Incorporating spatial and temporal variability in analyses of the relationship between biodiversity and ecosystem functioning

In the last few decades, a growing literature has examined how biodiversity influences ecosystem functioning. This body of work has greatly improved our understanding of ecosystem functioning and its modulation by biodiversity. In particular, there is nowa- days large consensus that biodiversity increases ecosystem productivity, and stabilises ecosystems. Early investigations were largely theoretical or involved simple experiments run in laboratory conditions, but over time biodiversity ecosystem-functioning experiments evolved to more realistic field experiments that better represent the real conditions found in natural ecosystems. In particular, these experiments are often run on larger spatial scales and over longer time frames allowing for the effect of environmental heterogeneity and temporal fluctuations to be explored. The designs of these experiments evolved along with the questions addressed in this field of research. However, the analytical tools used in the analyses of these experi- ments followed a slightly different path. In particular, most of the metrics currently used to analyse biodiversity ecosystem functioning experiments are not entirely suited to properly deal with the complexity of modern designs as they make a number of assumptions that are not met any more. In my thesis I developed a unified framework, based on the tailored use of Linear Mixed Effects Models, to analyse biodiversity-ecosystem functioning experiments such that the new complexities of these experiments can be taken into account. This thesis aimed to bring the focus of the analysis back to the biological interpretation of the results. I successfully applied my approach to several data sets. The framework developed here is expected to improve greatly our understanding of ecosystem functioning and how biodiversity modulates it. It also sheds new light on past research in this field. The great flexibility of the new approach makes it possible to let these experiments to evolve such that new biological questions can be addressed

Dupilumab for Chronic Prurigo: Case Series on Effectiveness, Safety, and Quality of Life

Background: Chronic prurigo (CPG) is a pruritic skin disease, characterized by an itch-scratch cycle and scarring. It reduces patients’ quality of life (QoL). Dupilumab is a monoclonal human IgG antibody that inhibits signaling of the interleukin 4 (IL-4) and interleukin 13 (IL-13) pathways through blockade of the IL-4 receptor. Patients with CPG who receive dupilumab often report great improvement in itch and overall QoL. We therefore reviewed our experience in order to follow up on QoL, safety, and treatment response in patients with CPG who received dupilumab. Methods: We conducted a real-world retrospective single-center case series. Outcomes were assessed by phone interviews and photographs using validated questionnaires and scores. Demographic data were obtained from the hospital files. Follow-up was up to 2 years. We assessed QoL with the Dermatology Life Quality Index (DLQI) and the Itchy quality of life questionnaire (ItchyQoL). Numerical Rating Scale (NRS) was used to assess itch. Prurigo lesions were documented with the Prurigo activity and severity score (PAS). Results: Ten patients were included in this study. Results were reported up to 2 years after treatment with dupilumab. The response variables for DLQI, ItchyQoL, NRS, and PAS analyses showed a statistically significant decrease over time (DLQI: p ≤ 0.0001 [−0.84; −1.27], ItchyQoL: p ≤ 0.0001 [−9.89; −18.69], NRS maximum and average: p ≤ 0.0001 [−0.52; −0.86] and p ≤ 0.0001 [−0.55; −0.94], and PAS number of lesions: p = 0.0005 [−1.70; −5.28]). The percent decrease after 1 year of treatment (this estimate is based on model estimates) ranges from −42% to −82%. Four (40%) patients reported mild side effects. No serious side effects were reported. Conclusion: Dupilumab treatment of CGP for up to 2 years is associated with improved QoL and less itching

The value of biodiversity for the functioning of tropical forests: insurance effects during the first decade of the Sabah Biodiversity Experiment

One of the main environmental threats in the tropics is selective logging, which has degraded large areas of forest. In southeast Asia, enrichment planting with seedlings of the dominant group of dipterocarp tree species aims to accelerate restoration of forest structure and functioning. The role of tree diversity in forest restoration is still unclear, but the ‘insurance hypothesis’ predicts that in temporally and spatially varying environments planting mixtures may stabilize functioning owing to differences in species traits and ecologies. To test for potential insurance effects, we analyse the patterns of seedling mortality and growth in monoculture and mixture plots over the first decade of the Sabah biodiversity experiment. Our results reveal the species differences required for potential insurance effects including a trade-off in which species with denser wood have lower growth rates but higher survival. This trade-off was consistent over time during the first decade, but growth and mortality varied spatially across our 500 ha experiment with species responding to changing conditions in different ways. Overall, average survival rates were extreme in monocultures than mixtures consistent with a potential insurance effect in which monocultures of poorly surviving species risk recruitment failure, whereas monocultures of species with high survival have rates of self-thinning that are potentially wasteful when seedling stocks are limited. Longer-term monitoring as species interactions strengthen will be needed to more comprehensively test to what degree mixtures of species spread risk and use limited seedling stocks more efficiently to increase diversity and restore ecosystem structure and functioning

Incorporating spatial and temporal variability in analyses of the relationship between biodiversity and ecosystem functioning

In the last few decades, a growing literature has examined how biodiversity influences ecosystem functioning. This body of work has greatly improved our understanding of ecosystem functioning and its modulation by biodiversity. In particular, there is nowa- days large consensus that biodiversity increases ecosystem productivity, and stabilises ecosystems. Early investigations were largely theoretical or involved simple experiments run in laboratory conditions, but over time biodiversity ecosystem-functioning experiments evolved to more realistic field experiments that better represent the real conditions found in natural ecosystems. In particular, these experiments are often run on larger spatial scales and over longer time frames allowing for the effect of environmental heterogeneity and temporal fluctuations to be explored. The designs of these experiments evolved along with the questions addressed in this field of research. However, the analytical tools used in the analyses of these experi- ments followed a slightly different path. In particular, most of the metrics currently used to analyse biodiversity ecosystem functioning experiments are not entirely suited to properly deal with the complexity of modern designs as they make a number of assumptions that are not met any more. In my thesis I developed a unified framework, based on the tailored use of Linear Mixed Effects Models, to analyse biodiversity-ecosystem functioning experiments such that the new complexities of these experiments can be taken into account. This thesis aimed to bring the focus of the analysis back to the biological interpretation of the results. I successfully applied my approach to several data sets. The framework developed here is expected to improve greatly our understanding of ecosystem functioning and how biodiversity modulates it. It also sheds new light on past research in this field. The great flexibility of the new approach makes it possible to let these experiments to evolve such that new biological questions can be addressed.</p

Does no-till agriculture limit crop yields?

No-till is an agricultural practice widely promoted by governments, development agencies, and agricultural organisations worldwide. However, the costs and benefits to farmers adopting no-till are hotly debated 1–4. Using a meta-analysis of unprecedented study size, Pittelkow et al.5 reported that adopting no-till results in average yield losses of -5.7%, but that these losses can be limited with the added implementation of two additional conservation agriculture practices - crop rotation and crop residue retention, and in dry environments. They claimed that, as a result, resource limited smallholder farmers, that are unable to implement the whole suite of conservation agriculture practices are likely to experience yield losses under no-till. In a re-evaluation of their analysis, we found that they overly biased their results toward showing that no-till negatively impacts yields, and overlooked the practical significance of their findings. Strikingly, we find that all of the variables they used in their analysis (e.g. crop residue management, rotation, site aridity and study duration) are not much better than random for explaining the effect of no-till on crop yields. Our results suggest that their meta-analysis cannot be used as the basis for evidence-based decision-making in the agricultural community.</jats:p

From seed to plant to cob: analyses on maize data

&lt;p&gt;The scope of this series of documents is primarily didactic.&nbsp;&lt;br&gt;&lt;br&gt;Data is collected from the following experiment: maize seeds are planted in different soils and at different depths. Day of germination is recorded, together with other variables. Seedlings, as well as seeds that have not sprouted yet, are then transferred in a field. Finally, for each maize plant, its height and the weight of the cob are recorded.&lt;br&gt;&lt;br&gt;The reader can find information about&nbsp;&lt;br&gt;- the design of the experiment&lt;br&gt;- the data itself and how it was prepared&lt;br&gt;- some preliminary graphical analysis&lt;br&gt;- the modelling of different types of responses (normal linear models, binomial models, GAMs, normal linear models with random effects).&lt;/p&gt;&lt;p&gt;The data is accompanied by R scripts to reproduce all analyses.&lt;/p&gt;&lt;p&gt;Disclaimer: This is a first version, accomplished with a limited time budget. Updated versions might be uploaded in the future.&lt;/p&gt

Impact of Chronic Neonicotinoid Exposure on Honeybee Colony Performance and Queen Supersedure

Background Honeybees provide economically and ecologically vital pollination services to crops and wild plants. During the last decade elevated colony losses have been documented in Europe and North America. Despite growing consensus on the involvement of multiple causal factors, the underlying interactions impacting on honeybee health and colony failure are not fully resolved. Parasites and pathogens are among the main candidates, but sublethal exposure to widespread agricultural pesticides may also affect bees. Methodology/Principal Findings To investigate effects of sublethal dietary neonicotinoid exposure on honeybee colony performance, a fully crossed experimental design was implemented using 24 colonies, including sister-queens from two different strains, and experimental in-hive pollen feeding with or without environmentally relevant concentrations of thiamethoxam and clothianidin. Honeybee colonies chronically exposed to both neonicotinoids over two brood cycles exhibited decreased performance in the short-term resulting in declining numbers of adult bees (−28%) and brood (−13%), as well as a reduction in honey production (−29%) and pollen collections (−19%), but colonies recovered in the medium-term and overwintered successfully. However, significantly decelerated growth of neonicotinoid-exposed colonies during the following spring was associated with queen failure, revealing previously undocumented long-term impacts of neonicotinoids: queen supersedure was observed for 60% of the neonicotinoid-exposed colonies within a one year period, but not for control colonies. Linked to this, neonicotinoid exposure was significantly associated with a reduced propensity to swarm during the next spring. Both short-term and long-term effects of neonicotinoids on colony performance were significantly influenced by the honeybees’ genetic background. Conclusions/Significance Sublethal neonicotinoid exposure did not provoke increased winter losses. Yet, significant detrimental short and long-term impacts on colony performance and queen fate suggest that neonicotinoids may contribute to colony weakening in a complex manner. Further, we highlight the importance of the genetic basis of neonicotinoid susceptibility in honeybees which can vary substantially

Effectiveness of integrated Aedes albopictus management in southern Switzerland

Abstract Background The exotic invasive tiger mosquito, Aedes albopictus, appeared in southern Switzerland in 2003. The spread of the mosquito has been surveyed constantly since then, and an integrated vector management (IVM) has been implemented to control its numbers. The control measures focus on the aquatic phase of the mosquito with removal of breeding sites and applications of larvicides in public areas whereas private areas are reached through extensive public information campaigns. Here, we evaluated the efficacy of the IVM. Methods Since all the municipalities with Ae. albopictus in southern Switzerland are currently implementing the IVM, Italian municipalities just across the Swiss-Italian border, where Ae. albopictus is present but no coordinated intervention programme is in place, served as control. Ovitraps and adult female traps were used to measure mosquito abundance in 2019. Generalised mixed-effects models were used to model the numbers of Ae. albopictus eggs and adult females collected. These numbers of Ae. albopictus eggs were compared to the numbers of eggs collected in 2012 and 2013 in a previous assessment of the IVM, using a hurdle model. Results Mean numbers of Ae. albopictus eggs and adult females in 2019 were consistently higher in the municipalities not following an IVM programme. In these municipalities, there were about four times (3.8) more eggs than in the municipalities implementing an IVM programme. Also, the numbers of eggs and adult females increased steadily from the beginning of the Ae. albopictus reproductive season, reaching a peak in August. In contrast, the increase in numbers of Ae. albopictus was much more contained in the municipalities implementing an IVM programme, without reaching an evident peak. Comparison with data from 2012 and 2013 indicates that the gap between intervention and non-intervention areas may have almost doubled in the past 6 years. Conclusions The results of the survey strongly support the efficacy of the IVM programme implemented in southern Switzerland compared to municipalities without defined control measures. With the constant implementation of an IVM, it appears possible to contain the numbers of Ae. albopictus at a manageable level, reducing the nuisance for the human population and the risk of arbovirus epidemics. Graphical Abstract </jats:sec

Effectiveness of Integrated Aedes albopictus Management in Southern Switzerland

Abstract BackgroundThe exotic invasive tiger mosquito, Aedes albopictus, appeared in southern Switzerland in 2003. The spread of the mosquito has been surveyed constantly since then and an integrated vector management (IVM) has been implemented to control its numbers. The control measures focus on the aquatic phase of the mosquito with removal of breeding sites and larvicide applications in public areas. Private areas are reached through extensive information campaigns to citizens. Here, we evaluated the efficacy of the IVM.MethodsSince all the municipalities with Ae. albopictus in southern Switzerland are currently implementing the IVM, Italian municipalities just across the Swiss-Italian border, where Ae. albopictus is present but no coordinated intervention programme is in place, served as control. Ovitraps and adult female traps were used to measure mosquito abundance in 2019. Generalised Mixed-Effects Models were used to model the numbers of Ae. albopictus eggs and adult females collected. The numbers of Ae. albopictus eggs were then compared to the numbers of eggs collected in 2012-2013 in a previous assessment of the IVM, using a hurdle model.ResultsMean Ae. albopictus egg and adult female numbers in 2019 were consistently higher in the municipalities not following an IVM programme. In these municipalities, there were about four times (3.8) more eggs than in the municipalities implementing an IVM programme. Also, the numbers of eggs and adult females increased steadily from the beginning of the Ae. albopictus reproductive season, reaching a peak in August. In contrast, the increase in numbers of Ae. albopictus was much more contained in the municipalities implementing an IVM programme, without reaching an evident peak. Comparison with data from 2012 and 2013 showed that the gap between intervention and non-intervention areas has almost doubled in the past six years.ConclusionsThe results of the survey demonstrate the efficacy of the IVM programme implemented in southern Switzerland, compared to municipalities not implementing defined control measures. With the constant implementation of an IVM, it is possible to contain the numbers of Ae. albopictus at a manageable level, reducing the nuisance for the human population and the risk of arbovirus epidemics.</jats:p