Articles

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

Long-term experimental evolution in Escherichia coli. X. Quantifying the fundamental and realized niche

Twelve populations of the bacterium, Escherichia coli, adapted to a simple, glucose-limited, laboratory environment over 10,000 generations. As a consequence, these populations tended to lose functionality on alt...

Authors: Vaughn S Cooper

Modelling developmental instability as the joint action of noise and stability: a Bayesian approach

Fluctuating asymmetry is assumed to measure individual and population level developmental stability. The latter may in turn show an association with stress, which can be observed through asymmetry-stress corre...

Authors: Stefan Van Dongen and Luc Lens

Craniodental variation among Macaques (Macaca), nonhuman primates

In terms of structure and function, the skull is one of the most complicated organs in the body. It is also one of the most important parts in terms of developmental and evolutionary origins. This complexity m...

Authors: Ruliang Pan and Charles E Oxnard

The diversity of microorganisms associated with Acromyrmex leafcutter ants

Molecular biological techniques are dramatically changing our view of microbial diversity in almost any environment that has so far been investigated. This study presents a systematic survey of the microbial d...

Authors: Steven Van Borm, Johan Billen and Jacobus J Boomsma

Structural, functional, and evolutionary analysis of moeZ, a gene encoding an enzyme required for the synthesis of the Pseudomonas metabolite, pyridine-2,6-bis(thiocarboxylic acid)

Pyridine-2,6-bis(thiocarboxylic acid) (pdtc) is a small secreted metabolite that has a high affinity for transition metals, increases iron uptake efficiency by 20% in Pseudomonas stutzeri, has the ability to redu...

Authors: Marc S Cortese, Allan B Caplan and Ronald L Crawford

The evolutionary position of nematodes

The complete genomes of three animals have been sequenced by global research efforts: a nematode worm (Caenorhabditis elegans), an insect (Drosophila melanogaster), and a vertebrate (Homo sapiens). Remarkably, th...

Authors: Jaime E Blair, Kazuho Ikeo, Takashi Gojobori and S Blair Hedges

Aminoadipate reductase gene: a new fungal-specific gene for comparative evolutionary analyses

In fungi, aminoadipate reductase converts 2-aminoadipate to 2-aminoadipate 6-semialdehyde. However, other organisms have no homologue to the aminoadipate reductase gene and this pathway appears to be restricte...

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

Evidence for the adaptive significance of an LTR retrotransposon sequence in a Drosophila heterochromatic gene

The potential adaptive significance of transposable elements (TEs) to the host genomes in which they reside is a topic that has been hotly debated by molecular evolutionists for more than two decades. Recent g...

Authors: Andrea M McCollum, Eric W Ganko, Paula A Barrass, Jose M Rodriguez and John F McDonald

Phylogenetic relationships between Hapalemur species and subspecies based on mitochondrial DNA sequences

Phylogenetic relationships of the genus Hapalemur remains controversial, particularly within the Hapalemur griseus species group. In order to obtain more information on the taxonomic status within this genus, and...

Authors: Jean-Luc Fausser, Prosper Prosper, Giuseppe Donati, Jean-Baptiste Ramanamanjato and Yves Rumpler

Sequence permutations in the molecular evolution of DNA methyltransferases

DNA methyltransferases (MTases), unlike MTases acting on other substrates, exhibit sequence permutation. Based on the sequential order of the cofactor-binding subdomain, the catalytic subdomain, and the target...

Authors: Janusz M Bujnicki

Evidence for an evolutionarily conserved interaction between cell wall biosynthesis and flowering in maize and sorghum

Factors that affect flowering vary among different plant species, and in the grasses in particular the exact mechanism behind this transition is not fully understood. The brown midrib (bm) mutants of maize (Zea m...

Authors: Wilfred Vermerris, Karen J Thompson, Lauren M McIntyre and John D Axtell

Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp

The cosmopolitan moon jelly Aurelia is characterized by high degrees of morphological and ecological plasticity, and subsequently by an unclear taxonomic status. The latter has been revised repeatedly over the la...

Authors: Werner Schroth, Gerhard Jarms, Bruno Streit and Bernd Schierwater

A family of putative K_ir potassium channels in prokaryotes

Prior to this report, members of the inward rectifier family, or Kir, have been found only in eukaryotes. Like most K⁺ channels, the pore-forming part of the protein is formed by four identical, or closely relate...

Authors: Stewart R Durell and H Robert Guy

High correlation between the turnover of nucleotides under mutational pressure and the DNA composition

Any DNA sequence is a result of compromise between the selection and mutation pressures exerted on it during evolution. It is difficult to estimate the relative influence of each of these pressures on the rate...

Authors: Maria Kowalczuk, Pawel Mackiewicz, Dorota Mackiewicz, Aleksandra Nowicka, Malgorzata Dudkiewicz, Miroslaw R Dudek and Stanislaw Cebrat

A model combining cell physiology and population genetics to explain Escherichia coli laboratory evolution

Laboratory experiments under controlled conditions during thousands of generations are useful tools to assess the processes underlying bacterial evolution. As a result of these experiments, the way in which th...

Authors: Martín Graña and Luis Acerenza

Concordance between genetic relatedness and phenotypic similarities of Trichomonas vaginalis strains

Despite the medical importance of trichomoniasis, little is known about the genetic relatedness of Trichomonas vaginalis strains with similar biological characteristics. Furthermore, the distribution of endobiont...

Authors: Vladimír Hampl, Štěpánka Vaňáčová, Jaroslav Kulda and Jaroslav Flegr

Wolbachia: Evolutionary novelty in a rickettsial bacteria

Although closely related, the alpha-proteobacteria Wolbachia and the Rickettsiacae (Rickettsia and Ehrlichia), employ different evolutionary life history strategies. Wolbachia are obligate endocellular symbionts ...

Authors: Cort L Anderson and Timothy L Karr

PCR primers for an aldolase-B intron in acanthopterygian fishes

Nuclear DNA sequences provide genetic information that complements studies using mitochondrial DNA. Some 'universal' primer sets have been developed that target introns within protein-coding loci, but many sim...

Authors: Joseph M Quattro, William J Jones and Kenneth J Oswald

Genome trees constructed using five different approaches suggest new major bacterial clades

The availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of co...

Authors: Yuri I Wolf, Igor B Rogozin, Nick V Grishin, Roman L Tatusov and Eugene V Koonin

Potential of (GATA)_n microsatellites from rice for inter- and intra-specific variability studies

The microsatellite, (GATA)_n has been frequently used for DNA fingerprinting. However, very few attempts have been made to analyze (GATA)_n-containing loci in rice.

Authors: Armaity P Davierwala, Wusirika Ramakrishna, Venkat Chowdari, Prabhakar K Ranjekar and Vidya S Gupta

Polytene chromosomes as indicators of phylogeny in several species groups of Drosophila

Polytene chromosome banding patterns have long been used by Drosophila evolutionists to infer degree of relatedness among taxa. Recently, nucleotide sequences have preempted this traditional method. We place the ...

Authors: Patrick M O'Grady, Richard H Baker, Celeste M Durando, William J Etges and Robert DeSalle

Parallel evolution of histophagy in ciliates of the genus Tetrahymena

Species of Tetrahymena were grouped into three complexes based on morphological and life history traits: the pyriformis complex of microstomatous forms; the patula complex of microstome-macrostome transformers; a...

Authors: Michaela C Strüder-Kypke, André-Denis G Wright, Cheryl A Jerome and Denis H Lynn

A genomic timescale for the origin of eukaryotes

Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are uncl...

Authors: S Blair Hedges, Hsiong Chen, Sudhir Kumar, Daniel YC Wang, Amanda S Thompson and Hidemi Watanabe