Fixation dynamics of beneficial alleles in prokaryotic polyploid chromosomes and plasmids

Theoretical population genetics has been mostly developed for sexually reproducing diploid and for monoploid (haploid) organisms, focusing on eukaryotes. The evolution of bacteria and archaea is often studied by models for the allele dynamics in monoploid populations. However, many prokaryotic organisms harbor multicopy replicons—chromosomes and plasmids—and theory for the allele dynamics in populations of polyploid prokaryotes remains lacking. Here, we present a population genetics model for replicons with multiple copies in the cell. Using this model, we characterize the fixation process of a dominant beneficial mutation at 2 levels: the phenotype and the genotype. Our results show that depending on the mode of replication and segregation, the fixation of the mutant phenotype may precede genotypic fixation by many generations; we term this time interval the heterozygosity window. We furthermore derive concise analytical expressions for the occurrence and length of the heterozygosity window, showing that it emerges if the copy number is high and selection strong. Within the heterozygosity window, the population is phenotypically adapted, while both alleles persist in the population. Replicon ploidy thus allows for the maintenance of genetic variation following phenotypic adaptation and consequently for reversibility in adaptation to fluctuating environmental conditions

Social media as a means of understanding park visitors: an evaluation of user-generated content related to two low use, remote national parks

Master of ScienceDepartment of Horticulture and Natural ResourcesRyan L. SharpUsing two remote and sparsely visited backcountry and wilderness areas in Alaska as a case study, this manuscript evaluates data from one season of online user-generated content. Social media posts from Twitter and Flickr were collected, coded for content, and mapped where geographic data was available. The resulting dataset was assessed for its quality, and results were compared with visitor use information reported by commercial use operators. Overall, out of 4,008 users in the dataset, 223 were on-site visitors to one or both parks, and 144 visited the backcountry. Social media content overrepresented wildlife viewing behaviors, and very little spatial data emerged. User-generated content in the study of very remote wilderness may have some application for managers, but the entire volume of related user-generate content may not represent on-site visitors, especially on Twitter. More research is needed to understand limitations in application of publicly available social media data

Characterizing Scales of Genetic Recombination and Antibiotic Resistance in Pathogenic Bacteria Using Topological Data Analysis

Pathogenic bacteria present a large disease burden on human health. Control of these pathogens is hampered by rampant lateral gene transfer, whereby pathogenic strains may acquire genes conferring resistance to common antibiotics. Here we introduce tools from topological data analysis to characterize the frequency and scale of lateral gene transfer in bacteria, focusing on a set of pathogens of significant public health relevance. As a case study, we examine the spread of antibiotic resistance in Staphylococcus aureus. Finally, we consider the possible role of the human microbiome as a reservoir for antibiotic resistance genes.Comment: 12 pages, 6 figures. To appear in AMT 2014 Special Session on Advanced Methods of Interactive Data Mining for Personalized Medicin

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts

Colonization dynamics of Pantoea agglomeransin the wheat root habitat

Plants are colonized by microbial communities that have diverse implications for plant development and health. The establishment of a stable plant–bacteria interaction depends on a continuous coexistence over generations. Transmission via the seed is considered as the main route for vertical inheritance of plant-associated bacteria. Nonetheless, the ecological principles that govern the plant colonization by seed endophytes remain understudied. Here we quantify the contribution of arrival time and colonization history to bacterial colonization of the wheat root. Establishing a common seed endophyte, Pantoea agglomerans, and wheat as a model system enabled us to document bacterial colonization of the plant roots during the early stages of germination. Using our system, we estimate the carrying capacity of the wheat roots as 108 cells g−1, which is robust among individual plants and over time. Competitions in planta reveal a significant advantage of early incoming colonizers over late-incoming colonizers. Priming for the wheat environment had little effect on the colonizer success. Our experiments thus provide empirical data on the root colonization dynamics of a seed endophyte. The persistence of seed endophyte bacteria with the plant population over generations may contribute to the stable transmission that is one route for the evolution of a stable host-associated lifestyle

Organization and oscillations in simulated shallow convective clouds

Physical insights into processes governing temporal organization and evolution of cloud fields are of great importance for climate research. Here using large eddy simulations with a bin microphysics scheme, we show that warm convective cloud fields exhibit oscillations with two distinct periods (~10 and ~90 min, for the case studied here). The shorter period dominates the nonprecipitating phase, and the longer period is related to the precipitating phase. We show that rain processes affect the domain\u27s thermodynamics, hence forcing the field into a low‐frequency recharge‐discharge cycle of developing cloudiness followed by precipitation‐driven depletion. The end result of precipitation is stabilization of the lower atmosphere by warming of the cloudy layer (due to latent heat release) and cooling of the subcloud layer (by rain evaporation, creating cold pools). As the thermodynamic instability weakens, so does the cloudiness, and the rain ceases. During the nonprecipitating phase of the cycle, surface fluxes destabilize the boundary layer until the next precipitation cycle. Under conditions that do not allow development of precipitation (e.g., high aerosol loading), high‐frequency oscillations dominate the cloud field. Clouds penetrating the stable inversion layer trigger gravity waves with a typical period of ~10 min. In return, the gravity waves modulate the clouds in the field by modifying the vertical velocity, temperature, and humidity fields. Subsequently, as the polluted nonprecipitating simulations evolve, the thermodynamic instability increases and the cloudy layer deepens until precipitation forms, shifting the oscillations from high to low frequency. The organization of cold pools and the spatial scale related to these oscillations are explored

Seed-derived microbial colonization of Wild Emmer and domesticated bread wheat (Triticum dicoccoides and T. aestivum) seedlings shows pronounced differences in overall diversity and composition

The composition of the plant microbiota may be altered by ecological and evolutionary changes in the host population. Seed-associated microbiota, expected to be largely vertically transferred, have the potential to coadapt with their host over generations. Strong directional selection and changes in the genetic composition of plants during domestication and cultivation may have impacted the assembly and transmission of seed-associated microbiota. Nonetheless, the effect of plant speciation and domestication on the composition of these microbes is poorly understood. Here, we have investigated the composition of bacteria and fungi associated with the wild emmer wheat (Triticum dicoccoides) and domesticated bread wheat (Triticum aestivum). We show that vertically transmitted bacteria, but not fungi, of domesticated bread wheat species T. aestivum are less diverse and more inconsistent among individual plants compared to those of the wild emmer wheat species T. dicoccoides. We propagated wheat seeds under sterile conditions to characterize the colonization of seedlings by seed-associated microbes. Hereby, we show markedly different community compositions and diversities of leaf and root colonizers of the domesticated bread wheat compared to the wild emmer wheat. By propagating the wild emmer wheat and domesticated bread wheat in two different soils, we furthermore reveal a small effect of plant genotype on microbiota assembly. Our results suggest that domestication and prolonged breeding have impacted the vertically transferred bacteria, but only to a lesser extent have affected the soil-derived microbiota of bread wheat.IMPORTANCE Genetic and physiological changes associated with plant domestication have been studied for many crop species. Still little is known about the impact of domestication on the plant-associated microbiota. In this study, we analyze the seed-associated and soil-derived bacterial and fungal microbiota of domesticated bread wheat and wild emmer wheat. We show a significant difference in the seed-associated, but not soil-derived, bacterial communities of the wheat species. Interestingly, we find less pronounced effects on the fungal communities. Overall, this study provides novel insight into the diversity of vertically transmitted microbiota of wheat and thereby contributes to our understanding of wheat as a “}metaorganism.{” Insight into the wheat microbiota is of fundamental importance for the development of improved crops

Bringing Forecasting Into the Future: Using Google to Predict Visitation in U.S. National Parks

In recent years, visitation to U.S. National Parks has been increasing, with the majority of this increase occurring in a subset of parks. As a result, managers in these parks must respond quickly to increasing visitor-related challenges. Improved visitation forecasting would allow managers to more proactively plan for such increases. In this study, we leverage internet search data that is freely available through Google Trends to create a forecasting model. We compare this Google Trends model to a traditional autoregressive forecasting model. Overall, our Google Trends model accurately predicted 97% of the total visitation variation to all parks one year in advance from 2013 to 2017 and outperformed the autoregressive model by all metrics. While our Google Trends model performs better overall, this was not the case for each park unit individually; the accuracy of this model varied significantly from park to park. We hypothesized that park attributes related to trip planning would correlate with the accuracy of our Google Trends model, but none of the variables tested produced overly compelling results. Future research can continue exploring the utility of Google Trends to forecast visitor use in protected areas, or use methods demonstrated in this paper to explore alternative data sources to improve visitation forecasting in U.S. National Parks

Spin correlations in the electron-doped high-transition-temperature superconductor Nd{2-x}Ce{x}CuO{4+/-delta}

High-transition-temperature (high-Tc) superconductivity develops near antiferromagnetic phases, and it is possible that magnetic excitations contribute to the superconducting pairing mechanism. To assess the role of antiferromagnetism, it is essential to understand the doping and temperature dependence of the two-dimensional antiferromagnetic spin correlations. The phase diagram is asymmetric with respect to electron and hole doping, and for the comparatively less-studied electron-doped materials, the antiferromagnetic phase extends much further with doping [1, 2] and appears to overlap with the superconducting phase. The archetypical electron-doped compound Nd{2-x}Ce{x}CuO{4\pm\delta} (NCCO) shows bulk superconductivity above x \approx 0.13 [3, 4], while evidence for antiferromagnetic order has been found up to x \approx 0.17 [2, 5, 6]. Here we report inelastic magnetic neutron-scattering measurements that point to the distinct possibility that genuine long-range antiferromagnetism and superconductivity do not coexist. The data reveal a magnetic quantum critical point where superconductivity first appears, consistent with an exotic quantum phase transition between the two phases [7]. We also demonstrate that the pseudogap phenomenon in the electron-doped materials, which is associated with pronounced charge anomalies [8-11], arises from a build-up of spin correlations, in agreement with recent theoretical proposals [12, 13].Comment: 5 pages, 4 figure