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Joseph Felsenstein is Professor in the Departments of Genome Sciences and Biology and Adjunct Professor in the Departments of Computer Science and Statistics at the University of Washington in Seattle. He is best known for his work on phylogenetic inference, and is the author of Inferring Phylogenies, and principal author and distributor of the package of phylogenetic inference programs called PHYLIP, and is currently serving as the President of the Society for Molecular Biology & Evolution.
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James McInerney is the principle investigator of the Bioinformatics and Molecular Evolution Laboratories at NUI Maynooth. He was one of the founding directors of the Irish Centre for High End Computing, an Associate Editor of Molecular Biology and Evolution, Biology Direct, and Journal of Experimental Zoology, and is currently serving as the Secretary for the Society for Molecular Biology and Evolution.
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Juliette de Meaux is interested in the molecular basis of Darwinian adaptation in natural plant systems. Her works combines the approaches of population, quantitative and molecular genetics to dissect the underpinning of adaptive changes. She completed her PhD at AgroParisTech, under the supervision of Prof. Claire Neema and studied the molecular basis of host-pathogen coevolution in natural populations of common bean. She then spent her Postdoc time in the lab of Prof. Tom Mitchell-Olds at the Max Planck Institute of Chemical Ecology in Jena and worked on the evolution of cis-regulatory DNA. Since 2005, she runs her own lab, first at the Max Planck Institute of Plant Breeding in Cologne and then at the University of Münster. In January 2015, she relocated her lab at the University of Cologne. She is currently serving as the Treasurer for the Society for Molecular Biology and Evolution.
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We are delighted to announce that the SMBE 2019 Meeting will be taking place in Manchester, United Kingdom. The Meeting will be held at the state of the art Manchester Central venue.
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Today HHMI announced its 2013 Investigator awards and we were pleased to see SMBE council member Harmit Malik and plenary lecturer at SMBE12 in Dublin, Hopi Hoekstra being honored with these awards. The awards have been made to only 27 of America's top biomedical scientists and represents an investment of $150 Million over the next five years.
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Dear SMBE Members:
SMBE is accepting proposals to host its International Meeting in 2015. The meeting is usually held in June or July and attracts ~1500 scientists from throughout the world. The Society will accept proposals from any location, but the successful location will need to have a lecture venue of sufficient size to host plenary lectures for all attendees and will also need to be near housing, preferably with a wide variety of options.
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Dear SMBE members,
*Nominations for Pres-elect and 2 councillors due by May 22 2013*
I am writing to solicit nominations for SMBE President-Elect and 2 counsillors whose terms will begin on January 1, 2014. As the society grows and thrive, members of council play very important roles in guiding its development and in soliciting and implementing programs that support our members, enrich opportunities for young scientists from around the world, oversee our two excellent journals (MBE and GBE) as well as our annual meeting and new satellite meeting program.
Call for 2013 SMBE Satellite Meetings (this message to also be distributed via email to the membership)
The Society for Molecular Biology and Evolution (SMBE) exists to "…provide facilities for association and conference among molecular evolutionists and to further the goals of molecular evolutionary biology and its practitioners, including the publication of two journals, Molecular Biology and Evolution, and Genome Biology and Evolution" (Society By-Laws, amended November 7, 2008). In addition to supporting its annual meeting, SMBE Council will provide funds in aid of one or more workshops or small meetings per calendar year, that number depending on total cost. SMBE's first satellite meeting sponsored under this competition was "Phylomedicine" held March 2012 at Arizona State University (http://www.smbe.org/phylomed). In spring 2013, SMBE supported three satellite symposia: "Eukaryotic Metagenomics"...
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Mechanisms of Protein Evolution II was held as an SMBE Satellite Meeting February 7-9, 2013 on the campus of University of Colorado School of Medicine in Aurora, CO. An amusing video describing the meeting was produced by James McInerney:
Dear friends and colleagues,
Registration is now open for EVOLUZIONE2103 (www.evoluzione2013.it), the biennial congress of the Italian Society for Evolutionary Biology (SIBE). The congress will be held at the end of August (28-31) in the historical town of Trento, in the heart of the Italian Alps, a region renowned for its excellent wine, castles, and the beautiful dolomite mountains.
Molecular Biology and Evolution, Volume 35, Issue 9, 1 September 2018, Pages 2230–2239, https://doi.org/10.1093/molbev/msy123
AbstractFungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size, or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.
AbstractVertebrate estrogen receptors (ERs) perform numerous cell signaling and transcriptional regulatory functions. ERɑ (Esr1) and ERβ (Esr2) likely evolved from an ancestral receptor that duplicated and diverged at the protein and cis-regulatory levels, but the evolutionary history of ERs, including the timing of proposed duplications, remains unresolved. Here we report on identification of two distinct ERs in cartilaginous fishes and demonstrate their orthology to ERα and ERβ. Phylogenetic analyses place the ERα/ERβ duplication near the base of crown gnathostomes (jawed vertebrates). We find that ERα and ERβ from little skate (Leucoraja erinacea) and mammals share key subtype-specific residues, indicating conserved protein evolution. In contrast, jawless fishes have multiple non-orthologous Esr genes that arose by parallel duplications. Esr1 and Esr2 are expressed in subtype-specific and sexually dimorphic patterns in skate embryos, suggesting that ERs might have functioned in sexually dimorphic development before the divergence of cartilaginous and bony fishes.
AbstractEnzymes are known to fine-tune their sequences to optimize catalytic function, yet quantitative evolutionary design principles of enzymes remain elusive on the proteomic scale. Recently, it was found that the catalytic site in enzymes induces long-range evolutionary constraint, where even sites distant to the catalytic site are more conserved than expected. Given that protein-fold usage is generally different between enzymes and nonenzymes, it remains an open question to what extent this long-range evolutionary constraint in enzymes is dictated, either directly or indirectly, by the special three-dimensional structure of the enzyme. To investigate this question, we have compared evolutionary properties of enzymes with those of counterpart pseudoenzymes that share the same protein fold but are catalytically inactive. We found that the long-range evolutionary constraint observed in enzymes is significantly reduced in pseudoenzyme counterparts, despite very high structural similarity (∼1.5 Å RMSD on average). Furthermore, this significant reduction in long-range evolutionary constraint is observed even in pseudoenzyme counterparts which retain the ligand-binding ability of enzymes. Finally, the distance between the site that induces the highest gradient of sequence conservation and the pseudocatalytic site in pseudoenzymes is significantly larger than the corresponding distance in enzymes. Taken together, our results suggest that the long-range evolutionary constraint in enzymes is induced mainly by the presence of the catalytic site rather than by the special three-dimensional structure of the enzyme, and that such long-range evolutionary constraint in enzymes depends mainly on the catalytic function of the active site rather than on the ligand-binding ability of the enzyme.
AbstractA key question in molecular evolutionary biology concerns the relative roles of mutation and selection in shaping genomic data. Moreover, features of mutation and selection are heterogeneous along the genome and over time. Mechanistic codon substitution models based on the mutation–selection framework are promising approaches to separating these effects. In practice, however, several complications arise, since accounting for such heterogeneities often implies handling models of high dimensionality (e.g., amino acid preferences), or leads to across-site dependence (e.g., CpG hypermutability), making the likelihood function intractable. Approximate Bayesian Computation (ABC) could address this latter issue. Here, we propose a new approach, named Conditional ABC (CABC), which combines the sampling efficiency of MCMC and the flexibility of ABC. To illustrate the potential of the CABC approach, we apply it to the study of mammalian CpG hypermutability based on a new mutation-level parameter implying dependence across adjacent sites, combined with site-specific purifying selection on amino-acids captured by a Dirichlet process. Our proof-of-concept of the CABC methodology opens new modeling perspectives. Our application of the method reveals a high level of heterogeneity of CpG hypermutability across loci and mild heterogeneity across taxonomic groups; and finally, we show that CpG hypermutability is an important evolutionary factor in rendering relative synonymous codon usage. All source code is available as a GitHub repository (https://github.com/Simonll/LikelihoodFreePhylogenetics.git).
AbstractFor 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.
AbstractMeiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5′ ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ∼100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 × 10−5). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny.
AbstractThe oxymonad Monocercomonoides exilis was recently reported to be the first eukaryote that has completely lost the mitochondrial compartment. It was proposed that an important prerequisite for such a radical evolutionary step was the acquisition of the SUF Fe–S cluster assembly pathway from prokaryotes, making the mitochondrial ISC pathway dispensable. We have investigated genomic and transcriptomic data from six oxymonad species and their relatives, composing the group Preaxostyla (Metamonada, Excavata), for the presence and absence of enzymes involved in Fe–S cluster biosynthesis. None possesses enzymes of mitochondrial ISC pathway and all apparently possess the SUF pathway, composed of SufB, C, D, S, and U proteins, altogether suggesting that the transition from ISC to SUF preceded their last common ancestor. Interestingly, we observed that SufDSU were fused in all three oxymonad genomes, and in the genome of Paratrimastix pyriformis. The donor of the SUF genes is not clear from phylogenetic analyses, but the enzyme composition of the pathway and the presence of SufDSU fusion suggests Firmicutes, Thermotogae, Spirochaetes, Proteobacteria, or Chloroflexi as donors. The inventory of the downstream CIA pathway enzymes is consistent with that of closely related species that retain ISC, indicating that the switch from ISC to SUF did not markedly affect the downstream process of maturation of cytosolic and nuclear Fe–S proteins.
AbstractThe genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and pure species, that illuminates the complete composition of genomes. sppIDer maps short-read sequencing data to a combination genome built from reference genomes of several species of interest and assesses the genomic contribution and relative ploidy of each parental species, producing a series of colorful graphical outputs ready for publication. As a proof-of-concept, we use the genus Saccharomyces to detect and visualize both interspecies hybrids and pure strains, even with missing parental reference genomes. Through simulation, we show that sppIDer is robust to variable reference genome qualities and performs well with low-coverage data. We further demonstrate the power of this approach in plants, animals, and other fungi. sppIDer is robust to many different inputs and provides visually intuitive insight into genome composition that enables the rapid identification of species and their interspecies hybrids. sppIDer exists as a Docker image, which is a reusable, reproducible, transparent, and simple-to-run package that automates the pipeline and installation of the required dependencies (https://github.com/GLBRC/sppIDer; last accessed September 6, 2018).
AbstractUnderstanding how microalgae adapt to rapidly changing environments is not only important to science but can help clarify the potential impact of climate change on the biology of primary producers. We sequenced and analyzed the nuclear genome of multiple Picochlorum isolates (Chlorophyta) to elucidate strategies of environmental adaptation. It was previously found that coordinated gene regulation is involved in adaptation to salinity stress, and here we show that gene gain and loss also play key roles in adaptation. We determined the extent of horizontal gene transfer (HGT) from prokaryotes and their role in the origin of novel functions in the Picochlorum clade. HGT is an ongoing and dynamic process in this algal clade with adaptation being driven by transfer, divergence, and loss. One HGT candidate that is differentially expressed under salinity stress is indolepyruvate decarboxylase that is involved in the production of a plant auxin that mediates bacteria–diatom symbiotic interactions. Large differences in levels of heterozygosity were found in diploid haplotypes among Picochlorum isolates. Biallelic divergence was pronounced in P. oklahomensis (salt plains environment) when compared with its closely related sister taxon Picochlorum SENEW3 (brackish water environment), suggesting a role of diverged alleles in response to environmental stress. Our results elucidate how microbial eukaryotes with limited gene inventories expand habitat range from mesophilic to halophilic through allelic diversity, and with minor but important contributions made by HGT. We also explore how the nature and quality of genome data may impact inference of nuclear ploidy.
AbstractMolluscan shells, mainly composed of calcium carbonate, also contain organic components such as proteins and polysaccharides. Shell organic matrices construct frameworks of shell structures and regulate crystallization processes during shell formation. To date, a number of shell matrix proteins (SMPs) have been identified, and their functions in shell formation have been studied. However, previous studies focused only on SMPs extracted from adult shells, secreted after metamorphosis. Using proteomic analyses combined with genomic and transcriptomic analyses, we have identified 31 SMPs from larval shells of the pearl oyster, Pinctada fucata, and 111 from the Pacific oyster, Crassostrea gigas. Larval SMPs are almost entirely different from those of adults in both species. RNA-seq data also confirm that gene expression profiles for larval and adult shell formation are nearly completely different. Therefore, bivalves have two repertoires of SMP genes to construct larval and adult shells. Despite considerable differences in larval and adult SMPs, some functional domains are shared by both SMP repertoires. Conserved domains include von Willebrand factor type A (VWA), chitin-binding (CB), carbonic anhydrase (CA), and acidic domains. These conserved domains are thought to play crucial roles in shell formation. Furthermore, a comprehensive survey of animal genomes revealed that the CA and VWA–CB domain-containing protein families expanded in molluscs after their separation from other Lophotrochozoan linages such as the Brachiopoda. After gene expansion, some family members were co-opted for molluscan SMPs that may have triggered to develop mineralized shells from ancestral, nonmineralized chitinous exoskeletons.
AbstractAs are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our data set. Individuals from this data set came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identified previously unrecognized population structure along the East–West axis of China, demonstrated a general pattern of isolation-by-distance among Han Chinese, and reported unique regional signals of admixture, such as European influences among the Northwestern provinces of China. Furthermore, we identified a number of highly differentiated, putatively adaptive, loci (e.g., MTHFR, ADH7, and FADS, among others) that may be driven by immune response, climate, and diet in the Han Chinese. Finally, we have made available allele frequency estimates stratified by administrative divisions across China in the Geography of Genetic Variant browser for the broader community. By leveraging the largest currently available genetic data set for Han Chinese, we have gained insights into the history and population structure of the world's largest ethnic group.
AbstractHuman populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the nonrecombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic exogamy, a marital practice in which men are required to marry women speaking a different language. We identified 2,969 SNPs in the NRY sequences, only 925 of which were previously described. The NRY and mtDNA data showed different sex-specific demographic histories: female effective population size has been larger than that of males through time, which might reflect larger variance in male reproductive success. Both markers show an increase in lineage diversification beginning ∼5,000 years ago, which may reflect the intensification of agriculture, technological innovations, and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, we find similar excesses of NRY versus mtDNA between-population divergence at both the local and continental scale, suggesting long-term stability of female versus male migration. We also find evidence of the impact of sociocultural practices on diversity patterns. Finally, our study highlights the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between sexes.
AbstractBacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness–expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.
AbstractUnder the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (Ne). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by ∼45% as Ne is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.
AbstractPhylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
AbstractAdaptive divergence between marine and freshwater (FW) environments is important in generating phyletic diversity within fishes, but the genetic basis of this process remains poorly understood. Genome selection scans can identify adaptive loci, but incomplete knowledge of genotype–phenotype connections makes interpreting their significance difficult. In contrast, association mapping (genome-wide association mapping [GWAS], random forest [RF] analyses) links genotype to phenotype, but offer limited insight into the evolutionary forces shaping variation. Here, we combined GWAS, RF, and selection scans to identify loci important in adaptation to FW environments. We utilized FW-native and brackish water (BW)-native populations of Atlantic killifish (Fundulus heteroclitus) as well as a naturally admixed population between the two. We measured morphology and multiple physiological traits that differ between populations and may contribute to osmotic adaptation (salinity tolerance, hypoxia tolerance, metabolic rate, body shape) and used a reduced representation approach for genome-wide genotyping. Our results show patterns of population divergence in physiological capabilities that are consistent with local adaptation. Population genomic scans between BW-native and FW-native populations identified genomic regions evolving by natural selection, whereas association mapping revealed loci that contribute to variation for each trait. There was substantial overlap in the genomic regions putatively under selection and loci associated with phenotypic traits, particularly for salinity tolerance, suggesting that these regions and genes are important for adaptive divergence between BW and FW environments. Together, these data provide insight into the mechanisms that enable diversification of fishes across osmotic boundaries.
AbstractCytolytic pore-forming proteins are widespread in living organisms, being mostly involved in both sides of the host–pathogen interaction, either contributing to the innate defense or promoting infection. In venomous organisms, such as spiders, insects, scorpions, and sea anemones, pore-forming proteins are often secreted as key components of the venom. Coluporins are pore-forming proteins recently discovered in the Mediterranean hematophagous snail Cumia reticulata (Colubrariidae), highly expressed in the salivary glands that discharge their secretion at close contact with the host. To understand their putative functional role, we investigated coluporins' molecular diversity and evolutionary patterns. Coluporins is a well-diversified family including at least 30 proteins, with an overall low sequence similarity but sharing a remarkably conserved actinoporin-like predicted structure. Tracking the evolutionary history of the molluscan porin genes revealed a scattered distribution of this family, which is present in some other lineages of predatory gastropods, including venomous conoidean snails. Comparative transcriptomic analyses highlighted the expansion of porin genes as a lineage-specific feature of colubrariids. Coluporins seem to have evolved from a single ancestral porin gene present in the latest common ancestor of all Caenogastropoda, undergoing massive expansion and diversification in this colubrariid lineage through repeated gene duplication events paired with widespread episodic positive selection. As for other parasites, these findings are congruent with a "one-sided arms race," equipping the parasite with multiple variants in order to broaden its host spectrum. Overall, our results pinpoint a crucial adaptive role for coluporins in the evolution of the peculiar trophic ecology of vampire snails.
AbstractVariola virus is at risk of re-emergence either through accidental release, bioterrorism, or synthetic biology. The use of phylogenetics and phylogeography to support epidemic field response is expected to grow as sequencing technology becomes miniaturized, cheap, and ubiquitous. In this study, we aimed to explore the use of common VARV diagnostic targets hemagglutinin (HA), cytokine response modifier B (CrmB), and A-type inclusion protein (ATI) for phylogenetic characterization as well as the representativeness of modelling strategies in phylogeography to support epidemic response should smallpox re-emerge. We used Bayesian discrete-trait phylogeography using the most complete data set currently available of whole genome (n = 51) and partially sequenced (n = 20) VARV isolates. We show that multilocus models combining HA, ATI, and CrmB genes may represent a useful heuristic to differentiate between VARV Major and subclades of VARV Minor which have been associated with variable case-fatality rates. Where whole genome sequencing is unavailable, phylogeography models of HA, ATI, and CrmB may provide preliminary but uncertain estimates of transmission, while supplementing whole genome models with additional isolates sequenced only for HA can improve sample representativeness, maintaining similar support for transmission relative to whole genome models. We have also provided empirical evidence delineating historic international VARV transmission using phylogeography. Due to the persistent threat of re-emergence, our results provide important research for smallpox epidemic preparedness in the posteradication era as recommended by the World Health Organisation.
AbstractGenes are "born," and eventually they "die." These processes shape the phenotypic evolution of organisms and are hence of great biological interest. If genes die in plants, they generally do so quite rapidly. Here, we describe the fate of GOA-like genes that evolve in a dramatically different manner. GOA-like genes belong to the subfamily of Bsister genes of MIKC-type MADS-box genes. Typical MIKC-type genes encode conserved transcription factors controlling plant development. We show that ABS-like genes, a clade of Bsister genes, are indeed highly conserved in crucifers (Brassicaceae) maintaining the ancestral function of Bsister genes in ovule and seed development. In contrast, their closest paralogs, the GOA-like genes, have been undergoing convergent gene death in Brassicaceae. Intriguingly, erosion of GOA-like genes occurred after millions of years of coexistence with ABS-like genes. We thus describe Delayed Convergent Asymmetric Degeneration, a so far neglected but possibly frequent pattern of duplicate gene evolution that does not fit classical scenarios. Delayed Convergent Asymmetric Degeneration of GOA-like genes may have been initiated by a reduction in the expression of an ancestral GOA-like gene in the stem group of Brassicaceae and driven by dosage subfunctionalization. Our findings have profound implications for gene annotations in genomics, interpreting patterns of gene evolution and using genes in phylogeny reconstructions of species.
Nature provides countless examples of evolutionary arms races, in which species develop adaptations and counter-adaptations in a struggle for survival and reproduction. Such arms races are common between predator and prey or between parasite and host. Understanding this coevolutionary process can aid in our ability to develop necessary countermeasures, such as overcoming bacterial resistance to antibiotics.
AbstractGene duplication and loss contribute to gene content differences as well as phenotypic divergence across species. However, the extent to which gene content varies among closely related plant species and the factors responsible for such variation remain unclear. Here, using the Solanaceae family as a model and Pfam domain families as a proxy for gene families, we investigated variation in gene family sizes across species and the likely factors contributing to the variation. We found that genes in highly variable families have high turnover rates and tend to be involved in processes that have diverged between Solanaceae species, whereas genes in low-variability families tend to have housekeeping roles. In addition, genes in high- and low-variability gene families tend to be duplicated by tandem and whole genome duplication, respectively. This finding together with the observation that genes duplicated by different mechanisms experience different selection pressures suggest that duplication mechanism impacts gene family turnover. We explored using pseudogene number as a proxy for gene loss but discovered that a substantial number of pseudogenes are actually products of pseudogene duplication, contrary to the expectation that most plant pseudogenes are remnants of once-functional duplicates. Our findings reveal complex relationships between variation in gene family size, gene functions, duplication mechanism, and evolutionary rate. The patterns of lineage-specific gene family expansion within the Solanaceae provide the foundation for a better understanding of the genetic basis underlying phenotypic diversity in this economically important family.
AbstractEndogenous viral sequences in eukaryotic genomes, such as those derived from plant pararetroviruses (PRVs), can serve as genomic fossils to study viral macroevolution. Many aspects of viral evolutionary rates are heterogeneous, including substitution rate differences between genes. However, the evolutionary dynamics of this viral gene rate heterogeneity (GRH) have been rarely examined. Characterizing such GRH may help to elucidate viral adaptive evolution. In this study, based on robust phylogenetic analysis, we determined an ancient endogenous PRV group in Oryza genomes in the range of being 2.41–15.00 Myr old. We subsequently used this ancient endogenous PRV group and three younger groups to estimate the GRH of PRVs. Long-term substitution rates for the most conserved gene and a divergent gene were 2.69 × 10−8 to 8.07 × 10−8 and 4.72 × 10−8 to 1.42 × 10−7 substitutions/site/year, respectively. On the basis of a direct comparison, a long-term GRH of 1.83-fold was identified between these two genes, which is unexpectedly low and lower than the short-term GRH (>3.40-fold) of PRVs calculated using published data. The lower long-term GRH of PRVs was due to the slightly faster rate decay of divergent genes than of conserved genes during evolution. To the best of our knowledge, we quantified for the first time the long-term GRH of viral genes using paleovirological analyses, and proposed that the GRH of PRVs might be heterogeneous on time scales (time-dependent GRH). Our findings provide special insights into viral gene macroevolution and should encourage a more detailed examination of the viral GRH.
AbstractVitellogenin (Vtg) is a glycolipophosphoprotein produced by oviparous and ovoviviparous species and is the precursor protein of the yolk, an essential nutrient reserve for embryonic development and early larval stages. Vtg is encoded by a family of paralog genes whose number varies in the different vertebrate lineages. Its evolution has been the subject of considerable analyses but it remains still unclear. In this work, microsyntenic and phylogenetic analyses were performed in order to increase our knowledge on the evolutionary history of this gene family in vertebrates. Our results support the hypothesis that the vitellogenin gene family is expanded from two genes both present at the beginning of vertebrate radiation through multiple independent duplication events occurred in the diverse lineages.
AbstractIt is often unavoidable to combine data from different sequencing centers or sequencing platforms when compiling data sets with a large number of individuals. However, the different data are likely to contain specific systematic errors that will appear as SNPs. Here, we devise a method to detect systematic errors in combined data sets. To measure quality differences between individual genomes, we study pairs of variants that reside on different chromosomes and co-occur in individuals. The abundance of these pairs of variants in different genomes is then used to detect systematic errors due to batch effects. Applying our method to the 1000 Genomes data set, we find that coding regions are enriched for errors, where ∼1% of the higher frequency variants are predicted to be erroneous, whereas errors outside of coding regions are much rarer (<0.001%). As expected, predicted errors are found less often than other variants in a data set that was generated with a different sequencing technology, indicating that many of the candidates are indeed errors. However, predicted 1000 Genomes errors are also found in other large data sets; our observation is thus not specific to the 1000 Genomes data set. Our results show that batch effects can be turned into a virtue by using the resulting variation in large scale data sets to detect systematic errors.
AbstractChlamydiae are an example of obligate intracellular bacteria that possess highly reduced, compact genomes (1.0–3.5 Mbp), reflective of their abilities to sequester many essential nutrients from the host that they no longer need to synthesize themselves. The Chlamydiae is a phylum with a very wide host range spanning mammals, birds, fish, invertebrates, and unicellular protists. This ecological and phylogenetic diversity offers ongoing opportunities to study intracellular survival and metabolic pathways and adaptations. Of particular evolutionary significance are Chlamydiae from the recently proposed Ca. Parilichlamydiaceae, the earliest diverging clade in this phylum, species of which are found only in aquatic vertebrates. Gill extracts from three Chlamydiales-positive Australian aquaculture species (Yellowtail kingfish, Striped trumpeter, and Barramundi) were subject to DNA preparation to deplete host DNA and enrich microbial DNA, prior to metagenome sequencing. We assembled chlamydial genomes corresponding to three Ca. Parilichlamydiaceae species from gill metagenomes, and conducted functional genomics comparisons with diverse members of the phylum. This revealed highly reduced genomes more similar in size to the terrestrial Chlamydiaceae, standing in contrast to members of the Chlamydiae with a demonstrated cosmopolitan host range. We describe a reduction in genes encoding synthesis of nucleotides and amino acids, among other nutrients, and an enrichment of predicted transport proteins. Ca. Parilichlamydiaceae share 342 orthologs with other chlamydial families. We hypothesize that the genome reduction exhibited by Ca. Parilichlamydiaceae and Chlamydiaceae is an example of within-phylum convergent evolution. The factors driving these events remain to be elucidated.
AbstractPrediction of evolutionary trajectories has been an elusive goal, requiring a deep knowledge of underlying mechanisms that relate genotype to phenotype plus understanding how phenotype impacts organismal fitness. We tested our ability to predict molecular regulatory evolution in a bacteriophage (T7) whose RNA polymerase (RNAP) was altered to recognize a heterologous promoter differing by three nucleotides from the wild-type promoter. A mutant of wild-type T7 lacking its RNAP gene was passaged on a bacterial strain providing the novel RNAP in trans. Higher fitness rapidly evolved. Predicting the evolutionary trajectory of this adaptation used measured in vitro transcription rates of the novel RNAP on the six promoter sequences capturing all possible one-step pathways between the wild-type and the heterologous promoter sequences. The predictions captured some of the regulatory evolution but failed both in explaining 1) a set of T7 promoters that consistently failed to evolve and 2) some promoter evolution that fell outside the expected one-step pathways. Had a more comprehensive set of transcription assays been undertaken initially, all promoter evolution would have fallen within predicted bounds, but the lack of evolution in some promoters is unresolved. Overall, this study points toward the increasing feasibility of predicting evolution in well-characterized, simple systems.
AbstractThe Lennoaceae, a small monophyletic plant family of root parasites endemic to the Americas, are one of the last remaining independently evolved lineages of parasitic angiosperms lacking a published plastome. In this study, we present the assembled and annotated plastomes of two species spanning the crown node of Lennoaceae, Lennoa madreporoides and Pholisma arenarium, as well as their close autotrophic relative from the sister family Ehretiaceae, Tiquilia plicata. We find that the plastomes of L. madreporoides and P. arenarium are similar in size and gene content, and substantially reduced compared to T. plicata, consistent with trends seen in other holoparasitic lineages. In particular, most plastid genes involved in photosynthesis function have been lost, whereas housekeeping genes (ribosomal protein-coding genes, rRNAs, and tRNAs) are retained. One notable exception is the persistence of a rbcL open reading frame in P. arenarium but not L. madreporoides suggesting a nonphotosynthetic function for this gene. Of the retained coding genes, dN/dS ratios indicate that some remain under purifying selection, whereas others show relaxed selection. Overall, this study supports the mounting evidence for convergent plastome evolution in flowering plants following the shift to heterotrophy.
AbstractFeather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.
AbstractAphids are a diverse group of taxa that contain agronomically important species, which vary in their host range and ability to infest crop plants. The genome evolution underlying agriculturally important aphid traits is not well understood. We generated draft genome assemblies for two aphid species: Myzus cerasi (black cherry aphid) and the cereal specialist Rhopalosiphum padi. Using a de novo gene prediction pipeline on both these, and three additional aphid genome assemblies (Acyrthosiphon pisum, Diuraphis noxia, and Myzus persicae), we show that aphid genomes consistently encode similar gene numbers. We compare gene content, gene duplication, synteny, and putative effector repertoires between these five species to understand the genome evolution of globally important plant parasites. Aphid genomes show signs of relatively distant gene duplication, and substantial, relatively recent, gene birth. Putative effector repertoires, originating from duplicated and other loci, have an unusual genomic organization and evolutionary history. We identify a highly conserved effector pair that is tightly physically linked in the genomes of all aphid species tested. In R. padi, this effector pair is tightly transcriptionally linked and shares an unknown transcriptional control mechanism with a subset of ∼50 other putative effectors and secretory proteins. This study extends our current knowledge on the evolution of aphid genomes and reveals evidence for an as-of-yet unknown shared control mechanism, which underlies effector expression, and ultimately plant parasitism.
AbstractThe frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.
AbstractPlastid genomes display remarkable organizational stability over evolutionary time. From green algae to angiosperms, most plastid genomes are largely collinear, with only a few cases of inversion, gene loss, or, in extremely rare cases, gene addition. These plastome insertions are mostly clade-specific and are typically of nuclear or mitochondrial origin. Here, we expand on these findings and present the first family-level survey of plastome evolution in ferns, revealing a novel suite of dynamic mobile elements. Comparative plastome analyses of the Pteridaceae expose several mobile open reading frames that vary in sequence length, insertion site, and configuration among sampled taxa. Even between close relatives, the presence and location of these elements is widely variable when viewed in a phylogenetic context. We characterize these elements and refer to them collectively as Mobile Open Reading Frames in Fern Organelles (MORFFO). We further note that the presence of MORFFO is not restricted to Pteridaceae, but is found across ferns and other plant clades. MORFFO elements are regularly associated with inversions, intergenic expansions, and changes to the inverted repeats. They likewise appear to be present in mitochondrial and nuclear genomes of ferns, indicating that they can move between genomic compartments with relative ease. The origins and functions of these mobile elements are unknown, but MORFFO appears to be a major driver of structural genome evolution in the plastomes of ferns, and possibly other groups of plants.
AbstractThe transcriptome of the venom duct of the Atlantic piscivorous cone species Chelyconus ermineus (Born, 1778) was determined. The venom repertoire of this species includes at least 378 conotoxin precursors, which could be ascribed to 33 known and 22 new (unassigned) protein superfamilies, respectively. Most abundant superfamilies were T, W, O1, M, O2, and Z, accounting for 57% of all detected diversity. A total of three individuals were sequenced showing considerable intraspecific variation: each individual had many exclusive conotoxin precursors, and only 20% of all inferred mature peptides were common to all individuals. Three different regions (distal, medium, and proximal with respect to the venom bulb) of the venom duct were analyzed independently. Diversity (in terms of number of distinct members) of conotoxin precursor superfamilies increased toward the distal region whereas transcripts detected toward the proximal region showed higher expression levels. Only the superfamilies A and I3 showed statistically significant differential expression across regions of the venom duct. Sequences belonging to the alpha (motor cabal) and kappa (lightning-strike cabal) subfamilies of the superfamily A were mainly detected in the proximal region of the venom duct. The mature peptides of the alpha subfamily had the α4/4 cysteine spacing pattern, which has been shown to selectively target muscle nicotinic-acetylcholine receptors, ultimately producing paralysis. This function is performed by mature peptides having a α3/5 cysteine spacing pattern in piscivorous cone species from the Indo-Pacific region, thereby supporting a convergent evolution of piscivory in cones.
AbstractThis work presents a systematic approach to study the conservation of genes between fruit flies and mammals. We have listed 971 Drosophila genes involved in female reproduction at the ovarian level and systematically looked for orthologs in the Ciona, zebrafish, coelacanth, lizard, chicken, and mouse. Depending on the species, the percentage of these Drosophila genes with at least one ortholog varies between 69% and 78%. In comparison, only 42% of all the Drosophila genes have an ortholog in the mouse genome (P < 0.0001), suggesting a dramatically higher evolutionary conservation of ovarian genes. The 177 Drosophila genes that have no ortholog in mice and other vertebrates correspond to genes that are involved in mechanisms of oogenesis that are specific to the fruit fly or the insects. Among 759 genes with at least one ortholog in the zebrafish, 73 have an expression enriched in the ovary in this species (RNA-seq data). Among 760 genes that have at least one ortholog in the mouse; 76 and 11 orthologs are reported to be preferentially and exclusively expressed in the mouse ovary, respectively (based on the UniGene expressed sequence tag database). Several of them are already known to play a key role in murine oogenesis and/or to be enriched in the mouse/zebrafish oocyte, whereas others have remained unreported. We have investigated, by RNA-seq and real-time quantitative PCR, the exclusive ovarian expression of 10 genes in fish and mammals. Overall, we have found several novel candidates potentially involved in mammalian oogenesis by an evolutionary approach and using the fruit fly as an animal model.


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(CPJ/IFEX) - The following is a 20 April 2007 CPJ press release:
In Rwanda, publication of a letter draws a prison term
New York, April 20, 2007 - A court in the capital, Kigali, today sentenced Agnès Nkusi-Uwimana, director of the bi-monthly journal Umurabyo, to a year in prison on charges linked to the publication of a reader's letter critical of the government, according to local journalists and press freedom group Journaliste en Danger. Nkusi-Uwimana has been jailed since January 12 on the charges.
Convicted of divisionism, sectarianism, and libel, Nkusi-Uwimana was also ordered to pay damages of 400,000 Rwandan francs (US$760), according to the same sources. She had pleaded guilty to the charges in exchange for a reduction in the five-year sentence sought by the state prosecutor. Nkusi-Uwimana did not have a defense lawyer present in court, but she planned to file an appeal, local journalists told CPJ.
"It is completely unacceptable that Agnès Nkusi-Uwimana should spend a year behind bars for publishing a reader's letter," said CPJ Executive Director Joel Simon. "Her conviction is another troubling example of the authorities' use of charges of sectarianism and criminal libel to silence crucial journalism. This must stop."
The charges stemmed from an unsigned letter published on January 1 that compared ethnic killings during President Paul Kagame's Tutsi-dominated administration to those of the previous Hutu regime, according to CPJ research.
Kagame's regime has continually used accusations of "divisionism" and "sectarianism" to silence critics, including those in the media. In a statement released last month, the Rwandan League for the Promotion and Defense of Human Rights stated that "some independent newspapers like Umuco and Rushyashya are being accused of an ideology of genocide and of separatism, without relevant evidence, in a scheme to muzzle them," according to the pro-government daily The New Times.
CPJ is a New York-based, independent, nonprofit organization that works to safeguard press freedom worldwide. For more information, visit http://www.cpj.org.
Court sentences newspaper director to one year in prison for publishing letter criticising government
(CPJ/IFEX) - The following is a 20 April 2007 CPJ press release:

subset: commoncrawl


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Perfect pick: Izzo's son makes right call as Duke pulls away for 71-61 win over Michigan St.
INDIANAPOLIS – Friday night was the one time Tom Izzo hoped his only son made the wrong choice.
Turns out, the 12-year-old got it exactly right.
Just days after word leaked that Izzo's son had picked Duke to beat his dad's team in the Midwest Regional final, Seth Curry scored 29 points to lead the Blue Devils to a 71-61 victory over the Spartans.
"I felt we never got on track," Izzo said. "We were in foul trouble the whole game and that seemed like that wasn't going to end."
For the Spartans (27-9), it never really did.
Keith Appling scored 16 points despite playing with a brace over his injured right shoulder. Adreian Payne had 14 points and 10 rebounds. But the rest of the Spartans struggled on a night they were just flat out of sync.
Curry "made great shots and he had good looks at the basket," Payne said. "When someone's making shots like that and we had the momentum, yeah, it is deflating."
Curry's big game put coach Mike Krzyzewski on the verge of a 12th Final Four appearance, which would equal John Wooden's record. Krzyzewski is tied for second with North Carolina's Dean Smith.
Next up for the second-seeded Blue Devils is Louisville (32-5), a 77-69 winner over Oregon in the night's first game, and it could be a virtual home game for the top-seeded Cardinals just about 100 miles from their campus. Plus, Louisville coach Rick Pitino is trying for his seventh Final Four, which would tie him for fourth with Roy Williams.
But Duke beat Louisville 76-71 on Nov. 24, and with Curry shooting like this, the Blue Devils just might have the advantage.
"Seth was just at a different level than anyone else on the court offensively tonight," Krzyzewski said. "To get 29 points in a game like this against a good team is just incredible."
The win comes 16 months after Duke beat Michigan State to give Krzyzewski the NCAA record for wins. And now, one year after falling to Lehigh in the second round of the tournament, Duke has reached the regional final in the same venue where it won its fourth national title — just as Izzo's son predicted.
Third-seeded Michigan State couldn't keep up with Curry and Duke's other shooters. Rasheed Sulaimon had 16 points for the Blue Devils, making 12 of 14 from the free-throw line, and Mason Plumlee finished with 14 points and seven rebounds in the return to his home state.
And the biggest difference was Curry.
"Curry's a fifth-year senior. He's wise. He knows how to come off things and get open," Izzo said after falling to 1-3 in NCAA tourney play against Krzyzewski. "I think our freshmen got a little lesson tonight."
Curry's sixth 3-pointer of the game broke a 38-38 tie early in the second half, sending Duke on a 9-0 run. It also matched the school record for most 3s in an NCAA tourney game, most recently accomplished by Jason Williams on March 22, 2001, against UCLA.
The Blue Devils never trailed again.
"Honestly, I was just trying to help my shot. I got a few to go early," Curry said. "I feel like every time I take a shot it's going to go down and nothing felt different tonight."
The game was billed as an entertaining contest between two of college basketball's most successful coaches — and it lived up to the hype.
The first half was played to a near draw with four ties and eight lead changes.
Michigan State grabbed an 18-17 lead on Derrick Nix's tip-in with 9:52 left in the first half, but Curry then scored nine points in an 11-2 run for the Blue Devils. He was fouled by Travis Trice while attempting a 3-pointer and made all three free throws to make it 28-20 with 4:59 remaining.
Back came the Spartans, who clamped down on defense and closed to 32-31 at halftime.
But Curry's early second-half scoring spree forced Michigan State to play catch-up the rest of the way. The Spartans pulled within seven with 1:32 to go, but couldn't get any closer after trailing by as much as 13 in the second half.
"We knew we would have to play at that level. They're a little more athletic than we are," Krzyzewski said. "We had to try to match that and tonight we were able to do that. I'm glad it's not a seven-game series because I'm not sure we'd be able to continue to do it. But tonight we were able to do it."


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Alumni & Parent Programs
The Howard Years at Lewis & Clark: 1960-1981
Date: 3:00pm - 6:00pm PDT November 1, 2013
Join us for special events honoring and celebrating the legacy of President John R. Howard, who led Lewis & Clark from 1960 to 1981. His accomplishments include the launching of the overseas study program, the merger with Northwestern School of Law, construction of major buildings, and many more.
Friday, November 1
3 p.m. - exhibition of President Howard's accomplishments at Lewis & Clark. Diane Gregg Pavilion.
4 p.m. - program featuring faculty, administrators, and alumni, including President Barry Glassner, life trustee Robert B. Pamplin '64, Stephen Dow Beckham, Dinah Dodds, Vern Jones, Ron Lansing, and Jean Ward. Agnes Flanagan Chapel.
5 p.m. - reception. Stamm Dining Room.
Please let us know if you are planning on attending so that we may plan the space and catering in advance. All of the events are free.


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Stat Surveys Upgrading Its Divisional Reporting
October 19, 2013 by Justin Leighty Comments Off on Stat Surveys Upgrading Its Divisional Reporting
Statistical Surveys Inc. (SSI) has rolled out a new feature with the release Friday (Oct. 18) of August's retail RV sales report, according to Tom Walworth, president of the Grand Rapids, Mich.-based firm.
The report now has a page detailing sales numbers by divisions of RV companies on the towable side.
"We're adding this to segregate the data in a little bit different fashion on that one page so that people can look at the strength of (various) divisions," Walworth said.
The goal, he added, is to make data comparisons easier.
"We've never had that page before. For us it's a little scary. It's a change in reporting," Walworth said, adding that all the old preexisting data will remain.
"I think when we were talking to our customer base, they said that there was some confusion developing in using the reports, and we thought, 'well, what can we do to minimize that?' We were going to put a whole new system in place, but I thought we could address it by something as simple as a new division section.
"By adding this divisional page, we certainly didn't want to drop anybody out of the reports. We defined them differently so dealers, manufacturers and lenders can look at it and it gives them a better feel for the market," Walworth explained.
The divisional section will display unit volume and market share, including two-year percentage of change for volume and share.
With this new approach, SSI also will change the definitions in the model section to keep things consistent, Walworth noted.
Manufacturers who choose to break out their models will have the benefit of being compared to competitive models. "The model section has kind of been a division of models, divisions and manufacturers," Walworth said. "When the dealers are looking to buy product and they see XYZ product is performing so and so, they'll have a better idea. It cleans up the model page.
"What was happening before is some of the manufacturers were trying to improve their ranking by combining models together. So, let's say they had six models they combined into two or into one. Well, guess what? Their ranking goes up in the model page," he said.
All in all, the changes will allow SSI's subscribers to get more of an apples-to-apples comparison, Walworth said.


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RM419.00 RM649.00 You Save 35% (RM230.00)
The Ergobaby Organic Carrier has all the advantages of the Ergobaby Original Carrier, crafted with soft 100% certified organic cotton twill and sateen.
The carrier has padded shoulder straps and a waist belt to comfortably distribute baby's weight between your shoulders and hips.
The carrier holds and cradles your baby just the way you do, with your baby's legs properly supported in a natural sitting position.


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Extra Points: Aztecs' Escobar in the mix with top tight ends
Philadelphia, PA – Most of the attention surrounding the tight ends available in the upcoming NFL Draft has focused on the two potential first round picks -- Notre Dame's Tyler Eifert and Stanford's Zach Ertz.
San Diego State's Gavin Escobar, however, may provide the most bang for the buck when it's all said and done.
Although he's not quite as athletic as Eifert and doesn't have the high- profile program on his resume like the Fighting Irish star or Ertz, the 6- foot-6, 253-pound Escobar compares favorably to his peers.
A 2012 All-Mountain West first-team selection and a semifinalist for the Mackey Award as the nation's top collegiate tight end, Escobar led the Aztecs in receptions, yards and touchdowns as a junior before deciding to come out a year early.
"Ultimately I was just really confident in my abilities to play at the next level," Escobar said when discussing why he decided to leave college behind. "Over the few seasons I've been playing, I've been playing against guys in the NFL now."
A high school basketball background has a lot of people comparing Escobar to another San Diego tight end, the Chargers' Antonio Gates.
Like the five-time NFL All-Pro, who was once named runner-up for Mr. Basketball in the state of Michigan, the hardwood seems to have helped Escobar develop excellent hand-eye coordination, body control and leaping ability, which makes him a great jump-ball player in red zone situations.
"The way they use tight ends these days is really translating with my body frame and abilities," Escobar said, "being able to be a red zone target and threat, being able to create mismatches."
Meanwhile, Escobar's hands, perhaps the best of any tight end in this draft class, really fits the role of today's slot threats, making Escobar a potential seam-buster and matchup headache in the mold of the Saints' Jimmy Graham or the Patriots' Aaron Hernandez.
"Watching him catch a football is like ballet." NFL Network draft analyst Mike Mayock said.
A slower than expected 40-time (4.84) at the NFL's Scouting Combine certainly gave some scouts reason to hit pause but Escobar answered at least some of the questions by improving his time to the 4.7 range at San Diego State's pro day late last month.
The bigger knock on Escobar, though, is the fact that he rarely lined up as a traditional tight end with the Aztecs so his technique as a blocker is very raw, and his ability to hold up and block consistently at the NFL level is suspect.
That said, he has the frame to eventually excel with sound and patient coaching and the continued specialization of the game may make his greatest deficiency less of a black mark than it would have been in past years.
"They moved me around a lot," Escobar said when talking about the Aztecs' system. "I'm fine with my hand in the dirt. I think some people look past my blocking ability because of my pass catching ability. It' something I'm willing to do and I'm always working hard to get better at."
Well over 20 teams were represented at San Diego State's pro day and all of them reportedly spoke to Escobar.
Local reporters indicated that the NFC champion San Francisco 49ers, who lost backup Delanie Walker in free agency, along with Tampa Bay and Miami showed the most interest in Escobar, a player who seems to have now cemented himself as a likely second-round pick.
"The feedback I've been getting from most teams is they like my pass catching ability," Escobar said. "They're a little concerned with the run game. I've been trying to tell them I'm willing to do that and I've been working hard at that, and over time I can only improve."
1. - Tyler Eifert, Notre Dame
2. - Zach Ertz, Stanford
3. - Gavin Escobar, San Diego State
4. - Travis Kelce, Cincinnati
5. - Vance McDonald, Rice
6. - Jordan Reed, Florida
7. - Levine Toilolo, Stanford
8. - Chris Gragg, Arkansas
9. - Dion Sims, Michigan State
10. - Ryan Otten, San Kose State
Best Route Runner: Zach Ertz, Stanford
Fastest: Jordan Reed, Florida
Best Hands: Gavin Escobar, San Diego State
Best Blocker: Levine Toilolo, Stanford
Underrated: Nick Kasa, Colorado
Biggest Risk: Dion Sims, Michigan State


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A Simple Single-Child Model
Consider the following logical data model:
There are multiple Companies
Each Company has many Projects
Each Project has many Tasks
Each Task has a Status, selected from a global list of pre-defined Statuses.
Status Companies
\ |
\ |
\ Projects
\ |
\ |
Let us say that we decide that the primary key of Companies, Projects, Tasks, and Status are all Identity (auto-number) columns, since we would like to auto-generate primary keys for those tables.
So, we have something like...
posted @ Wednesday, August 13, 2008 11:06 AM | Feedback (51) |
Filed Under [
Database Design
Most people know about cascading updates and deletes, but did you know there are two other foreign key constraint options you can use to maintain referential integrity?
Read all about them in my latest article over at SQLTeam.com.
These features, introduced with SQL Server 2005, haven't got a lot of publicity, but they can be very useful. I just used the SET NULL option recently for the first time (inspiring me to put together an article on it) and it works great.
posted @ Wednesday, August 13, 2008 9:56 AM | Feedback (3) |
Filed Under [
Database Design
Always remember that the column names returned in a result set do not have to be the same as what you eventually output at your presentation layer.
For example, suppose you have stored procedure that accepts a @CurrentYear parameter and returns a sales variance between the current year and the previous year for each customer. I often see programmers struggling with writing dynamic SQL to produce output like this:
CustomerID 2008 Total 2007 Total Variance
---------- ---------- ---------- --------
That is, the names of the columns vary based on the data; that is not a good way...
posted @ Wednesday, August 06, 2008 11:43 AM | Feedback (3) |
Filed Under [
Report Writing
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Copyright © Jeff Smith


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The Poet Laureate and the Fraygrants
Robert Pinsky goes toe-to-toe with participants in "The Fray."
Monday, Poet Laureate Robert Pinsky entered "The Fray," Slate's reader-discussion forum, for an hourlong discussion. The following is an edited transcript of the chat.
Robert Pinsky was named poet laureate of the United States in March 1997. His special project as poet laureate is the Favorite Poem Project, which will create an audio and video archive featuring Americans from all walks of life reading aloud a beloved poem. He is the author of five books of poetry, including The Figured Wheel: New and Collected Poems 1965-1995, which was nominated for the Pulitzer Prize and received the 1997 Lenore Marshall Poetry Prize. He is Slate's poetry editor.
What have you been reading lately?
The letters between Ezra Pound and William Carlos Williams: They met in college, and it's wonderful as well as a little sad to follow the devotion, the ups and downs ... Pound spent his last night in America at Williams' house.
Excellent, I will look for it. I used a WCW video--"Voices and Visions," I think--to work with talented middle school students this summer. I also used your poem "Shirt" with the same students.
I find some of the Voices and Visions series wonderful. A video/audio project of my own that I hope we get to is the Favorite Poem Project: The idea is to tape 1,000 Americans of all ages, professions, regions--not necessarily poets--each saying aloud a favorite poem, with a sentence or two about why he/she loves the poem. Bless you for using my "Shirt"--it was on a recent College Board exam. ... I'm both pleased by that and a little dismayed to think I'm being used by ETS to torment the young!
Do you speak your work aloud as you write to hear those sounds?
I do write--and read--with my voice. For me, this is a vocal art.
Mr. Pinsky,
I find the statement that you view poetry as a vocal art quite interesting. Are you saying that what comes out of you as poetry is a thing designed to be spoken? I have said something similar myself, but I was referring to the inner voice we all carry around with us. Is this the voice you speak of, or do you literally mean poetry should be vocalized physically?
I mean "voice" quite literally. I think that part of poetry's unique appeal is that it is a bodily art in which the medium is the audience's body--that is, our voice. When I say a Dickinson poem aloud, my breath is her art's medium. So when I write, I am trying to make something in my voice that will sound good in the reader's own voice, as he/she says or imagines saying the words.
This makes poetry a uniquely intimate, yet public or civic, art.
Mr. Pinsky,
Like NuPlanet, I find this statement most interesting:
"But along with that intellectual pull, there's the physical attraction of the sounds of words; and the two are related, because the allure of the riddle is partly the physical, mysterious presence of sounds that are just beginning to mean something."
It's this line of thought that has led to my interest in "Sound Poetry," exemplified by the works of Tzara, Schwitters, Heidsieck, Haussmann, etc. Strangely enough, this kind of poem is generally met with resistance and/or disapproval from those primarily interested in less marginalized forms. Do you have any thoughts on these poets or on this field in general?
I guess I consider all poetry sound poetry, and there are examples or schools in any art that emphasize one aspect (e.g., the physical) at the expense of others, validly. But the Pinsky family motto is "All of the Above."
Mr. Pinsky,
I think I understand what you say about "our" voice becoming the medium in a bodily sense. I suppose where I differ is that I consider poetry that is specifically designed to be read aloud, as in a public forum, just a different category within the medium. This is partly because I am never consciously aware that the voice I am using to conceive a poem is anything more than just my own private vocalization. Also, I always seem to miss half of what's going on when poetry is presented in any type of theatrical milieu. I find my consciousness interacting with the body or vocal language of the speaker, as well as the environment in which it is presented. The voice option in Slate is a typical example of this. I have read some of the poems and then listened to the author's reading of the same poem. Aside from finding the personality was exactly opposite to what I had conjured during the reading, I now found myself trying to fathom inflections and emphasis in places where I had previously not found any. I guess my question, at this point, would be, am I unique in writing poetry as something I expect to be simply read, rather than recited aloud? And have you encountered this type of resistance(?) or question in your travels within the various poetry circles?
Mr. Pinsky,
I grew up with poetry (my father frequently quoted Eliot and Frost) but fell away for about the last 15 years. Can you recommend any poets, anthologies, magazines, or books to help me catch up? I recently bought Thomas Lux's New and Selected and loved it.
I'm glad you enjoyed Tom Lux's book. Louise Glück has a book about to come out, Vita Nova, that I like a lot, as I did her Meadowlands. I'll also recommend Frank Bidart's Desire. Her publisher is Ecco and his Farrar, Straus. As to anthologies, I've just done one that comes out this month, from Morrow: The Handbook of Heartbreak: 101 Poems of Lost Love and Sorrow. Though the material is sad, I hope the book gives pleasure.
dpiette, Blaise, others,
I hope you consider volunteering to read a poem for my Favorite Poem Project. You can learn about it at http://www.nefa.org, the site of my sponsoring agency, the New England Foundation for the Arts. Or just send the author and title of the poem you'd like to read, and your address name and phone number to me at firstname.lastname@example.com. The volunteers--I have thousands already--will be a valuable archive, aside from the video and audio.
Hello Mr. Pinsky,
I'd like to know your thoughts, as general or as specific as they may be, on canonicity. What works or authors do you consider to be an integral part thereof? What do you think of the notion of "sexiness" in relation to the canon's constituents?
My question springs from a desire to know the ways in which we redefine the canon every so often. Also, as a follow-up, what elements of a work of poetry (or fiction for that matter) make that work canon-worthy? Are there such elements?
As to the canon, it is always changing, always different for each person, always suggests some social core. Like culture, or a culture or a nation, it is made out of motion. It is a form of change.
Mr. Pinsky,
You say that the canon is "always different for each person." How could it be, then, that Chaucer, Shakespeare, Milton, Blake, Wordsworth, et al., are so universally agreed upon? Just how personal is the canon when these literary figures are such a large part of our common epistemology?
What does it mean to be a Jewish poet in an America where ethnicity seems increasingly less important?
As to the idea "How could it be, then, that Chaucer, Shakespeare, Milton, Blake, Wordsworth, et al. are so universally agreed upon." Well, some people think Chaucer is outdated; I personally think Shakespeare though a great, great artist in the plays is often second rate in the sonnets; Pound deprecated Wordsworth and Milton; and some people think Blake is a scoundrel; etc., etc. What lasts is what doesn't bore people, I guess.
Horowitz, I hope you are right that ethnicity is less important. I do think that our terms for these things will seem quaint to our grandchildren. I find "Jewish" an immensely rich, fascinating historical reality that I will be thinking about as long as I live--"ethnicity" is an inadequate term for all these threads and influences from the past that make up any one person: George Herbert through his poetry, and Coleman Hawkins through his music, are our ancestors, too.
Why are you happy to see ethnicity disappear? An America without it would seem awfully bland. Do you envision a day when there are no countries or religions (kudos to John Lennon), nothing to kill or die for?
I don't welcome any cultural reality "disappearing"--I remember your original terms as "less important" and that phrase made me think of racism, blood-hatred, snobbery, etc. Remember, my family motto is "All of the Above," so my Chinese and Hindu and African-American and Islamic heritage is important to me, too.
By the way, if any of you are librarians or teachers, etc., and would like to have a public Favorite Poem reading in your community, my helper Maggie Dietz will send you a how-to kit: firstname.lastname@example.com, or FPP, 236 Bay State Road, Boston, MA 02215.
Let me clarify: To say it is a vocal art does not mean that it is a performative art. I am not thinking of the expert actor or poet or orator performing in a hall so much as I am the person muttering a few lines or a whole memorized poem while in the shower, or driving--or the person reading the poem aloud to a lover, child, one or two friends. "Do you know these lines of Whitman ..." and then the reading. Or just the way I comfort my mind with a few snatches of "Sailing to Byzantium" or whatever ... that's near the center of the art, for me.
That is a perfect clarification. Thank you.
I also do not want anyone to go away with the image that I look down upon the practice of reading poetry aloud. I think what you are trying to do with your "Favorite" poem project is excellent, and very important. Especially for, though not limited to, children. Now here is an area where I know reading poetry aloud has a meaningful and lasting effect. Having spent uncountable hours reciting too many rhymes, riddles, and tattered Golden Books to my kids, I am well aware that it does make a difference. In any case, thanks for dropping in this evening, and I really think you should just pop into the other poetry thread from time to time (you do lurk there, I hope?) and let us pick your brain or vice versa. Ciao.
"The Unseen" is a devastating poem about your visit to Krakow--the concentration camps. The title is perfect--because it's almost what you didn't see that evokes the pain and anger. This kind of poem seems so hard to write. I've tried and failed for the most part.
On a lighter note: Do you still play the sax?
I think there are subjects and feelings one carries around for many years, perhaps noticing them sometimes no more than a limb of one's body, and then one day the opportunity to write that poem somehow appears. I feel as if "The Unseen" is as you say about what one cannot get at--to return to the haunted ruin idea, the part that is left in ruin. And at Auschwitz, the proportion of what is lost, and the dimension of it, is like a cry as big as the universe ...
I do still play the sax, take a lesson with the Boston jazz player Steve Tully whenever I can ... though there is so much travel that I often neglect it ...
A couple of years ago, Garrison Keillor (yes, the Minnesota boy) wrote a scathing article in the Atlantic Monthly called "The Poetry Judge" (it is not online unfortunately) where he had been asked to judge a local poetry competition in XXX town somewhere. He said he wished that he could have given NO awards, because all the poetry was so bad. Is this because he is a crotchety Midwesterner or because poetry is so "easy" to write that anyone who strings a rhyming couplet together is a poet?
And then, why is it so HARD to write good poetry?
Garrison Keillor is a serious lover of poetry and knows what he is talking about; if you ever hear him read a poem aloud, you will know what I mean. He gets it. I can imagine him (he is a grouchy chap) becoming a bit bearish if his beloved art seemed to be taken lightly, or treated as if it were easy, or an amusing sideline, etc.
Something that ties into Garrison Keillor's gruff attitude toward judging a poetry competition is the current phenomenon of poetry "Slams," which appears to be quite fashionable among the young hipster set. While I definitely think it's a good thing for these kids to be channeling their energy into artistic pursuits, I find the competitive attitude at these events rather distasteful. To me it misses the point and fatally detracts from the art. I'll assume there's an element of competition among established poets, as there is in any vocation, but that's not quite the same as these verbal mud-wrestling exhibitions. What other readily available options do you suppose young people interested in honing their poetic skills have today?
Let me say something about the discourse on this thread, where I have lurked from time to time. (Eavesdropping inspired me to suggest this format.) Sometimes the Web leads people to that insulated rudeness so familiar on the highway: People who would be polite on the grocery line are brutish in the anonymity of the car. But this group has attained a generous, courteous kind of discourse, serious without being strident. So I congratulate you all. Thank you all--and as NuPlanet suggests, I hope we can do this again some time.
And please do help with the FPP--addresses and information above.
Good night!
Robert Pinsky


text:
The word brief comes from the Latin brevis (short) that derives from the ancient Greek brahis (short).
From the same root: briefing, briefly, brevity, briefcase, briefness.
In modern Greek:
a) brahis: short
b) brahitis: shortness, brevity
c) brahino: to shorten, to cut down
brahis --> brevis --> brief
See the blog: English words of no apparent Greek origin at: http://ewonago.blogspot.com/