BMC Evolutionary Biology (BMC EVOL BIOL)

Publisher: BioMed Central

Journal description

BMC Evolutionary Biology publishes original research articles in all aspects of molecular and non-molecular evolution of all organisms, as well as phylogenetics and palaeontology.

Current impact factor: 3.41

Impact Factor Rankings

2015 Impact Factor Available summer 2015
2013 / 2014 Impact Factor 3.407
2012 Impact Factor 3.285
2011 Impact Factor 3.521
2010 Impact Factor 3.702
2009 Impact Factor 4.294
2008 Impact Factor 4.05
2007 Impact Factor 4.091
2006 Impact Factor 4.455
2005 Impact Factor 4.447

Impact factor over time

Impact factor
Year

Additional details

5-year impact 4.43
Cited half-life 4.40
Immediacy index 0.30
Eigenfactor 0.05
Article influence 1.67
Website BMC Evolutionary Biology website
Other titles BMC evolutionary biology, BioMed Central evolutionary biology, Evolutionary biology
ISSN 1471-2148
OCLC 47657384
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

BioMed Central

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Publisher's version/PDF may be used
    • Eligible UK authors may deposit in OpenDepot
    • Creative Commons Attribution License
    • Copy of License must accompany any deposit.
    • All titles are open access journals
    • 'BioMed Central' is an imprint of 'Springer Verlag (Germany)'
  • Classification
    ​ green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Dinoflagellates are eukaryotes with unusual cell biology and appear to rely on translational rather than transcriptional control of gene expression. The eukaryotic translation initiation factor 4E (eIF4E) plays an important role in regulating gene expression because eIF4E binding to the mRNA cap is a control point for translation. eIF4E is part of an extended, eukaryote-specific family with different members having specific functions, based on studies of model organisms. Dinoflagellate eIF4E diversity could provide a mechanism for dinoflagellates to regulate gene expression in a post-transcriptional manner. Accordingly, eIF4E family members from eleven core dinoflagellate transcriptomes were surveyed to determine the diversity and phylogeny of the eIF4E family in dinoflagellates and related lineages including apicomplexans, ciliates and heterokonts. The survey uncovered eight to fifteen (on average eleven) different eIF4E family members in each core dinoflagellate species. The eIF4E family members from heterokonts and dinoflagellates segregated into three clades, suggesting at least three eIF4E cognates were present in their common ancestor. However, these three clades are distinct from the three previously described eIF4E classes, reflecting diverse approaches to a central eukaryotic function. Heterokonts contain four clades, ciliates two and apicomplexans only a single recognizable eIF4E clade. In the core dinoflagellates, the three clades were further divided into nine sub-clades based on the phylogenetic analysis and species representation. Six of the sub-clades included at least one member from all eleven core dinoflagellate species, suggesting duplication in their shared ancestor. Conservation within sub-clades varied, suggesting different selection pressures. Phylogenetic analysis of eIF4E in core dinoflagellates revealed complex layering of duplication and conservation when compared to other eukaryotes. Our results suggest that the diverse eIF4E family in core dinoflagellates may provide a toolkit to enable selective translation as a strategy for controlling gene expression in these enigmatic eukaryotes.
    BMC Evolutionary Biology 12/2015; 15(1). DOI:10.1186/s12862-015-0301-9
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    ABSTRACT: Morphological divergence often increases with phylogenetic distance, thus making morphology taxonomically informative. However, transitions to asexual reproduction may complicate this relationship because asexual lineages capture and freeze parts of the phenotypic variation of the sexual populations from which they derive. Parasitoid wasps belonging to the genus Lysiphlebus Foerster (Hymenoptera: Braconidae: Aphidiinae) are composed of over 20 species that exploit over a hundred species of aphid hosts, including many important agricultural pests. Within Lysiphlebus, two genetically and morphologically well-defined species groups are recognised: the "fabarum" and the "testaceipes" groups. Yet within each group, sexual as well as asexual lineages occur, and in L. fabarum different morphs of unknown origin and status have been recognised. In this study, we selected a broad sample of specimens from the genus Lysiphlebus to explore the relationship between genetic divergence, reproductive mode and morphological variation in wing size and shape (quantified by geometric morphometrics). The analyses of mitochondrial and nuclear gene sequences revealed a clear separation between the "testaceipes" and "fabarum" groups of Lysiphlebus, as well as three well-defined phylogenetic lineages within the "fabarum" species group and two lineages within the "testaceipes" group. Divergence in wing shape was concordant with the deep split between the "testaceipes" and "fabarum" species groups, but within groups no clear association between genetic divergence and wing shape variation was observed. On the other hand, we found significant and consistent differences in the shape of the wing between sexual and asexual lineages, even when they were closely related. Mapping wing shape data onto an independently derived molecular phylogeny of Lysiphlebus revealed an association between genetic and morphological divergence only for the deepest phylogenetic split. In more recently diverged taxa, much of the variation in wing shape was explained by differences between sexual and asexual lineages, suggesting a mechanistic link between wing shape and reproductive mode in these parasitoid wasps.
    BMC Evolutionary Biology 12/2015; 15(1). DOI:10.1186/s12862-015-0293-5
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    ABSTRACT: Genetic analyses of DNA sequences make use of an increasingly complex set of nucleotide substitution models to estimate the divergence between gene sequences. However, there is currently no way to assess the validity of nucleotide substitution models over short time-scales and with limited mutational accumulation. We show that quantifying the decline in the ratio of transitions to transversions (ti/tv) over time provides an in-built measure of mutational saturation and hence of substitution model accuracy. We tested this through detailed phylogenetic analyses of 10 representative virus data sets comprising recently sampled and closely related sequences. In the majority of cases our estimates of ti/tv decrease with time, even under sophisticated time-reversible models of nucleotide substitution. This indicates that high levels of saturation are attained extremely rapidly in viruses, sometimes within decades. In contrast, we did not find any temporal patterns in selection pressures or CG-content over these short time-frames. To validate the temporal trend of ti/tv across a broader taxonomic range, we analyzed a set of 76 different viruses. Again, the estimate of ti/tv scaled negatively with evolutionary time, a trend that was more pronounced for rapidly-evolving RNA viruses than slowly-evolving DNA viruses. Our study shows that commonly used substitution models can underestimate the number of substitutions among closely related sequences, such that the time-scale of viral evolution and emergence may be systematically underestimated. In turn, estimates of ti/tv provide an effective internal control of substitution model performance in viruses because of their high sensitivity to mutational saturation.
    BMC Evolutionary Biology 12/2015; 15(1):312. DOI:10.1186/s12862-015-0312-6
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    ABSTRACT: Long-term monitoring of the biological impacts of the radioactive pollution caused by the Fukushima nuclear accident in March 2011 is required to understand what has occurred in organisms living in the polluted areas. Here, we investigated spatial and temporal changes of the abnormality rate (AR) in both field-caught adult populations and laboratory-reared offspring populations of the pale grass blue butterfly, Zizeeria maha, which has generation time of approximately one month. We monitored 7 localities (Fukushima, Motomiya, Hirono, Iwaki, Takahagi, Mito, and Tsukuba) every spring and fall over 3 years (2011-2013). The adult ARs of these localities quickly increased and peaked in the fall of 2011, which was not observed in non-contaminated localities. In the offspring generation, the total ARs, which include deaths at the larval, prepupal, and pupal stages and morphological abnormalities at the adult stage, peaked either in the fall of 2011 or in the spring of 2012, with much higher levels than those of the parent field populations, suggesting that high incidence of deaths and abnormalities might have occurred in the field populations. Importantly, the elevated ARs of the field and offspring populations settled back to a normal level by the fall of 2012 and by the spring of 2013, respectively. Similar results were obtained not only in the spatiotemporal dynamics of the number of individuals caught per minute but also in the temporal dynamics of the correlation coefficient between the adult abnormality rate and the ground radiation dose or the distance from the Power Plant. These results demonstrated an occurrence and an accumulation of adverse physiological and genetic effects in early generations, followed by their decrease and leveling off at a normal level, providing the most comprehensive record of biological dynamics after a nuclear accident available today. This study also indicates the importance of considering generation time and adaptive evolution in evaluating the biological impacts of artificial pollution in wild organisms.
    BMC Evolutionary Biology 12/2015; 15(1). DOI:10.1186/s12862-015-0297-1
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    ABSTRACT: RPB1, the largest subunit of RNA polymerase II, contains a highly modifiable C-terminal domain (CTD) that consists of variations of a consensus heptad repeat sequence (Y1S2P3T4S5P6S7). The consensus CTD repeat motif and tandem organization represent the ancestral state of eukaryotic RPB1, but across eukaryotes CTDs show considerable diversity in repeat organization and sequence content. These differences may reflect lineage-specific CTD functions mediated by protein interactions. Mammalian CTDs contain eight non-consensus repeats with a lysine in the seventh position (K7). Posttranslational acetylation of these sites was recently shown to be required for proper polymerase pausing and regulation of two growth factor-regulated genes. To investigate the origins and function of RPB1 CTD acetylation (acRPB1), we computationally reconstructed the evolution of the CTD repeat sequence across eukaryotes and analyzed the evolution and function of genes dysregulated when acRPB1 is disrupted. Modeling the evolutionary dynamics of CTD repeat count and sequence content across diverse eukaryotes revealed an expansion of the CTD in the ancestors of Metazoa. The new CTD repeats introduced the potential for acRPB1 due to the appearance of distal repeats with lysine at position seven. This was followed by a further increase in the number of lysine-containing repeats in developmentally complex clades like Deuterostomia. Mouse genes enriched for acRPB1 occupancy at their promoters and genes with significant expression changes when acRPB1 is disrupted are enriched for several functions, such as growth factor response, gene regulation, cellular adhesion, and vascular development. Genes occupied and regulated by acRPB1 show significant enrichment for evolutionary origins in the early history of eukaryotes through early vertebrates. Our combined functional and evolutionary analyses show that RPB1 CTD acetylation was possible in the early history of animals, and that the K7 content of the CTD expanded in specific developmentally complex metazoan lineages. The functional analysis of genes regulated by acRPB1 highlight functions involved in the origin of and diversification of complex Metazoa. This suggests that acRPB1 may have played a role in the success of animals.
    BMC Evolutionary Biology 12/2015; 15(1):327. DOI:10.1186/s12862-015-0327-z
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    ABSTRACT: Polycomb repressive complex 1 (PRC1) is an essential protein complex for plant development. It catalyzes ubiquitination of histone H2A that is an important part of the transcription repression machinery. Absence of PRC1 subunits in Arabidopsis thaliana plants causes severe developmental defects. Many aspects of the plant PRC1 are elusive, including its origin and phylogenetic distribution. We established the evolutionary history of the plant PRC1 subunits (LHP1, Ring1a-b, Bmi1a-c, EMF1, and VRN1), enabled by sensitive phylogenetic methods and newly sequenced plant genomes from previously unsampled taxonomic groups. We showed that all PRC1 core subunits exist in gymnosperms, earlier than previously thought, and that VRN1 is a recent addition, found exclusively in eudicots. The retention of individual subunits in chlorophytes, mosses, lycophytes and monilophytes indicates that they can moonlight as part of other complexes or processes. Moreover, we showed that most PRC1 subunits underwent a complex, duplication-rich history that differs significantly between Brassicaceae and other eudicots. PRC1 existed in the last common ancestor of seed plants where it likely played an important regulatory role, aiding their radiation. The presence of LHP1, Ring1 and Bmi1 in mosses, lycophytes and monilophytes also suggests the presence of a primitive yet functional PRC1.
    BMC Evolutionary Biology 12/2015; 15(1):319. DOI:10.1186/s12862-015-0319-z
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    ABSTRACT: Many butterflies possess striking structures called eyespots on their wings, and several studies have sought to understand the selective forces that have shaped their evolution. Work over the last decade has shown that a major function of eyespots is their ability to reduce predation by being intimidating to attacking predators. Two competing hypotheses seek to explain the cause of intimidation, one suggesting 'eye-mimicry' and the other their 'conspicuousness' as the reason. There is an on-going debate about which of these better explains the effectiveness of eyespots against predation. We undertook a series of indoor experiments to understand the relative importance of conspicuousness and eye-mimicry, and therefore how predator perception may have influenced the evolution of eyespots. We conducted choice tests where artificial paper models mimicking Junonia almana butterflies were presented to chickens and their preference of attack recorded. We first established that birds avoided models with a pair of eyespots. However, contrary to previous, outdoor experiments, we found that the total area of eyespots did not affect their effectiveness. Non-eye-like, fan shaped patterns derived from eyespots were found to be just as effective as eye-like circular patterns. Furthermore, we did not find a significant effect of symmetry of patterns, again in discordance with previous work. However, across all experiments, models with a pair of patterns, symmetric or asymmetric, eyelike or non-eye-like, suffered from fewer attacks compared with other models. The study highlights the importance of pairedness of eyespots, and supports the hypothesis that two is a biologically significant number that is important in prey-predator signalling. We discuss the implications of our results for the understanding of eyespot evolution.
    BMC Evolutionary Biology 12/2015; 15(1):307. DOI:10.1186/s12862-015-0307-3
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    ABSTRACT: Shelled pteropods are planktonic gastropods that are potentially good indicators of the effects of ocean acidification. They also have high potential for the study of zooplankton evolution because they are metazoan plankton with a good fossil record. We investigated phenotypic and genetic variation in pteropods belonging to the genus Cuvierina in relation to their biogeographic distribution across the world's oceans. We aimed to assess species boundaries and to reconstruct their evolutionary history. We distinguished six morphotypes based on geometric morphometric analyses of shells from 926 museum and 113 fresh specimens. These morphotypes have distinct geographic distributions across the Atlantic, Pacific and Indian oceans, and belong to three major genetic clades based on COI and 28S DNA sequence data. Using a fossil-calibrated phylogeny, we estimated that these clades separated in the Late Oligocene and Early to Middle Miocene. We found evidence for ecological differentiation among all morphotypes based on ecological niche modelling with sea surface temperature, salinity and phytoplankton biomass as primary determinants. Across all analyses, we found highly congruent patterns of differentiation suggesting species level divergences between morphotypes. However, we also found distinct morphotypes (e.g. in the Atlantic Ocean) that were ecologically, but not genetically differentiated. Given the distinct ecological and phenotypic specializations found among both described and undescribed Cuvierina taxa, they may not respond equally to future ocean changes and may not be equally sensitive to ocean acidification. Our findings support the view that ecological differentiation may be an important driving force in the speciation of zooplankton.
    BMC Evolutionary Biology 12/2015; 15(1):310. DOI:10.1186/s12862-015-0310-8
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    ABSTRACT: During the speciation process several types of isolating barriers can arise that limit gene flow between diverging populations. Studying recently isolated species can inform our understanding of how and when these barriers arise, and which barriers may be most important to limiting gene flow. Here we focus on Drosophila suboccidentalis and D. occidentalis, which are closely related mushroom-feeding species that inhabit western North America and are not known to overlap in geographic range. We investigate patterns of reproductive isolation between these species, including premating, postmating prezygotic, and postzygotic barriers to gene flow. Using flies that originate from a single population of each species, we find that the strength of premating sexual isolation between these species is asymmetric: while D. occidentalis females mate with D. suboccidentalis males at a reduced but moderate rate, D. suboccidentalis females discriminate strongly against mating with D. occidentalis males. Female hybrids will mate at high rates with males of either species, indicating that this discrimination has a recessive genetic basis. Hybrid males are accepted by females of both species. We do not find evidence for postmating prezygotic or postzygotic isolating barriers, as females use the sperm of heterospecific males and both male and female hybrids are fully fertile. Premating isolation is substantial but incomplete, and appears to be the primary form of reproductive isolation between these species. If these species do hybridize, the lack of postzygotic barriers may allow for gene flow between them. Given that these species are recently diverged and are not known to be sympatric, the level of premating isolation is relatively strong given the lack of intrinsic post-zygotic isolation. Further work is necessary to characterize the geographic and genetic variation in reproductive isolating barriers, as well as to determine the factors that drive reproductive isolation and the consequences that isolating barriers as well as geographic isolation have had on patterns of gene flow between these species.
    BMC Evolutionary Biology 12/2015; 15(1):328. DOI:10.1186/s12862-015-0328-y