Articles

Structure-function evolution of the Transforming acidic coiled coil genes revealed by analysis of phylogenetically diverse organisms

Examination of ancient gene families can provide an insight into how the evolution of gene structure can relate to function. Functional homologs of the evolutionarily conserved transforming acidic coiled coil (TA...

Authors: Ivan H Still, Ananthalakshmy K Vettaikkorumakankauv, Anthony DiMatteo and Ping Liang

Section-level relationships of North American Agalinis (Orobanchaceae) based on DNA sequence analysis of three chloroplast gene regions

The North American Agalinis are representatives of a taxonomically difficult group that has been subject to extensive taxonomic revision from species level through higher sub-generic designations (e.g., subsectio...

Authors: Maile C Neel and Michael P Cummings

Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response

A response to Fraser HB, Hirsh AE: Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol Biol 2004, 4: 13

Authors: Jesse D Bloom and Christoph Adami

Evolutionary rate depends on number of protein-protein interactions independently of gene expression level

Whether or not a protein's number of physical interactions with other proteins plays a role in determining its rate of evolution has been a contentious issue. A recent analysis suggested that the observed corr...

Authors: Hunter B Fraser and Aaron E Hirsh

Adaptation of a South American malaria vector to laboratory colonization suggests faster-male evolution for mating ability

Anopheles (Nyssorhynchus) albitarsis (Diptera: Culicidae) is one of the very few South American mosquito vectors of malaria successfully colonized in the laboratory. These vectors are very hard to breed because t...

Authors: José BP Lima, Denise Valle and Alexandre A Peixoto

Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans

Comparative genomic data among organisms allow the reconstruction of their phylogenies and evolutionary time scales. Molecular timings have been recently used to suggest that environmental global change have s...

Authors: Frédéric Delsuc, Sergio F Vizcaíno and Emmanuel JP Douzery

A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry

Plant natriuretic peptides (PNPs) are systemically mobile molecules that regulate homeostasis at nanomolar concentrations. PNPs are up-regulated under conditions of osmotic stress and PNP-dependent processes i...

Authors: Victoria Nembaware, Cathal Seoighe, Muhammed Sayed and Chris Gehring

Upstream plasticity and downstream robustness in evolution of molecular networks

Gene duplication followed by the functional divergence of the resulting pair of paralogous proteins is a major force shaping molecular networks in living organisms. Recent species-wide data for protein-protein...

Authors: Sergei Maslov, Kim Sneppen, Kasper Astrup Eriksen and Koon-Kiu Yan

The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae) have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have general...

Authors: Elisabeth Arévalo, Yong Zhu, James M Carpenter and Joan E Strassmann

The iron-sulfur cluster assembly genes iscS and iscU of Entamoeba histolytica were acquired by horizontal gene transfer

Iron-sulfur (FeS) proteins are present in all living organisms and play important roles in electron transport and metalloenzyme catalysis. The maturation of FeS proteins in eukaryotes is an essential function ...

Authors: Mark van der Giezen, Siân Cox and Jorge Tovar

Evolutionary and functional relationships within the DJ1 superfamily

Inferences about protein function are often made based on sequence homology to other gene products of known activities. This approach is valuable for small families of conserved proteins but can be difficult t...

Authors: Sourav Bandyopadhyay and Mark R Cookson

Acetylcholinesterase alterations reveal the fitness cost of mutations conferring insecticide resistance

Insecticide resistance is now common in insects due to the frequent use of chemicals to control them, which provides a useful tool to study the adaptation of eukaryotic genome to new environments. Although num...

Authors: Ming An Shi, Andrée Lougarre, Carole Alies, Isabelle Frémaux, Zhen Hua Tang, Jure Stojan and Didier Fournier

Mutations of acetylcholinesterase which confer insecticide resistance in Drosophila melanogaster populations

Organophosphate and carbamate insecticides irreversibly inhibit acetylcholinesterase causing death of insects. Resistance-modified acetylcholinesterases(AChEs) have been described in many insect species and se...

Authors: Philippe Menozzi, Ming An Shi, Andrée Lougarre, Zhen Hua Tang and Didier Fournier

A scale invariant clustering of genes on human chromosome 7

Vertebrate genes often appear to cluster within the background of nontranscribed genomic DNA. Here an analysis of the physical distribution of gene structures on human chromosome 7 was performed to confirm the...

Authors: Wayne S Kendal

A molecular timescale of eukaryote evolution and the rise of complex multicellular life

The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated ...

Authors: S Blair Hedges, Jaime E Blair, Maria L Venturi and Jason L Shoe

Direct selection on male attractiveness and female preference fails to produce a response

Theoretical studies suggest that direct and indirect selection have the potential to cause substantial evolutionary change in female mate choice. Similarly, sexual selection is considered a strong force in the...

Authors: Matthew Hall, Anna K Lindholm and Robert Brooks

The tyranny of adenosine recognition among RNA aptamers to coenzyme A

Understanding the diversity of interactions between RNA aptamers and nucleotide cofactors promises both to facilitate the design of new RNA enzymes that utilize these cofactors and to constrain models of RNA W...

Authors: Dayal Saran, Joseph Frank and Donald H Burke

Automated measurement of Drosophila wings

Many studies in evolutionary biology and genetics are limited by the rate at which phenotypic information can be acquired. The wings of Drosophila species are a favorable target for automated analysis because ...

Authors: David Houle, Jason Mezey, Paul Galpern and Ashley Carter

Evolution of phage with chemically ambiguous proteomes

The widespread introduction of amino acid substitutions into organismal proteomes has occurred during natural evolution, but has been difficult to achieve by directed evolution. The adaptation of the translati...

Authors: Jamie M Bacher, James J Bull and Andrew D Ellington

Phylogeography of competing sexual and parthenogenetic forms of a freshwater flatworm: patterns and explanations

Models of the maintenance of sex predict that one reproductive strategy, sexual or parthenogenetic, should outcompete the other. Distribution patterns may reflect the outcome of this competition as well as the...

Authors: Norbert Pongratz, Martin Storhas, Salvador Carranza and Nicolaas K Michiels

Analysis of disruptive selection in subdivided populations

Analytical methods have been proposed to determine whether there are evolutionarily stable strategies (ESS) for a trait of ecological significance, or whether there is disruptive selection in a population appr...

Authors: Émile Ajar

Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein–protein interactions data sets

Several studies have suggested that proteins that interact with more partners evolve more slowly. The strength and validity of this association has been called into question. Here we investigate how biases in ...

Authors: Jesse D Bloom and Christoph Adami

Evolutionary experimentation through hybridization under laboratory condition in Drosophila: Evidence for Recombinational Speciation

Drosophila nasuta nasuta (2n = 8) and Drosophila nasuta albomicans (2n = 6) are a pair of sibling allopatric chromosomal cross-fertile races of the nasuta subgroup of immigrans species group of Drosophila. Interr...

Authors: Ballagere P Harini and Nallur B Ramachandra

Position specific variation in the rate of evolution in transcription factor binding sites

The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational metho...

Authors: Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S Lander and Michael B Eisen

Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase

The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance a...

Authors: Colin R Jackson and Sandra L Dugas

Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families

Dof proteins are a family of plant-specific transcription factors that contain a particular class of zinc-finger DNA-binding domain. Members of this family have been found to play diverse roles in gene regulat...

Authors: Diego Lijavetzky, Pilar Carbonero and Jesús Vicente-Carbajosa

Inter-familial relationships of the shorebirds (Aves: Charadriiformes) based on nuclear DNA sequence data

Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have ...

Authors: Per GP Ericson, Ida Envall, Martin Irestedt and Janette A Norman

Theory of genomic imprinting conflict in social insects

Genomic imprinting refers to the differential expression of genes inherited from the mother and father (matrigenes and patrigenes). The kinship theory of genomic imprinting treats parent-specific gene expressi...

Authors: David C Queller

Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes

Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replac...

Authors: Jan O Andersson and Andrew J Roger

Sexual selection on land snail shell ornamentation: a hypothesis that may explain shell diversity

Many groups of land snails show great interspecific diversity in shell ornamentation, which may include spines on the shell and flanges on the aperture. Such structures have been explained as camouflage or def...

Authors: Menno Schilthuizen

Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light

A key event in the origin of life on this planet has been formation of self-replicating RNA-type molecules, which were complex enough to undergo a Darwinian-type evolution (origin of the "RNA world"). However,...

Authors: Armen Y Mulkidjanian, Dmitry A Cherepanov and Michael Y Galperin

A simple dependence between protein evolution rate and the number of protein-protein interactions

It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions a protein has correlates negatively with their rates of evolution. However, the generality of ...

Authors: Hunter B Fraser, Dennis P Wall and Aaron E Hirsh

Shape differences rather than size differences between castes in the Neotropical swarm-founding wasp Metapolybia docilis (Hymenoptera: Vespidae, Epiponini)

Swarm-founding epiponine wasps are an intriguing group of social insects in which colonies are polygynic (several queens share reproduction) and differentiation between castes is often not obvious. However, ca...

Authors: Mário V Baio, Fernando B Noll and Ronaldo Zucchi

Molecular evolution of adenylating domain of aminoadipate reductase

Aminoadipate reductase (Lys2) is a fungal-specific protein. This enzyme contains an adenylating domain. A similar primary structure can be found in some bacterial antibiotic/peptide synthetases. In this study,...

Authors: Kwang-Deuk An, Hiromi Nishida, Yoshiharu Miura and Akira Yokota

Evidence for survival of Pleistocene climatic changes in Northern refugia by the land snail Trochoidea geyeri (Soós 1926) (Helicellinae, Stylommatophora)

The study of organisms with restricted dispersal abilities and presence in the fossil record is particularly adequate to understand the impact of climate changes on the distribution and genetic structure of sp...

Authors: Markus Pfenninger, David Posada and Frédéric Magnin

The exon context and distribution of Euascomycetes rRNA spliceosomal introns

We have studied spliceosomal introns in the ribosomal (r)RNA of fungi to discover the forces that guide their insertion and fixation.

Authors: Debashish Bhattacharya, Dawn Simon, Jian Huang, Jamie J Cannone and Robin R Gutell

Sexual selection, germline mutation rate and sperm competition

An important component of sexual selection arises because females obtain viability benefits for their offspring from their mate choice. Females choosing extra-pair fertilization generally favor males with exag...

Authors: AP Møller and JJ Cuervo

Erratum to: No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

Authors: I King Jordan, Yuri I Wolf and Eugene V Koonin

The evolution of Runx genes I. A comparative study of sequences from phylogenetically diverse model organisms

Runx genes encode proteins defined by the highly conserved Runt DNA-binding domain. Studies of Runx genes and proteins in model organisms indicate that they are key transcriptional regulators of animal develop...

Authors: Jessica Rennert, James A Coffman, Arcady R Mushegian and Anthony J Robertson

Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding

The rate at which fitness declines as an organism's genome accumulates random mutations is an important variable in several evolutionary theories. At an intuitive level, it might seem natural that random mutat...

Authors: Claus O Wilke, Richard E Lenski and Christoph Adami

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Comparative analysis of sequenced genomes reveals numerous instances of apparent horizontal gene transfer (HGT), at least in prokaryotes, and indicates that lineage-specific gene loss might have been even more...

Authors: Boris G Mirkin, Trevor I Fenner, Michael Y Galperin and Eugene V Koonin

No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

It has been suggested that rates of protein evolution are influenced, to a great extent, by the proportion of amino acid residues that are directly involved in protein function. In agreement with this hypothes...

Authors: I King Jordan, Yuri I Wolf and Eugene V Koonin

The relationship of protein conservation and sequence length

In general, the length of a protein sequence is determined by its function and the wide variance in the lengths of an organism's proteins reflects the diversity of specific functional roles for these proteins....

Authors: David J Lipman, Alexander Souvorov, Eugene V Koonin, Anna R Panchenko and Tatiana A Tatusova

Long-term experimental evolution in Escherichia coli. XI. Rejection of non-transitive interactions as cause of declining rate of adaptation

Experimental populations of Escherichia coli have evolved for 20,000 generations in a uniform environment. Their rate of improvement, as measured in competitions with the ancestor in that environment, has decline...

Authors: J Arjan GM de Visser and Richard E Lenski

Birth and death of protein domains: A simple model of evolution explains power law behavior

Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connect...

Authors: Georgy P Karev, Yuri I Wolf, Andrey Y Rzhetsky, Faina S Berezovskaya and Eugene V Koonin

Molecular phylogeny of Subtribe Artemisiinae (Asteraceae), including Artemisia and its allied and segregate genera

Subtribe Artemisiinae of Tribe Anthemideae (Asteraceae) is composed of 18 largely Asian genera that include the sagebrushes and mugworts. The subtribe includes the large cosmopolitan, wind-pollinated genus Artemi...

Authors: Linda E Watson, Paul L Bates, Timothy M Evans, Matthew M Unwin and James R Estes

Little qualitative RNA misexpression in sterile male F₁ hybrids of Drosophila pseudoobscura and D. persimilis

Although the genetics of hybrid sterility has been the subject of evolutionary studies for over sixty years, no one has shown the reason(s) why alleles that operate normally within species fail to function in ...

Authors: Jane Reiland and Mohamed AF Noor

Individual variation evades the Prisoner's Dilemma

The Prisoner's Dilemma (PD) is a widely used paradigm to study cooperation in evolutionary biology, as well as in fields as diverse as moral philosophy, sociology, economics and politics. Players are typically...

Authors: Dominic DP Johnson, Pavel Stopka and Josh Bell

Carbon and nitrogen substrate utilization by archival Salmonella typhimurium LT2 cells

A collection of over 20,000 Salmonella typhimurium LT2 mutants, sealed for four decades in agar stabs, is a unique resource for study of genetic and evolutionary changes. Previously, we reported extensive diversi...

Authors: Breca S Tracy, Kelly K Edwards and Abraham Eisenstark

Phylogenetic relationships and taxonomic position of Chlorella-like isolates from low pH environments (pH < 3.0)

Little is known about phytoplankton communities inhabiting low pH environments such as volcanic and geothermal sites or acidic waters. Only specialised organisms are able to tolerate such extreme conditions. T...

Authors: Volker AR Huss, Claudia Ciniglia, Paola Cennamo, Salvatore Cozzolino, Gabriele Pinto and Antonino Pollio