Invasive species and biodiversity crises: testing the link in the late devonian

During the Late Devonian Biodiversity Crisis, the primary driver of biodiversity decline was the dramatic reduction in speciation rates, not elevated extinction rates; however, the causes of speciation decline have been previously unstudied. Speciation, the formation of new species from ancestral populations, occurs by two primary allopatric mechanisms: vicariance, where the ancestral population is passively divided into two large subpopulations that later diverge and form two daughter species, and dispersal, in which a small subset of the ancestral population actively migrates then diverges to form a new species. Studies of modern and fossil clades typically document speciation by vicariance in much higher frequencies than speciation by dispersal. To assess the mechanism behind Late Devonian speciation reduction, speciation rates were calculated within stratigraphically constrained species-level phylogenetic hypotheses for three representative clades and mode of speciation at cladogenetic events was assessed across four clades in three phyla: Arthropoda, Brachiopoda, and Mollusca. In all cases, Devonian taxa exhibited a congruent reduction in speciation rate between the Middle Devonian pre-crisis interval and the Late Devonian crisis interval. Furthermore, speciation via vicariance is almost entirely absent during the crisis interval; most episodes of speciation during this time were due to dispersal. The shutdown of speciation by vicariance during this interval was related to widespread interbasinal species invasions. The lack of Late Devonian vicariance is diametrically opposed to the pattern observed in other geologic intervals, which suggests the loss of vicariant speciation attributable to species invasions during the Late Devonian was a causal factor in the biodiversity crisis. Similarly, modern ecosystems, in which invasive species are rampant, may be expected to exhibit similar shutdown of speciation by vicariance as an outcome of the modern biodiversity crisis.     

Improving and integrating data on invasive species collected by citizen scientists

Limited resources make it difficult to effectively document, monitor, and control invasive species across large areas, resulting in large gaps in our knowledge of current and future invasion patterns. We surveyed 128 citizen science program coordinators and interviewed 15 of them to evaluate their potential role in filling these gaps. Many programs collect data on invasive species and are willing to contribute these data to public databases. Although resources for education and monitoring are readily available, groups generally lack tools to manage and analyze data. Potential users of these data also retain concerns over data quality. We discuss how to address these concerns about citizen scientist data and programs while preserving the advantages they afford. A unified yet flexible national citizen science program aimed at tracking invasive species location, abundance, and control efforts could be designed using centralized data sharing and management tools. Such a system could meet the needs of multiple stakeholders while allowing efficiencies of scale, greater standardization of methods, and improved data quality testing and sharing. Finally, we present a prototype for such a system (see ).     

Biaryl guanidine inhibitors of in vitro HCV-IRES activity

A structure-activity relationship analysis was carried out on a high-throughput small molecule screening lead for HCV-IRES translation inhibition. The study led to the identification of a guanidine-based structure with low microM inhibitory activity.     

Antibacterial activity of quinolone-macrocycle conjugates

Novel quinolone-macrocycle conjugates displayed submicromolar antibacterial activity against Escherichia coli and Staphylococcus aureus bacterial strains. An analogous open-chain structure was not active at 100 microM against the same pathogenic strains.     

Balancing data sharing requirements for analyses with data sensitivity

Data sensitivity can pose a formidable barrier to data sharing. Knowledge of species current distributions from data sharing is critical for the creation of watch lists and an early warning/rapid response system and for model generation for the spread of invasive species. We have created an on-line system to synthesize disparate datasets of non-native species locations that includes a mechanism to account for data sensitivity. Data contributors are able to mark their data as sensitive. This data is then ‘fuzzed’ in mapping applications and downloaded files to quarter-quadrangle grid cells, but the actual locations are available for analyses. We propose that this system overcomes the hurdles to data sharing posed by sensitive data.     

Structural and Mechanical Improvements to Bone Are Strain Dependent with Axial Compression of the Tibia in Female C57BL/6 Mice

Strain-induced adaption of bone has been well-studied in an axial loading model of the mouse tibia. However, most outcomes of these studies are restricted to changes in bone architecture and do not explore the mechanical implications of those changes. Herein, we studied both the mechanical and morphological adaptions of bone to three strain levels using a targeted tibial loading mouse model. We hypothesized that loading would increase bone architecture and improve cortical mechanical properties in a dose-dependent fashion. The right tibiae of female C57BL/6 mice (8 week old) were compressively loaded for 2 weeks to a maximum compressive force of 8.8N, 10.6N, or 12.4N (generating periosteal strains on the anteromedial region of the mid-diaphysis of 1700 με, 2050 με, or 2400 με as determined by a strain calibration), while the left limb served as an non-loaded control. Following loading, ex vivo analyses of bone architecture and cortical mechanical integrity were assessed by micro-computed tomography and 4-point bending. Results indicated that loading improved bone architecture in a dose-dependent manner and improved mechanical outcomes at 2050 με. Loading to 2050 με resulted in a strong and compelling formation response in both cortical and cancellous regions. In addition, both structural and tissue level strength and energy dissipation were positively impacted in the diaphysis. Loading to the highest strain level also resulted in rapid and robust formation of bone in both cortical and cancellous regions. However, these improvements came at the cost of a woven bone response in half of the animals. Loading to the lowest strain level had little effect on bone architecture and failed to impact structural- or tissue-level mechanical properties. Potential systemic effects were identified for trabecular bone volume fraction, and in the pre-yield region of the force-displacement and stress-strain curves. Future studies will focus on a moderate load level which was largely beneficial in terms of cortical/cancellous structure and cortical mechanical function.     

Analyzing niche stability and biogeography of Late Ordovician brachiopod species using ecological niche modeling

Gauging the potential impacts of environmental change on the geographic distributions of species is a central area of modern biogeographic analysis, often involving complex models of species–environment interactions. The geographic distribution of fossil species can also provide a framework to test the impact of environmental change on biogeography and ecological niches of species, yet few paleontological analyses have attacked this question in deep time. Herein we present a quantitative biogeographic analysis to examine the stability of ecological niches and geographic ranges of rhynchonelliform brachiopods during an interval of sea level change preserved in Upper Ordovician strata of the Cincinnati Arch.The intensive sampling, excellent preservation, and numerous prior paleoecological and sedimentological analyses within the tri-state region of Kentucky, Indiana, and Ohio provide a robust framework for detailed paleobiogeographic study. Quantitative biogeographic modeling methods incorporating GIS (Geographic Information Systems) are utilized in order to spatially analyze the geographic ranges of brachiopod species of the Corryville and Mt. Auburn Formations of the C3 (uppermost Maysvillian) depositional sequence.This study employs the ecological niche modeling program GARP (Genetic Algorithm using Rule-set Prediction) to predict the geographic distribution of eight brachiopod species during three time slices within the C3 sequence. This method estimates a species’ geographic range by modeling the ecological niche of the species based on a set of known species occurrence data coupled with environmental data inferred from sedimentologic proxies. Once environmental tolerances for a species are modeled; the species is predicted to occur wherever its preferred set of environmental conditions occurs within the study region.Distributional patterns were reconstructed for three time slices during the C3 sequence. Recovered range predictions were quantitatively analyzed for evidence of temporal range changes. Results indicate that average species range within the study area decreased and species tracked their preferred niche with high fidelity during the transition from the early to middle portions of the C3 depositional sequence, an interval of rapid relative sea level change. However, during the transition from the middle to late portions of the sequence, gradual shallowing within the basin and development of discontinuous habitat patches correlates with niche evolution of five of the eight species modeled. The average area a species occupied within the basin increased during this interval, but there is a mixed response including both increases and decreases in range size within the study group. In general, the species that exhibit niche evolution increased their geographic range size while those that continue to track their niche with high fidelity experience a decrease in geographic range size. During the latter half of the C3 sequence, previously continuous habitats become fragmented, thereby isolating individual populations and providing a mechanism for niche evolution. The rate of sea level change and the corresponding fragmentation of previously continuous habitats into isolated patches appear to be the primary controls on both mean geographic range size and relative degree of niche evolution.     

Only one of five groEL genes is required for viability and successful symbiosis in Sinorhizobium meliloti

Many bacterial species contain multiple copies of the genes that encode the chaperone GroEL and its cochaperone, GroES, including all of the fully sequenced root-nodulating bacteria that interact symbiotically with legumes to generate fixed nitrogen. In particular, in Sinorhizobium meliloti there are four groESL operons and one groEL gene. To uncover functional redundancies of these genes during growth and symbiosis, we attempted to construct strains containing all combinations of groEL mutations. Although a double groEL1 groEL2 mutant cannot be constructed, we demonstrate that the quadruple groEL1 groESL3 groEL4 groESL5 and groEL2 groESL3 groEL4 groESL5 mutants are viable. Therefore, like E. coli and other species, S. meliloti requires only one groEL gene for viability, and either groEL1 or groEL2 will suffice. The groEL1 groESL5 double mutant is more severely affected for growth at both 30 degrees C and 40 degrees C than the single mutants, suggesting overlapping functions in stress response. During symbiosis the quadruple groEL2 groESL3 groEL4 groESL5 mutant acts like the wild type, but the quadruple groEL1 groESL3 groEL4 groESL5 mutant acts like the groEL1 single mutant, which cannot fully induce nod gene expression and forms ineffective nodules. Therefore, the only groEL gene required for symbiosis is groEL1. However, we show that the other groE genes are expressed in the nodule at lower levels, suggesting minor roles during symbiosis. Combining our data with other data, we conclude that groESL1 encodes the housekeeping GroEL/GroES chaperone and that groESL5 is specialized for stress response.     

Modelling invasion for a habitat generalist and a specialist plant species

Predicting suitable habitat and the potential distribution of invasive species is a high priority for resource managers and systems ecologists. Most models are designed to identify habitat characteristics that define the ecological niche of a species with little consideration to individual species' traits. We tested five commonly used modelling methods on two invasive plant species, the habitat generalist Bromus tectorum and habitat specialist Tamarix chinensis , to compare model performances, evaluate predictability, and relate results to distribution traits associated with each species. Most of the tested models performed similarly for each species; however, the generalist species proved to be more difficult to predict than the specialist species. The highest area under the receiver-operating characteristic curve values with independent validation data sets of B. tectorum and T. chinensis was 0.503 and 0.885, respectively. Similarly, a confusion matrix for B. tectorum had the highest overall accuracy of 55%, while the overall accuracy for T. chinensis was 85%. Models for the generalist species had varying performances, poor evaluations, and inconsistent results. This may be a result of a generalist's capability to persist in a wide range of environmental conditions that are not easily defined by the data, independent variables or model design. Models for the specialist species had consistently strong performances, high evaluations, and similar results among different model applications. This is likely a consequence of the specialist's requirement for explicit environmental resources and ecological barriers that are easily defined by predictive models. Although defining new invaders as generalist or specialist species can be challenging, model performances and evaluations may provide valuable information on a species' potential invasiveness.     

Evaluating dominance as a component of non-native species invasions

Many studies have quantified plant invasions by determining patterns of non‐native species establishment (i.e. richness and absolute cover). Until recently, dominance has been largely overlooked as a significant component of invasion. Therefore, we re‐examined a 6‐year data set of 323 0.1 ha plots within 18 vegetation types collected in the Grand Staircase‐Escalante National Monument from 1998 to 2003, including dominance (i.e. relative cover) in our analyses. We specifically focused on the non‐native species Bromus tectorum, a notable dominant annual grass in this system. We found that non‐native species establishment and dominance are both occurring in species‐rich, mesic vegetation types. Therefore, non‐native species dominance may result despite many equally abundant native species rather than a dominant few, and competitive exclusion does not seem to be a primary control on either non‐native species establishment or dominance in this study. Unlike patterns observed for non‐native species establishment, relative non‐native species cover could not be predicted by native species richness across vegetation types (R² < 0.001; P = 0.45). However, non‐native species richness was found to be positively correlated with relative non‐native species cover and relative B. tectorum cover (R² = 0.46, P < 0.01; R² = 0.17, P < 0.01). Analyses within vegetation types revealed predominantly positive relationships among these variables for the correlations that were significant. Regression tree analyses across vegetation types that included additional biotic and abiotic variables were a little better at predicting non‐native species dominance (PRE = 0.49) and B. tectorum dominance (PRE = 0.39) than at predicting establishment. Land managers will need to set priorities for control efforts on the more productive, species‐rich vegetation types that appear to be susceptible to both components of invasion.