most Pong elements contain two open reading frames (ORFs). One encodes a transposase (ORF2) that catalyzes transposition of Pong and related non-autonomous elements, while the function of the second is unknown. Little is known about the evolutionary history of Pong elements in flowering plants. In this work, we present the first comprehensive analysis of the diversity, abundance, and evolution of the Pong-like transposase gene in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of nuclear-encoded Pong elements in any organism. A phylogenetic analysis of nearly 300 Pong sequences based on a conserved region of the transposase domain revealed a complex evolutionary history of Pong elements that can be best explained by ancestral polymorphism, followed by differential evolutionary success of some transposase lineages, and by occasional horizontal transfer between phylogenetically distant genera. In addition, we used transposon display to estimate the abundance of the transposase gene within Triticeae genomes, and our results revealed varying levels of Pong proliferation, with numbers of transposase copies ranging from 22 to 92. Comparisons of Pong transposase abundance to flow cytometry estimates of genome size revealed that larger Triticeae genome size was not correlated with transposase abundance. Copyright © 2015. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 07/2015; DOI:10.1016/j.ympev.2015.07.008
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    ABSTRACT: Despite the recent focus on phylogenetic niche conservatism in macroevolutionary studies, many clades have diversified widely along multiple niche dimensions. The factors underlying lineage-specific niche lability are still not well understood. We examined morphological and climate niche evolution in Montiaceae (Caryophyllales), an ecologically variable plant lineage distributed primarily along the mountain chains of the western Americas. Core Montiaceae inhabit a broader range of temperatures than their relatives, with an increase in the evolutionary rate of temperature niche diversification at the node subtending this clade. Within Montiaceae, life history is highly labile and significantly correlated with temperature, with perennials consistently occurring in cooler environments. This elevated evolutionary lability facilitated repeated shifts between habitats as new environments were created by post-Eocene orogenic events and aridification in the western Americas. The shifts between annual and perennial forms are elaborations of an underlying rosette body plan in most cases, and may involve simple alterations in biomass allocation. Montiaceae stand as another clear counterexample to phylogenetic niche conservatism, and demonstrate a mechanism by which pronounced ecological shifts may occur frequently and rapidly among closely related species. Copyright © 2015. Published by Elsevier Inc.
    Molecular Phylogenetics and Evolution 07/2015; DOI:10.1016/j.ympev.2015.06.006
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    ABSTRACT: The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous-Paleogene (K-Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K-Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1 - 3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K-Pg mass extinction, in the Paleocene-Eocene (65.5 - 33.9 Ma) or in association with the Eocene-Oligocene transition (33.9 Ma). Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 06/2015; DOI:10.1016/j.ympev.2015.06.005
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    ABSTRACT: Mitochondrial DNA (mtDNA) sequence data are widely used to delimit species. However, owing to its strict maternal inheritance in most species, mtDNA tracks female dispersion and dispersal only. The accuracy of mtDNA-derived species delimitation is often not explicitly tested using other independent evidence, such as nuclear DNA (nDNA) data, morphological data, or ecological data. Because species are independent evolutionary lineages that can form testable hypotheses, we present a multi-evidence case study on species delimitation that combines statistical approaches with spatially explicit ecological analysis. Montane salamanders of the Pachytriton brevipes complex (Salamandridae) from southeastern China exhibit conservative morphology and variable color patterning that impede species diagnosis. Recent studies proposed splitting P. brevipes into four species based on deep mtDNA divergence but also found discordance between mtDNA and nDNA trees. In this study, we test evolutionary independence of these hypothesized species lineages using two coalescent-based Bayesian methods (Bayes factor and BP&P). Despite significant conflict between mtDNA gene tree and the species phylogeny, the results reinforce the inference of at least four species in the complex as opposed to the one species recognized for over 130 years. Correlative ecological niche modeling and statistical analysis of environmental data indicate that suitable habitats for each species are isolated by incompatible intervening lowland regions, so the likelihood of gene flow among species is very low, and means species lineages should maintain their evolutionary independence. We demonstrate that concordance among independent evidence confirms species status, which forms the basis for accurate assessment of regional biodiversity. Copyright © 2015 Elsevier Inc. All rights reserved.
    Molecular Phylogenetics and Evolution 06/2015; DOI:10.1016/j.ympev.2015.06.010