Mapping diversity indices: not a trivial issue

Mapping diversity indices, that is estimating values in all locations of a given area from some sampled locations, is central to numerous research and applied fields in ecology. Two approaches are used to map diversity indices without including abiotic or biotic variables: (i) the indirect approach, which consists in estimating each individual species distribution over the area, then stacking the distributions of all species to estimate and map a posteriori the diversity index, (ii) the direct approach, which relies on computing a diversity index in each sampled locations and then to interpolate these values to all locations of the studied area for mapping. For both approaches, we document drawbacks from theoretical and practical viewpoints and argue about the need for adequate interpolation methods. First, we point out that the indirect approach is problematic because of the high proportion of rare species in natural communities. This leads to zero-inflated distributions, which cannot be interpolated using standard statistical approaches. Secondly, the direct approach is inaccurate because diversity indices are not spatially additive, that is the diversity of a studied area (e.g. region) is not the sum of the local diversities. Therefore, the arithmetic variance and some of its derivatives, such as the variogram, are not appropriate to ecologically measure variation in diversity indices. For the direct approach, we propose to consider the -diversity, which quantifies diversity variations between locations, by the mean of a -gram within the interpolation procedure. We applied this method, as well as the traditional interpolation methods for comparison purposes on different faunistic and floristic data sets collected from scientific surveys. We considered two common diversity indices, the species richness and the Rao\u27s quadratic entropy, knowing that the above issues are true for complementary species diversity indices as well as those dealing with other biodiversity levels such as genetic diversity. We conclude that none of the approaches provided an accurate mapping of diversity indices and that further methodological developments are still needed. We finally discuss lines of research that may resolve this key issue, dealing with conditional simulations and models taking into account biotic and abiotic explanatory variables

Historical summer distribution of the endangered North Atlantic right whale (Eubalaena glacialis): a hypothesis based on environmental preferences of a congeneric species

Aim: To obtain a plausible hypothesis for the historical distribution of North Atlantic right whales (NARWs) (Eubalaena glacialis) in their summer feeding grounds. Previously widespread in the North Atlantic, after centuries of hunt- ing, these whales survive as a small population off eastern North America. Because their exploitation began before formal records started, information about their historical distribution is fragmentary

Особенности процесса распылительной сушки высоковлажной биомассы Spirulina platensis

Проведен комплекс исследований по распылительному обезвоживанию биомассы Spirulina platensis, включающий исследование кинетических особенностей обезвоживания и теплотехнологических параметров распылительного способа сушки. Получены опытные партии порошков, проведен анализ дисперсионных и структурно-механических характеристик полученных порошков, показано, что процесс обезвоживания осуществляется при достаточно “мягких” термических условиях.Проведено комплекс досліджень розпилювального зневоднення біомаси Spirulina platensis, стосовно кінетичних особливостей сушіння та теплотехнологічних параметрів розпилювального способу сушки. Отримано дослідні партії порошків, проведено аналіз дисперсних та структурно-механічних характеристик отриманих порошків, виявлено, що процес зневоднення здійснюється при достатньо “м’яких” термічних умовах.A complex investigation of the spray drying of Spirulina platensis biomass have been carried out, which included studying of the kinetic properties of the dehydration process as well as the heat exchanging technological parametrs of spray drying technique. By using a pilot dryer, development types of the dry powdered product have been obtained. A analysis of the dispersion and mechanical characteristics of the powdered product being obtained has been performed. It has been shown that the drying processes has to be carried out at fairly soft dehydration regimes

A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes

The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ∼100–80 Mya, and most Perciformes families originated 80–50 Mya. Two important clade origin events were detected. The first at 100–80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot

Genome-Wide Association Study Identifies Genetic Loci Associated with Iron Deficiency

The existence of multiple inherited disorders of iron metabolism in man, rodents and other vertebrates suggests genetic contributions to iron deficiency. To identify new genomic locations associated with iron deficiency, a genome-wide association study (GWAS) was performed using DNA collected from white men aged ≥25 y and women ≥50 y in the Hemochromatosis and Iron Overload Screening (HEIRS) Study with serum ferritin (SF) ≤ 12 µg/L (cases) and iron replete controls (SF>100 µg/L in men, SF>50 µg/L in women). Regression analysis was used to examine the association between case-control status (336 cases, 343 controls) and quantitative serum iron measures and 331,060 single nucleotide polymorphism (SNP) genotypes, with replication analyses performed in a sample of 71 cases and 161 controls from a population of white male and female veterans screened at a US Veterans Affairs (VA) medical center. Five SNPs identified in the GWAS met genome-wide statistical significance for association with at least one iron measure, rs2698530 on chr. 2p14; rs3811647 on chr. 3q22, a known SNP in the transferrin (TF) gene region; rs1800562 on chr. 6p22, the C282Y mutation in the HFE gene; rs7787204 on chr. 7p21; and rs987710 on chr. 22q11 (GWAS observed P<1.51×10−7 for all). An association between total iron binding capacity and SNP rs3811647 in the TF gene (GWAS observed P = 7.0×10−9, corrected P = 0.012) was replicated within the VA samples (observed P = 0.012). Associations with the C282Y mutation in the HFE gene also were replicated. The joint analysis of the HEIRS and VA samples revealed strong associations between rs2698530 on chr. 2p14 and iron status outcomes. These results confirm a previously-described TF polymorphism and implicate one potential new locus as a target for gene identification

Bringing macroecology into agricultural science: promises and challenges

National audienceGiven the multiple challenges imposed by global changes, including climate change, land use conversion, biological invasions, and habitat loss, ecology has received more societal attention in the last decades than ever before. Indeed, global change imposes a number of new challenges for global food security, including the need to adapt agricultural systems to new environmental conditions and potentially new pests and diseases. Planning for these changes requires a better understanding of the factors influencing agricultural productivity and stability, as well as the design and use of predictive tools to allow forecasting and comparisons between potential management strategies. More importantly, the goals of sustainability, along with the need to adapt and forecast, impose a need to abandon the case-by-case approaches and to come up with broader, more generalizable strategies that will allow maintaining and increasing productivity in a more biodiversity-friendly manner. Macroecology focuses on finding general patterns across ecological communities at large scales, in particular with respect to abundance, distributions and biodiversity. It is therefore particularly well suited to study and answer questions of global change as applied to agricultural landscapes. However, as in many other fields in ecology, macroecologists have focused largely on the study of natural or semi-natural systems. Here I review major macroecological fields of study that can contribute to a more predictive agricultural management strategy. The main goals of this review will be to (1) synthesize what we know about macroecological patterns that need to be tested and applied to agricultural systems; (2) identify areas where macroecological research has already been contributing to agricultural planning as well as (3) identifying gaps where we can bring more macroecology into agricultural sciences. The emphasis will be on the particular challenges and opportunities that agricultural settings can provide for such a macroecological perspective

Comparing alternative systematic conservation planning strategies against a politically driven conservation plan

Decisions regarding the level of detail included in conservation planning and the importance given to feasibility considerations can greatly influence management in terms of total area required, achievement of conservation targets and costs. This work had two main objectives: (1) to compare priority sites proposed by the Chilean commission for the environment in a politically driven process to the results of alternative systematic conservation planning scenarios; and (2) to compare the efficacy of systematic conservation planning based on different types of conservation targets (forest types and bird species) and minimum area thresholds. To address these issues, we used vegetation cover as well as field data on forest birds in central Chile. Bird species distributions were modeled using a variety of climatic and environmental layers, allowing for the integration of environmental heterogeneity into the planning process. We then ran several conservation planning scenarios considering conservation targets based on vegetation types alone, birds alone, or a combination of vegetation and birds. Collectively these results show that conservation planning results differ significantly when considering birds or vegetation types, and that minimum area requirements for each conservation feature has a great influence on the final results. Moreover, important conservation sites are not represented in the current government plan, and these sites are related to the small representation of rare vegetation types. This study suggests that using appropriate minimum area requirements can greatly affect the results of a conservation planning exercise and therefore represents a key knowledge gap in the region

A theoretical framework for upscaling species distribution models

enThis link goes to a English sectionesThis link goes to a Spanish section Species distribution models (SDM) have become one of the most popular predictive tools in ecology. With the advent of new computation and remote sensing technology, high-resolution environmental data sets are becoming more and more common predictors in these modelling efforts. Understanding how scaling affects their outputs is therefore fundamental to understand their applicability. Here, we develop a theoretical basis to understand the consequences of aggregating occurrence and environmental data at different resolutions. We provide a theoretical framework, along with numerical simulations and a real-world case study, to show how these scaling rules influence predictive outputs. We show that the properties of the environment–occurrence relationships change when the data are aggregated: the mean probability of occurrence and species prevalence increases, the optimal environmental values shift and classification rates increase at coarser resolutions up to a certain level. Furthermore, and contrary to the widespread expectation that high-resolution data would produce better predictions, we show here that model performance may increase using coarser resolution data sets rather than the inverse. Finally, we also show that model performance depends not only on the environment–occurrence relationship but also on the interaction between this and the geography and distribution of the available environment. This theoretical framework helps understanding previously incoherent results regarding SDM upscaling and model performance, and illustrates how theoretical and empirical results can provide important feedbacks to advance in understanding scaling issues in macroecology. The interaction between the shape of the environment–occurrence relationship and the rates of change of the environment is fundamental to understand the effects of upscaling in model performance, and may explain why some models are more difficult to transfer to different regions. Most importantly, we argue that there are conceptual choices related to scaling and SDM fitting that require expert knowledge and further explorations between theory and practice in macroecology.enThis link goes to a English sectionesThis link goes to a Spanish section Los modelos de distribución de especies (SDM) se han convertido en una de las herramientas predictivas más populares en ecología. Con el advenimiento de nueva tecnología, entre ellas en teledetección e informática, los datos ambientales de alta resolución a grandes escalas se han convertido en predictores cada vez más comunes en estos esfuerzos de modelización. Por lo tanto, es fundamental entender la influencia de los cambios de escala, y en particular de la resolución, sobre el éxito predictivo de los resultados, para comprender mejor su aplicabilidad y generalidad. En este estudio desarrollamos una base teórica para comprender las consecuencias de agregar datos ambientales y de ocurrencia a diferentes resoluciones. Proporcionamos un marco teórico, junto con simulaciones numéricas y un estudio de caso del mundo real, para mostrar cómo estas reglas de escala influyen sobre los resultados predictivos. Mostramos que las propiedades de las relaciones ambiente-ocurrencia cambian cuando los datos se agregan a resoluciones más gruesas: la probabilidad media de ocurrencia y la prevalencia de las especies aumentan, los valores ambientales óptimos cambian, y las tasas de clasificación (éxito predictivo en términos de presencia-ausencia) aumentan hasta cierto nivel. Además, y contrariamente a la expectativa generalizada de que los datos de alta resolución producirían universalmente mejores predicciones, aquí mostramos que el éxito predictivo de estos modelos puede aumentar utilizando datos de resolución más gruesa. Finalmente, también mostramos que el desempeño de un modelo depende no solo de la relación ambiente-ocurrencia, sino también de la interacción entre ésta y la geografía y distribución del ambiente disponible. Este marco teórico ayuda a comprender resultados que parecían previamente incoherentes con respecto a la mejora del poder predictivo de los SDM cuando se utilizan datos de menor resolución, e ilustra cómo los resultados teóricos y empíricos pueden proporcionar elementos importantes para avanzar en la comprensión de los problemas de escala en macroecología. La interacción entre la forma de la relación ambiente-ocurrencia y las tasas de cambio del gradiente ambiental es fundamental para comprender los efectos del aumento de escala en el éxito predictivo de los modelos y puede explicar por qué algunos modelos son más difíciles de transferir a diferentes regiones. Aún más importante, argumentamos que existen nociones conceptuales relacionadas con la escala y el ajuste de los modelos que requieren del conocimiento de los expertos taxonómicos, al igual que más exploraciones entre la teoría y la práctica en macroecología

An increase in management actions has compensated for past climate change effects on desert locust gregarization in western Africa

In response to high population density, the desert locust, Schistocerca gregaria, becomes gregarious and forms swarms that can cause significant damage to crops and pastures, threatening food security of human populations from western Africa to India. This switch from solitary to gregarious populations is highly dependent on favorable weather conditions. Climate change, which has been hypothesized to shift conditions towards increasing risks of gregarization, is therefore likely to have significant impacts on the spatial distribution and likelihood of outbreak events. However, the desert locust is intensely managed at large scales, which possibly counteracts any increased risk of outbreaks due to a more favorable climate. Consequently, understanding the changes in risks in the future involves teasing out the effects of climate change and management actions. Here we studied the dynamics of gregarization at the very early stages of potential outbreaks, in parallel with trends in climate and management, between 1985 and 2018 in western Africa. We used three different spatial scales, with the goal to have a better understanding of the potential effects of climate change per se while controlling for management. Our first approach was to look at a regional scale, where we observed an overall decrease in gregarization events. However, this scale includes very heterogeneous environments and management efforts. To consider this heterogeneity, we divided the area into a grid of 0.5° cells. For each cell, a climate analysis was performed for rainfall and temperature, with trends obtained by a harmonic decomposition model on monthly data. Analyses of gregarization showed only a few significant trends, both positive and negative, mainly found in western Mauritania where management effort has increased. To improve the statistical power, these cells were then grouped into larger homogeneous climatic clusters, i.e. groups of cells with similar climatic conditions and similar climatic trends over the study period. At this scale, gregarization events depend on the intersection between climate conditions and management efforts. The clusters where gregarization increased were also the ones with the highest increase of management. These results highlight the important effect of preventive management, which may counteract the positive effects of climate change on locust proliferation