Meeting Name 2010 Caenorhabditis evolution meeting Corresponding author name asdf Corresponding author email asdasdfasdf Title as Author asdf (asd) Author azs (zsd) Author (zsd) Author aszser (zsdf) Abstract asdfa asdfa sdf a asdf asdfasdf asdf DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name asdf Presenting author email asd@boop.com Title title Author first mid last 1234 somewhere somewhere Author f2 m2 la2 no Author f3 l3 affi Abstract long text th thing DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Baer Presenting author email cbaer@ufl.edu Title FASTER MUTATIONAL DECAY OF FITNESS IN GONOCHORISTIC THAN IN SELF-FERTILIZING CAENORHABDITIS Author Charles F. Baer University of Florida Author Joanna Joyner-Matos Eastern Washington University Author Dejerianne Ostrow University of Florida Author Matthew P Salomon University of Florida Author Ambuj Upadhyay University of Nottingham Author Veronica Grigaltchik University of Florida Abstract Evolutionary theory predicts that, all else equal, the mutation rate should evolve to zero because deleterious mutations are so much more prevalent than beneficial mutations. All else is not equal: the mutation rate is never zero. Further, mutation rate demonstrably varies between and within species. In principle, the strength of natural selection to reduce the mutation rate should be stronger in self-fertilizing organisms than in related outcrossing organisms, perhaps much stronger. However, the relative efficacy of selection on mutation rate relative to the many other factors influencing the evolution of any species is poorly understood - that is, what is the empirical relevance of the theory? To address this question we allowed mutations to accumulate in the relative absence of natural selection for ~100 generations in several sets of "mutation accumulation" (MA) lines in several species of gonochoristic Caenorhabditis (C. remanei, C. brenneri, C. sp5); we have previously conducted similar experiments in self-compatible rhabditids. The results are very clear: in every case the rate of mutational decay is substantially greater in the gonochoristic taxa than in the self-compatible C. elegans (~4X greater) and C. briggsae (~2X greater). Residual heterozygosity in the ancestral controls of these MA lines introduces some complications in interpreting the results, but there is reason to believe the results are not primarily due to inbreeding depression resulting from ancestral variation. The results suggest that natural selection operates to optimize the mutation rate in Caenorhabditis and that the strength (or efficiency) of selection differs consistently on the basis of mating system, as predicted by theory. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name DIAZ Presenting author email bzsad@bristol.ac.uk Title DOES THE COST OF PHENOTYPIC PLASTICITY KEEP THE JACK OF ALL TRADES FROM BEING A MASTER OF ANY? AN EXPERIMENT ON Caenorhabditis remanei Author Anaid Diaz University of Bristol Author Jan Lindstrom University of Glasgow Author Daniel T. Haydon University of Glasgow Abstract Virtually all organisms live in a heterogeneous environment. It is commonly assumed that phenotypic plasticity is associated with environments variable in space and/or time, and that such a 'Jack of all trades' genotype would do better than a fixed genotype. On the other hand, a genotype with phenotypic plasticity is expected do worse in a constant environment than a fixed would. The cost of maintaining phenotypic plasticity is commonly associated with the maintenance and production of genetic and cellular machinery to detect and produce the ‘best’ phenotype for the environment. Although the idea of the cost of maintaining phenotypic responses in a constant environment is widely recognised, it has not been demonstrated experimentally. We addressed this question by using long-term selection experiments on a gonochoristic nematode species (Caenorhabditis remanei). Initially, replicates of worms were maintained for 50 generations under two temperature regimes: constant temperature (mean 15°C) and fluctuating environment with the same mean but temperature fluctuating between 5 and 25°C every 12 hours. The objective of this experiment was to select for individuals with different levels of plasticity. Plasticity levels were measured by comparing the ability of a line to maintain high fitness across a temperature gradient. After 50 generations in each environment, populations were transposed between these environments. The objective was to compare differences in fitness of individuals from the two regimes before and after the selection experiment. Comparisons of fitness across the environments will enable to determine if selection for plasticity is costly in a constant environment, and if specialisation to a constant environment carries a cost when transferred to a fluctuating environment. The results of the first experiment showed changes in fitness across temperatures; worms from a fluctuating environment showed wider thermal breath compared to worms selected for a constant environment. This suggests that phenotypic plasticity was favoured in a fluctuating environment and it had some genetic basis. Comparisons of fitness before and after the selection experiment showed that increased phenotypic plasticity potentially incurred a fitness cost. Worms cultured in a fluctuating environment for 50 generations showed reduced fitness when cultured in a constant environment compared to worms in a constant environment at the beginning of the experiment. However, worms cultured in the constant regime and moved to the fluctuating environment showed no differences with worms in a fluctuating environment at the beginning of the experiment. These results suggest that, for this system, there is a potential cost of adapting via phenotypic plasticity but there is not a cost for becoming a fixed genotype. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Wharton Presenting author email david.wharton@stonebow.otago.ac.nz Title Panagrolaimus davidi, an Antarctic nematode model for the survival of extreme environmental stress Author David Alan Wharton Department of Zoology, University of Otago, Dunedin, New Zealand Abstract Nematodes are found in almost all environments, including those where they are often exposed to extreme environmental stress. Panagrolaimus davidi is an Antarctic nematode living associated with moss and algae in terrestrial habitats on the Victoria Land coast that are free of snow and ice for part of the year. It has to survive very variable thermal and hydric environments where liquid water and temperatures suitable for growth are only periodically available. P. davidi can survive complete water loss (anhydrobiosis) and is the only organism that has been shown to survive intracellular ice formation throughout its tissues. It has several cold tolerance strategies, including; freeze avoidance, cryoprotective dehydration, freezing tolerance and anhydrobiosis. The mechanisms involved may include the production of trehalose, ice active proteins and the control of ice nucleation. Do the different survival strategies of P. davidi represent the expression of different gene sets or does the production of stress-related compounds provide protection against a variety of environmental challenges? Other nematodes, including Caenorhabditis elegans, are not so resistant to desiccation and freezing. Comparing the genomes of P. davidi and C. elegans may thus highlight the adaptations that are necessary for the survival of extreme environmental stress. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Schiffer Presenting author email p.schiffer@uni-koeln.de Title 959 NEMATODE GENOMES Author Philipp Heinrich Schiffer Universität zu Köln, Zoologisches Institut, Köln, NRW, Germany Author Sujai Kumar The University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, Scotland, UK Author Mark Blaxter The University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, Scotland, UK Abstract There are 23,000 described species of nematodes, and an estimated 2-10 million species exist. Established model organisms (particularly Caenorhabditis elegans) have given invaluable new insights into core biological processes and underpinned advances in biomedical science. Being the first metazoan for which the genome was fully sequenced, C. elegans founded metazoan genomic research. Recently nematologists have turned their attention from a few model species to a diverse array of nematodes. Some have already sequenced ‘their’ nematode of interest, or are in the process of doing so (we have counted over 60 species with significant sequencing efforts underway). Next generation sequencing technologies can already deliver 100-fold coverage of ten new genomes in under a week on a single instrument, and costs per genome are declining rapidly. Consequently, the time has come to call for a large number of nematode genomes to be sequenced in the imminent future – 959 is an appealing mark to set, being the number of somatic cells in the female hermaphrodite C. elegans and thus standing for a milestone in developmental biology (the embryonic lineage of C. elegans from fertilized zygote to fertile adult). Just as the tree of the C. elegans embryonic lineage was a key underpinning of later work on this model nematode, we hope that a Nematoda phylogeny decorated with 959 genome-sequenced taxa will underpin the phylogenetically-informed investigation of nematode biology in general. [Obviously, more is always better, so 1031 genomes (the number of cells in male C. elegans) would be fine also…] This nematode genomic programme will offer an opportunity for coordinated and targeted analyses: either bringing experts on one particular process, pathway or gene family together to examine diversity across species, or nucleating interest groups focusing on particular clades of the nematode tree. The addition of even more nematode genomes will allow the specific instance of C. elegans to be contextualised and will, amongst other fields, fuel research on comparative genomics, the evolutionary biology of genome change, the phylogeny of nematodes, developmental pathways, and the biology of the many parasitic nematodes. We invite everyone to make their plans and dreams public: visit the wiki website http://1000.nematodegenomes.org and join this initiative. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Camps Presenting author email Julia.Camps@uni-koeln.de Title THE WAY HOW TO ESTABLISH DIFFERENCES ALONG THE A-P AXIS VARIES AMONG CLOSELY RELATED NEMATODES Author Julia Camps University of Cologne, Zoological Institute Author Michael Kroiher University of Cologne, Zoological Institute Author Einhard Schierenberg University of Cologne, Zoological Institute Abstract Asymmetric cell division plays a crucial role in axis determination during the early embryonic development of Caenorhabditis elegans. Prior to the first division an asymmetric distribution of cytoplasmatic components takes place in the embryo which leads to a germline soma separation already in the 2 cell stage. The mRNA of the mex 3 gene is only found in the anterior part of the early C. elegans embryo. This localisation of the mex 3 gene product is necessary for correct anterior pattern formation. MEX 3 Protein, a posttranscriptional regulator of the pal 1 gene, binds the 3’ untranslated region of the pal 1 mRNA and initiates its degradation. Due to this interaction no co localisation of mex 3 and pal 1 gene products is found in C. elegans. Instead, expression domains are clearly separated during early developmental stages. Mex 3 mRNA is located in the anterior, while pal 1 mRNA can be detected only in the posterior part. In contrast, in Diploscapter coronatus the distribution of mex 3 mRNA differs dramatically from C. elegans even although belong to the same phylogenetic clade. In D. coronatus mex 3 mRNA is located in the posterior part of the embryo. We could show, that mex 3 and pal 1 mRNA are co localised in the early D. coronatus embryo suggesting major differences in the cell specification mechanisms of D. coronatus and C. elegans at this stage of development. Much later, during morphogenesis, we found a second expression domain of mex 3 and pal 1 mRNA absent in C. elegans. At this time mex 3 mRNA is located in the anterior and pal 1 mRNA in the posterior region of the developing D. coronatus embryo. These results lead to the question to what extend mex 3 and pal 1 are involved in the establishment of the anterior-posterior body axis in D. coronatus or whether they fulfil a different function in cell specification during embryogenesis in this species. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Holroyd Presenting author email neh@sanger.ac.uk Title Parasitic Helminth Genomes at the Wellcome Trust Sanger Institute Abstract Despite their importance globally, both medically and economically, parasitic helminth research has remained relatively untouched by genomics. The Wellcome Trust Sanger Institute (WTSI) is committed to producing reference genomes using de novo sequencing approaches for a cross-phyla list of parastic helminths that include hookworms, whipworms, threadworms and the filarial parasites. We aim to uncover the genomic basis for differences in the biology of these parasites. Presented here will be an overview of nematode genomic projects at WTSI and the approaches we are employing. The reference genomes are being produced using a mixture of sequencing technologies (Illumina, 454 and limited capillary sequence data). Manual improvement of the assemblies is being performed in silica and employing custom capillary sequencing. Several software packages support this process, enabling both large scale global viewing of the genomic and associated data, and in depth manipulation down to the base level. De novo sequencing relies heavily upon reliable mapping information. We are using a number of different mapping sources including genetic markers, happy map markers, large insert read pairs and fingerprint maps. We are also developing a new physical mapping approach based on second generation sequencing that could provide a powerful additional tool for de novo genome sequencing. Gene prediction is a major challenge in genome analysis. Second generation sequencing technologies are being employed to directly sequence transcriptomes and identify coding regions by alignment to the genome sequence. Comparative sequencing of related strains or species will be undertaken to identify candidate genes or other sequences relating to species-specific differences. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Thomas Presenting author email cristel.thomas@gmail.com Title How do males and females do it ? A phylo-genomic screen for reproductive genes lost in hermaphrodite lineages. Author Cristel G Thomas 8347 University Of Maryland, Department of Biology, College Park, Maryland, United States of America Author Ian Korf 3191 UC Davis Genome Center, University of California Davis, Davis, CA, USA Author Eric S Haag 227 University Of Maryland, Department of Biology, College Park, Maryland, United States of America Abstract Both C. elegans and less famous C. briggsae are androdioecious species within the Caenorhabditis genus, while their common ancestor and most extant species are gonochoristic. A complete understanding of the emergence of hermaphrodite species requires both determining how the regulation of sex determination has been modified to allow for germline bisexuality and also identifying other traits that may have been deemed useless after the loss of obligate outcrossing. This assertion is supported by evidence from several labs that C. elegans and C. briggsae suffered a weakening of their overall mating efficiency and ability. The genes underlying these mating-related traits are most likely not identifiable in either of these androdioecious species. However, using an extant gonochoristic species like C. remanei as a proxy for the gonochoristic ancestors of C. elegans and C. briggsae may allow their identification. In this study, we assumed that genes involved in sexual traits lost in hermaphrodites are likely to be strongly sex-biased in their expression, and that they will be lost in C. elegans and/or C. briggsae. We used transcriptome deep-sequencing technology to identify genes with extreme sex-biased expression in C. remanei, and defined candidates for hermaphrodite loss based on their phylogenetic distribution within the Caenorhabditis genus. The most promising genes to emerge from our pipeline so far all encode proteins essentially specific to males. We used in situ hybridization as well as quantitative RT-PCR to show that these genes are all associated with maturation of the adult. Ongoing motif analysis may reveal potential binding sites in the promoter and 3' UTRs of these genes, and shed some light on the regulation of their expression. We suggest that understanding the evolutionary loss of ancestral traits in the wake of an adaptation is an important complement to the identification of the developmental and genetic novelties that directly produce the adaptation. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Harvey Presenting author email simon.harvey@canterbury.ac.uk Title Thermal stress responses in Caenorhabditis elegans: reproductive effects, natural variation and the costs of hormesis. Author Simon Crawford Harvey WBPerson3440 Department of Geographical and Life Science, Canterbury Christ Church University, North Holmes Road, Canterbury, Kent, CT1 1QU, UK. Abstract Species have different thermal niches and these appear to be flexible. Extensive natural variation exists between even closely related species in both the position (i.e. the absolute upper and lower temperature limits) and breadth (i.e. the difference between the upper and lower temperature limits) of the thermal niche and in their responses to thermal stress. Understanding how this variation has arisen and how temperature responses evolve requires knowledge of the mechanistic bases of the temperature interactions and of how different aspects of such interactions are related. In C. elegans, the response to high temperature stress has been shown to be closely linked to lifespan and this interaction has been studied in great detail. These analyses have primarily focussed on the effects of mutations that alter either the stress response or longevity. However, it is not clear to what extent the stress response varies in natural populations or how variation within the thermal niche in other life history traits relates to variation in the response to thermal stress. Further, the effect of thermal stress on reproductive traits, such as lifetime fecundity and the timing of progeny production, has not been systematically studied. Here I show that fecundity is much more strongly affected by thermal stress than either lifespan or survival and that the effect of thermal stress depends on the growth conditions. Interestingly, these analyses also demonstrate a reproductive cost in response to short duration heat shocks that extend lifespan. i.e. the hormetic effects of thermal stress are associated with reduced fecundity. Further, extensive natural variation in resistance to thermal stress is identified in very recent "wild" isolates of C. elegans and the relationship between this variation and variation in other life history traits is explored. This work will help to understand how traits related to temperature evolve. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Elling Presenting author email elling@wsu.edu Title COMPARATIVE GENOMICS BETWEEN CAENORHABDITIS ELEGANS AND HETERODERA GLYCINES Author Axel A Elling Department of Plant Pathology, Washington State University, Pullman, WA, U.S.A. Author Thomas J Baum Department of Plant Pathology, Iowa State University, Ames, IA, U.S.A. Abstract Parasitic nematodes have a major impact on human and animal health and crop productivity. Many of the most important parasitic nematodes are endoparasites, which makes them generally inaccessible to molecular techniques once they are inside their hosts. With the exception of RNA interference, forward and reverse genetics and transgenesis have so far proven to be impossible with parasitic nematodes, which represents a significant technological hurdle. Comparative genomics between the model nematode Caenorhabditis elegans and parasitic species is a powerful approach to circumvent some of these problems and to gain insights into fundamental biological processes that are conserved in the Nematoda. We have conducted a comparative analysis between C. elegans and the plant-parasitic nematode Heterodera glycines. Using microarrays and sequence analyses we identified 788 H. glycines candidate genes with putative roles in parasitism for further studies. Furthermore, we found that a significant number of genes that are enriched for the dauer stage in C. elegans have putative orthologs in H. glycines but that their expression signatures were not uniformly conserved when the developmentally arrested infective stage of H. glycines and the C. elegans dauer stage were compared. This suggests that the molecular mechanisms governing developmental arrest in C. elegans and H. glycines might have undergone more divergent evolution than previously thought and points at the need for more detailed analyses of parasitic species. Sequencing the genomes of more non-parasitic and parasitic nematodes to capture the enormous diversity in trophic ecology, habitats and life styles found in the phylum Nematoda will allow a better understanding of the evolutionary changes that have occurred between the dauer stage in C. elegans and the infective stage of parasitic nematodes. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Schierenberg Presenting author email e.schierenberg@uni-koeln.de Title Many roads lead to Rome: Variations of how to design a nematode Abstract For a long time it was thought that embryogenesis as found in Ascaris and C. elegans is typical for nematodes in general. We initiated a comparative study of representatives from various nematode clades and found a multitude of unexpected variations demonstrating that within this phylum many ways lead to a rather uniform hatching larva. These variations cover essentially all prominent early embryonic processes, e.g. establishment of polarity, symmetry formation, soma-germline separation, cell specification and gastrulation but also gene expression patterns and genome organization. The observed differences can often but not always be correlated to phylogenetic position, i.e. also members of the same clade may show considerable developmental differences. Only part of the variations can be interpreted as heterochronic shifts. Our data indicate that a high plasticity in the developmental program during the first half of embryogenesis can easily be accomodated but only as long as it does not compromise the elaboration of the general nematode body plan and that during evolution a network of developmental strategies was established from a slow developing embryo with late fixation of cell fate to embryos with rapid cell cycles and early cell specification. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Rodriguez Presenting author email miriam.rodriguezsanchez@wur.nl Title Natural variation of genome-wide transcription underlying longevity and stress response in C. elegans Author Miriam Rodriguez Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands Author L. Basten Snoek Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands. Author Joost A.G. Riksen Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands. Author Jan E. Kammenga Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands. Abstract Induced mutant analyses in C. elegans wildtype N2 have revealed a strong relationship between prolonged lifespan and increased stress tolerance. For instance, long living mutants display a higher tolerance to heat and many other stress factors. But induced mutations in a single genetic background do not reveal genome-wide allelic effects that segregate in natural populations and contribute to variation in longevity and stress tolerance. We measured gene transcription profiles and stress tolerance to heat shock in wildtypes N2 and CB4856, and their recombinant offspring (recombinant inbred lines or RILs). Different heat shock responses were found in both parentals, they differed in lifespan average, offspring and transcriptional profile after the heat shock. The heat shocked RILs showed an increase in average lifespan by 4.85% after surviving the first three days after the heat shock and a 51.5% reduction in viable offspring. The mechanisms which involved in these responses pointed at two pathways, the Insulin like pathway (ILP) and induction of heat shock response. These results pave the way towards further experimentation and analysis of natural variation in stress tolerance and aging. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Felix Presenting author email felix@ijm.univ-paris-diderot.fr Title Nodaviruses naturally infecting Caenorhabditis nematodes Author Marie-Anne Félix 172 Author Alyson Ashe Author Joséphine Piffaretti Author Guang Wu Author Isabelle Nuez Author Tony Bélicard Author Yanfang Jiang Author Guoyan Zhao Author Leonard Goldstein Author Mabel Sanroman Author Eric Miska Author David Wang Abstract Nodaviruses naturally infecting Caenorhabditis nematodes Marie-Anne Félix*1, Alyson Ashe*2, Joséphine Piffaretti*1, Guang Wu3, Isabelle Nuez1, Tony Bélicard1, Yanfang Jiang3, Guoyan Zhao3, Leonard Goldstein2, Mabel Sanroman1, Eric Miska2, David Wang3 * First authors 1: Institut Jacques Monod, CNRS- University of Paris-Diderot, France 2: Gurdon Institute, University of Cambridge, UK 3: Departments of Molecular Microbiology and Pathology & Immunology,Washington University School of Medicine, Saint-Louis, USA We found natural viral infections in wild isolates of both C. elegans and C. briggsae. The infections visibly affect the intestinal cells. Infected worm lysates passed through 0.2 m filters could be used to infect uninfected worms, which could be further passaged for many generations. Two highly divergent but related RNA viruses in the family Nodaviridae, tentatively named Orsay nodavirus and Santeuil nodavirus, were detected and sequenced. The viruses were subject to processing by the RNAi machinery as evidenced by the detection of virally derived small RNAs that mapped to the entire viral genome. These data demonstrate that nodaviruses are natural parasites of nematodes in the wild. We detect intra-specific variation in sensitivity to the virus among different C. elegans or C. briggsae isolates. Further study of the interactions between these viruses and nematodes is likely to provide insight into the natural ecology of nematodes and may reveal novel innate immune mechanisms that respond to viral infection. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Baer Presenting author email cbaer@ufl.edu Title FASTER MUTATIONAL DECAY OF FITNESS IN GONOCHORISTIC THAN IN SELF-FERTILIZING CAENORHABDITIS Author Charles F Baer University of Florida Author Joanna Joyner-Matos Eastern Washington University Author Dejerianne Ostrow University of Florida Author Matthew P Salomon University of Florida Author Ambuj Upadhyay University of Florida Author Veronica Grigaltchik University of Florida Abstract Evolutionary theory predicts that, all else equal, the mutation rate should evolve to zero because deleterious mutations are so much more prevalent than beneficial mutations. All else is not equal: the mutation rate is never zero. Further, mutation rate demonstrably varies between and within species. In principle, the strength of natural selection to reduce the mutation rate should be stronger in self-fertilizing organisms than in related outcrossing organisms, perhaps much stronger. However, the relative efficacy of selection on mutation rate relative to the many other factors influencing the evolution of any species is poorly understood - that is, what is the empirical relevance of the theory? To address this question we allowed mutations to accumulate in the relative absence of natural selection for ~100 generations in several sets of "mutation accumulation" (MA) lines in several species of gonochoristic Caenorhabditis (C. remanei, C. brenneri, C. sp5); we have previously conducted similar experiments in self-compatible rhabditids. The results are very clear: in every case the rate of mutational decay is substantially greater in the gonochoristic taxa than in the self-compatible C. elegans (~4X greater) and C. briggsae (~2X greater). Residual heterozygosity in the ancestral controls of these MA lines introduces some complications in interpreting the results, but there is reason to believe the results are not primarily due to inbreeding depression resulting from ancestral variation. The results suggest that natural selection operates to optimize the mutation rate in Caenorhabditis and that the strength (or efficiency) of selection differs consistently on the basis of mating system, as predicted by theory. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Pénigault Presenting author email penigault@ijm.univ-paris-diderot.fr Title QUANTITATIVE VARIATION OF DEVELOPMENTAL CELL COMPETENCE: THE CASE OF THE VULVAL PRECURSOR CELLS IN C. ELEGANS AND OTHER CAENORHABDITIS SPECIES. Author Jean-Baptiste Pénigault WBPerson6406 Institut Jacques Monod - CNRS - Paris-Diderot University, Paris, France Author Marie-Anne Félix WBPerson172 Institut Jacques Monod - CNRS - Paris-Diderot University, Paris, France Abstract Developmental competence is often thought to be equal among cells of an "equivalence" group. Yet in Caenorhabditis elegans, the six vulval precursor cells, P(3-6).p, present different degrees of competence to respond to the induction from the gonad. P3.p, the most anterior vulval precursor cell, displays the highest variability in competence in C. elegans N2. To determine the evolutionary stability of this phenomenon, we assessed it in twenty Caenorhabditis species. Studying relative anterior-posterior vulval precursor cell competence, we find a reduction of P3.p and P4.p competence in the Elegans group a clade of six species including C. elegans and C. briggsae. Within the Elegans group anterior competence reduction is varying quantitatively affecting more or less P3.p and in some strains P3.p and P4.p. P3.p competence also varies intra-specifically and in C. elegans lines evolved in the lab from N2, suggesting this trait is highly sensitive to the genetic background. Thus, intra-specific variation of anterior competence is likely to be neutral, although inter-specific variation in positioning defects of the inducing cell may provide a selective pressure for anterior competence variation. We further wished to determine the molecular factors underlying competence variations in the Caenorhabditis genus. In C. elegans, vulval precursor cells are maintained competent by the combined activity of lin-39/Hox5 and of Wnt signals, which form a long-range gradient from the posterior region until P3.p. In all the species displaying a reduced anterior competence, LIN-39 protein level is very low in anterior vulval precursor cells. Modulation of Wnt and LIN-39 dosages in C. elegans and C. briggsae confirmed that vulval precursor cell competence is highly sensitive to their level. In C. elegans, the activity of the Wnt pathway on P3.p and P4.p competence and the level of LIN-39 protein in these cells are independent. Variations in a long-range Wnt gradient and in the level of Homeodomain protein may thus both and independently involved in the evolutionary variation of competence. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Carvalho Presenting author email saracarvalho@igc.gulbenkian.pt Title Patterns of life-history evolution of inbred and outbred populations of C. elegans Author Sara Nunes Lança Carvalho WBPerson10812 Instituto Gulbenkiande Ciencia, Oeiras, Portugal Author Diogo Manoel Institut de Biologie du Développement de Marseille-Luminy CNRS UMR, Marseille, France Author Miguel Roque Author Henrique Teotonio WBPerson9834 Instituto Gulbenkiande Ciencia, Oeiras, Portugal Abstract The diversity of life forms we find in space and time ultimately stems from genetic differences among individuals within breeding groups. Natural selection operates on the phenotypes generated by such genetic differences leading to changes in the genetic composition of populations with time. Mutations and recombination events are important phenomena in generating new genotypes upon which natural selection can act. We investigated the influence of both mutation and rates of recombination from standing genetic variation on patterns of phenotypic evolution and rates of adaptation to a novel environment. We performed experimental evolution in populations of C. elegans which differed in their starting levels of heterozigocity and breeding-mode – androcioecious or dioecious. Replicate populations were maintained in a laboratory environment at high and constant population sizes (N=104) during 100 discrete and non-overlapping generations. The survivorship and reproduction fitness components were measured during experimental evolution, as well as the genotype frequencies at 6 microsatellite loci. Evolved populations reveal extensive phenotypic evolution for most of the measured phenotypes, with differences in phenotypic changes being on average more prominent between inbred vs outbred populations than between populations with different mating systems. An increase in the fraction of males was observed for both the inbred and outbred androdioecious populations, which exhibited frequencies of male of approximately 18% by generation 100. These males, and similarly among males from inbred and outbred dioecious populations, showed an increased ability to fertilize hermaphrodites/females. Female reproductive component under conditions of outcrossing with males also showed a significant increase with evolution, but not the self-reproduction component. Egg-to-adult survivorship does not show consistent evolution, probably representing an optimum for this fitness component. Overall, standing levels of genetic variation have an effect in evolutionary rates and extension of adaptation, but not mating system. The different patterns and rates of phenotypic evolution revealed by the experimental populations will be discussed in the light of the laboratory ecology, mutation rates and effective recombination rates estimated from the molecular data. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Dutilleul Presenting author email morgan.dutilleul@irsn.fr Title Expression of life-history and behaviour traits to environmental constraints of a Caenorhabditis elegans population affected by chronic toxicity of uranium Author Morgan Dutilleul Lab. de Radioécologie et d’Ecotoxicologie - Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, Bâtiment 190, BP 3, 13115 Saint Paul Lez Durance Cedex, France Author Simon Galas Université Montpellier 1, Faculté de Pharmacie-CRBM-CNRS UMR5237, 1919 route de Mende, F34293 Montpellier cedex 5, France Author Catherine Lecomte-Pradines Lab. de Radioécologie et d’Ecotoxicologie - Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, Bâtiment 190, BP 3, 13115 Saint Paul Lez Durance Cedex, France Author Simon Descamps Université Montpellier 1, Faculté de Pharmacie-CRBM-CNRS UMR5237, 1919 route de Mende, F34293 Montpellier cedex 5, France Author Mathias Gauduchon Lab. de Microbiologie, Géochimie et Ecologie marine - UMR 6117, OSU, Case 901 Campus de Luminy, 13288 Marseille Cedex 9, France Author Denis Réale Département des Sciences Biologiques, Université du Québec à Montréal, CP-8888 succursale centre-ville, Montréal, Qc, Canada, H3C 3P8 Author Jean-Marc Bonzom Lab. de Radioécologie et d’Ecotoxicologie - Institut de Radioprotection et de Sûreté Nucléaire, Cadarache, Bâtiment 190, BP 3, 13115 Saint Paul Lez Durance Cedex, France Abstract Local adaptation, which is a major cause of population differentiation, is one of the basic principles of modern evolutionary biology. Natural selection is widely acknowledged to be the primary cause of phenotypic changes in natural populations and to drive adaptive processes. Pollution can play an important role as a factor of natural selection, as stress-induced toxicity of the pollutant amplifies selection pressures in organisms. This amplification can lead to rapid genetic changes associated with increased tolerance to the pollutant. In this context, the main aim of this PhD project is to study the expression of life-history traits (brood and body size, life span, generation time…) and behavioural responses (chemotaxis, basic movements…) to environmental constraints (starvation and temperature variation) of a Caenorhabditis elegans population affected by chronic toxicity of uranium. Several experiments are designed to study this question. We will first provide a thorough examination of the effects of uranium on life-history and behaviour traits, as there have not been well studied yet. Then we will determine the proportion of endpoint values transmitted to offspring using quantitative genetics. Thanks to a multigenerational experience the phenotypic and genetic changes will also be examined in a population exposed to uranium over several generations. After that the occurrence of specializations will be identified. We will play on environmental constraints, competition between contaminated and uncontaminated populations. The aim will be to evaluate the costs of specializations and the evolutionary potential to integrate into the population. In the context of global change a comparison will be required between the frequency of constraints and their severity in order to prioritize their impact factor on a population. At the same time we will use an adaptive dynamic model to predict the response of experimental populations to exposure to uranium in the presence of environmental constraints. All these works should enable us to evaluate how chronic toxic stress impacts the adaptive response of C. elegans. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Snoek Presenting author email basten.snoek@wur.nl Title Next-gen transcriptome sequencing reveals polymorphisms and expression differences between two C.elegans wildtype isolates, CB4856 and N2. Author L. Basten Snoek WBPerson10344 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author Joost A.G. Riksen WBPerson5837 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author Jan E. Kammenga WBPerson1742 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Abstract The development of the next generation sequencers and subsequent reduction in time and costs enabled us to sequence the total RNA pool of wildtypes Hawaii (CB4856) and Bristol (N2). First, it allowed us to study the expression differences between the two isolates and compare transcriptomics by sequencing to microarrays. Secondly, we could find the polymorphisms between CB4856 and N2 in the coding regions of the expressed genes. Of the Single Nucleotide Polymorphisms (SNPs) the silent and those that change an amino acid could be found. Furthermore, we could find inter and intra specific differences in spliced variant usage. Thirdly we could find genes that were not expressed (present) in N2 but could be found in CB4856. These differences between CB4856 and N2 will speed up the identification of natural occurring functionally different alleles and subsequent “cloning of a (e)QTL”. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Haag Presenting author email ehaag@umd.edu Title High-density genotyping in Caenorhabditis briggsae advanced-intercross recombinant inbred lines reveals unexpected inter-strain genomic incompatibilities Author Joseph A. Ross Department of Biology, University of Maryland, College Park Author Daniel C. Koboldt Department of Genetics, Washington University School of Medicine, St. Louis MO Author Julia E. Staisch Department of Genetics, Washington University School of Medicine, St. Louis MO Author Scott E. Baird Department of Biological Sciences, Wright State University, Dayton OH Author Helen M. Chamberlin Department of Molecular Genetics, Ohio State University, Columbus OH Author Bhagwati P. Gupta Department of Biology, McMaster University, Hamilton ON Author Raymond D. Miller Department of Genetics, Washington University School of Medicine, St. Louis MO Author Eric S. Haag Department of Biology, University of Maryland, College Park Abstract Caenorhabditis briggsae is a useful species with which to pursue evolutionary and genomic questions by comparison with C. elegans. However, in C. briggsae the genetic maps and genome assembly necessary for robustly conducting experiments, such as mapping mutations, are not of comparable quality to those available for C. elegans. To improve the genetic map and genome assembly of C. briggsae, 180 AF16xHK104 and HK104xAF16 advanced-intercross recombinant inbred lines (AI-RIL) were genotyped at 1,536 single nucleotide polymorphism (SNP) markers using the Illumina GoldenGate platform. Following quality control, the final dataset comprised 167 AI-RIL typed at 1,034 markers. Employing AI-RIL increased the number and decreased the size of haplotype blocks per chromosome, and the dense panel of genetic markers allowed most previously unplaced sequence contigs to be ordered within chromosome assemblies. Additional issues with the present genome assembly, including contig misassignment to chromosomes, have been resolved to produce a new genome assembly (cb4). Our genotyping data also reveal interesting population genetic phenomena. Analysis of parental allele fraction of the AI-RIL reveals strong bias of three autosomes in favor of the HK104 parental allele. The bias of one autosome is independent of cross direction and due to a slow-growth phenotype elicited in a hybrid genome. The bias of the other two autosomes is strongly dependent on cross direction. Comparison of inter-chromosomal linkage disequilibrium (LD) in the AI-RIL also reveals the presence of cross-direction-specific LD. Together, the genome-wide study of marker segregation in C. briggsae AI-RIL reveals evidence of inter-strain genomic incompatibilities that suggest the onset of genomic divergence and potentially incipient speciation. Efforts are currently under way to identify the incompatibility loci involved. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Jens Schulze Presenting author email JensSchulze@gmx.de Title Evolution of embryonic development in nematodes Author Jens Schulze Author Einhard Schierenberg Abstract Nematodes are well suited for a comparative study of early embryogenesis. Analyzing development of a model system like C.elegans alone allows no conclusions about evolutionary modification within the taxon nematoda. For better understanding evolution of development among nematodes and identification of plesiomorphic and apomorphic characters, data from suitable representatives have to be related to their phylogenetic position. The approach of using developmental markers constitutes a chance to compare our findings without groups like tardigrades and rotifers, in search of embryonic support for the Ecdysozoa or Articulata hypothesis. Our data show that embryogenesis in nematodes is unexpectedly variable with floating transitions which can be interpreted as frozen images of evolutionary change. However, some basic similarities with respect to embryogenesis are found among them, e.g. the general existence of cell lineages and early separation of soma from germline along the a-p axis. The comparison between the basal nematode Tobrilus stefanskii and published data on the tardigrade Hypsibius dujardini (classical view: phylogenetically distant) concerninge arly pattern formation revealed obvious similarities in contrast to rotifers (classical view: close relatives of nematodes). This may be considered as an embryological support for the Ecdysozoa hypothesis (tardigrades and nematodes: close relatives). DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Green Presenting author email j.w.green3@canterbury.ac.uk Title Population growth and dauer larvae development in Caenorhabditis elegans. Author James WM Green Department of Geographical and Life Science, Canterbury Christ Church University, North Holmes Road, Canterbury, Kent CT1 1QU, UK. Author Simon Crawford Harvey WBPerson3440 Department of Geographical and Life Science, Canterbury Christ Church University, North Holmes Road, Canterbury, Kent CT1 1QU, UK. Abstract The study of the ecology of C. elegans is of increasing interest and the species has the potential to allow analyses that directly relate genetic and ecological variation. Natural populations of C. elegans are believed to be typified by a “boom and bust” strategy, with rapid population growth within resource-rich patches of decaying organic material and subsequent dispersal, as developmentally-arrested dauer larvae, between patches. Given this, the fitness of a particular genotype will depend on how quickly and efficiently resources are used, the timing of dispersal stage production, the number of dispersal stages produced and the subsequent success of these dispersal stages at colonising new patches. The properties of growing populations of C. elegans are however poorly understood. It is known that predicted population sizes, calculated from analyses of individual worms, are significantly greater than those actually observed. This indicates that there are strong density dependent effects on population growth. Further, these effects differ between worm genotypes. It is not however clear when these density dependent effects arise, which life-history traits underlie them or how differences between isolates are produced. The timing and rate of dauer larvae development in growing populations is also not known. We are investigating these issues to determine the causes and consequences of variation in population dynamics across environments and genotypes and how dauer larvae develop in growing populations. Preliminary results indicate that as food patch size increases, dauer larvae are formed prior to patch exhaustion. Further, the number of dauer larvae present increases after the patch is exhausted, i.e. worms that had not completed development as a dauer larvae when the food was exhausted continue development in the absence of food. These analyses will determine the properties of growing C. elegans populations across a range of conditions, investigate the role of competition between isolates and place dauer larvae development in an ecological context. This proposal will allow much more ecologically relevant analyses of variation in C. elegans to be undertaken, increasing the utility of the species for answering ecological questions. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Kiontke Presenting author email kk52@nyu.edu Title Caenorhabditis: New Species, Phylogeny, Biogeography and Evolution Author Karin C. Kiontke 2076 New York University, New York, USA Abstract Since 2007, 13 new Caenorhabditis species have been discovered, bringing the total number of Caenorhabditis species in culture to 24. The majority of these new species were found through searches focusing on rotting fruits. To elucidate the relationships of the new species to the five species with sequenced genomes, we used sequence data from two rRNA genes and nine protein-coding genes. Several of these genes were identified as well-conserved, single-copy orthologs in the genomes of the five genome-sequenced species. With this dataset, we obtain almost complete resolution of the Caenorhabditis phylogeny. Our updated phylogeny confirms the existence of two major groups within Caenorhabditis. One group, contains all genome sequenced species and 10 further species. We call this group the Elegans group. The second group, the Drosophilae group, comprises C. drosophilae C. sp. 3 (PS1010) and 5 additional species. C. sp. 1 and C. plicata form the first two branches of the Caenorhabditis tree. C. elegans and C. briggsae have a cosmopolitan distribution. C. remanei and C. brenneri are also widely distributed, but C. remanei is found only in temperate zones whereas C. brenneri lives in tropical zones. Among the new species, some have been encountered several times, esp. C. sp. 11, found on La Réunion in the Indian Ocean, the Cape de Verde Islands in the Atlantic, Guyana in S. America, and on Hawaii. Other species appear to have more limited distributions, for example C. sp. 5 appears to be restricted to China, C. sp. 7 to West Africa and C. sp. 8 to the Eastern United States. Several species can co-occur in the same location or even in the same fruit. So far, it is not possible to infer a center of origin for the genus. Hermaphroditism evolved three times independently in Caenorhabditis, each time in a terminal lineage: C. elegans, C. briggsae, and C. sp. 11. The evolution of only two morphological features is fully congruent with the molecular phylogeny. A pointed spicule. evolved prior to the branch to C. elegans; a narrow fan and spiral copulation evolved in the stem species of C. sp. 3, 8 and 12. All other features show some degree of homoplasy, e.g. the serrated edge of the fan, the anteriorly closed fan, the position of the anterior dorsal ray and the hook. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Kiontke Presenting author email kk52@nyu.edu Title Caenorhabditis: New Species, Phylogeny, Biogeography and Evolution Author Karin C. Kiontke 2076 New York University, New York, New York, USA Author Marie-Anne Félix 172 Institut J. Monod, Paris, France Author Michael Alion University of Utah, Salt Lake City, Utah, USA Author David H. A. Fitch 178 New York University, New York, New York, USA Abstract Since 2007, 13 new Caenorhabditis species have been discovered, bringing the total number of Caenorhabditis species in culture to 24. The majority of these new species were found through searches focusing on rotting fruits. To elucidate the relationships of the new species to the five species with sequenced genomes, we used sequence data from two rRNA genes and nine protein-coding genes. Several of these genes were identified as well-conserved, single-copy orthologs in the genomes of the five genome-sequenced species. With this dataset, we obtain almost complete resolution of the Caenorhabditis phylogeny. Our updated phylogeny confirms the existence of two major groups within Caenorhabditis. One group, contains all genome sequenced species and 10 further species. We call this group the Elegans group. The second group, the Drosophilae group, comprises C. drosophilae C. sp. 3 (PS1010) and 5 additional species. C. sp. 1 and C. plicata form the first two branches of the Caenorhabditis tree. C. elegans and C. briggsae have a cosmopolitan distribution. C. remanei and C. brenneri are also widely distributed, but C. remanei is found only in temperate zones whereas C. brenneri lives in tropical zones. Among the new species, some have been encountered several times, esp. C. sp. 11, found on La Réunion in the Indian Ocean, the Cape de Verde Islands in the Atlantic, Guyana in S. America, and on Hawaii. Other species appear to have more limited distributions, for example C. sp. 5 appears to be restricted to China, C. sp. 7 to West Africa and C. sp. 8 to the Eastern United States. Several species can co-occur in the same location or even in the same fruit. So far, it is not possible to infer a center of origin for the genus. Hermaphroditism evolved three times independently in Caenorhabditis, each time in a terminal lineage: C. elegans, C. briggsae, and C. sp. 11. The evolution of only two morphological features is fully congruent with the molecular phylogeny. A pointed spicule. evolved prior to the branch to C. elegans; a narrow fan and spiral copulation evolved in the stem species of C. sp. 3, 8 and 12. All other features show some degree of homoplasy, e.g. the serrated edge of the fan, the anteriorly closed fan, the position of the anterior dorsal ray and the hook. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Andersen Presenting author email eca@princeton.edu Title AN UNBIASED GENOME-WIDE INVESTIGATION OF WORLD-WIDE C. ELEGANS POPULATION STRUCTURE AND GENOMICS Author Erik C Andersen WBPerson1730 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA Author Justin P Gerke Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA Author Joshua A Shapiro Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA Author Marie-Anne Felix WBPerson172 Institut Jacque Monod, Paris, France Author Leonid Kruglyak WBPerson5224 Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA Abstract We leveraged next-generation sequencing technology to obtain a genome-wide and unbiased understanding of C. elegans population structure. Through collaboration and generous donations, we obtained a set of 202 wild isolates from throughout the world. In order to reduce the 100 Mb genome to a manageable size amenable to multiplexing, we employed Restriction-Assisted DNA marker sequencing (1) where the genome of each strain was cut using EcoRI and sequenced in both directions from each restriction site. This method allowed us to sequence the same eight megabases from each strain in two runs of an Illumina Genome Analyzer. We sequenced to an average of 12.6X coverage of each region, and SNPs were identified using SAMtools after mapping to the C. elegans genome using bwa. We will present the results of our analysis of population structure, linkage disequilibrium, and indications of genome-wide selection using the roughly 20,000 identified SNPs with minor allele frequencies greater than 5%. So far, we found the average pair-wise differences between strains is roughly 1/900 base pairs, as compared to the reference N2 genome. However, there is a wide range in the pair-wise differences with some strains being much more divergent from the reference N2 than the Hawaiian strain CB4856. These data will allow us to pursue genome-wide association studies and new recombinant inbred line crosses with maximally diverse wild isolates. (1) Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, et al. 2008 Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers. PLoS ONE 3(10): e3376. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Phillips Presenting author email pphil@uoregon.edu Title Creating a sexy model: Genetic and genomic resources in C. remanei Author Patrick C. Phillips WBPerson484 Center for Ecology and Evolutionary Biology, University of Oregon Abstract Although C. elegans has served as a wonderful model for genetic and functional analysis, it is clear that most of recent and current evolutionary history is dominated by its selfing mode of reproduction, especially from the standpoint of population genetics. A growing number of studies have shown that the closely related gonochoristic, fully outcrossing species C. remanei displays orders of magnitude more molecular and quantitative genetic variation. Indeed, levels of polymorphism within C. remanei exceed those of most animals, providing unique opportunities, as well as serious difficulties (such as profound inbreeding depression). Here, I summarize what is known about the evolutionary genetics of this species and present an update on the efforts that my lab has made in creating a set of canonical recombinant inbred lines, using next generation sequencing to produce a high density genetic map, in fully assembling the genome, and in creating a drug-based transformation system. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Samuel Presenting author email bsamuel@molbio.mgh.harvard.edu Title Defining the natural microbiota of wild C. elegans Author Buck S. Samuel WBPerson10314 Author Christian Braendle WBPerson3263 Author Marie-Anne Felix WBPerson172 Author Gary Ruvkun WBPerson545 Abstract Like all of us, C. elegans lives in a microbially dominated world. It naturally colonizes habitats rich in microbes, such as rotting fruits and vegetation. Interactions with these as yet unnamed microbes undoubtedly span a spectrum from constant confrontation (pathogens) to relative indifference (food) and perhaps even mutual benefit (symbionts). Many other animals, including some nematodes, acquire fitness benefits by relying on microbes for nutrients, protection from pathogen colonization, and detoxification of harmful xenobiotics. Indeed, C. elegans adults have been observed to harbor undigested microbes in their intestines under some circumstances. In any case, C. elegans has certainly adapted to be highly tuned to microbial cues in order to evaluate their ‘food quality’ or potential to support growth. However, little is known about how this complex microbial calculus occurs with natural microbes. To more broadly examine the microbes encountered by wild C. elegans populations, we performed both culture-based and comprehensive culture-independent sequencing of microbial SSU rDNA from habitats with proliferating and non-proliferating (mostly dauer) wild C. elegans populations. In addition, we isolated animals away from their habitats to directly sequence their more closely associated microbes and potential natural microbiota. Preliminary analyses of all habitats indicate that these animals most commonly encounter bacteria belonging to four phylogenetic divisions (phyla), Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria, along with seven more rare divisions. However, there are also great variations in the diversity and richness of bacteria found within the habitats: some rotting apples have more simple microbial communities (<10 phylotypes) while other rotting vegetation harbors nearly 100 phylotypes. Additionally, several phylotypes were identified from quite disparate habitats (e.g., a snail, a rotting apple and a rotting orange), which could indicate their close association with C. elegans animals themselves. Further analyses of enrichment of specific microbes in isolated worms compared to their habitats (natural or culture-based mimics) will inform these correlations. Determination of what microbes C. elegans associate with naturally is a first step in elaborating the ecological pressures that they may both instigate and ameliorate. Further, by comparing responses of lab-raised strains that have been domesticated on E. coli and wild strains with their naturally associated microbes, we hope to identify conserved host-microbial response pathways that influence C. elegans physiology and metabolism. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Rane Presenting author email hrane@unm.edu Title Gene conversion and DNA sequence polymorphism in the sex-determination gene fog-2 and its paralog ftr-1 in Caenorhabditis elegans Author Hallie S. Rane WBPerson11309 University of New Mexico Author Jessica M. Smith WBPerson11310 Author Ulfar Bergthorsson WBPerson11308 Author Vaishali Katju WBPerson4723 Abstract Gene conversion, a form of concerted evolution, bears enormous potential to shape the trajectory of sequence and functional divergence of gene paralogs subsequent to duplication events. fog-2 , a sex-determination gene unique to Caenorhabditis elegans and implicated in the origin of hermaphroditism in this species, resulted from the duplication of ftr-1, an upstream gene of unknown function. Synonymous sequence divergence in regions of fog-2 and ftr-1 (excluding recent gene conversion tracts) suggests that the duplication occurred 46 million generations ago. Gene conversion between fog-2 and ftr-1 was previously discovered in experimental fog-2 knockout lines of C. elegans, whereby hermaphroditism was restored in mutant obligately-outcrossing male-female populations. We analyzed DNA sequence variation in fog-2 and ftr-1 within 40 isolates of C. elegans from diverse geographic locations in order to evaluate the contribution of gene conversion to genetic variation in the two gene paralogs. The analysis shows that gene conversion contributes significantly to DNA sequence diversity in fog-2 and ftr-1 (22% and 34%, respectively) and may have the potential to alter sexual phenotypes in natural populations. A radical amino acid change in a conserved region of the F-box domain of fog-2 was found in natural isolates of C. elegans with significantly lower fecundity. We hypothesize that the lowered fecundity is due to reduced masculinization and less sperm production, and that amino acid replacement substitutions and gene conversion in fog-2 may contribute significantly to variation in the degree of inbreeding and outcrossing in natural populations. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Viñuela Presenting author email ana.vinuela@wur.nl Title Heritable expression regulation in aging C. elegans Author Ana Viñuela WBPerson10381 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author L. Basten Snoek WBPerson10344 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author Joost A.G. Riksen WBPerson5837 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author Jan E. Kammenga WBPerson1742 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Abstract Gene expression becomes more variable with age and it is widely assumed that this is due to a decrease in expression regulation. But currently there is no understanding how gene expression regulatory patterns progress with age. Here we explored genome-wide gene expression variation and regulatory loci (eQTL) in a population of developing and aging C.elegans recombinant inbred worms. We found almost 900 genes with an eQTL of which almost half were found to have a genotype-by-age effect (gxaeQTL). The total number of eQTL decreased with age whereas the variation in expression increased. In developing worms, the number of genes with increased expression variation was similar to the ones with decreased expression variation. In aging worms the number of genes with increased variation was nearly 5 times higher than the number of genes with a decreased expression variation. The number of cis-acting eQTL in juveniles decreased by almost 50% in old worms whereas the number of trans-acting loci decreased by ~27%, indicating that cis-regulation becomes relatively less frequent than trans-regulation in aging worms. Of the genes with decreased expression level variation in aging worms, ~39% had an eQTL compared to ~14% in developing worms. gxaeQTL were found for ~21% of these genes in aging worms compared to only ~6% in developing worms. Our findings demonstrate that eQTL patterns are strongly affected by age and suggest that gene network regulation vary with age. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Viñuela Presenting author email ana.vinuela@wur.nl Title Transcriptional consequences of recombination in aging C. elegans Author Ana Viñuela WBPerson10381 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author L. Basten Snoek WBPerson10344 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author Joost A.G. Riksen WBPerson5837 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Author Jan E. Kammenga WBPerson1742 Laboratory of Nematology. Wageningen University. Droevendaalsesteeg 1. 6708PB, Wageningen. The Netherlands. Abstract Recently, we explored genome-wide gene expression variation and regulatory loci (eQTL) in an N2 x CB4856 recombinant inbred population of developing and aging C.elegans worms (Viñuela, et al., Genome Research, 2010). Here we present gene expression profiles of the two parental strains. We explored gene expression heritability and transgression as genetic parameters for the analysis of gene expression divergence in natural isolates. Moreover, we investigated the progression of those parameters with age. Preliminary results showed a strong influence of age in the transcriptional profile as well as a changed influence of the genotype in gene expression divergences in older worms. Research is ongoing to understand those results in a context of evolutionary forces affecting gene transcription divergences between two natural isolates. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Levin Presenting author email michalxlevin@gmail.com Title Transcriptomics on a phylogeny: comparative gene expression in the Caenorhabditis embryo Author Michal Levin Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel Author Tamar Hashimshony Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel Author Florian Wagner Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel Abstract Metazoan development is a highly conserved process governed by gene regulatory circuits comprised of similar genes across species, with precise temporal and spatial gene regulation. Comparing developmental regulatory programs of both phenotypically similar and divergent organisms is a powerful test of the hypothesis that morphological evolution is predominantly based upon modulation of gene expression across time and space. Further it can provide insights into the plasticity of the genomic program for encoding phenotypically similar organisms with different underlying programs. We are exploring embryonic gene expression programs of a stable set of orthologs and quickly evolving paralogs across a phylogeny of five completely sequenced Caenorhabditis species (C.elegans, C.briggsae, C.remanei, C.brenneri and C.japonica). Custom-designed microarrays containing the entire gene set of each of the species were used to obtain expression levels of all genes across ten embryonic stages of development (4-cell stage to first larvae) of precisely staged embryos. Analysis of this data set has enabled the screening for gene expression conservation and divergence across gene families. Further, the consensus of orthologous gene expression profiles appear to be more correlated with the timings of known functions in C. elegans than the actual C. elegans gene expression profile, suggesting that gene expression profiles across species can be analyzed like gene sequences and queried for the signature of selection through observed patterns of conservations and divergences. We propose that genetic drift of the transcriptome is an important developmental principle with implications to other principles such as robustness and modularity. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Levin Presenting author email michalxlevin@gmail.com Title Transcriptomics on a phylogeny: comparative gene expression in the Caenorhabditis embryo Author Michal Levin Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel Author Tamar Hashimshony Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel Author Florian Wagner Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel Abstract Metazoan development is a highly conserved process governed by gene regulatory circuits comprised of similar genes across species, with precise temporal and spatial gene regulation. Comparing developmental regulatory programs of both phenotypically similar and divergent organisms is a powerful test of the hypothesis that morphological evolution is predominantly based upon modulation of gene expression across time and space. Further it can provide insights into the plasticity of the genomic program for encoding phenotypically similar organisms with different underlying programs. We are exploring embryonic gene expression programs of a stable set of orthologs and quickly evolving paralogs across a phylogeny of five completely sequenced Caenorhabditis species (C.elegans, C.briggsae, C.remanei, C.brenneri and C.japonica). Custom-designed microarrays containing the entire gene set of each of the species were used to obtain expression levels of all genes across ten embryonic stages of development (4-cell stage to first larvae) of precisely staged embryos. Analysis of this data set has enabled the screening for gene expression conservation and divergence across gene families. Further, the consensus of orthologous gene expression profiles appear to be more correlated with the timings of known functions in C. elegans than the actual C. elegans gene expression profile, suggesting that gene expression profiles across species can be analyzed like gene sequences and queried for the signature of selection through observed patterns of conservations and divergences. We propose that genetic drift of the transcriptome is an important developmental principle with implications to other principles such as robustness and modularity. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Sanchez-Flores Presenting author email as9@sanger.ac.uk Title Assembly of the Strongyloides ratti genome Author Alejandro Sanchez-Flores Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK Author Nancy Holroyd Parasite Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK Author Mark Viney School of Biological Sciences, University of Bristol, Woodland Road, Bristol Abstract Strongyloides ratti is the rat analogue of the human gastro-intestinal threadworm S. stercoralis. Occurring principally in the tropics and sub-tropics, S. stercoralis infections are widespread: some 100-200 million people are infected worldwide. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis, in which worms occur throughout the body. This can be fatal unless anti-Strongyloides therapy is given. S. ratti has a complex life cycle including parasitic and free-living stages. The adult parasites are female only and live in the mucosa of the small intestine. These parasites produce eggs that pass out of the host in its faeces. We have used a Whole Genome Shotgun strategy and three different DNA sequencing technologies (Sanger, 454 and Illumina) for this genome. Although, the use of second generation sequencing technologies offers an alternative to Sanger sequencing for larger genomes, the results vary depending on the size and complexity of the genome and greater demands are made on computational and software resources. We merged the three technologies into a draft genome with ~50 million base pairs (haploid). The hybrid assembly approach produced significant benefits compared with separate assemblies of the component datasets. Each sequencing technology has limitations and artifacts that can be complemented and corrected by data from another technology. We also included recently published information of the genetic map, assigning all 74 molecular markers unambiguously to assembly scaffolds. We mapped a set of clustered ESTs for S. ratti and S. stercoralis, obtained from NemBase3, against the draft genome 95% of the ESTs from S.ratti mapped at least in 70% of their length. For the S. stercoralis ESTs set, 50% of them mapped in similar conditions. Within the assembly, sequences from a possible S. ratti endosymbiont were found, similar to those of other nematodes. Currently, the draft genome is in a process of finishing and manual curation that will result in a high quality reference genome for other species. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name rane Presenting author email Title Abstract DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Streit Presenting author email adrian.streit@tuebingen.mpg.de Title CHROMATIN DIMINUTION AND SEX CHROMOSOME EVOLUTION IN THE PARASITIC NEMATODE GENUS STRONGYLOIDES Author Adrian Streit 629 Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany Author Mark E Viney 672 School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK Author Alexander G Eberhardt 9306 Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany Author Linda Nemetschke 9329 Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany Abstract The clade four nematode genus Strongyloides consists of parasites that live as parthenogenetic females in the small intestines of their vertebrate hosts. In addition to producing all female parasitic offspring, Strongyloides sp. can also form a facultative free-living generation consisting of both males and females. Usually the entire progeny of the free-living generation is female and parasitic. This complex life cycle gives these worms an interesting "choice" between a parasitic life style associated with clonal reproduction and a free-living existence with sexual reproduction. The presence of a free-living generation offers a unique opportunity for the experimental manipulation of a true parasite. We combine molecular and genetic approaches to study life history switches, i. e. the switch between the parasitic and the free-living cycle and sex determination. To this end we established methods for genetic mapping and a genetic linkage map for S. ratti. Sex determination differs within the genus. Some species (e. g. S. ratti, a parasite of rats and S. stercoralis, a parasite of humans) have three chromosomes of roughly equal size and employ XX/XO sex determination like C. elegans. In S. papillosus, a parasite of sheep, there are only two pairs of chromosomes, one of which is considerably larger than the other. It had been speculated that the longer chromosome is the result of a fusion of the ancestral X chromosome with one of the autosomes. Here we demonstrate genetically that S. papillosus employs male-specific chromatin diminution to eliminate an internal portion of one of the two homologs of the longer chromosome pair, as has been proposed by some but contested by other authors based on cytological observations. We found extensive local syntheny and conservation of genetic linkage between S. ratti and S. papillosus but not between C. elegans and these Strongyloides species. Further, we demonstrate that the region that undergoes chromatin diminution in S. papillosus males is homologous to the X chromosome of S. ratti. Our findings suggest that in the evolution leading to S. papillosus the X chromosome was integrated into the autosome that corresponds to chromosome I of S. ratti. It appears that in S. papillosus only the non-diminuted chromosome is present in sperm. Consequentially, for loci that are genetically linked to the eliminated region, males pass on preferentially (in the extreme cases exclusively) one of their two alleles to their all-female progeny. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Mayer Presenting author email melanie.mayer@tuebingen.mpg.de Title Natural Variation in Dauer Entry and Dauer Exit in the Nematode Pristionchus pacificus Author Melanie G. Mayer Max Planck Institute for Developmental Biology, Tübingen, Germany Author Akira Ogawa Max Planck Institute for Developmental Biology, Tübingen, Germany Author Ralf J. Sommer Max Planck Institute for Developmental Biology, Tübingen, Germany Abstract Evolutionary ecology investigates how the developmental response to the environment and the ecological interactions of an organism shape the evolution of new phenotypes. Under harsh environmental conditions, the diplogastrid nematode Pristionchus pacificus is able to arrest its development in the third larval stage and form dauer juveniles (Ogawa et al. 2009). The well-known association of P. pacificus with scarab beetles is exclusively in the dauer stage, indicating that the dauer stage is essential not only for enduring unfavorable conditions but also for dispersal. The supernatant prepared from P. pacificus liquid cultures contains dauer pheromone, which induces J2 larvae to enter the dauer stage. To study natural variation in dauer entry, we tested 18 P. pacificus strains with the dauer pheromone of each strain. Interestingly, these strains show a high level of natural variation regarding dauer entry, even in response to the same dauer pheromone. We will report recombinant-inbred-line experiments, which try to identify the molecular basis of natural variation in dauer entry. Furthermore, we investigated the ability of P. pacificus to exit the dauer stage after different periods of time and at different temperatures, an experiment that is still ongoing. As with dauer entry, the 10 tested strains show a wide range of natural variation regarding dauer exit. However, in nearly all of the strains, many dauers were still able to recover and reproduce after 28 weeks at 8°C. Some strains display a distinct trade-off between survival (the ability to exit the dauer stage) and recovery (the ability to develop into J4 larvae) or between recovery and brood size. When incubated at higher temperatures, P. pacificus dauers seem to compensate for lower survival and recovery by increasing their brood size. These studies provide a better understanding of the ecologically most important nematode stage, the dauer stage. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Bayes Presenting author email jbayes@berkeley.edu Title A Comparative Evolutionary Model for the Study of Meiotic Mechanisms Author Joshua J Bayes Howard Hughes Medical Institute, Univ. of California, Berkeley; Dept. of Molecular and Cell Biology, Univ. of California, Berkeley Author Abby F Dernburg 136 Howard Hughes Medical Institute, Univ. of California, Berkeley; Dept. of Molecular and Cell Biology, Univ. of California, Berkeley; Lawrence Berkeley National Lab Abstract Meiosis is a specialized cell division that reduces a diploid cell to haploid gametes, which is a critical evolutionary innovation for genetic diversity. Critical features of the meiosis include homologous chromosome recognition (pairing), establishment of the synaptonemal complex (SC) between paired homologs (synapsis), and formation of physical linkages, or chiasmata, between paired chromosomes. Surprisingly, despite its important function and some shared commonalities, many meiotic mechanisms and genes are not conserved between species. To address why these differences exist and how evolution has tailored the mechanistic details of meiosis between species, I have initiated studies to develop the nematode Pristionchus pacificus as a comparative model to Caenorhabditis elegans. In silico searches against the P. pacificus genome using known meiotic gene sequences from C. elegans have identified orthologous genes primarily encoding the class of proteins involved in recombination and sister chromatid cohesion. Interestingly, the P. pacificus genome lacks homologous sequences to genes encoding products that function in pairing or are constituents of the SC, suggesting that these particular processes may evolve quite rapidly and involve novel genes. Genetic and cytological tools are currently under development to elucidate how these processes may mechanistically differ from our understanding of C. elegans pairing and synapsis. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name dtbzpgzlk Presenting author email qnciwe@poiusk.com Title yLfCUXxJOxnmhjq Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author qnciwe@poiusk.com qnciwe@poiusk.com qnciwe@poiusk.com qnciwe@poiusk.com qnciwe@poiusk.com Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Author dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk dtbzpgzlk Abstract m9V8VC ugbbjwdlrhza, [url=http://dlhsbjcerzxv.com/]dlhsbjcerzxv[/url], [link=http://aykifxkbpnap.com/]aykifxkbpnap[/link], http://aibsneikqepn.com/ DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Herman Presenting author email mherman@ksu.edu Title BACTERIAL-RESPONSIVE TRANSCRIPTOMES OF RHABDITID SOIL NEMATODES Author Michael A Herman 251 Division of Biology, Kansas State University, Manhattan, KS 66506 Author Brian Darby Division of Biology, Kansas State University, Manhattan, KS 66506 Author David Wheeler Division of Biology, Kansas State University, Manhattan, KS 66506 Abstract Nematodes, the most abundant metazoans on earth, are responsive to both biotic and abiotic environmental stimuli. Soil bacteria are an important part of the biotic environment for bacterial feeding soil nematodes, serving not only as food sources but also as potential pathogens. Interactions between nematodes and bacteria, therefore, are of significant importance to understand the ecological dynamics of the soil community. In order to dissect this complexity, we used C. elegans to model the interactions of native soil nematodes with soil bacteria and identified C. elegans genes responsive to various soil bacteria (Coolon et al, 2009 PLoS Genet 5(6): e1000503). Using mutations that inactivate many of the identified genes in C. elegans, we showed that most contribute to fitness and/or defense in a given bacterial environment. Moreover, we showed that for many genes the degree of differential gene expression between two bacterial environments predicted the magnitude of the effect of the loss of gene function on life history traits in those environments. This observation has important implications for interpreting the results of transcriptional profiling experiments of populations of organisms in their native environments, where in many cases the genetic tools to disrupt gene function have not yet been fully developed or that interfering with gene functions in nature may not be feasible. To test this observation we have isolated four rhabditid nematodes (Oscheius tipulae, Oscheius sp. 2, Rhabditis sp, and Mesorhabditis sp.) from soils collected at Konza Prairie Biological Station and used transcriptome sequencing to investigate their responses to native soil bacteria. Specifically, we grew nematodes on a mix of gram-positive and gram-negative bacteria and sequenced normalized cDNA libraries using a Roche GS-FLX Genome Sequencer. Preliminary analysis detected about 12,000 genes expressed in each taxa with an average 10x sequence coverage. Approximately 60-70 percent of transcripts significantly matched database sequences, while another 30 percent may be lineage specific, some of which might shared among these nematodes. Our short-term goal is to use this information to determine patterns of gene expression in response to soil bacteria in the lab and in the field. In addition, these transcriptome sequences will complement genomic information available within the Rhabditid family and be useful in comparative genome studies. Ultimately, our studies will help us understand the gene functions involved in the formation and maintenance of dynamic soil nematode communities in changing environments. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Semple Presenting author email jennifer.semple@crg.es Title RAPID TRANSGENE SELECTION WITH PUROMYCIN IN CAENORHABDITIS SPECIES Author Jennifer Isabel Semple Author Rosa Garcia-Verdugo Author Ben Lehner Abstract We have developed a drug selection system for transgene expression in nematodes. Worms carrying an extrachromosomal array containing the puromycin resistance gene are efficiently selected from a mixed population. This approach has a number of advantages over existing methods for transgene selection: 1) Large numbers of transgenic worms can be easily selected without the need for expensive, specialised equipment such as a worm-sorter. 2) Strains carrying extrachromosomal arrays with puromycin resistance can be maintained on puromycin plates without needing to pick individual worms. 3) Puromycin selection does not require a particular genetic background, eliminating the need to generate particular mutant strains for different species, which are often laborious to work with. We have successfully tested puromycin selection in both C. elegans and C. briggsae and anticipate that this system could be useful for transgenesis in a variety of Caenorhabditis species. 4) We have developed a protocol for rapid drug selection following bombardment of N2 worms. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Teotonio Presenting author email teotonio@igc.gulbenkian.pt Title RECOMBINATION LOAD IN C.ELEGANS EXPERIMENTAL POPULATIONS Author Ivo M Chelo Instituto Gulbenkian de Ciência, Oeiras Portugal Author Sara - Carvalho Instituto Gulbenkian de Ciência, Oeiras Portugal Author Henrique - Teotonio WBPerson9834 Instituto Gulbenkian de Ciência, Oeiras Portugal Abstract The interaction of recombination and natural selection in large populations is poorly understood at the empirical level. We have constructed populations of C. elegans that segregate large amounts of genetic variation and alternative mating systems. Upon these populations experimental evolution was performed, in well-defined laboratory conditions, for 100 generations, and patterns of DNA sequence diversity were characterized for two chromosomes at a density of approximately 100kb. We observe that there is extensive natural selection in single-marker frequencies which cannot be explained by initial gametic linkage disequilibrium. With standing genetic variation outcrossing rates have no differential effects on adaptation, unless effective recombination rates are explicitly sought by inbreeding of evolving outbred populations. When this is done we find that higher outcrossing leads to higher recombination that is responsible for the break-up of several high fitness polygenic polymorphisms during initial experimental evolution, while lower effective recombination appears to generate the same kind of balanced polymorphisms after 100 generations. These observations will be briefly discussed in the context of evolutionary theory. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Pollard Presenting author email dp96@nyu.edu Title Unraveling of an ancient regulatory pathway: RNAi insensitivity in the germline of C. elegans Author Daniel Avery Pollard WBPerson9860 New York University, New York, NY Author Maxwell J Kramer New York University, New York, NY Author Matthew V Rockman WBPerson7165 New York University, New York, NY Abstract The round worm Caenorhabditis elegans has played a central role in the elucidation of the RNAi and microRNA pathways and yet a Hawaiian natural isolate exhibits a dramatic loss of sensitivity to RNAi in the germline. We sought to expand the characterization of the loss of RNAi sensitivity in C. elegans to identify new genes involved in the pathway and better understand the genetics underlying the loss of this pathway in the population. Using quantitative trait locus mapping techniques we first examined the genetics underlying the difference in germline RNAi sensitivity between the fully sensitive N2 lab strain and the fully insensitive Hawaiian isolate. Although the insensitivity does not segregate as a single locus Mendelian trait (implying complexity), mapping revealed only one large-effect QTL, centered over the argonaute gene ppw-1 (previously implicated in this insensitivity by Tijsterman et al. 2002). A survey of germline RNAi sensitivity in 41 natural isolates representing distinct C. elegans haplotypes revealed the insensitivity is common (38%) and geographically widespread in natural populations. Association mapping with the natural isolates implicated no significant genomic regions, suggesting a high level of genetic complexity or heterogeneity. Complementation tests with a ppw-1 null strain (NL2557) suggest germline RNAi insensitivity may have been gained multiple times through separate mechanisms. We are currently performing QTL mapping of RNAi sensitivity in natural isolates whose insensitivity is ppw-1 independent. We conclude that germline RNAi insensitivity is a widespread and genetically complex trait in C. elegans. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Barkoulas Presenting author email barkoulas@ijm.paris-univ-diderot.fr Title TOWARDS A QUANTITATIVE UNDERSTANDING OF THE VULVA CELL FATE PATTERNING NETWORK Author Michalis Barkoulas Institut Jacques Monod, CNRS-University of Paris-Diderot, Paris, France Author Marie-Anne Felix Institut Jacques Monod, CNRS-University of Paris-Diderot, Paris, France Abstract The C. elegans vulva is the egg-laying and copulatory organ of the adult hermaphrodite that is specified during the third larval stage of postembryonic development from a row of six vulva precursor cells (P3.p-P8.p). These six cells are all competent to adopt vulva fates, but only three of these cells (P5-7.p) will normally generate vulva tissues, by adopting two distinct cell fates; the 1° cell fate, which is acquired by P6.p, or the 2° fate which is adopted by P5.p and P7.p. Two major signalling pathways have been shown to be critical in specifying the vulva precursor cell fate pattern. Firstly, an inductive signal from the uterine anchor cell activates the 1° cell fate in P6.p through EGF-RAS-Map kinase signalling. Secondly, Notch signalling is involved in lateral signalling among the Pn.p cells, resulting in acquisition of the 2° cell fate in P5.p and P7.p. Extensive genetic analyses over the last thirty years have revealed both the key molecular components of these two pathways, and also the ways via which these pathways positively or negatively interact within a single or neighbouring Pn.p cells. Nonetheless, even in such a well-studied system, a quantitative understanding of the molecular network is still lacking. We have started addressing this question experimentally by systematically varying the doses of Ras and Notch pathway activities using transgenic manipulations and we present here our first, preliminary results. Our aim is to establish Ras and Notch pathway dose-response curves and study their interaction, combining our experimental results with a computational model of the vulva cell fate network that we have recently developed. The final vulva cell fate pattern is conserved across many Caenorhabditis species, although differences can be revealed upon experimental manipulations. These results suggest that within a shared vulva molecular network among closely related species, the quantitative strengths of the lateral and inductive pathways may differ. We would like eventually to extend the quantitative knowledge of the C. elegans network to other species to understand the evolution of the vulva. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name Lo Presenting author email te-wen.lo@berkeley.edu Title Heritable gene disruption using zinc finger nucleases reveals evolutionary conservation of dosage compensation machinery among Caenorhabditis species Author Te-Wen Lo WBPerson1221 Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, CA, USA Author Andrew J. Wood Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, CA, USA; King's College London, London, UK Author Bryan Zeitler Sangamo BioSciences, Inc., Richmond, CA, USA Author Catherine S. Pickle Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, CA, USA Author Andrew H. Lee Sangamo BioSciences, Inc., Richmond, CA, USA Author Jeffrey C. Miller Sangamo BioSciences, Inc., Richmond, CA, USA Author Lei Zhang Sangamo BioSciences, Inc., Richmond, CA, USA Author Edward J. Rebar Sangamo BioSciences, Inc., Richmond, CA, USA Author Qinwen Liu University of Maryland, College Park, MD, USA Author Eric S. Haag University of Maryland, College Park, MD, USA Author Philip D. Gregory Sangamo BioSciences, Inc., Richmond, CA, USA Author Fyodor D. Urnov D. Urnov Sangamo BioSciences, Inc., Richmond, CA, USA Author Barbara J. Meyer Howard Hughes Medical Institute, University of California-Berkeley, Berkeley, CA, USA Abstract Evolutionary studies within the nematode phylum have been hampered by the lack of efficient gene targeting technologies outside of C. elegans. To this end, we have employed zinc finger nucleases (ZFNs) to achieve heritable, single-step gene targeting in C. briggsae. ZFNs consist of custom-designed DNA binding motifs based on the C2H2 zinc finger as a scaffold, fused to the cleavage domain of the FokI restriction enzyme. These molecules have recently been applied to other model systems to generate double-strand breaks at pre-determined loci, which are then subject to imperfect repair via the non-homologous end-joining pathway to generate short insertions and deletions at the target site. To demonstrate the versatility of ZFN technology, we studied the evolution of dosage compensation (DC), an essential process that equalizes X-linked gene expression between sexes. In C. elegans, X-linked gene expression is reduced by approximately half in the XX hermaphrodite to equal the expression of the single X in the XO male. This process is mediated by the dosage compensation complex (DCC) and regulated by the developmental switch gene, Ce-xol-1. Although C. elegans and C. briggsae have diverged 15-30 MYA, we found the DC machinery and genetic hierarchy controlling DC to be conserved. By isolating deletion alleles of Cbr-dpy-27 and Cbr-mix-1, homologs of two C. elegans DCC components, raising antibodies, and developing FISH probes, we showed that Cbr-DPY-27 associates with the C. briggsae X in a XX-specific manner and in the absence of either Cbr-dpy-27 or Cbr-mix-1, DCC localization is disrupted causing XX-specific lethality. Furthermore, a mutation in Cbr-xol-1 results in XO-specific lethality due to DCC mislocalization onto the single X suggesting that the regulatory role of xol-1 is conserved. Since previous screens failed to identify mutations in the homolog of Ce-sdc-2, a DCC component required to target all remaining subunits to X, we utilized ZFNs to isolate mutations in Cbr-sdc-2. Loss of Cbr-sdc-2 results in the failure of the DCC to load and rescues the male lethality caused by a mutation in Cbr-xol-1, indicating that Cbr-sdc-2’s role in DC is conserved. Despite the conservation of DCC subunits, their binding sites on X appear diverged. X DNA fragments that recruit and completely titrate the DCC from the endogenous C. elegans X chromosome cannot do so when expressed in C. briggsae. Taken together, these data not only provide insights into the evolution of dosage compensation, but also demonstrate the successful application of ZFN technology to C. briggsae and thus add a new dimension to the reverse genetic toolkit for nematodes. DIVIDER Meeting Name 2010 Caenorhabditis evolution meeting Presenting author name felix Presenting author email Title Abstract DIVIDER