Ground beetles (carabids) constitute an important functional component of biodiversity in agroeco... more Ground beetles (carabids) constitute an important functional component of biodiversity in agroecosystems, mainly because of their role as predators of pests, but also as consumers of weed seeds and as prey to other organisms. Over the past few decades, there has been a marked and continuous decline of ground beetles in Europe, and many species of this insect family are threatened by intensive agricultural practices. The effect of soil tillage, a standard technique in arable farming, on carabids has been investigated in many experimental studies. However, there is currently no clear and differentiated picture of how ground beetles are affected by tillage operations in direct and indirect ways. In this review, we narrow this gap of knowledge and show that the effects of intensive tillage on ground beetles—especially the use of mouldboard ploughing—are extremely variable. Nonetheless, on balance across multiple studies, greater tillage intensity tends to have a negative effect on abund...
Investigating how interactions among plants depend on environmental conditions is key to understa... more Investigating how interactions among plants depend on environmental conditions is key to understand and predict plant communities’ response to climate change. However, while many studies have shown how direct interactions change along climatic gradients, indirect interactions have received far less attention. In this study, we aim at contributing to a more complete understanding of how biotic interactions are modulated by climatic conditions. We investigated both direct and indirect effects of adult tree canopy and ground vegetation on seedling growth and survival in five tree species in the French Alps. To explore the effect of environmental conditions, the experiment was carried out at 10 sites along a climatic gradient closely related to temperature. While seedling growth was little affected by direct and indirect interactions, seedling survival showed significant patterns across multiple species. Ground vegetation had a strong direct competitive effect on seedling survival under warmer conditions. This effect decreased or shifted to facilitation at lower temperatures. While the confidence intervals were wider for the effect of adult canopy, it displayed the same pattern. The monitoring of micro-environmental conditions revealed that competition by ground vegetation in warmer sites could be related to reduced water availability; and weak facilitation by adult canopy in colder sites to protection against frost. For a cold-intolerant and shade-tolerant species (Fagus sylvatica), adult canopy indirectly facilitated seedling survival by suppressing ground vegetation at high temperature sites. The other more cold tolerant species did not show this indirect effect (Pinus uncinata, Larix decidua and Abies alba). Our results support the widely observed pattern of stronger direct competition in more productive climates. However, for shade tolerant species, the effect of direct competition may be buffered by tree canopies reducing the competition of ground vegetation, resulting in an opposite trend for indirect interactions across the climatic gradient
Species recorded in the field survey under different environmental conditions. DRY/WET – plots wi... more Species recorded in the field survey under different environmental conditions. DRY/WET – plots with low/high flooding probabilities respectively; M+/ M– – plots with/without mole activity respectively. For each species listed, its abundance (number of individuals found in the survey plots) per environmental condition is given
Abstract Forecasting spring phenology of temperate fruit trees is of high concern for orchard pla... more Abstract Forecasting spring phenology of temperate fruit trees is of high concern for orchard plannersand fruit producers, particularly in the context of climate change. Responding to this need, horticultural researchers have developed models to estimate chill and heat requirements and project dormancy release. Despite some successes in dormancy modeling, several shortcomings still hamper reliable forecasts. Many widely used models rely on oversimplified and inflexible assumptions and are neither validated nor parameterized for most species or cultivars. More complex models are often poorly accessible due to a lack of guidance on calibration and application. Moreover, most approaches do not provide estimates of uncertainty. We aimed to develop a dormancy model that (a) is based on the best available biological understanding and experimental evidence on dormancy dynamics, (b) can flexibly adapt to species- and cultivar-specific physiology, (c) comes with a detailed description of the work-flow and (d) is open-source. The result is the new modeling framework PhenoFlex. It combines the Dynamic Model for chill accumulation with the Growing-Degree-Hours model for heat accumulation by a flexible transition. PhenoFlex is accompanied by a framework for calibrating the 12 model parameters. It is published as part of the chillR package, which contains a detailed vignette. We tested the predictive performance of PhenoFlex with 60 years of apple and pear bloom data and compared results to several benchmark models. With Root Mean Square Error values for projected bloom dates of 4.0 days for pears and 3.8 days for apples, PhenoFlex outperformed all other models including the StepChill model (10.2 and 7.7 days, respectively), and a machine learning approach (5.6 and 6.3 days). Some temperature response dynamics appeared unrealistic, indicating the need for larger training datasets with more temperature variation. We hope that PhenoFlex will facilitate further research on the temperature response dynamics of temperate tree species.
In the face of a changing climate, yield stability is becoming increasingly important for farmers... more In the face of a changing climate, yield stability is becoming increasingly important for farmers and breeders. Long-term field experiments (LTEs) generate data sets that allow the quantification of stability for different agronomic treatments. However, there are no commonly accepted guidelines for assessing yield stability in LTEs. The large diversity of options impedes comparability of results and reduces confidence in conclusions. Here, we review and provide guidance for the most commonly encountered methodological issues when analysing yield stability in LTEs. The major points we recommend and discuss in individual sections are the following: researchers should (1) make data quality and methodological approaches in the analysis of yield stability from LTEs as transparent as possible; (2) test for and deal with outliers; (3) investigate and include, if present, potentially confounding factors in the statistical model; (4) explore the need for detrending of yield data; (5) account...
Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21(... more Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21(st) century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally...
Canadian Journal of Fisheries and Aquatic Sciences, 2015
Spatial and temporal management measures to reduce nontarget catch are important strategies for r... more Spatial and temporal management measures to reduce nontarget catch are important strategies for rebuilding overfished rockfish (Sebastes spp.) populations in the Northeast Pacific. We describe efforts to support reducing rockfish bycatch in central California trawl fisheries by testing the efficacy of move-on rules on catch data from 2002 to 2010. Move-on rules are regulations or guidelines that trigger the temporary closure of a fishery in a targeted area when a bycatch threshold is reached, without the closure of the entire fishery. Move-on rules based on spatiotemporal autocorrelation (clustering) were effective in reducing bycatch with modest impact on target catch, removing between 35% and 77% of future hauls with bycatch within a specified distance and time of a bycatch-containing haul, while foregoing target catch by an average of 12%. The spatial and temporal peak clustering scales show correlation with the level of schooling behavior by each species; however, the efficiency...
ALADYN is a freely available cross-platform C++ modeling framework for stochastic simulation of j... more ALADYN is a freely available cross-platform C++ modeling framework for stochastic simulation of joint allelic and demographic dynamics of spatially-structured populations. Juvenile survival is linked to the degree of match between an individual's phenotype and the local phenotypic optimum. There is considerable flexibility provided for the demography of the considered species and the genetic architecture of the traits under selection. ALADYN facilitates the investigation of adaptive processes to spatially and/or temporally changing conditions and the resulting niche and range dynamics. To our knowledge ALADYN is so far the only model that allows a continuous resolution of individuals' locations in a spatially explicit landscape together with the associated patterns of selection.
Ground beetles (carabids) constitute an important functional component of biodiversity in agroeco... more Ground beetles (carabids) constitute an important functional component of biodiversity in agroecosystems, mainly because of their role as predators of pests, but also as consumers of weed seeds and as prey to other organisms. Over the past few decades, there has been a marked and continuous decline of ground beetles in Europe, and many species of this insect family are threatened by intensive agricultural practices. The effect of soil tillage, a standard technique in arable farming, on carabids has been investigated in many experimental studies. However, there is currently no clear and differentiated picture of how ground beetles are affected by tillage operations in direct and indirect ways. In this review, we narrow this gap of knowledge and show that the effects of intensive tillage on ground beetles—especially the use of mouldboard ploughing—are extremely variable. Nonetheless, on balance across multiple studies, greater tillage intensity tends to have a negative effect on abund...
Investigating how interactions among plants depend on environmental conditions is key to understa... more Investigating how interactions among plants depend on environmental conditions is key to understand and predict plant communities’ response to climate change. However, while many studies have shown how direct interactions change along climatic gradients, indirect interactions have received far less attention. In this study, we aim at contributing to a more complete understanding of how biotic interactions are modulated by climatic conditions. We investigated both direct and indirect effects of adult tree canopy and ground vegetation on seedling growth and survival in five tree species in the French Alps. To explore the effect of environmental conditions, the experiment was carried out at 10 sites along a climatic gradient closely related to temperature. While seedling growth was little affected by direct and indirect interactions, seedling survival showed significant patterns across multiple species. Ground vegetation had a strong direct competitive effect on seedling survival under warmer conditions. This effect decreased or shifted to facilitation at lower temperatures. While the confidence intervals were wider for the effect of adult canopy, it displayed the same pattern. The monitoring of micro-environmental conditions revealed that competition by ground vegetation in warmer sites could be related to reduced water availability; and weak facilitation by adult canopy in colder sites to protection against frost. For a cold-intolerant and shade-tolerant species (Fagus sylvatica), adult canopy indirectly facilitated seedling survival by suppressing ground vegetation at high temperature sites. The other more cold tolerant species did not show this indirect effect (Pinus uncinata, Larix decidua and Abies alba). Our results support the widely observed pattern of stronger direct competition in more productive climates. However, for shade tolerant species, the effect of direct competition may be buffered by tree canopies reducing the competition of ground vegetation, resulting in an opposite trend for indirect interactions across the climatic gradient
Species recorded in the field survey under different environmental conditions. DRY/WET – plots wi... more Species recorded in the field survey under different environmental conditions. DRY/WET – plots with low/high flooding probabilities respectively; M+/ M– – plots with/without mole activity respectively. For each species listed, its abundance (number of individuals found in the survey plots) per environmental condition is given
Abstract Forecasting spring phenology of temperate fruit trees is of high concern for orchard pla... more Abstract Forecasting spring phenology of temperate fruit trees is of high concern for orchard plannersand fruit producers, particularly in the context of climate change. Responding to this need, horticultural researchers have developed models to estimate chill and heat requirements and project dormancy release. Despite some successes in dormancy modeling, several shortcomings still hamper reliable forecasts. Many widely used models rely on oversimplified and inflexible assumptions and are neither validated nor parameterized for most species or cultivars. More complex models are often poorly accessible due to a lack of guidance on calibration and application. Moreover, most approaches do not provide estimates of uncertainty. We aimed to develop a dormancy model that (a) is based on the best available biological understanding and experimental evidence on dormancy dynamics, (b) can flexibly adapt to species- and cultivar-specific physiology, (c) comes with a detailed description of the work-flow and (d) is open-source. The result is the new modeling framework PhenoFlex. It combines the Dynamic Model for chill accumulation with the Growing-Degree-Hours model for heat accumulation by a flexible transition. PhenoFlex is accompanied by a framework for calibrating the 12 model parameters. It is published as part of the chillR package, which contains a detailed vignette. We tested the predictive performance of PhenoFlex with 60 years of apple and pear bloom data and compared results to several benchmark models. With Root Mean Square Error values for projected bloom dates of 4.0 days for pears and 3.8 days for apples, PhenoFlex outperformed all other models including the StepChill model (10.2 and 7.7 days, respectively), and a machine learning approach (5.6 and 6.3 days). Some temperature response dynamics appeared unrealistic, indicating the need for larger training datasets with more temperature variation. We hope that PhenoFlex will facilitate further research on the temperature response dynamics of temperate tree species.
In the face of a changing climate, yield stability is becoming increasingly important for farmers... more In the face of a changing climate, yield stability is becoming increasingly important for farmers and breeders. Long-term field experiments (LTEs) generate data sets that allow the quantification of stability for different agronomic treatments. However, there are no commonly accepted guidelines for assessing yield stability in LTEs. The large diversity of options impedes comparability of results and reduces confidence in conclusions. Here, we review and provide guidance for the most commonly encountered methodological issues when analysing yield stability in LTEs. The major points we recommend and discuss in individual sections are the following: researchers should (1) make data quality and methodological approaches in the analysis of yield stability from LTEs as transparent as possible; (2) test for and deal with outliers; (3) investigate and include, if present, potentially confounding factors in the statistical model; (4) explore the need for detrending of yield data; (5) account...
Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21(... more Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21(st) century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally...
Canadian Journal of Fisheries and Aquatic Sciences, 2015
Spatial and temporal management measures to reduce nontarget catch are important strategies for r... more Spatial and temporal management measures to reduce nontarget catch are important strategies for rebuilding overfished rockfish (Sebastes spp.) populations in the Northeast Pacific. We describe efforts to support reducing rockfish bycatch in central California trawl fisheries by testing the efficacy of move-on rules on catch data from 2002 to 2010. Move-on rules are regulations or guidelines that trigger the temporary closure of a fishery in a targeted area when a bycatch threshold is reached, without the closure of the entire fishery. Move-on rules based on spatiotemporal autocorrelation (clustering) were effective in reducing bycatch with modest impact on target catch, removing between 35% and 77% of future hauls with bycatch within a specified distance and time of a bycatch-containing haul, while foregoing target catch by an average of 12%. The spatial and temporal peak clustering scales show correlation with the level of schooling behavior by each species; however, the efficiency...
ALADYN is a freely available cross-platform C++ modeling framework for stochastic simulation of j... more ALADYN is a freely available cross-platform C++ modeling framework for stochastic simulation of joint allelic and demographic dynamics of spatially-structured populations. Juvenile survival is linked to the degree of match between an individual's phenotype and the local phenotypic optimum. There is considerable flexibility provided for the demography of the considered species and the genetic architecture of the traits under selection. ALADYN facilitates the investigation of adaptive processes to spatially and/or temporally changing conditions and the resulting niche and range dynamics. To our knowledge ALADYN is so far the only model that allows a continuous resolution of individuals' locations in a spatially explicit landscape together with the associated patterns of selection.
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