Divergent adaptation promotes reproductive isolation among experimental populations of the filamentous fungus Neurospora

<p>Abstract</p> <p>Background</p> <p>An open, focal issue in evolutionary biology is how reproductive isolation and speciation are initiated; elucidation of mechanisms with empirical evidence has lagged behind theory. Under ecological speciation, reproductive isolation between populations is predicted to evolve incidentally as a by-product of adaptation to divergent environments. The increased genetic diversity associated with interspecific hybridization has also been theorized to promote the development of reproductive isolation among independent populations. Using the fungal model <it>Neurospora</it>, we founded experimental lineages from both intra- and interspecific crosses, and evolved them in one of two sub-optimal, selective environments. We then measured the influence that initial genetic diversity and the direction of selection (parallel versus divergent) had on the evolution of reproductive isolation.</p> <p>Results</p> <p>When assayed in the selective environment in which they were evolved, lineages typically had greater asexual fitness than the progenitors and the lineages that were evolved in the alternate, selective environment. Assays for reproductive isolation showed that matings between lineages that were adapted to the same environment had greater sexual reproductive success than matings between lineages that were adapted to different environments. Evidence of this differential reproductive success was observed at two stages of the sexual cycle. For one of the two observed incompatibility phenotypes, results from genetic analyses were consistent with a two-locus, two-allele model with asymmetric (gender-specific), antagonistic epistasis. The effects of divergent adaptation on reproductive isolation were more pronounced for populations with greater initial genetic variation.</p> <p>Conclusion</p> <p>Divergent selection resulted in divergent adaptation and environmental specialization, consistent with fixation of different alleles in different environments. When brought together by mating, these alleles interacted negatively and had detrimental effects on sexual reproductive success, in agreement with the Dobzhansky-Muller model of genetic incompatibilities. As predicted by ecological speciation, greater reproductive isolation was observed among divergent-adapted lineages than among parallel-adapted lineages. These results support that, given adequate standing genetic variation, divergent adaptation can indirectly cause the evolution of reproductive isolation, and eventually lead to speciation.</p

Seasonality of precipitation in the southwestern United States during the late Pleistocene inferred from stable isotopes in herbivore tooth enamel

The late Pleistocene was a climatically dynamic period, with abrupt shifts between cool-wet and warmdry conditions. Increased effective precipitation supported large pluvial lakes and long-lived spring ecosystems in valleys and basins throughout the western and southwestern U.S., but the source and seasonality of the increased precipitation are debated. Increases in the proportions of C4/(C4+ C3) grasses in the diets of large grazers have been ascribed both to increases in summer precipitation and lower atmospheric CO2 levels. Here we present stable carbon and oxygen isotope data from tooth enamel of late Pleistocene herbivores recovered from paleowetland deposits at Tule Spring Fossil Beds National Monument in the Las Vegas Valley of southern Nevada, as well as modern herbivores from the surrounding area. We use these data to investigate whether winter or summer precipitation was responsible for driving the relatively wet hydroclimate conditions that prevailed in the region during the late Pleistocene. We also evaluate whether late Pleistocene grass C4/(C4+ C3) was higher than today, and potential drivers of any changes. Tooth enamel δ18O values for Pleistocene Equus, Bison, and Mammuthus are generally low (average 22.0 ± 0.7‰, 2 s.e., VSMOW) compared to modern equids (27.8 ± 1.5‰), and imply lower water δ18O values (-16.1 ± 0.8‰) than modern precipitation (-10.5‰) or in waters present in active springs and wells in the Las Vegas Valley (-12.9‰), an area dominated by winter precipitation. In contrast, tooth enamel of Camelops (a browser) generally yielded higher δ18O values (23.9 ± 1.1‰), possibly suggesting drought tolerance. Mean δ13C values for the Pleistocene grazers (-6.6 ± 0.7‰, 2 s.e., VPDB) are considerably higher than for modern equids (-9.6 ± 0.4‰) and indicate more consumption of C4 grass (17 ± 5%) than today (4 ± 4%). However, calculated C4 grass consumption in the late Pleistocene is strikingly lower than the proportion of C4 grass taxa currently present in the valley (55-60%). δ13C values in Camelops tooth enamel (-7.7 ± 1.0‰) are interpreted as reflecting moderate consumption (14 ± 8%) of Atriplex (saltbush), a C4 shrub that flourishes in regions with hot, dry summers. Lower water δ18O values, lower abundance of C4 grasses, and the inferred presence of Atriplex are all consistent with general circulation models for the late Pleistocene that show enhanced delivery of winter precipitation, sourced from the north Pacific, into the interior western U.S. but do not support alternative models that infer enhanced delivery of summer precipitation, sourced from the tropics. In addition, we hypothesize that dietary competition among the diverse and abundant Pleistocene fauna may have driven the grazers analyzed here to feed preferentially on C4 grasses. Dietary partitioning, especially when combined with decreased pCO2 levels during the late Pleistocene, can explain the relatively high δ13C values observed in late Pleistocene grazers in the Las Vegas Valley and elsewhere in the southwestern U.S. without requiring additional summer precipitation. Pleistocene hydroclimate parameters derived from dietary and floral records may need to be reevaluated in the context of the potential effects of dietary preferences and lower pCO2 levels on the stability of C3 vs. C4 plants

A Process Calculus for Molecular Interaction Maps

We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs), a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks.Comment: 15 pages; 8 figures; To be published on EPTCS, proceedings of MeCBIC 200

Projection on Segre varieties and determination of holomorphic mappings between real submanifolds

It is shown that a germ of a holomorphic mapping sending a real-analytic generic submanifold of finite type into another is determined by its projection on the Segre variety of the target manifold. A necessary and sufficient condition is given for a germ of a mapping into the Segre variety of the target manifold to be the projection of a holomorphic mapping sending the source manifold into the target. An application to the biholomorphic equivalence problem is also given.Comment: 16 page

Theoretical Study of Cubic Structures Based on Fullerene Carbon Clusters: C28_{28}C and (C28)2_{28})_{2}

We study a new hypothetical form of solid carbon \csc, with a unit cell which is composed of the \cs \ fullerene cluster and an additional single carbon atom arranged in the zincblende structure. Using {\it ab initio} calculations, we show that this new form of solid carbon has lower energy than hyperdiamond, the recently proposed form composed of \cs \ units in the diamond structure. To understand the bonding character of of these cluster-based solids, we analyze the electronic structure of \csc \ and of hyperdiamond and compare them to the electronic states of crystalline cubic diamond.Comment: 15 pages, latex, no figure

Pathogens and pharmaceuticals in source-separated urine in eThekwini, South Africa

In eThekwini, South Africa, the production of agricultural fertilizers from human urine collected from urine-diverting dry toilets is being evaluated at a municipality scale as a way to help finance a decentralized, dry sanitation system. The present study aimed to assess a range of human and environmental health hazards in source-separated urine, which was presumed to be contaminated with feces, by evaluating the presence of human pathogens, pharmaceuticals, and an antibiotic resistance gene. Composite urine samples from households enrolled in a urine collection trial were obtained from urine storage tanks installed in three regions of eThekwini. Polymerase chain reaction (PCR) assays targeted 9 viral and 10 bacterial human pathogens transmitted by the fecal-oral route. The most frequently detected viral pathogens were JC polyomavirus, rotavirus, and human adenovirus in 100%, 34% and 31% of samples, respectively. Aeromonas spp. and Shigella spp. were frequently detected gram negative bacteria, in 94% and 61% of samples, respectively. The gram positive bacterium, Clostridium perfringens, which is known to survive for extended times in urine, was found in 72% of samples. A screening of 41 trace organic compounds in the urine facilitated selection of 12 priority pharmaceuticals for further evaluation. The antibiotics sulfamethoxazole and trimethoprim, which are frequently prescribed as prophylaxis for HIV-positive patients, were detected in 95% and 85% of samples, reaching maximum concentrations of 6800 µg/L and 1280 µg/L, respectively. The antiretroviral drug emtricitabine was also detected in 40% of urine samples. A sulfonamide antibiotic resistance gene (sul1) was detected in 100% of urine samples. By coupling analysis of pathogens and pharmaceuticals in geographically dispersed samples in eThekwini, this study reveals a range of human and environmental health hazards in urine intended for fertilizer production. Collection of urine offers the benefit of sequestering contaminants from environmental release and allows for targeted treatment of potential health hazards prior to agricultural application. The efficacy of pathogen and pharmaceutical inactivation, transformation or removal during urine nutrient recovery processes is thus briefly reviewed

Hematopoietic Cell Transplantation in Patients With Primary Immune Regulatory Disorders (PIRD): A Primary Immune Deficiency Treatment Consortium (PIDTC) Survey.

Primary Immune Regulatory Disorders (PIRD) are an expanding group of diseases caused by gene defects in several different immune pathways, such as regulatory T cell function. Patients with PIRD develop clinical manifestations associated with diminished and exaggerated immune responses. Management of these patients is complicated; oftentimes immunosuppressive therapies are insufficient, and patients may require hematopoietic cell transplant (HCT) for treatment. Analysis of HCT data in PIRD patients have previously focused on a single gene defect. This study surveyed transplanted patients with a phenotypic clinical picture consistent with PIRD treated in 33 Primary Immune Deficiency Treatment Consortium centers and European centers. Our data showed that PIRD patients often had immunodeficient and autoimmune features affecting multiple organ systems. Transplantation resulted in resolution of disease manifestations in more than half of the patients with an overall 5-years survival of 67%. This study, the first to encompass disorders across the PIRD spectrum, highlights the need for further research in PIRD management

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea–specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.Fil: Ten Have, Arjen. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Mar del Plata. Instituto de Investigaciones Biológicas; Argentina. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Biológicas; ArgentinaFil: Amselem, Joelle. Institut National de la Recherche Agronomique; FranciaFil: Cuomo, Christina A.. Broad Institute of MIT and Harvard; Estados UnidosFil: Jan, A. L. van Kan. Wageningen University; Países BajosFil: Viaud, Muriel. Institut National de la Recherche Agronomique; FranciaFil: Benito, Ernesto P.. Universidad de Salamanca; EspañaFil: Couloux, Arnaud. Centre National de Séquençage. Genoscope; FranciaFil: Coutinho, Pedro M.. Centre National de la Recherche Scientifique; FranciaFil: Vries, Ronald P. de. Microbiology and Kluyver Centre for Genomics of Industrial Fermentations; Países Bajos. Fungal Biodiversity Centre; Países BajosFil: Dyer, Paul S.. The University Of Nottingham; Reino UnidoFil: Fillinger, Sabine. Institut National de la Recherche Agronomique; FranciaFil: Fournier, Elisabeth. Institut National de la Recherche Agronomique; Francia. Centre de coopération internationale en recherche agronomique pour le développement; FranciaFil: Gout, Lilian. Institut National de la Recherche Agronomique; FranciaFil: Hahn, Matthias. University Of Kaiserlautern; AlemaniaFil: Kohn, Linda. University Of Toronto; CanadáFil: Lapalu, Nicolas. Institut National de la Recherche Agronomique; FranciaFil: Plummer, Kim M.. la Trobe University; AustraliaFil: Pradier, Jean-Marc. Institut National de la Recherche Agronomique; FranciaFil: Quévillon, Emmanuel. Institut National de la Recherche Agronomique; Francia. Centre National de la Recherche Scientifique; FranciaFil: Sharon, Amir. Tel Aviv University. Department of Molecular Biology and Ecology of Plants; IsraelFil: Simon, Adeline. Institut National de la Recherche Agronomique; FranciaFil: Tudzynski, Bettina. Institut für Biologie und Biotechnologie der Pflanzen; AlemaniaFil: Tudzynski, Paul. Institut für Biologie und Biotechnologie der Pflanzen; AlemaniaFil: Wincker, Patrick. Centre National de Séquençage. Genoscope; FranciaFil: Andrew, Marion. University Of Toronto; CanadáFil: Anthouard, Véronique. Centre National de Séquençage. Genoscope; FranciaFil: Beever, Ross E.. Landcare Research; Nueva ZelandaFil: Beffa, Rolland. Centre National de la Recherche Scientifique; FranciaFil: Benoit, Isabelle . Microbiology and Kluyver Centre for Genomics of Industrial Fermentations; Países BajosFil: Bouzid, Ourdia. Microbiology and Kluyver Centre for Genomics of Industrial Fermentations; Países Bajo

Evaluation of Protocol Uniformity Concerning Laparoscopic Cholecystectomy in The Netherlands

Background: Iatrogenic bile duct injury remains a current complication of laparoscopic cholecystectomy. One uniform and standardized protocol, based on the "critical view of safety" concept of Strasberg, should red