http://www.biomedcentral.com/bmcevolbiol/ The most accessed research articles published by BMC Evolutionary Biology 2009-11-06T00:00:00Z This is an RSS newsfeed from BioMed Central It is intended to be used with an RSS reader. For more information about RSS newsfeeds from BioMed Central, visit http://www.biomedcentral.com/info/about/rss/ Background: The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago. Results: To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and 2.23 nuclear genes per genus. Our analyses of mitochondrial DNA place Tarsiiformes as the sister group of Strepsirrhini. Within Haplorrhini, we find support for the primary divergence of Pitheciidae in Platyrrhini, and our results suggest a sister grouping of African and non-African colobines within Colobinae and of Cercopithecini and Papionini within Cercopthecinae. Date estimates for nodes within each family and genus are presented, with estimates for key splits including: Strepsirrhini-Haplorrhini 64 million years ago (MYA), Lemuriformes-Lorisiformes 52 MYA, Platyrrhini-Catarrhini 43 MYA and Cercopithecoidea-Hominoidea 29 MYA. Conclusion: We present an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history. Although considerable gaps remain in our knowledge of the primate phylogeny, increased data sampling, particularly from nuclear loci, will be able to provide further resolution. http://www.biomedcentral.com/1471-2148/9/259 Helen Chatterjee Simon Ho Ian Barnes Colin Groves BMC Evolutionary Biology 2009, 9:259 2009-10-27T00:00:00Z doi:10.1186/1471-2148-9-259 BMC Evolutionary Biology 1471-2148 9 259 2009-10-27T00:00:00Z XML Background: Cooperative hunting and foraging in spiders is rare and prone to cheating such that the actions of selfish individuals negatively affect the whole group. The resulting social dilemma may be mitigated by kin selection since related individuals lose indirect fitness benefits by acting selfishly. Indeed, cooperation with genetic kin reduces the disadvantages of within-group competition in the subsocial spider Stegodyphus lineatus, supporting the hypothesis that high relatedness is an important pre-adaptation in the transition to sociality in spiders. In this study we examined the consequences of group size and relatedness on cooperative feeding in the subsocial spider S. tentoriicola, a species suggested to be at the transition to permanent sociality. Results: We formed groups of 3 and 6 spiders that were either siblings or non-siblings. We found that increasing group size negatively affected feeding efficiency but that these negative effects were reduced in sib-groups. Sib groups were more likely to feed cooperatively and all group members grew more homogenously than groups of unrelated spiders. The measured differences did not translate into differential growth or mortality during the experimental period of 8 weeks. Conclusion: The combination of our results with those from previous studies indicates that the conflict between individual interests and group interests may be reduced by nepotism and that the latter promote the maintenance of the social community. http://www.biomedcentral.com/1471-2148/9/257 Jasmin Ruch Lisa Heinrich Trine Bilde Jutta Schneider BMC Evolutionary Biology 2009, 9:257 2009-10-27T00:00:00Z doi:10.1186/1471-2148-9-257 BMC Evolutionary Biology 1471-2148 9 257 2009-10-27T00:00:00Z XML Background: Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion: The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding. http://www.biomedcentral.com/1471-2148/9/258 Cristiane Thompson Ana Carolina Vicente Rangel Souza Ana Tereza Vasconcelos Tammi Vesth Nelson Alves David Ussery Tetsuya Iida Fabiano Thompson BMC Evolutionary Biology 2009, 9:258 2009-10-27T00:00:00Z doi:10.1186/1471-2148-9-258 BMC Evolutionary Biology 1471-2148 9 258 2009-10-27T00:00:00Z XML Background: The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. A large number of popular stochastic models of sequence evolution are provided and tree-based models suitable for both within- and between-species sequence data are implemented. Results: BEAST version 1.4.6 consists of 81000 lines of Java source code, 779 classes and 81 packages. It provides models for DNA and protein sequence evolution, highly parametric coalescent analysis, relaxed clock phylogenetics, non-contemporaneous sequence data, statistical alignment and a wide range of options for prior distributions. BEAST source code is object-oriented, modular in design and freely available at http://beast-mcmc.googlecode.com/ under the GNU LGPL license. Conclusion: BEAST is a powerful and flexible evolutionary analysis package for molecular sequence variation. It also provides a resource for the further development of new models and statistical methods of evolutionary analysis. http://www.biomedcentral.com/1471-2148/7/214 Alexei Drummond Andrew Rambaut BMC Evolutionary Biology 2007, 7:214 2007-11-08T00:00:00Z doi:10.1186/1471-2148-7-214 BMC Evolutionary Biology 1471-2148 7 214 2007-11-08T00:00:00Z XML Background: The Nme family, previously known as Nm23 or NDPK, is involved in various molecular processes including tumor metastasis and some members of the family, but not all, exhibit a Nucleoside Diphosphate Kinase (NDPK) activity. Ten genes are known in humans, in which some members have been extensively studied. In non-mammalian species, the Nme protein family has received, in contrast, far less attention. The picture of the vertebrate Nme family remains thus incomplete and orthology relationships with mammalian counterparts were only partially characterized. The present study therefore aimed at characterizing the Nme gene repertoire in vertebrates with special interest for teleosts, and providing a comprehensive overview of the Nme gene family evolutionary history in vertebrates. Results: In the present study, we present the evolutionary history of the Nme family in vertebrates and characterize the gene family repertoire for the first time in several non-mammalian species. Our observations show that vertebrate Nme genes can be separated in two evolutionary distinct groups. Nme1, Nme2, Nme3, and Nme4 belong to Group I while vertebrate Nme5, Nme6, Nme7, Nme8, and Nme9 belong to Group II. The position of Nme10 is in contrast more debatable due to its very specific evolutionary history. The present study clearly indicates that Nme5, Nme6, Nme7, and Nme8 originate from duplication events that occurred before the chordate radiation. In contrast, Nme genes of the Group I have a very different evolutionary history as our results suggest that they all arise from a common gene present in the chordate ancestor. In addition, expression patterns of all zebrafish nme transcripts were studied in a broad range of tissues by quantitative PCR and discussed in the light of the function of their mammalian counterparts. Conclusion: This work offers an evolutionary framework that will pave the way for future studies on vertebrate Nme proteins and provides a unified vertebrate Nme nomenclature that is consistent with the nomenclature in use in mammals. Based on protein structure and expression data, we also provide new insight into molecular functions of Nme proteins among vertebrates and raise intriguing questions on the roles of Nme proteins in gonads. http://www.biomedcentral.com/1471-2148/9/256 Thomas Desvignes Pierre Pontarotti Christian Fauvel Julien Bobe BMC Evolutionary Biology 2009, 9:256 2009-10-23T00:00:00Z doi:10.1186/1471-2148-9-256 BMC Evolutionary Biology 1471-2148 9 256 2009-10-23T00:00:00Z XML Background: Protein secretion is a universal cellular process involving vesicles which bud and fuse between organelles to bring proteins to their final destination. Vesicle budding is mediated by protein coats; vesicle targeting and fusion depend on Rab GTPase, tethering factors and SNARE complexes. The Génolevures II sequencing project made available entire genome sequences of four hemiascomycetous yeasts, Yarrowia lipolytica, Debaryomyces hansenii, Kluyveromyces lactis and Candida glabrata. Y. lipolytica is a dimorphic yeast and has good capacities to secrete proteins. The translocation of nascent protein through the endoplasmic reticulum membrane was well studied in Y. lipolytica and is largely co-translational as in the mammalian protein secretion pathway. Results: We identified S. cerevisiae proteins involved in vesicular secretion and these protein sequences were used for the BLAST searches against Génolevures protein database (Y. lipolytica, C. glabrata, K. lactis and D. hansenii). These proteins are well conserved between these yeasts and Saccharomyces cerevisiae. We note several specificities of Y. lipolytica which may be related to its good protein secretion capacities and to its dimorphic aspect. An expansion of the Y. lipolytica Rab protein family was observed with autoBLAST and the Rab2- and Rab4-related members were identified with BLAST against NCBI protein database. An expansion of this family is also found in filamentous fungi and may reflect the greater complexity of the Y. lipolytica secretion pathway. The Rab4p-related protein may play a role in membrane recycling as rab4 deleted strain shows a modification of colony morphology, dimorphic transition and permeability. Similarly, we find three copies of the gene (SSO) encoding the plasma membrane SNARE protein. Quantification of the percentages of proteins with the greatest homology between S. cerevisiae, Y. lipolytica and animal homologues involved in vesicular transport shows that 40% of Y. lipolytica proteins are closer to animal ones, whereas they are only 13% in the case of S. cerevisiae. Conclusion: These results provide further support for the idea, previously noted about the endoplasmic reticulum translocation pathway, that Y. lipolytica is more representative of vesicular secretion of animals and other fungi than is S. cerevisiae. http://www.biomedcentral.com/1471-2148/7/219 Dominique Swennen Jean-Marie Beckerich BMC Evolutionary Biology 2007, 7:219 2007-11-12T00:00:00Z doi:10.1186/1471-2148-7-219 BMC Evolutionary Biology 1471-2148 7 219 2007-11-12T00:00:00Z XML Background: Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Results: Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. Conclusion: For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference. http://www.biomedcentral.com/1471-2148/9/245 Sarah Kingston Lara Adams Patricia Rosel BMC Evolutionary Biology 2009, 9:245 2009-10-07T00:00:00Z doi:10.1186/1471-2148-9-245 BMC Evolutionary Biology 1471-2148 9 245 2009-10-07T00:00:00Z XML Background: Recent phylogenetic studies have revealed that the mitochondrial genome of the angiosperm Silene noctiflora (Caryophyllaceae) has experienced a massive mutation-driven acceleration in substitution rate, placing it among the fastest evolving eukaryotic genomes ever identified. To date, it appears that other species within Silene have maintained more typical substitution rates, suggesting that the acceleration in S. noctiflora is a recent and isolated evolutionary event. This assessment, however, is based on a very limited sampling of taxa within this diverse genus. Results: We analyzed the substitution rates in 4 mitochondrial genes (atp1, atp9, cox3 and nad9) across a broad sample of 74 species within Silene and related genera in the tribe Sileneae. We found that S. noctiflora shares its history of elevated mitochondrial substitution rate with the closely related species S. turkestanica. Another section of the genus (Conoimorpha) has experienced an acceleration of comparable magnitude. The phylogenetic data remain ambiguous as to whether the accelerations in these two clades represent independent evolutionary events or a single ancestral change. Rate variation among genes was equally dramatic. Most of the genus exhibited elevated rates for atp9 such that the average tree-wide substitution rate for this gene approached the values for the fastest evolving branches in the other three genes. In addition, some species exhibited major accelerations in atp1 and/or cox3 with no correlated change in other genes. Rates of non-synonymous substitution did not increase proportionally with synonymous rates but instead remained low and relatively invariant. Conclusion: The patterns of phylogenetic divergence within Sileneae suggest enormous variability in plant mitochondrial mutation rates and reveal a complex interaction of gene and species effects. The variation in rates across genomic and phylogenetic scales raises questions about the mechanisms responsible for the evolution of mutation rates in plant mitochondrial genomes. http://www.biomedcentral.com/1471-2148/9/260 Daniel Sloan Bengt Oxelman Anja Rautenberg Douglas Taylor BMC Evolutionary Biology 2009, 9:260 2009-10-31T00:00:00Z doi:10.1186/1471-2148-9-260 BMC Evolutionary Biology 1471-2148 9 260 2009-10-31T00:00:00Z XML Background: Culex pipiens L. is the most widespread mosquito vector in temperate regions. This species consists of two forms, denoted molestus and pipiens, that exhibit important behavioural and physiological differences. The evolutionary relationships and taxonomic status of these forms remain unclear. In northern European latitudes molestus and pipiens populations occupy different habitats (underground vs. aboveground), a separation that most likely promotes genetic isolation between forms. However, the same does not hold in southern Europe where both forms occur aboveground in sympatry. In these southern habitats, the extent of hybridisation and its impact on the extent of genetic divergence between forms under sympatric conditions has not been clarified. For this purpose, we have used phenotypic and genetic data to characterise Cx. pipiens collected aboveground in Portugal. Our aims were to determine levels of genetic differentiation and the degree of hybridisation between forms occurring in sympatry, and to relate these with both evolutionary and epidemiological tenets of this biological group. Results: Autogeny and stenogamy was evaluated in the F1 progeny of 145 individual Cx. pipiens females. Bayesian clustering analysis based on the genotypes of 13 microsatellites revealed two distinct genetic clusters that were highly correlated with the alternative traits that define pipiens and molestus. Admixture analysis yielded hybrid rate estimates of 8-10%. Higher proportions of admixture were observed in pipiens individuals suggesting that more molestus genes are being introgressed into the pipiens form than the opposite. Conclusion: Both physiological/behavioural and genetic data provide evidence for the sympatric occurrence of molestus and pipiens forms of Cx. pipiens in the study area. In spite of the significant genetic differentiation between forms, hybridisation occurs at considerable levels. The observed pattern of asymmetric introgression probably relates to the different mating strategies adopted by each form. Furthermore, the differential introgression of molestus genes into the pipiens form may induce a more opportunistic biting behaviour in the latter thus potentiating its capacity to act as a bridge-vector for the transmission of arboviral infections. http://www.biomedcentral.com/1471-2148/9/262 Bruno Gomes Carla Sousa Maria Novo Ferdinando Freitas Ricardo Alves Ana Corte-Real Patricia Salgueiro Martin Donnelly Antonio Almeida Joao Pinto BMC Evolutionary Biology 2009, 9:262 2009-11-06T00:00:00Z doi:10.1186/1471-2148-9-262 BMC Evolutionary Biology 1471-2148 9 262 2009-11-06T00:00:00Z XML Background: Mutualisms are inherently conflictual as one partner always benefits from reducing the costs imposed by the other. Despite the widespread recognition that mutualisms are essentially reciprocal exploitation, there are few documented examples of traits that limit the costs of mutualism. In plant/seed-eating pollinator interactions the only mechanisms reported so far are those specific to one particular system, such as the selective abortion of over-exploited fruits. Results: This study shows that plant chemical defence against developing larvae constitutes another partner sanction mechanism in nursery mutualisms. It documents the chemical defence used by globeflower Trollius europaeus L. (Ranunculaceae) against the seed-eating larvae of six pollinating species of the genus Chiastocheta Pokorny (Anthomyiidae). The correlative field study carried out shows that the severity of damage caused by Chiastocheta larvae to globeflower fruits is linked to the accumulation in the carpel walls of a C-glycosyl-flavone (adonivernith), which reduces the larval seed predation ability per damaged carpel. The different Chiastocheta species do not exploit the fruit in the same way and their interaction with the plant chemical defence is variable, both in terms of induction intensity and larval sensitivity to adonivernith. Conclusion: Adonivernith accumulation and larval predation intensity appear to be both the reciprocal cause and effect. Adonivernith not only constitutes an effective chemical means of partner control, but may also play a key role in the sympatric diversification of the Chiastocheta genus. http://www.biomedcentral.com/1471-2148/9/261 Sebastien Ibanez Christiane Gallet Fanny Dommanget Laurence Despres BMC Evolutionary Biology 2009, 9:261 2009-11-03T00:00:00Z doi:10.1186/1471-2148-9-261 BMC Evolutionary Biology 1471-2148 9 261 2009-11-03T00:00:00Z XML