Showing papers by "Marinez Ferreira de Siqueira published in 2020"

modleR: a modular workflow to perform ecological niche modeling in R

Abstract: Ecological niche models (ENM) use the environmental variables associated with the currently known distribution of a species to model its ecological niche and project it into the geographic space. Widely used and misused, ENM has become a common tool for ecologists and decision-makers. Many ENM platforms have been developed over the years, first as standalone programs, later as packages within script-based programming languages and environments. The democratization of these programming tools and the advent of Open Science brought a growing concern regarding the reproducibility, transparency, robustness, portability, and interoperability in ENM workflows.ENM workflows have some core components that are replicated between projects. However, they have a large internal variation due to the variety of research questions and applications. Any ecological niche modeling platform should take into account this trade-off between stability and reproducibility on one hand, and flexibility and decision-making on the other. Here, we present modleR, a four-step workflow that wraps some of the common phases executed during an ecological niche model procedure. We have divided the process into (1) data setup, (2) model fitting and projection, (3) partition joining and(4) ensemble modeling (consensus between algorithms). modleR is highly adaptable and replicable depending on the user9s needs and is open to deeper internal parametrization. It can be used as a testing platform due to its consistent folder structure and its capacity to control some sources of variation while changing others. It can be run in interactive local sessions and in high-performance or high-throughput computational (HPC/HTC) platforms and parallelized by species or algorithms. It can also communicate with other tools in the field, allowing the user to enter and exit the workflow at any phase, and execute complementary routines outside the package. Finally, it records metadata and session information at each step, ensuring reproducibility beyond the use of script-based applications.

Defining endemism levels for biodiversity conservation: tree species in the Atlantic Forest hotspot

Abstract: Endemic species are important for biodiversity conservation. Yet, quantifying endemism remains challenging because endemism concepts can be too strict (i.e., pure endemism) or too subjective (i.e., near endemism). We propose a data-driven approach to objectively estimate the proportion of records inside a given the target area (i.e., endemism level) that optimizes the separation of near-endemics from non-endemic species. We apply this approach to the Atlantic Forest tree flora using millions of herbarium records retrieved from multiple sources. We first report an updated checklist of 5044 species for the Atlantic Forest tree flora and then we compare how species-specific endemism levels obtained from herbarium data match species-specific endemism accepted by taxonomists. We show that an endemism level of 90% separates well pure and near-endemic from non-endemic species, which in the Atlantic Forest revealed an overall endemism ratio of 45% for its tree flora. We also found that the diversity of pure and near endemics and of endemics and overall species was congruent in space. Our results for the Atlantic Forest reinforce that pure and near endemic species can be combined to quantify regional endemism and therefore to set conservation priorities taking into account endemic species distribution. We provided general guidelines on how the proposed approach can be used to assess endemism levels of regional biotas in other parts of the world.

Could Protected Areas in Brazil’s Semi-Arid Conserve Endangered Birds Facing Climatic and Land Cover Changes?

Abstract: Las areas protegidas actuan como pilares sobre los cuales se construyen las estrategias de conservacion. Ademas de las actividades humanas, los cambios climaticos globales son una preocupacion adicional para la conservacion de las especies. En el noreste de Brasil, el cambio climatico deberia conducir a un reemplazo de la vegetacion nativa actual por vegetacion semidesertica. Este estudio evalua si las areas protegidas de Caatinga pueden contribuir al mantenimiento de condiciones climaticas adecuadas para las aves en peligro de extincion a lo largo del tiempo frente a los cambios climaticos globales y el cambio de la cubierta terrestre. Utilizamos modelos de nicho ecologicos como capas de entrada en un programa de priorizacion espacial, en el que se utilizaron indices de estabilidad para ponderar los objetivos. Los resultados pronosticaron que la mayoria de lostaxa (18) tendran su idoneidad reducida en el futuro, y todos los taxa (23) tendran su nicho ecologico desplazado geograficamente. Sin embargo, nuestros resultados mostraron que el sistema de areas protegidas de Caatinga integrado con un conjunto de areas prioritarias puede mantener condiciones climaticas adecuadas para las aves en peligro de extincion ante el cambio climatico y el cambio de la cubierta terrestre. En promedio, el sistema de areas protegidas de Caatinga podria proteger las areas de estabilidad climatica al menos 1.7 veces mayor que los escenarios sin ella. Esto refuerza la importancia de las areas protegidas como estrategia de conservacion de la biodiversidad.