Articles

PHOG-BLAST – a new generation tool for fast similarity search of protein families

The need to compare protein profiles frequently arises in various protein research areas: comparison of protein families, domain searches, resolution of orthology and paralogy. The existing fast algorithms can...

Authors: Igor V Merkeev and Andrey A Mironov

Differentiated evolutionary rates in alternative exons and the implications for splicing regulation

Alternatively spliced exons play an important role in the diversification of gene function in most metazoans and are highly regulated by conserved motifs in exons and introns. Two contradicting properties have...

Authors: Mireya Plass and Eduardo Eyras

Mitochondrial phylogeny and phylogeography of East African squeaker catfishes (Siluriformes: Synodontis)

Squeaker catfishes (Pisces, Mochokidae, Synodontis) are widely distributed throughout Africa and inhabit a biogeographic range similar to that of the exceptionally diverse cichlid fishes, including the three East...

Authors: Stephan Koblmüller, Christian Sturmbauer, Erik Verheyen, Axel Meyer and Walter Salzburger

ESTimating plant phylogeny: lessons from partitioning

While Expressed Sequence Tags (ESTs) have proven a viable and efficient way to sample genomes, particularly those for which whole-genome sequencing is impractical, phylogenetic analysis using ESTs remains diff...

Authors: Jose EB de la Torre, Mary G Egan, Manpreet S Katari, Eric D Brenner, Dennis W Stevenson, Gloria M Coruzzi and Rob DeSalle

Mitochondrial sequence data expose the putative cosmopolitan polychaete Scoloplos armiger (Annelida, Orbiniidae) as a species complex

Polychaetes assigned as Scoloplos armiger (Orbiniidae) show a cosmopolitan distribution and have been encountered in all zoogeographic regions. Sibling S. armiger-like species have been revealed by recent studies...

Authors: Christoph Bleidorn, Inken Kruse, Sylvia Albrecht and Thomas Bartolomaeus

Comparative rates of evolution in endosymbiotic nuclear genomes

The nucleomorphs associated with secondary plastids of cryptomonads and chlorarachniophytes are the sole examples of organelles with eukaryotic nuclear genomes. Although not as widespread as their prokaryotic ...

Authors: Nicola J Patron, Matthew B Rogers and Patrick J Keeling

The evolution of activity breaks in the nest cycle of annual eusocial bees: a model of delayed exponential growth

Social insects show considerable variability not only in social organisation but also in the temporal pattern of nest cycles. In annual eusocial sweat bees, nest cycles typically consist of a sequence of disti...

Authors: Oliver Mitesser, Norbert Weissel, Erhard Strohm and Hans-Joachim Poethke

Computing Ka and Ks with a consideration of unequal transitional substitutions

Approximate methods for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) among protein-coding sequences have adopted different mutation (substitution) models. In the past two decades, sev...

Authors: Zhang Zhang, Jun Li and Jun Yu

A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank

Since thermodynamic stability is a global property of proteins that has to be conserved during evolution, the selective pressure at a given site of a protein sequence depends on the amino acids present at othe...

Authors: Ugo Bastolla, Markus Porto, H Eduardo Roman and Michele Vendruscolo

The distribution and evolutionary history of the PRP8 intein

We recently described a mini-intein in the PRP8 gene of a strain of the basidiomycete Cryptococcus neoformans, an important fungal pathogen of humans. This was the second described intein in the nuclear genome of...

Authors: Margaret I Butler, Jeremy Gray, Timothy JD Goodwin and Russell TM Poulter

Core set approach to reduce uncertainty of gene trees

A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because intraspecific sequences are more cl...

Authors: Takahisa Okabayashi, Yasuhiro Kitazoe, Hirohisa Kishino, Teruaki Watabe, Noriaki Nakajima, Yoshiyasu Okuhara, Samantha O'Loughlin and Catherine Walton

JMATING: a software for the analysis of sexual selection and sexual isolation effects from mating frequency data

Many different sexual isolation and sexual selection statistics have been proposed in the past. However, there is no available software that implements all these statistical estimators and their corresponding ...

Authors: Antonio Carvajal-Rodriguez and Emilio Rolan-Alvarez

Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron

Ribosomal DNA of several species of the free-living Naegleria amoeba harbors an optional group I intron within the nuclear small subunit ribosomal RNA gene. The intron (Nae.S516) has a complex organization of two...

Authors: Odd-Gunnar Wikmark, Christer Einvik, Johan F De Jonckheere and Steinar D Johansen

Differential gene transfers and gene duplications in primary and secondary endosymbioses

Most genes introduced into phototrophic eukaryotes during the process of endosymbiosis are either lost or relocated into the host nuclear genome. In contrast, gro EL homologues are found in different genome compa...

Authors: Stefan Zauner, Peter Lockhart, Bettina Stoebe-Maier, Paul Gilson, Geoffrey I McFadden and Uwe G Maier

The complete chloroplast genome sequence of the chlorophycean green alga Scenedesmus obliquus reveals a compact gene organization and a biased distribution of genes on the two DNA strands

The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. While the basal position of the Prasinophyceae is well established, the divergence order of the Ulvophyceae, Tr...

Authors: Jean-Charles de Cambiaire, Christian Otis, Claude Lemieux and Monique Turmel

A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects

A full understanding of the patterns and processes of biological diversification requires the dating of evolutionary events, yet the fossil record is inadequate for most lineages under study. Alternatively, a ...

Authors: Kathleen M Kay, Justen B Whittall and Scott A Hodges

Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes)

Anther smuts of the basidiomycetous genus Microbotryum on Caryophyllaceae are important model organisms for many biological disciplines. Members of Microbotryum are most commonly found parasitizing the anthers of...

Authors: Martin Kemler, Markus Göker, Franz Oberwinkler and Dominik Begerow

A high density of ancient spliceosomal introns in oxymonad excavates

Certain eukaryotic genomes, such as those of the amitochondriate parasites Giardia and Trichomonas, have very low intron densities, so low that canonical spliceosomal introns have only recently been discovered th...

Authors: Claudio H Slamovits and Patrick J Keeling

Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

Thrombospondins (TSPs) are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tis...

Authors: Patrick McKenzie, Seetharam C Chadalavada, Justin Bohrer and Josephine C Adams

Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids

The Vitaceae (grape) is an economically important family of angiosperms whose phylogenetic placement is currently unresolved. Recent phylogenetic analyses based on one to several genes have suggested several a...

Authors: Robert K Jansen, Charalambos Kaittanis, Christopher Saski, Seung-Bum Lee, Jeffrey Tomkins, Andrew J Alverson and Henry Daniell

A phylogenomic profile of globins

Globins occur in all three kingdoms of life: they can be classified into single-domain globins and chimeric globins. The latter comprise the flavohemoglobins with a C-terminal FAD-binding domain and the gene-r...

Authors: Serge N Vinogradov, David Hoogewijs, Xavier Bailly, Raúl Arredondo-Peter, Julian Gough, Sylvia Dewilde, Luc Moens and Jacques R Vanfleteren

A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage

The evolution of type II MADS box genes has been extensively studied in angiosperms. One of the best-understood subfamilies is that of the Arabidopsis gene APETALA3 (AP3). Previous work has demonstrated that the ...

Authors: Elena M Kramer, Huei-Jiun Su, Cheng-Chiang Wu and Jer-Ming Hu

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution m...

Authors: Thomas M Keane, Christopher J Creevey, Melissa M Pentony, Thomas J Naughton and James O Mclnerney

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1

Genetic diversity of the human immunodeficiency virus type 1 (HIV-1) population within an individual is lost during transmission to a new host. The demography of transmission is an important determinant of evo...

Authors: Charles TT Edwards, Edward C Holmes, Daniel J Wilson, Raphael P Viscidi, Elaine J Abrams, Rodney E Phillips and Alexei J Drummond

Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes

Lateral gene transfer (LGT) in eukaryotes from non-organellar sources is a controversial subject in need of further study. Here we present gene distribution and phylogenetic analyses of the genes encoding the ...

Authors: Jan O Andersson, Robert P Hirt, Peter G Foster and Andrew J Roger

Multiple lineage specific expansions within the guanylyl cyclase gene family

Guanylyl cyclases (GCs) are responsible for the production of the secondary messenger cyclic guanosine monophosphate, which plays important roles in a variety of physiological responses such as vision, olfacti...

Authors: David A Fitzpatrick, Damien M O'Halloran and Ann M Burnell

Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics

The exchange of nucleotides at synonymous sites in a gene encoding a protein is believed to have little impact on the fitness of a host organism. This should be especially true for synonymous transitions, wher...

Authors: Tang Li, Stephen G Chamberlin, M Daniel Caraco, David A Liberles, Eric A Gaucher and Steven A Benner

No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation

The mitochondrial DNA (mtDNA) of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea...

Authors: Michael E Hellberg

Multi-character perspectives on the evolution of intraspecific differentiation in a neotropical hylid frog

Multi-character empirical studies are important contributions to our understanding of the process of speciation. The relatively conserved morphology of, and importance of the mate recognition system in anurans...

Authors: Stephen C Lougheed, James D Austin, James P Bogart, Peter T Boag and Andrew A Chek

Paths of lateral gene transfer of lysyl-aminoacyl-tRNA synthetases with a unique evolutionary transition stage of prokaryotes coding for class I and II varieties by the same organisms

While the premise that lateral gene transfer (LGT) is a dominant evolutionary force is still in considerable dispute, the case for widespread LGT in the family of aminoacyl-tRNA synthetases (aaRS) is no longer...

Authors: Shaul Shaul, Ruth Nussinov and Tal Pupko

Evolution of the P-type II ATPase gene family in the fungi and presence of structural genomic changes among isolates of Glomus intraradices

The P-type II ATPase gene family encodes proteins with an important role in adaptation of the cell to variation in external K⁺, Ca²⁺ and Na²⁺ concentrations. The presence of P-type II gene subfamilies that are sp...

Authors: Nicolas Corradi and Ian R Sanders

Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

Papillomaviruses (PVs) infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the ...

Authors: Santiago García-Vallvé, José R Iglesias-Rozas, Ángel Alonso and Ignacio G Bravo

Immune function and parasite resistance in male and polymorphic female Coenagrion puella

Colour polymorphisms are widespread and one of the prime examples is the colour polymorphism in female coenagrionid damselflies: one female morph resembles the male colour (andromorph) while one, or more, fema...

Authors: Gerrit Joop, Andreas Mitschke, Jens Rolff and Michael T Siva-Jothy

The evolution of the histone methyltransferase gene Su(var)3-9 in metazoans includes a fusion with and a re-fission from a functionally unrelated gene

In eukaryotes, histone H3 lysine 9 (H3K9) methylation is a common mechanism involved in gene silencing and the establishment of heterochromatin. The loci of the major heterochromatic H3K9 methyltransferase Su(...

Authors: Veiko Krauss, Anne Fassl, Petra Fiebig, Ina Patties and Heinz Sass

Molecular phylogeny and taxonomic revision of the sportive lemurs (Lepilemur, Primates)

The number of species within the Malagasy genus Lepilemur and their phylogenetic relationships is disputed and controversial. In order to establish their evolutionary relationships, a comparative cytogenetic and ...

Authors: Nicole Andriaholinirina, Jean-Luc Fausser, Christian Roos, Dietmar Zinner, Urs Thalmann, Clément Rabarivola, Iary Ravoarimanana, Jörg U Ganzhorn, Bernhard Meier, Roland Hilgartner, Lutz Walter, Alphonse Zaramody, Christoph Langer, Thomas Hahn, Elke Zimmermann, Ute Radespiel…

Tracking the evolution of alternatively spliced exons within the Dscam family

The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17), potent...

Authors: Mack E Crayton III, Bradford C Powell, Todd J Vision and Morgan C Giddings

Phylogenetic identification of lateral genetic transfer events

Lateral genetic transfer can lead to disagreements among phylogenetic trees comprising sequences from the same set of taxa. Where topological discordance is thought to have arisen through genetic transfer even...

Authors: Robert G Beiko and Nicholas Hamilton

Rate of promoter class turn-over in yeast evolution

Phylogenetic conservation at the DNA level is routinely used as evidence of molecular function, under the assumption that locations and sequences of functional DNA segments remain invariant in evolution. In pa...

Authors: Georgii A Bazykin and Alexey S Kondrashov

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach

Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a larg...

Authors: Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B Stern and Claude W dePamphilis

Evolution of the NANOG pseudogene family in the human and chimpanzee genomes

The NANOG gene is expressed in mammalian embryonic stem cells where it maintains cellular pluripotency. An unusually large family of pseudogenes arose from it with one unprocessed and ten processed pseudogenes in...

Authors: Daniel J Fairbanks and Peter J Maughan

The complete mitochondrial genome of the enigmatic bigheaded turtle (Platysternon): description of unusual genomic features and the reconciliation of phylogenetic hypotheses based on mitochondrial and nuclear DNA

The big-headed turtle (Platysternon megacephalum) from east Asia is the sole living representative of a poorly-studied turtle lineage (Platysternidae). It has no close living relatives, and its phylogenetic posit...

Authors: James F Parham, Chris R Feldman and Jeffrey L Boore

Polyphyly of the hawk genera Leucopternis and Buteogallus (Aves, Accipitridae): multiple habitat shifts during the Neotropical buteonine diversification

The family Accipitridae (hawks, eagles and Old World vultures) represents a large radiation of predatory birds with an almost global distribution, although most species of this family occur in the Neotropics. ...

Authors: Fabio S Raposo do Amaral, Matthew J Miller, Luís Fábio Silveira, Eldredge Bermingham and Anita Wajntal

Erratum to: Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages

Authors: Revathi Rajkumar, Jheelam Banerjee, Hima Bindu Gunturi, R Trivedi and VK Kashyap

Stable evolutionary signal in a Yeast protein interaction network

The recently emerged protein interaction network paradigm can provide novel and important insights into the innerworkings of a cell. Yet, the heavy burden of both false positive and false negative protein-prot...

Authors: Stefan Wuchty, Albert-Laszlo Barabási and Michael T Ferdig

Genome-wide acceleration of protein evolution in flies (Diptera)

The rate of molecular evolution varies widely between proteins, both within and among lineages. To what extent is this variation influenced by genome-wide, lineage-specific effects? To answer this question, we...

Authors: Joël Savard, Diethard Tautz and Martin J Lercher

Molecular phylogenetics and comparative modeling of HEN1, a methyltransferase involved in plant microRNA biogenesis

Recently, HEN1 protein from Arabidopsis thaliana was discovered as an essential enzyme in plant microRNA (miRNA) biogenesis. HEN1 transfers a methyl group from S-adenosylmethionine to the 2'-OH or 3'-OH group of ...

Authors: Karolina L Tkaczuk, Agnieszka Obarska and Janusz M Bujnicki

Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of...

Authors: Etienne GJ Danchin, Philippe Gouret and Pierre Pontarotti

Diversity begets diversity: host expansions and the diversification of plant-feeding insects

Plant-feeding insects make up a large part of earth's total biodiversity. While it has been shown that herbivory has repeatedly led to increased diversification rates in insects, there has been no compelling e...

Authors: Niklas Janz, Sören Nylin and Niklas Wahlberg

Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio

Integrons are genetic elements capable of the acquisition, rearrangement and expression of genes contained in gene cassettes. Gene cassettes generally consist of a promoterless gene associated with a recombina...

Authors: Yan Boucher, Camilla L Nesbø, Michael J Joss, Andrew Robinson, Bridget C Mabbutt, Michael R Gillings, W Ford Doolittle and HW Stokes

A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear th...

Authors: James W Wilson and Cheryl A Nickerson