Mapping linkages between biodiversity and nature’s contributions to people: a ValPar.CH perspective

The approach of Nature's Contributions to People (NCP) has been developed to emphasize human dependence on nature and to better target environmental conservation efforts. While the methods used for NCP assessments have evolved greatly over the last 20 years, the challenge of how to best link and predict NCP to and from individual species or biotic communities still remains largely unmet. Current NCP-based conservation prioritization methods tend to fail to account for individual species and many other dimensions of biodiversity (BD). Therefore, land-management policies based on simple NCP mapping are unlikely to properly account for the full complexity of ecosystems and can ultimately lead to biodiversity loss. Furthermore, as landscapes are increasingly modified by anthropogenic forces, the remaining (semi-)natural ecosystems represent a potential ecological ‘infrastructure’ to be maintained and kept functional. In this working paper, we provide i) a review on the BD-NCP spatial relationships, ii) the main methods used for their study, iii) the main research gaps, and iv) recommendations on how the study of their relationships can be improved, especially when considering a national ecological infrastructure (EI), and a roadmap about how we will approach this subject within the ValPar.CH project. The roadmap focuses on the EI mapping objectives of ValPar.CH, and its main stakeholders

Too many candidates: Embedded covariate selection procedure for species distribution modelling with the covsel R package

1. Selecting the best subset of covariates out of a panel of many candidates is a key and highly influential stage of the species distribution modelling process. Yet, there is currently no commonly accepted and widely adopted standard approach by which to perform this selection. 2. We introduce a two-step “embedded” covariate selection procedure aimed at optimizing the predictive ability and parsimony of species distribution models fitted in a context of high-dimensional candidate covariate space. The procedure combines a collinearity-filtering algorithm (Step A) with three model-specific embedded regularization techniques (Step B), including generalized linear model with elastic net regularization, generalized additive model with null-space penalization, and guided regularized random forest. 3. We evaluated the embedded covariate selection procedure through an example application aimed at modelling the habitat suitability of 50 species in Switzerland from a suite of 123 candidate covariates. We demonstrated the ability of the embedded covariate selection procedure to provide significantly more accurate species distribution models as compared to models obtained with alternative procedures. Model performance was independent of the characteristics of the species data, such as the number of occurrence records or their spatial distribution across the study area. 4. We implemented and streamlined our embedded covariate selection procedure in the covsel R package, paving the way for a ready-to-use, automated, covariate selection tool that was missing in the field of species distribution modelling. All the information required for installing and running the covsel R package is openly available on the GitHub repository https://github.com/N-SDM/covsel

N‐SDM: a high‐performance computing pipeline for Nested Species Distribution Modelling

Predicting contemporary and future species distributions is relevant for science and decision making, yet the development of high‐resolution spatial predictions for numerous taxonomic groups and regions is limited by the scalability of available modelling tools. Uniting species distribution modelling (SDM) techniques into one high‐performance computing (HPC) pipeline, we developedN‐SDM, an SDM platform aimed at delivering reproducible outputs for standard biodiversity assessments.N‐SDMwas built around a spatially‐nested framework, intended at facilitating the combined use of species occurrence data retrieved from multiple sources and at various spatial scales.N‐SDMallows combining two models fitted with species and covariate data retrieved from global to regional scales, which is useful for addressing the issue of spatial niche truncation. The set of state‐of‐the‐art SDM features embodied inN‐SDMincludes a newly devised covariate selection procedure, five modelling algorithms, an algorithm‐specific hyperparameter grid search, and the ensemble of small‐models approach.N‐SDMis designed to be run on HPC environments, allowing the parallel processing of thousands of species at the same time. All the information required for installing and runningN‐SDMis openly available on the GitHub repositoryhttps://github.com/N‐SDM/N‐SDM

Integrating ecosystem services within spatial biodiversity conservation prioritization in the Alps

As anthropogenic degradation of biodiversity and ecosystems increases, so does the potential threat to the supply of ecosystem services, a key contribution of nature to people. Biodiversity has often been used in spatial conservation planning and has been regarded as one among multiple services delivered by ecosystems. Hence, biodiversity conservation planning should be integrated in a framework of prioritizing services in order to inform decision-making. Here, we propose a prioritization approach based on scenarios maximising both the provision of ecosystem services and the conservation of biodiversity hotspots. Different weighting scenarios for the α-diversity in four taxonomic groups and 10 mapped ecosystem services were used to simulate varying priorities of policymakers in a mountain region. Our results illustrate how increasing priorities to ecosystem services can be disadvantageous to biodiversity. Moreover, the analysis to identify priority areas that best compromise the conservation of α-diversity and ecosystem services are predominantly not located within the current protected area network. Our analyses stress the need for an appropriate weighting of biodiversity within decision making that seek to integrate multiple ecosystem services. Our study paves the way toward further integration of multiple biodiversity groups and components, ecosystem services and various socio-economic scenarios, ultimately fuelling the development of more informed, evidence-based spatial planning decisions for conservation

N‐SDM: a high‐performance computing pipeline for Nested Species Distribution Modelling

Predicting contemporary and future species distributions is relevant for science and decision making, yet the development of high-resolution spatial predictions for numerous taxonomic groups and regions is limited by the scalability of available modelling tools. Uniting species distribution modelling (SDM) techniques into one high-performance computing (HPC) pipeline, we developed N-SDM, an SDM platform aimed at delivering reproducible outputs for standard biodiversity assessments. N-SDM was built around a spatially-nested framework, intended at facilitating the combined use of species occurrence data retrieved from multiple sources and at various spatial scales. N-SDM allows combining two models fitted with species and covariate data retrieved from global to regional scales, which is useful for addressing the issue of spatial niche truncation. The set of state-of-the-art SDM features embodied in N-SDM includes a newly devised covariate selection procedure, five modelling algorithms, an algorithm-specific hyperparameter grid search, and the ensemble of small-models approach. N-SDM is designed to be run on HPC environments, allowing the parallel processing of thousands of species at the same time. All the information required for installing and running N-SDM is openly available on the GitHub repository https://github.com/N-SDM/N-SDM

Overview of grapevine trunk diseases in France in the 2000s

The National Grapevine Trunk Disease Survey was conducted in France from 2003 to 2008 to monitor grapevine trunk diseases (GTDs), eutypa dieback and esca/black dead arm (BDA). Data collected from seven regions, 329 vineyards and 12 cultivars were analysed. There were great variations amongst regions in the incidence of GTDs. For esca/BDA, two groups were distinguished: vineyards in Jura and Charentes had greater incidence (93–95%) than those of Bordeaux, Alsace and Bourgogne (54–82%). Incidence increased in Charentes over the 6-year survey, with the highest values being recorded during the last 2 years. For eutypa dieback, all vineyards of Charentes were affected, with 17 to 25% of vines expressing symptoms; for the other regions, 52 to 80% of vineyards were affected, with incidences below 3%. Cultivars Savagnin and Trousseau in Jura were especially affected by esca/BDA. Instead, Ugni Blanc in Charentes was most affected by eutypa dieback. One cultivar could be significantly more affected in one region than in another. The global health status of the vineyards was also investigated. (i) For four regions, 82% (Jura) to 87% (Alsace) of the grapevines were healthy, but this percentage decreased steadily (67%) in Charentes. (ii) Plants infected by GTDs were 32 and 18% in Jura and Charentes respectively, and only 2.9% in the Bourgogne region. (iii) The unproductive plants, i.e. dead, missing, replanted or restored, represented a significant part of the losses (6.6% in Charentes to 9.9% in Jura). The extension of GTDs is discussed with regard to the abiotic and biotic factors that may favour the diseases

Network analysis of the associations between personality traits, cognitive functioning, and inflammatory markers in elderly individuals without dementia

IntroductionLower cognitive functioning in old age has been associated with personality traits or systemic inflammatory markers. Associations have also been found between personality traits and inflammatory markers. However, no study has explored the inter-relationships between these three components simultaneously. The present study aims to better understand the inter-relationships among personality traits, inflammatory markers, and cognitive performance in elderly individuals without dementia.MethodsThis study utilizes a network analysis approach, a statistical method that allows visualization of the data’s unique pairwise associations. We performed a cross-sectional analysis on 720 elderly individuals without dementia, using data from Colaus|PsyColaus, a population-based study conducted in Lausanne, Switzerland. The Revised NEO Five-Factor Inventory (NEO-FFI-R) was used to assess personality traits, and interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), and C-reactive protein (CRP) were used as peripheral inflammatory markers. Cognitive domains were investigated using the Mini-Mental State Examination (MMSE), the Verbal Fluency Test, the Stroop Test, the DO40, and the Free and Cued Selective Reminding (FCSR) test.ResultsOpenness was associated with verbal fluency and Agreeableness with immediate free recall. In contrast, no association between inflammatory markers and personality traits or cognition was identified.DiscussionIn elderly individuals without dementia, a high level of Openness or Agreeableness was associated with executive functioning/semantic memory and episodic memory, respectively

Overview of grapevine trunk diseases in France in the 2000s

The National Grapevine Trunk Disease Survey was conducted in France from 2003 to 2008 to monitor grapevine trunk diseases (GTDs), eutypa dieback and esca/black dead arm (BDA). Data collected from seven regions, 329 vineyards and 12 cultivars were analysed. There were great variations amongst regions in the incidence of GTDs. For esca/BDA, two groups were distinguished: vineyards in Jura and Charentes had greater incidence (93–95%) than those of Bordeaux, Alsace and Bourgogne (54–82%). Incidence increased in Charentes over the 6-year survey, with the highest values being recorded during the last 2 years. For eutypa dieback, all vineyards of Charentes were affected, with 17 to 25% of vines expressing symptoms; for the other regions, 52 to 80% of vineyards were affected, with incidences below 3%. Cultivars Savagnin and Trousseau in Jura were especially affected by esca/BDA. Instead, Ugni Blanc in Charentes was most affected by eutypa dieback. One cultivar could be significantly more affected in one region than in another. The global health status of the vineyards was also investigated. (i) For four regions, 82% (Jura) to 87% (Alsace) of the grapevines were healthy, but this percentage decreased steadily (67%) in Charentes. (ii) Plants infected by GTDs were 32 and 18% in Jura and Charentes respectively, and only 2.9% in the Bourgogne region. (iii) The unproductive plants, i.e. dead, missing, replanted or restored, represented a significant part of the losses (6.6% in Charentes to 9.9% in Jura). The extension of GTDs is discussed with regard to the abiotic and biotic factors that may favour the diseases

Front Aging Neurosci

INTRODUCTION: Lower cognitive functioning in old age has been associated with personality traits or systemic inflammatory markers. Associations have also been found between personality traits and inflammatory markers. However, no study has explored the inter-relationships between these three components simultaneously. The present study aims to better understand the inter-relationships among personality traits, inflammatory markers, and cognitive performance in elderly individuals without dementia. METHODS: This study utilizes a network analysis approach, a statistical method that allows visualization of the data's unique pairwise associations. We performed a cross-sectional analysis on 720 elderly individuals without dementia, using data from Colaus|PsyColaus, a population-based study conducted in Lausanne, Switzerland. The Revised NEO Five-Factor Inventory (NEO-FFI-R) was used to assess personality traits, and interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), and C-reactive protein (CRP) were used as peripheral inflammatory markers. Cognitive domains were investigated using the Mini-Mental State Examination (MMSE), the Verbal Fluency Test, the Stroop Test, the DO40, and the Free and Cued Selective Reminding (FCSR) test. RESULTS: Openness was associated with verbal fluency and Agreeableness with immediate free recall. In contrast, no association between inflammatory markers and personality traits or cognition was identified. DISCUSSION: In elderly individuals without dementia, a high level of Openness or Agreeableness was associated with executive functioning/semantic memory and episodic memory, respectively