Projecting future expansion of invasive species: Comparing and improving methodologies for species distribution modeling

Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships with four modeling methods run with multiple scenarios of (1) sources of occurrences and geographically isolated background ranges for absences, (2) approaches to drawing background (absence) points, and (3) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved by using a global dataset for model training, rather than restricting data input to the species’ native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e. into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g. boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post-hoc test conducted on a new Partenium dataset from Nepal validated excellent predictive performance of our “best” model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for Parthenium hysterophorus L. (Asteraceae; parthenium). However, discrepancies between model predictions and parthenium invasion in Australia indicate successful management for this globally significant weed. This article is protected by copyright. All rights reserved.

Projecting future expansion of invasive species: Comparing and improving methodologies for species distribution modeling

Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships with four modeling methods run with multiple scenarios of (1) sources of occurrences and geographically isolated background ranges for absences, (2) approaches to drawing background (absence) points, and (3) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved by using a global dataset for model training, rather than restricting data input to the species’ native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e. into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g. boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post-hoc test conducted on a new Partenium dataset from Nepal validated excellent predictive performance of our “best” model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for Parthenium hysterophorus L. (Asteraceae; parthenium). However, discrepancies between model predictions and parthenium invasion in Australia indicate successful management for this globally significant weed. This article is protected by copyright. All rights reserved.

Fluorescence Assay for Polymerase Arrival Rates

To engineer complex synthetic biological systems will require modular design, assembly, and characterization strategies. The RNA polymerase arrival rate (PAR) is defined to be the rate that RNA polymerases arrive at a specified location on the DNA. Designing and characterizing biological modules in terms of RNA polymerase arrival rates provides for many advantages in the construction and modeling of biological systems. PARMESAN is an in vitro method for measuring polymerase arrival rates using pyrrolo-dC, a fluorescent DNA base that can substitute for cytosine. Pyrrolo-dC shows a detectable fluorescence difference when in single-stranded versus double-stranded DNA. During transcription, RNA polymerase separates the two strands of DNA, leading to a change in the fluorescence of pyrrolo-dC. By incorporating pyrrolo-dC at specific locations in the DNA, fluorescence changes can be taken as a direct measurement of the polymerase arrival rate.

Implications of future climate for marine fish

Climate change has already been linked to significant impacts on Earth's ocean ecosystems including shifts in species geographic ranges, changes in population abundance, shits in timing of seasonal events, and establishment of introduced species (Walter et al. 2002, Parmesan and Yohe 2003). Global climate modelling for the Australian region has identified south-eastern Australia as the area that will be subject to the greatest impacts from climatic change (Lough 2009). The major changes predicted include warming of air and water, changes to wind patterns, changes to the strength and southerly extent of dominant oceanic currents flowing down the east and west coasts of Australia, changes to rainfall and run-off (distribution, timing and intensity), increasing ocean acidification, increasing exposure to UV light and sea level rise (Lough and Hobday 2011). Victorian species may be at greater risk than species in other areas of Australia, because Victorian marine waters are in a zone of predicted high climate change (Johnson et al. 2011, Wernberg et al. 2011).

Queijo Parmesão: caracterização físico-química, microbiológica e microestrutura

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Liberação das enzimas LDH e PepX e evolução da maturação de queijo parmesão adicionado de culturas autolíticas de Lactobacilus helveticus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo in situ de culturas autóctones de Lactobacillus helveticus autolíticus sobre a dinâmica bioquímica e sensorial do queijo Paramesão

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Queijos tipo parmesão ralados industrialmente e no ato da venda, adquiridos no comércio varejista, como fontes de agentes deteriorantes e patogênicos

Pós-graduação em Medicina Veterinária - FCAV

Caracterização de segurança e tecnológica de bactérias acidoláticas termofílicas autóctones e aplicação em queijo parmesão

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Ars pictoria, or, An academy treating of drawing, painting, limning, etching : to which are added XXXI copper plates, expressing the choicest, nearest, and most exact grounds and rules of symmetry /

Errata for Ars pictoria, p. [8] of preliminaries. Errata for Appendix, p. 39.

Scientific case for avoiding dangerous climate change to protect young people and nature

28 pages, 6 figures; version submitted to Proceedings of the National Academy of Sciences

Scientific case for avoiding dangerous climate change to protect young people and nature

28 pages, 6 figures; version submitted to Proceedings of the National Academy of Sciences