Applying spatial analysis of genetic and environmental data to predict connection corridors to the New World screwworm populations in South America

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

Environmental suitability of a highly fragmented and heterogeneous landscape for forest bird species in south-eastern Brazil

Assessment of the suitability of anthropogenic landscapes for wildlife species is crucial for setting priorities for biodiversity conservation. This study aimed to analyse the environmental suitability of a highly fragmented region of the Brazilian Atlantic Forest, one of the world's 25 recognized biodiversity hotspots, for forest bird species. Eight forest bird species were selected for the analyses, based on point counts (n = 122) conducted in April-September 2006 and January-March 2009. Six additional variables (landscape diversity, distance from forest and streams, aspect, elevation and slope) were modelled in Maxent for (1) actual and (2) simulated land cover, based on the forest expansion required by existing Brazilian forest legislation. Models were evaluated by bootstrap or jackknife methods and their performance was assessed by AUC, omission error, binomial probability or p value. All predictive models were statistically significant, with high AUC values and low omission errors. A small proportion of the actual landscape (24.41 +/- 6.31%) was suitable for forest bird species. The simulated landscapes lead to an increase of c. 30% in total suitable areas. In average, models predicted a small increase (23.69 +/- 6.95%) in the area of suitable native forest for bird species. Being close to forest increased the environmental suitability of landscapes for all bird species; landscape diversity was also a significant factor for some species. In conclusion, this study demonstrates that species distribution modelling (SDM) successfully predicted bird distribution across a heterogeneous landscape at fine spatial resolution, as all models were biologically relevant and statistically significant. The use of landscape variables as predictors contributed significantly to the results, particularly for species distributions over small extents and at fine scales. This is the first study to evaluate the environmental suitability of the remaining Brazilian Atlantic Forest for bird species in an agricultural landscape, and provides important additional data for regional environmental planning.

Modeling the Potential Geographic Distribution of Black Pepper (Piper nigrum) in Asia Using GIS Tools

Known as the "king of spices", black pepper (Piper nigrum), a perennial crop of the tropics, is economically the most important and the most widely used spice crop in the world. To understand its suitable bioclimatic distribution, maximum entropy based on ecological niche modeling was used to model the bioclimatic niches of the species in its Asian range. Based on known occurrences, bioclimatic areas with higher probabilities are mainly located in the eastern and western coasts of the Indian Peninsula, the east of Sumatra Island, some areas in the Malay Archipelago, and the southeast coastal areas of China. Some undocumented places were also predicted as suitable areas. According to the jackknife procedure, the minimum temperature of the coldest month, the mean monthly temperature range, and the precipitation of the wettest month were identified as highly effective factors in the distribution of black pepper and could possibly account for the crop's distribution pattern. Such climatic requirements inhibited this species from dispersing and gaining a larger geographical range.

Species Distribution Modeling for Conservation Purposes

Species distribution models (SDMs) can be useful for different conservation purposes. We discuss the importance of fitting spatial scale and using current records and relevant predictors aiming conservation. We choose jaguar (Panthera onca) as a target species and Brazil and Atlantic Forest biome as study areas. We tested two different extents (continent and biome) and resolutions (similar to 4 Km and similar to 1 Km) in Maxent with 186 records and 11 predictors (bioclimatic, elevation, land-use and landscape structure). All models presented satisfactory AUC values (>0.70) and low omission errors (<23%). SDMs were scale-sensitive as the use of reduced extent implied in significant gains to model performance generating more constrained and real predictive distribution maps. Continental-scale models performed poorly in predicting potential current jaguar distribution, but they reached the historic distribution. Specificity increased significantly from coarse to finer-scale models due to the reduction of overprediction. The variability of environmental space (E-space) differed for most of climatic variables between continental and biome-scale and the representation of the E-space by predictors differed significantly (t = 2.42, g.I. = 9, P < 0.05). Refining spatial scale, incorporating landscape variables and improving the quality of biological data are essential for improving model prediction for conservation purposes.

Pollination services at risk: Bee habitats will decrease owing to climate change in Brazil

Native bees are important providers of pollination services, but there are cumulative evidences of their decline. Global changes such as habitat losses, invasions of exotic species and climate change have been suggested as the main causes of the decline of pollinators. In this study, the influence of climate change on the distribution of 10 species of Brazilian bees was estimated with species distribution modelling. We used Maxent algorithm (maximum entropy) and two different scenarios, an optimistic and a pessimistic, to the years 2050 and 2080. We also evaluated the percentage reduction of species habitat based on the future scenarios of climate change through Geographic Information System (GIS). Results showed that the total area of suitable habitats decreased for all species but one under the different future scenarios. The greatest reductions in habitat area were found for Melipona bicolor bicolor and Melipona scutellaris, which occur predominantly in areas related originally to Atlantic Moist Forest. The species analysed have been reported to be pollinators of some regional crops and the consequence of their decrease for these crops needs further clarification. (C) 2012 Elsevier B.V. All rights reserved.

Enhanced Sensitivity by Nonuniform Sampling Enables Multidimensional MAS NMR Spectroscopy of Protein Assemblies

We report dramatic sensitivity enhancements in multidimensional MAS NMR spectra by the use of nonuniform sampling (NUS) and introduce maximum entropy interpolation (MINT) processing that assures the linearity between the time and frequency domains of the NUS acquired data sets. A systematic analysis of sensitivity and resolution in 2D and 3D NUS spectra reveals that with NUS, at least 1.5- to 2-fold sensitivity enhancement can be attained in each indirect dimension without compromising the spectral resolution. These enhancements are similar to or higher than those attained by the newest-generation commercial cryogenic probes. We explore the benefits of this NUS/MaxEnt approach in proteins and protein assemblies using 1-73-(U-C-13,N-15)/74-108-(U-N-15) Escherichia coil thioredoxin reassembly. We demonstrate that in thioredoxin reassembly, NUS permits acquisition of high-quality 3D-NCACX spectra, which are inaccessible with conventional sampling due to prohibitively long experiment times. Of critical importance, issues that hinder NUS-based SNR enhancement in 3D-NMR of liquids are mitigated in the study of solid samples in which theoretical enhancements on the order of 3-4 fold are accessible by compounding the NUS-based SNR enhancement of each indirect dimension. NUS/MINT is anticipated to be widely applicable and advantageous for multidimensional heteronuclear MAS NMR spectroscopy of proteins, protein assemblies, and other biological systems.

Enhancing Sensitivity In Natural Product Nmr: Exploring Optimal Non-Uniform Sampling

Recent optimizations of NMR spectroscopy have focused their attention on innovations in new hardware, such as novel probes and higher field strengths. Only recently has the potential to enhance the sensitivity of NMR through data acquisition strategies been investigated. This thesis has focused on the practice of enhancing the signal-to-noise ratio (SNR) of NMR using non-uniform sampling (NUS). After first establishing the concept and exact theory of compounding sensitivity enhancements in multiple non-uniformly sampled indirect dimensions, a new result was derived that NUS enhances both SNR and resolution at any given signal evolution time. In contrast, uniform sampling alternately optimizes SNR (t < 1.26T2) or resolution (t~3T2), each at the expense of the other. Experiments were designed and conducted on a plant natural product to explore this behavior of NUS in which the SNR and resolution continue to improve as acquisition time increases. Possible absolute sensitivity improvements of 1.5 and 1.9 are possible in each indirect dimension for matched and 2x biased exponentially decaying sampling densities, respectively, at an acquisition time of ¿T2. Recommendations for breaking into the linear regime of maximum entropy (MaxEnt) are proposed. Furthermore, examination into a novel sinusoidal sampling density resulted in improved line shapes in MaxEnt reconstructions of NUS data and comparable enhancement to a matched exponential sampling density. The Absolute Sample Sensitivity derived and demonstrated here for NUS holds great promise in expanding the adoption of non-uniform sampling.

Distribución potencial de los bosques de prosopis flexuosa en la provincia biogeográfica del monte

El objetivo de esta investigación fue generar un modelo de distribución potencial de los bosques de Prosopis flexuosa, en la provincia Biogeográfica del Monte, desde Catamarca hasta Mendoza, para luego comparar con distribuciones actuales y poder inferir acerca de los principales procesos y cambios en la distribución que pudieron haber sufrido estos bosques ya sea por causas naturales o antrópicas. Para obtener el mapa modelo se utilizó el software Maxent, el cual utiliza como datos los registros de presencia (georreferenciados) de la especie y las variables ambientales que se consideran relevantes para su distribución. Para correr el modelo, se utilizaron las variables bioclimáticas (obtenidas del sitio Worldclim) y las variables altura, pendiente, orientación, subórdenes de suelos y freática. Como registros, se utilizaron puntos de presencia de bosques (tomados con GPS) en diferentes zonas del Monte. El mapa de distribución potencial resultante concuerda con la ubicación de los principales valles, bolsones y llanuras del Monte, en donde se conoce la existencia actual de los bosques de Prosopis flexuosa. En comparación con estas distribuciones reales, existe una importante coincidencia pero, en general, el área abarcada por los bosques potenciales es superior a lo determinado por las imágenes actuales, como así también existen casos particulares en los cuales las probabilidades de ocurrencia de bosques son muy bajas y las imágenes nos muestran existencia de los mismos. A su vez, al comparar con fuentes y registros históricos, con documentos oficiales (cartas IGM) y estadísticas del ferrocarril se pueden inferir posibles procesos de desmontes, que estarían determinando la ausencia de bosques actuales en sitios donde nuestro mapa potencial presenta altas probabilidades.

Global habitat suitability of deep-water Antipatharia

Antipatharia are a diverse group of corals with many species found in deep water. Many Antipatharia are habitat for associates, have extreme longevity and some species can occur beyond 8500 m depth. As they are major constituents of 'coral gardens', which are Vulnerable Marine Ecosystems (VMEs), knowledge of their distribution and environmental requirements is an important pre-requisite for informed conservation planning particularly where the expense and difficulty of deep-sea sampling prohibits comprehensive surveys. This study uses a global database of Antipatharia distribution data to perform habitat suitability modelling using the Maxent methodology to estimate the global extent of black coral habitat suitability. The model of habitat suitability is driven by temperature but there is notable influence from other variables of topography, surface productivity and oxygen levels. This model can be used to predict areas of suitable habitat, which can be useful for conservation planning. The global distribution of Antipatharia habitat suitability shows a marked contrast with the distribution of specimen observations, indicating that many potentially suitable areas have not been sampled, and that sampling effort has been disproportionate to shallow, accessible areas inside marine protected areas (MPAs). Although 25% of Antipatharia observations are located in MPAs, only 7-8% of predicted suitable habitat is protected, which is short of the Convention on Biological Diversity target to protect 10% of ocean habitats by 2020.

Crabeater seals (Lobodon carcinophaga) in the Weddell Sea during DRE1998 campaign

The crabeater seal (Lobodon carcinophaga) is the most abundant Antarctic seal and inhabits the circumpolar pack ice zone of the Southern Ocean. Until now, information on important environmental factors affecting its distribution as well as on foraging behaviour is limited. In austral summer 1998, 12 crabeater seals of both sexes and different age classes were equipped with satellitelinked dive recorders at Drescher Inlet (72.85°S, 19.26°E), eastern Weddell Sea. To identify suitable habitat conditions within the Weddell Sea, a maximum entropy (Maxent) modelling approach was implemented. The model revealed that the eastern and southern Weddell Sea is especially suitable for crabeater seals. Distance to the continental shelf break and sea ice concentration were the two most important parameters in modelling species distribution throughout the study period. Model predictions demonstrated that crabeater seals showed a dynamic response to their seasonally changing environment emphasized by the favoured sea ice conditions. Crabeater seals utilized ice-free waters substantially, which is potentially explained by the comparatively low sea ice cover of the Weddell Sea during summer 1998. Diving behaviour was characterized by short (>90 % = 0-4 min) and shallow (>90 % = 0-51 m) dives. This pattern reflects the typical summer and autumn foraging behaviour of crabeater seals. Both the distribution and foraging behaviour corresponded well with the life history of the Antarctic krill (Euphausia superba), the preferred prey of crabeater seals. In general, predicted suitable habitat conditions were congruent with probable habitats of krill, which emphasizes the strong dependence on their primary prey.

Phytoplankton niches estimated from CPR data in the North Atlantic

We combine phytoplankton occurrence data for 119 species from the continuous plankton recorder with climatological environmental variables in the North Atlantic to obtain ecological response functions of each species using the MaxEnt statistical method. These response functions describe how the probability of occurrence of each species changes as a function of environmental conditions and can be reduced to a simple description of phytoplankton realized niches using the mean and standard deviation of each environmental variable, weighted by its response function. Although there was substantial variation in the realized niche among species within groups, the envelope of the realized niches of North Atlantic diatoms and dinoflagellates are mostly separate in niche space.

Lesson from the habitat suitability models to evaluate the environmental of Pinus nigra Arnold and Pinus sylvesris L. in the Iberian Peninsula

PREDICT POTENTIAL DISTRIBUTION. Spatial and temporal evolution of the species under different climate scenarios. Generation of habitat suitability models (HSM)  high degree of uncertainty and limitations. The importance of their validation has been stressed. In this work we discuss the present potential distribution of P. sylvestris and P. nigra in the Iberian Peninsula by using MaxEnt, and evaluate the influence of the different environmental variables. Our intention is to select a set of environmental variables that explains better their current distribution, to achieve the most accurate and reliable models. Then we project them to the past climatic conditions (21 to 0 kyrs BP), to evaluate the outputs with existing palaeo-ecological data.

Refining predictions of iberian plant distribution: lessons from p. nigra and p. sylvestris palaeoecological-based habitat suitability models

In recent years, challenged by the climate scenarios put forward by the IPCC and its potential impact on plant distribution, numerous predictive techniques -including the so called habitat suitability models (HSM)- have been developed. Yet, as the output of the different methods produces different distribution areas, developing validation tools are strong needs to reduce uncertainties. Focused in the Iberian Peninsula, we propose a palaeo-based method to increase the robustness of the HSM, by developing an ecological approach to understand the mismatches between the palaeoecological information and the projections of the HSMs. Here, we present the result of (1) investigating causal relationships between environmental variables and presence of Pinus sylvestris L. and P. nigra Arn. available from the 3rd Spanish Forest Inventory, (2) developing present and past presence-predictions through the MaxEnt model for 6 and 21 kyr BP, and (3) assessing these models through comparisons with biomized palaeoecological data available from the European Pollen Database for the Iberian Peninsula.

Evaluación del estado de conservación de dos especies forestales priorizadas participativamente en la sub-cuenca del río Quijos, provincia de Napo, Ecuador

El presente proyecto, enmarcado dentro del Programa INIAP/SENESCYT “Conservación y Uso Sostenible de Recursos Genéticos Forestales en áreas críticas de bosques húmedos y secos de los Andes y Amazonía”, a cargo del Departamento de Forestería del INIAP, nace de la necesidad de generar información sobre la pérdida de la biodiversidad de diversos ecosistemas de Ecuador. En concreto, de aquellos bosques de gran complejidad y elevada susceptibilidad como son los que se encuentran en la sub-cuenca del río Quijos: bosques húmedos de la región amazónica, fuentes de biodiversidad y sumideros de carbono, que se están viendo fuertemente amenazados por el cambio climático y por el cambio en el uso del suelo derivada de la intensa actividad humana que sufre la región desde hace décadas. Debido a esta complejidad, el proyecto se centra en las dos especies forestales más valoradas por los habitantes, aplicando metodología de Diagnóstico Rural Participativo, haciéndoles partícipes de esta forma de las decisiones y actuaciones de su región. Una vez determinadas las dos especies a estudiar (Cedrela montana y Erythrina edulis), se evaluó qué efectos tendrán las principales amenazas: el cambio climático y el cambio de uso del suelo, en las poblaciones de ambas. Para el estudio climático se han utilizado Modelos de Distribución de Especie, en concreto el programa Maxent, con el que se han modelizado dos situaciones: la probabilidad de idoneidad de hábitat actual y la probabilidad de idoneidad de hábitat futuro. Por comparación de ambos mapas se obtuvo una primera visión de cómo podría variar para el año 2070 la distribución potencial de ambas especies debido al cambio de las condiciones climáticas. Así mismo, se pudo determinar cuál de estas variables climáticas influye más en el modelo y, por lo tanto, en la distribución potencial. En el caso de Cedrela montana, en el año 2070 se prevé la desaparición total de hábitat idóneo en la zona de estudio, mientras que en Erythrina edulis, la reducción prevista es también casi total, de un 99,99%. A continuación, aplicando los Criterios de la Lista Roja de la UICN sobre los modelos, se ha determinado el estado de conservación de ambas especies, obteniendo el grado de amenaza que soportan, que en ambos casos es En Peligro Crítico (CR). Para el análisis del efecto del uso del suelo se procedió a la realización de muestreos en zonas con distinto grado antropogénico: el bosque natural y el bosque intervenido. Mediante comparación de las abundancias relativas y las distintas distribuciones diamétricas se han sacado conclusiones de cómo afecta la actividad humana a las poblaciones de ambas especies. Cedrela montana, por su excelente condición de maderable, desaparece en los bosques intervenidos y, si permanece, lo hace sólo con representación de diámetros bastante inferiores al de cortabilidad. Sin embargo, Erythrina edulis, por su condición de comestible, parece verse incluso beneficiada por la acción antrópica: desaparece con la eliminación del bosque, pero parece mantener o incrementar su abundancia en bosque intervenidos, en los que la curva de distribución diamétrica de la especie parece no variar con respecto al bosque primario. Con estas actividades se consigue comprender un poco más cómo sería la evolución de estas especies y el grado de amenaza a el que están sometidas, lo que constituye una fuente valiosa de información en la que basar futuras actividades de conservación de la biodiversidad y manejo sostenible del suelo.