Molecular Biology and Evolution
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Lineage-Specific Adaptive Evolution of the Centromeric Protein CENH3 in Diploid and Allotetraploid Oryza Species
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Centromeres in eukaryotic species are defined by the presence of a centromere-specific histone H3 variant, CENH3. CENH3 plays a key role in recruiting other centromeric proteins; thus, it is the central component in kinetochore formation and centromere function. The CENH3 proteins in several plant and animal species were found to be under positive selection, which was hypothesized to respond to the rapid changing of the repetitive DNA sequences associated with the centromeres. Here, we report the expression and evolution of the CenH3 genes in two allotetraploid rice species as well as their representative diploid progenito...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Hirsch, C. D., Wu, Y., Yan, H., Jiang, J. Tags: Research Articles Source Type: journals
Evolutionary Trajectories of Primate Genes Involved in HIV PathogenesisEmail this article to a colleague.
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The current availability of five complete genomes of different primate species allows the analysis of genetic divergence over the last 40 million years of evolution. We hypothesized that the interspecies differences observed in susceptibility to HIV-1 would be influenced by the long-range selective pressures on host genes associated with HIV-1 pathogenesis. We established a list of human genes (n = 140) proposed to be involved in HIV-1 biology and pathogenesis and a control set of 100 random genes. We retrieved the orthologous genes from the genome of humans and of four nonhuman primates (Pan troglodytes, Pongo pygmaeus ab...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Ortiz, M., Guex, N., Patin, E., Martin, O., Xenarios, I., Ciuffi, A., Quintana-Murci, L., Telenti, A. Tags: Research Articles Source Type: journals
mtDNA Data Indicate a Single Origin for Dogs South of Yangtze River, Less Than 16,300 Years Ago, from Numerous WolvesEmail this article to a colleague.
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There is no generally accepted picture of where, when, and how the domestic dog originated. Previous studies of mitochondrial DNA (mtDNA) have failed to establish the time and precise place of origin because of lack of phylogenetic resolution in the so far studied control region (CR), and inadequate sampling. We therefore analyzed entire mitochondrial genomes for 169 dogs to obtain maximal phylogenetic resolution and the CR for 1,543 dogs across the Old World for a comprehensive picture of geographical diversity. Hereby, a detailed picture of the origins of the dog can for the first time be suggested. We obtained evidence ...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Pang, J.-F., Kluetsch, C., Zou, X.-J., Zhang, A.-b., Luo, L.-Y., Angleby, H., Ardalan, A., Ekstrom, C., Skollermo, A., Lundeberg, J., Matsumura, S., Leitner, T., Zhang, Y.-P., Savolainen, P. Tags: Research Articles Source Type: journals
Novel Internal Regions of Fluorescent Proteins Undergo Divergent Evolutionary PatternsEmail this article to a colleague.
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Over the past decade, fluorescent proteins (FPs) have become ubiquitous tools in biological research. Yet, little is known about the natural function or evolution of this superfamily of proteins that originate from marine organisms. Using molecular phylogenetic analyses of 102 naturally occurring cyan fluorescent proteins, green fluorescent proteins, red fluorescent proteins, as well as the nonfluorescent (purple-blue) protein sequences (including new FPs from Lizard Island, Australia) derived from organisms with known geographic origin, we show that FPs consist of two distinct and novel regions that have evolved under opp...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Gruber, D. F., DeSalle, R., Lienau, E. K., Tchernov, D., Pieribone, V. A., Kao, H.-T. Tags: Research Articles Source Type: journals
Genic Incompatibilities in Two Hybrid BacteriophagesEmail this article to a colleague.
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Horizontal gene transfer and recombination play a major role in microbial evolution and have been detected in diverse groups, including many of medical relevance such as HIV and dengue virus. In the absence of mechanistic barriers, the evolutionary success of a particular recombination event is determined by whether the recombinant genotype suffers a fitness cost through the disruption of favorable epistatic interactions within the genome, and if so, the extent to which this fitness cost might be mitigated by subsequent compensatory evolution. To investigate the importance of epistatic interactions between genes and the ev...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Rokyta, D. R., Wichman, H. A. Tags: Research Articles Source Type: journals
Evolution of 7SK RNA and Its Protein Partners in MetazoaEmail this article to a colleague.
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7SK RNA is a key player in the regulation of polymerase II transcription. 7SK RNA was considered as a highly conserved vertebrate innovation. The discovery of poorly conserved homologs in several insects and lophotrochozoans, however, implies a much earlier evolutionary origin. The mechanism of 7SK function requires interaction with the proteins HEXIM and La-related protein 7. Here, we present a comprehensive computational analysis of these two proteins in metazoa, and we extend the collection of 7SK RNAs by several additional candidates. In particular, we describe 7SK homologs in Caenorhabditis species. Furthermore, we de...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Marz, M., Donath, A., Verstraete, N., Nguyen, V. T., Stadler, P. F., Bensaude, O. Tags: Research Articles Source Type: journals
Global Microsatellite Content Distinguishes Humans, Primates, Animals, and PlantsEmail this article to a colleague.
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Microsatellites are highly mutable, repetitive sequences commonly used as genetic markers, but they have never been studied en masse. Using a custom microarray to measure hybridization intensities of every possible repetitive nucleotide motif from 1-mers to 6-mers, we examined 25 genomes. Here, we show that global microsatellite content varies predictably by species, as measured by array hybridization signal intensities, correlating with established taxonomic relationships, and particular motifs are characteristic of one species versus another. For instance, hominid-specific microsatellite motifs were identified despite al...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Galindo, C.L., McIver, L.J., McCormick, J.F., Skinner, M.A., Xie, Y., Gelhausen, R.A., Ng, K., Kumar, N.M., Garner, H.R. Tags: Research Articles Source Type: journals
A Broadscale Phylogenetic Analysis of Group II Intron RNAs and Intron-Encoded Reverse TranscriptasesEmail this article to a colleague.
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In this study, we present a broadscale phylogenetic analysis of group II introns using sequence data from both the conserved RNA structure and the intron-encoded reverse transcriptase (RT). Two similar phylogenies are estimated for the RT open reading frame (ORF), based on either amino acid or nucleotide sequence, whereas one phylogeny is produced for the RNA. In making these estimates, we confronted nearly all the classic challenges to phylogenetic inference, including positional saturation, base composition heterogeneity, short internodes with low support, and sensitivity to taxon sampling. Although the major lineages ar...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Simon, D. M., Kelchner, S. A., Zimmerly, S. Tags: Research Articles Source Type: journals
A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox GenesEmail this article to a colleague.
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The full complement of homeobox transcription factor sequences, including genes and pseudogenes, was determined from the analysis of 10 complete genomes from flowering plants, moss, Selaginella, unicellular green algae, and red algae. Our exhaustive genome-wide searches resulted in the discovery in each class of a greater number of homeobox genes than previously reported. All homeobox genes can be unambiguously classified by sequence evolutionary analysis into 14 distinct classes also characterized by conserved intron–exon structure and by unique codomain architectures. We identified many new genes belonging to previ...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Mukherjee, K., Brocchieri, L., Burglin, T. R. Tags: Research Articles Source Type: journals
Tracing the History of Goat Pastoralism: New Clues from Mitochondrial and Y Chromosome DNA in North AfricaEmail this article to a colleague.
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We present the first study combining results from mitochondrial DNA (mtDNA) and Y chromosome loci for the genetic characterization of a domestic goat population. Our analyses indicate a remarkably high diversity of maternal and paternal lineages in a sample of indigenous goats from the northwestern fringe of the African continent. Median-joining networks and a multidimensional scaling of ours and almost 2000 published mtDNA sequences revealed a considerable genetic affinity between goat populations from the Maghreb (Northwest Africa) and the Near East. It has been previously shown that goats have a weak phylogeographic str...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Pereira, F., Queiros, S., Gusmao, L., Nijman, I. J., Cuppen, E., Lenstra, J. A., Consortium, E., Davis, S. J.M., Nejmeddine, F., Amorim, A. Tags: Research Articles Source Type: journals
Targets of Balancing Selection in the Human GenomeEmail this article to a colleague.
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Balancing selection is potentially an important biological force for maintaining advantageous genetic diversity in populations, including variation that is responsible for long-term adaptation to the environment. By serving as a means to maintain genetic variation, it may be particularly relevant to maintaining phenotypic variation in natural populations. Nevertheless, its prevalence and specific targets in the human genome remain largely unknown. We have analyzed the patterns of diversity and divergence of 13,400 genes in two human populations using an unbiased single-nucleotide polymorphism data set, a genome-wide approa...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Andres, A. M., Hubisz, M. J., Indap, A., Torgerson, D. G., Degenhardt, J. D., Boyko, A. R., Gutenkunst, R. N., White, T. J., Green, E. D., Bustamante, C. D., Clark, A. G., Nielsen, R. Tags: Research Articles Source Type: journals
Signal Conflicts in the Phylogeny of the Primary Photosynthetic EukaryotesEmail this article to a colleague.
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It is widely accepted that the first photosynthetic eukaryotes arose from a single primary endosymbiosis of a cyanobacterium in a phagotrophic eukaryotic host, which led to the emergence of three major lineages: Chloroplastida (green algae and land plants), Rhodophyta, and Glaucophyta. For a long time, Glaucophyta have been thought to represent the earliest branch among them. However, recent massive phylogenomic analyses of nuclear genes have challenged this view, because most of them suggested a basal position of Rhodophyta, though with moderate statistical support. We have addressed this question by phylogenomic analysis...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Deschamps, P., Moreira, D. Tags: Research Articles Source Type: journals
Benchmarking Next-Generation Transcriptome Sequencing for Functional and Evolutionary GenomicsEmail this article to a colleague.
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Next-generation sequencing has opened the door to genomic analysis of nonmodel organisms. Technologies generating long-sequence reads (200–400 bp) are increasingly used in evolutionary studies of nonmodel organisms, but the short-sequence reads (30–50 bp) that can be produced at lower cost are thought to be of limited utility for de novo sequencing applications. Here, we tested this assumption by short-read sequencing the transcriptomes of the tropical disease vectors Aedes aegypti and Anopheles gambiae, for which complete genome sequences are available. Comparison of our results to the reference genomes allowe...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Gibbons, J. G., Janson, E. M., Hittinger, C. T., Johnston, M., Abbot, P., Rokas, A. Tags: Research Articles Source Type: journals
A Phylogenomic Approach to Resolve the Basal Pterygote DivergenceEmail this article to a colleague.
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One of the most fascinating Bauplan transitions in the animal kingdom was the invention of insect wings, a change that also contributed to the success and enormous diversity of this animal group. However, the origin of insect flight and the relationships of basal winged insect orders are still controversial. Three hypotheses have been proposed to explain the phylogeny of winged insects: 1) the traditional Palaeoptera hypothesis (Ephemeroptera + Odonata, Neoptera), 2) the Metapterygota hypothesis (Ephemeroptera, Odonata + Neoptera), and 3) the Chiastomyaria hypothesis (Odonata, Ephemeroptera + Neoptera). Neither phylogeneti...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Simon, S., Strauss, S., von Haeseler, A., Hadrys, H. Tags: Research Articles Source Type: journals
Hemocyanin Suggests a Close Relationship of Remipedia and HexapodaEmail this article to a colleague.
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The Remipedia are enigmatic crustaceans from anchialine cave systems, first described only 30 years ago, whose phylogenetic affinities are as yet unresolved. Here we report the sequence of hemocyanin from Speleonectes tulumensis Yager, 1987 (Remipedia, Speleonectidae). This is the first proof of the presence of this type of respiratory protein in a crustacean taxon other than Malacostraca. Speleonectes tulumensis hemocyanin consists of multiple distinct (at least three) subunits (StuHc1–3; Hc, hemocyanin). Surprisingly, the sequences are most similar to hexapod hemocyanins. Phylogenetic analyses showed that the S. tu...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Ertas, B., von Reumont, B. M., Wagele, J.-W., Misof, B., Burmester, T. Tags: Research Articles Source Type: journals
Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within OpisthokontaEmail this article to a colleague.
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The shared ancestry between Fungi and animals has been unequivocally demonstrated by abundant molecular and morphological data for well over a decade. Along with the animals and Fungi, multiple protists have been placed in the supergroup Opisthokonta making it exceptionally diverse. In an effort to place the cellular slime mold Fonticula alba, an amoeboid protist with aggregative, multicellular fruiting, we sequenced five nuclear encoded genes; small subunit ribosomal RNA, actin, beta-tubulin, elongation factor 1-alpha, and the cytosolic isoform of heat shock protein 70 for phylogenetic analyses. Molecular trees demonstrat...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Brown, M. W., Spiegel, F. W., Silberman, J. D. Tags: Research Articles Source Type: journals
General Heterotachy and Distance Method AdjustmentsEmail this article to a colleague.
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Heterotachy is a general term to describe positions in a sequence that evolve at different rates in different lineages. Kolaczkowski and Thornton (2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431:980–984.) recently described an intriguing heterotachy model that leads to topological bias for likelihood-based methods and parsimony methods. In this article, we show that heterotachy can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for eac...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Wu, J., Susko, E. Tags: Research Articles Source Type: journals
Molecular Evolution of GYPC: Evidence for Recent Structural Innovation and Positive Selection in HumansEmail this article to a colleague.
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GYPC encodes two erythrocyte surface sialoglycoproteins in humans, glycophorin C and glycophorin D (GPC and GPD), via initiation of translation at two start codons on a single transcript. The malaria-causing parasite Plasmodium falciparum uses GPC as a means of invasion into the human red blood cell. Here, we examine the molecular evolution of GYPC among the Hominoidea (Greater and Lesser Apes) and also the pattern of polymorphism at the locus in a global human sample. We find an excess of nonsynonymous divergence among species that appears to be caused solely by accelerated evolution of GYPC in the human lineage. Moreover...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Wilder, J. A., Hewett, E. K., Gansner, M. E. Tags: Research Articles Source Type: journals
Transcription, Translation, and the Evolution of Specialists and GeneralistsEmail this article to a colleague.
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We used DNA microarrays to measure transcription and iTRAQ 2D liquid chromatography-mass spectrometry/mass spectrometry (a mass-tag labeling proteomic technique) to measure protein expression in 14 strains of Escherichia coli adapted for hundreds of generations to growth-limiting concentrations of either lactulose, methylgalactoside, or a 72:28 mixture of the two. The two ancestors, TD2 and TD10, differ only in their lac operons and have similar transcription and protein expression profiles. Changes in transcription and protein expression are observed at 30–250 genes depending on the evolved strain. Lactulose special...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Zhong, S., Miller, S. P., Dykhuizen, D. E., Dean, A. M. Tags: Research Articles Source Type: journals
Selection to Maintain Paralogous Amino Acid Differences Under the Pressure of Gene Conversion in the Heat-Shock Protein Genes in YeastEmail this article to a colleague.
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A genome scan for the signatures of selection for paralogous functional amino acid differences was performed with yeast genomes. This recently developed method makes it possible to localize the target sites of selection under the pressure of gene conversion. We found that two gene pairs have strong signatures of selection. The two pairs of duplicated genes happened to be heat shock genes (Ssa1/ Ssa2 and Ssb1/Ssb2), which have similar protein structures to each other, although the amino acid sequence identity between Ssa and Ssb is not high (~60%). Interestingly, the two gene pairs exhibit signature of selection at almost i...
Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Authors: Takuno, S., Innan, H. Tags: Letter Source Type: journals
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Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Cover Source Type: journals
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Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
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Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
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Source: Molecular Biology and Evolution - November 10, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
Age-Related Accumulation of Mutations Supports a Replication-Dependent Mechanism of Spontaneous Mutation at Tandem Repeat DNA Loci in MiceEmail this article to a colleague.
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Expanded simple tandem repeat (ESTR) loci belong to the class of highly unstable loci in the mouse genome. The mechanisms underlying the very high spontaneous instability at these loci still remain poorly understood. Using single-molecule polymerase chain reaction, here we have compared the pattern of mutation accumulation in tissues with different proliferation capacities in male mice of age 12, 26, 48, and 96 weeks. In the nonproliferating brain, we did not observe any measurable age-related accumulation of ESTR mutations. In contrast, a highly elevated frequency of ESTR mutation was detected in the sperm samples taken f...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Hardwick, R. J., Tretyakov, M. V., Dubrova, Y. E. Tags: Research Articles Source Type: journals
Pistillata--Duplications as a Mode for Floral Diversification in (Basal) AsteridsEmail this article to a colleague.
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Basal asterid families, and to a lesser extent the asterids as a whole, are characterized by a high variation in petal and stamen morphology. Moreover, the stamen number, the adnation of stamens to petals, and the degree of sympetaly vary considerably among basal asterid taxa. The B group genes, members of the APETALA3 (AP3) and PISTILLATA (PI) gene lineages, have been shown to specify petal and stamen identities in several core eudicot species. Duplicate genes in these lineages have been shown in some cases to have diversified in their function; for instance in Petunia, a PI paralog is required for the fusion of stamens t...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Viaene, T., Vekemans, D., Irish, V. F., Geeraerts, A., Huysmans, S., Janssens, S., Smets, E., Geuten, K. Tags: Research Articles Source Type: journals
Cross-Sectional Dating of Novel Haplotypes of HERV-K 113 and HERV-K 115 Indicate These Proviruses Originated in Africa before Homo sapiensEmail this article to a colleague.
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The human genome, human endogenous retroviruses (HERV), of which HERV-K113 and HERV-K115 are the only known full-length proviruses that are insertionally polymorphic. Although a handful of previously published papers have documented their prevalence in the global population; to date, there has been no report on their prevalence in the United States population. Here, we studied the geographic distribution of K113 and K115 among 156 HIV-1+ subjects from the United States, including African Americans, Hispanics, and Caucasians. In the individuals studied, we found higher insertion frequencies of K113 (21%) and K115 (35%) in A...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Jha, A. R., Pillai, S. K., York, V. A., Sharp, E. R., Storm, E. C., Wachter, D. J., Martin, J. N., Deeks, S. G., Rosenberg, M. G., Nixon, D. F., Garrison, K. E. Tags: Research Articles Source Type: journals
Reconciling Ecological and Genomic Divergence among Lineages of Listeria under an "Extended Mosaic Genome Concept"Email this article to a colleague.
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There is growing evidence for a discontinuity between genomic and ecological divergence in several groups of bacteria. This evidence is difficult to reconcile with the traditional concept that ecologically divergent species maintain a cohesive gene pool isolated from other gene pools by barriers to homologous recombination (HR). There have been several innovative models of bacterial divergence that permit such discontinuity; we refer to these, collectively, as "mosaic genome concepts" (MGCs). These concepts remain a point of contention. Here, we undertake an investigation among ecologically divergent lineages of genus List...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Dunn, K. A., Bielawski, J. P., Ward, T. J., Urquhart, C., Gu, H. Tags: Research Articles Source Type: journals
Quantitative Prediction of Molecular Clock and Ka/Ks at Short TimescalesEmail this article to a colleague.
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Recent empirical studies of taxa including humans, fish, and birds have shown elevated rates of molecular evolution between species that diverged recently. Using the Moran model, we calculate expected divergence as a function of time. Our findings suggest that the observed phenomenon of elevated rates at short timescales is consistent with standard population genetics theory. The apparent acceleration of the molecular clock at short timescales can be explained by segregating polymorphisms present at the time of the ancestral population, both neutral and slightly deleterious, and not newly arising slightly deleterious mutat...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Peterson, G. I., Masel, J. Tags: Research Articles Source Type: journals
Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0Email this article to a colleague.
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Sequence simulation is an important tool in validating biological hypotheses as well as testing various bioinformatics and molecular evolutionary methods. Hypothesis testing relies on the representational ability of the sequence simulation method. Simple hypotheses are testable through simulation of random, homogeneously evolving sequence sets. However, testing complex hypotheses, for example, local similarities, requires simulation of sequence evolution under heterogeneous models. To this end, we previously introduced indel-Seq-Gen version 1.0 (iSGv1.0; indel, insertion/deletion). iSGv1.0 allowed heterogeneous protein evo...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Strope, C. L., Abel, K., Scott, S. D., Moriyama, E. N. Tags: Research Articles Source Type: journals
Alu-Mediated Acquisition of Unstable ATTCT Pentanucleotide Repeats in the Human ATXN10 GeneEmail this article to a colleague.
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Spinocerebellar ataxia type 10 is caused by ATTCT repeat expansion in the ATXN10 gene in humans. We studied the evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable ATTCT repeats in the genome. We found that long interspersed element-1 (LINE-1) was inserted into ATXN10 intron 9; Alu was then inserted in the middle of LINE-1; and endogenous retrovilcus K was lastly retrotransposed in the middle of Alu. The ATTCT repeat was located on the boundary between the 3'-end of the Alu element and the direct repeat arising from LINE-1. We determined nucleotide sequences of the or...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Kurosaki, T., Matsuura, T., Ohno, K., Ueda, S. Tags: Research Articles Source Type: journals
Positive Selection and Gene Conversion Drive the Evolution of a Brain-Expressed snoRNAs ClusterEmail this article to a colleague.
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HBII-52 small nucleolar RNAs (snoRNAs) are brain-expressed posttranscriptional modifiers of serotonin receptor 2C RNA. They are organized in a cluster of 47 highly homologous gene copies spanning 100 kb at chromosome 15q11.2. Nucleotide diversity at HBII-52 snoRNA gene cluster in African and European descent populations was analyzed via resequencing of 25 functional snoRNA gene copies. Ninety-four variants were detected, from which 74 are novel. Only 16 variants are shared between Africans and Europeans. We also report a novel Yoruba-specific copy-number variant representing a 5.2-kb polymorphic deletion and resulting in a...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Ogorelkova, M., Navarro, A., Vivarelli, F., Ramirez-Soriano, A., Estivill, X. Tags: Research Articles Source Type: journals
Self-Recognition and Ca2+-Dependent Carbohydrate-Carbohydrate Cell Adhesion Provide Clues to the Cambrian ExplosionEmail this article to a colleague.
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The Cambrian explosion of life was a relatively short period approximately 540 Ma that marked a generalized acceleration in the evolution of most animal phyla, but the trigger of this key biological event remains elusive. Sponges are the oldest extant Precambrian metazoan phylum and thus a valid model to study factors that could have unleashed the rise of multicellular animals. One such factor is the advent of self-/non–self-recognition systems, which would be evolutionarily beneficial to organisms to prevent germ-cell parasitism or the introduction of deleterious mutations resulting from fusion with genetically diff...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Fernandez-Busquets, X., Kornig, A., Bucior, I., Burger, M. M., Anselmetti, D. Tags: Research Articles Source Type: journals
Dynamic Evolution of Immune System Regulators: The History of the Interferon Regulatory Factor FamilyEmail this article to a colleague.
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This manuscript presents the first extensive phylogenetics analysis of a key family of immune regulators, the interferon regulatory factor (IRF) family. The IRF family encodes transcription factors that play important roles in immune defense, stress responses, reproduction, development, and carcinogenesis. Several times during their evolution, the IRF genes have undergone expansion and diversification. These genes were also completely lost on two separate occasions in large groups of metazoans. The origin of the IRF family coincides with the appearance of multicellularity in animals. IRF genes are present in all principal ...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Nehyba, J., Hrdlickova, R., Bose, H. R. Tags: Research Articles Source Type: journals
Roles of Trans and Cis Variation in Yeast Intraspecies Evolution of Gene ExpressionEmail this article to a colleague.
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We examined whether genes regulated by a single transcription factor (TF; single input module, SIM genes) or genes regulated by multiple TFs (multiple input module, MIM genes) are more susceptible to trans variation. Because a SIM gene is regulated by a single immediate upstream TF, the chance for a change to occur in its trans-acting factors would, on average, be smaller than that for a MIM gene. We chose 232 genes that exhibited expression divergence between BY and RM to test this hypothesis. We examined the expression patterns of these genes in a BY–RM coculture system and in a BY–RM diploid hybrid. We found...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Sung, H.-M., Wang, T.-Y., Wang, D., Huang, Y.-S., Wu, J.-P., Tsai, H.-K., Tzeng, J., Huang, C.-J., Lee, Y.-C., Yang, P., Hsu, J., Chang, T., Cho, C.-Y., Weng, L.-C., Lee, T.-C., Chang, T.-H., Li, W.-H., Shih, M.-C. Tags: Research Articles Source Type: journals
Evolution of Duplicated {beta}-Globin Genes and the Structural Basis of Hemoglobin Isoform Differentiation in MusEmail this article to a colleague.
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The functional diversification of multigene families may be strongly influenced by mechanisms of concerted evolution such as interparalog gene conversion. The β-globin gene family of house mice (genus Mus) represents an especially promising system for evaluating the effects of gene conversion on the functional divergence of duplicated genes. Whereas the majority of mammalian species possess tandemly duplicated copies of the adult β-globin gene that are identical in sequence, natural populations of house mice are often polymorphic for distinct two-locus haplotypes that differ in levels of functional divergence bet...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Runck, A. M., Moriyama, H., Storz, J. F. Tags: Research Articles Source Type: journals
The Evolutionary Rates of Eukaryotic RNA Polymerases and of Their Transcription Factors Are Affected by the Level of Concerted Evolution of the Genes They TranscribeEmail this article to a colleague.
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A defining characteristic of all eukaryotes is the presence of three RNA polymerases, each of which transcribes a particular subset of nuclear genes. RNA polymerase I transcribes rRNA genes; RNA polymerase II transcribes mRNA, miRNA, snRNA, and snoRNA genes; and RNA polymerase III transcribes 5S rRNA and tRNA genes. Here, we use the sequences of up to 25 Ascomycete species to show that the type of genes transcribed by each RNA polymerase affects their evolutionary rates and those of their transcription factors (TFs). The RNA polymerase subunits and TFs of genes whose promoters experience higher levels of concerted evolutio...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Carter, R., Drouin, G. Tags: Research Articles Source Type: journals
Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora liniEmail this article to a colleague.
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Genetic variation for pathogen infectivity is an important driver of disease incidence and prevalence in both natural and managed systems. Here, we use the interaction between the rust pathogen, Melampsora lini, and two host plants, Linum marginale and Linum usitatissimum, to examine how host–pathogen interactions influence the maintenance of polymorphism in genes underlying pathogen virulence. Extensive sequence variation at two effector loci (AvrP123, AvrP4) was found in M. lini isolates collected from across the native range of L. marginale in Australia, as well as in isolates collected from a second host, the cul...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Barrett, L. G., Thrall, P. H., Dodds, P. N., van der Merwe, M., Linde, C. C., Lawrence, G. J., Burdon, J. J. Tags: Research Articles Source Type: journals
Evolution and Biochemistry of Family 4 Glycosidases: Implications for Assigning Enzyme Function in Sequence AnnotationsEmail this article to a colleague.
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This study emphasizes the importance of automatic annotation systems that by integrating phylogenetic analysis, functional motifs, and bioinformatics data, may lead to innovative experiments that further our understanding of biological systems. (Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Hall, B. G., Pikis, A., Thompson, J. Tags: Research Articles Source Type: journals
Population Genomics of the Arabidopsis thaliana Flowering Time Gene NetworkEmail this article to a colleague.
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The time to flowering is a key component of the life-history strategy of the model plant Arabidopsis thaliana that varies quantitatively among genotypes. A significant problem for evolutionary and ecological genetics is to understand how natural selection may operate on this ecologically significant trait. Here, we conduct a population genomic study of resequencing data from 52 genes in the flowering time network. McDonald–Kreitman tests of neutrality suggested a strong excess of amino acid polymorphism when pooling across loci. This excess of replacement polymorphism across the flowering time network and a skewed de...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Flowers, J. M., Hanzawa, Y., Hall, M. C., Moore, R. C., Purugganan, M. D. Tags: Research Articles Source Type: journals
MPF2-Like-A MADS-Box Genes Control the Inflated Calyx Syndrome in Withania (Solanaceae): Roles of Darwinian SelectionEmail this article to a colleague.
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The Chinese lantern, which is the inflated calyx syndrome (ICS) of Physalis, is formed by MPF2 in the presence of the plant hormones, cytokinin and gibberellin. MPF2 knockdown mutants of Physalis have small leaves, no ICS, and are male sterile, thus, revealing three MPF2-related functions. Of the close relatives of Physalis, Tubocapsicum has only a rudimentary calyx, whereas others, like the Withania species, have ICS. From all Withania samples tested, two classes of MPF2-like orthologs, MPF2-like-A and MPF2-like-B, were isolated, whereas only the latter class was obtained from tetraploid Tubocapsicum. Though distinct diff...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Khan, M. R., Hu, J.-Y., Riss, S., He, C., saedler, H. Tags: Research Articles Source Type: journals
Temporal Constraints on the Incorporation of Regulatory Mutants in Evolutionary PathwaysEmail this article to a colleague.
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Understanding the molecular details of the sequence of events in multistep evolutionary pathways can reveal the extent to which natural selection exploits regulatory mutations affecting expression, amino acid replacements affecting the active site, amino acid replacements affecting protein folding or stability, or variations affecting gene copy number. In experimentally exploring the adaptive landscape of the evolution of resistance to β-lactam antibiotics in enteric bacteria, we noted that a regulatory mutation that increases β-lactamase expression by about 2-fold has a very strong tendency to be fixed at or nea...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Brown, K. M., DePristo, M. A., Weinreich, D. M., Hartl, D. L. Tags: Research Articles Source Type: journals
Metabolic Adaptation after Whole Genome DuplicationEmail this article to a colleague.
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Whole genome duplications (WGDs) have been hypothesized to be responsible for major transitions in evolution. However, the effects of WGD and subsequent gene loss on cellular behavior and metabolism are still poorly understood. Here we develop a genome scale evolutionary model to study the dynamics of gene loss and metabolic adaptation after WGD. Using the metabolic network of Saccharomyces cerevisiae as an example, we primarily study the outcome of WGD on yeast as it currently is. However, similar results were obtained using a recontructed hypothetical metabolic network of the pre-WGD ancestor. We show that the retention ...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: van Hoek, M. J. A., Hogeweg, P. Tags: Research Articles Source Type: journals
Big and Slow: Phylogenetic Estimates of Molecular Evolution in Baleen Whales (Suborder Mysticeti)Email this article to a colleague.
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We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1–15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Jackson, J. A., Baker, C. S., Vant, M., Steel, D. J., Medrano-Gonzalez, L., Palumbi, S. R. Tags: Research Articles Source Type: journals
Peeling the Onion: Ribosomes Are Ancient Molecular FossilsEmail this article to a colleague.
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We describe a method to establish chronologies of ancient ribosomal evolution. The method uses structure-based and sequence-based comparison of the large subunits (LSUs) of Haloarcula marismortui and Thermus thermophilus. These are the highest resolution ribosome structures available and represent disparate regions of the evolutionary tree. We have sectioned the superimposed LSUs into concentric shells, like an onion, using the site of peptidyl transfer as the origin (the PT-origin). This spherical approximation combined with a shell-by-shell comparison captures significant information along the evolutionary time line reve...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Hsiao, C., Mohan, S., Kalahar, B. K., Williams, L. D. Tags: Research Articles Source Type: journals
Functioning and Evolutionary Significance of Nutrient TransceptorsEmail this article to a colleague.
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The discovery of nutrient transceptors, transporter-like proteins with a receptor function, suggests that receptors for chemical signals may have been derived in evolution from nutrient transporters. Several examples are now available of nutrient transporters with an additional nutrient signaling function, nutrient receptors with a transporter-like sequence and structure but without transport capacity, and G protein–coupled receptors (GPCRs) that have nutrients as ligands. Recent results have revealed that transceptor signaling requires a specific ligand-induced conformational change, which indicates that transceptor...
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Authors: Thevelein, J. M., Voordeckers, K. Tags: Review Source Type: journals
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(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
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(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
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(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Cover Source Type: journals
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(Source: Molecular Biology and Evolution)
Source: Molecular Biology and Evolution - October 12, 2009 Category: Molecular Biology Tags: Standing Material Source Type: journals
