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4.
  • Abbafati, Cristiana, et al. (författare)
  • 2020
  • Tidskriftsartikel (refereegranskat)
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  • Sepanlou, Sadaf G., et al. (författare)
  • The global, regional, and national burden of cirrhosis by cause in 195 countries and territories, 1990-2017 : a systematic analysis for the Global Burden of Disease Study 2017
  • 2020
  • Ingår i: The Lancet Gastroenterology & Hepatology. - 2468-1253. ; 5:3, s. 245-266
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Cirrhosis and other chronic liver diseases (collectively referred to as cirrhosis in this paper) are a major cause of morbidity and mortality globally, although the burden and underlying causes differ across locations and demographic groups. We report on results from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 on the burden of cirrhosis and its trends since 1990, by cause, sex, and age, for 195 countries and territories. Methods We used data from vital registrations, vital registration samples, and verbal autopsies to estimate mortality. We modelled prevalence of total, compensated, and decompensated cirrhosis on the basis of hospital and claims data. Disability-adjusted life-years (DALYs) were calculated as the sum of years of life lost due to premature death and years lived with disability. Estimates are presented as numbers and age-standardised or age-specific rates per 100 000 population, with 95% uncertainty intervals (UIs). All estimates are presented for five causes of cirrhosis: hepatitis B, hepatitis C, alcohol-related liver disease, non-alcoholic steatohepatitis (NASH), and other causes. We compared mortality, prevalence, and DALY estimates with those expected according to the Socio-demographic Index (SDI) as a proxy for the development status of regions and countries. Findings In 2017, cirrhosis caused more than 1.32 million (95% UI 1.27-1.45) deaths (440000 [416 000-518 000; 33.3%] in females and 883 000 [838 000-967 000; 66.7%] in males) globally, compared with less than 899 000 (829 000-948 000) deaths in 1990. Deaths due to cirrhosis constituted 2.4% (2.3-2.6) of total deaths globally in 2017 compared with 1.9% (1.8-2.0) in 1990. Despite an increase in the number of deaths, the age-standardised death rate decreased from 21.0 (19.2-22.3) per 100 000 population in 1990 to 16.5 (15.8-18-1) per 100 000 population in 2017. Sub-Saharan Africa had the highest age-standardised death rate among GBD super-regions for all years of the study period (32.2 [25.8-38.6] deaths per 100 000 population in 2017), and the high-income super-region had the lowest (10.1 [9.8-10-5] deaths per 100 000 population in 2017). The age-standardised death rate decreased or remained constant from 1990 to 2017 in all GBD regions except eastern Europe and central Asia, where the age-standardised death rate increased, primarily due to increases in alcohol-related liver disease prevalence. At the national level, the age-standardised death rate of cirrhosis was lowest in Singapore in 2017 (3.7 [3.3-4.0] per 100 000 in 2017) and highest in Egypt in all years since 1990 (103.3 [64.4-133.4] per 100 000 in 2017). There were 10.6 million (10.3-10.9) prevalent cases of decompensated cirrhosis and 112 million (107-119) prevalent cases of compensated cirrhosis globally in 2017. There was a significant increase in age-standardised prevalence rate of decompensated cirrhosis between 1990 and 2017. Cirrhosis caused by NASH had a steady age-standardised death rate throughout the study period, whereas the other four causes showed declines in age-standardised death rate. The age-standardised prevalence of compensated and decompensated cirrhosis due to NASH increased more than for any other cause of cirrhosis (by 33.2% for compensated cirrhosis and 54.8% for decompensated cirrhosis) over the study period. From 1990 to 2017, the number of prevalent cases snore than doubled for compensated cirrhosis due to NASH and more than tripled for decompensated cirrhosis due to NASH. In 2017, age-standardised death and DALY rates were lower among countries and territories with higher SDI. Interpretation Cirrhosis imposes a substantial health burden on many countries and this burden has increased at the global level since 1990, partly due to population growth and ageing. Although the age-standardised death and DALY rates of cirrhosis decreased from 1990 to 2017, numbers of deaths and DALYs and the proportion of all global deaths due to cirrhosis increased. Despite the availability of effective interventions for the prevention and treatment of hepatitis B and C, they were still the main causes of cirrhosis burden worldwide, particularly in low-income countries. The impact of hepatitis B and C is expected to be attenuated and overtaken by that of NASH in the near future. Cost-effective interventions are required to continue the prevention and treatment of viral hepatitis, and to achieve early diagnosis and prevention of cirrhosis due to alcohol-related liver disease and NASH.
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  • Burger, H. F., et al. (författare)
  • Bottom-up and top-down drivers of herbivory on Arabica coffee along an environmental and management gradient
  • 2022
  • Ingår i: Basic and Applied Ecology. - : Elsevier BV. - 1439-1791 .- 1618-0089. ; 59, s. 21-32
  • Tidskriftsartikel (refereegranskat)abstract
    • While sustainable agriculture relies on natural pest control, we lack insights into the relative importance of bottom-up and top-down factors on pest levels, especially along broad environmental and management gradients. To this aim, we focused on bottom-up and top-down control of herbivore damage in sixty sites in the centre of origin of Arabica coffee in southwestern Ethiopia, where coffee grows along a management gradient ranging from little or no management in the natural forest to commercial plantations. More specifically, we examined how canopy cover, percentage of surrounding forest and management intensity affected caffeine and chlorogenic acid concentration (bottom-up process) and attack of dummy caterpillars by ants and birds (top-down process), and how these in turn affected pest levels. Caffeine and chlorogenic acid concentrations were negatively related to canopy cover, while ant attack rate was positively related to canopy cover. Both ant and bird attack rate increased with the percentage of surrounding forest. Yet, secondary chemistry and caterpillar attack rates were unrelated to herbivory, and herbivory was only directly and positively affected by management intensity. Our study highlights that canopy cover can have contrasting effects on plant defence and predation, and that changes in bottom-up and top-down factors do – unlike often assumed – not necessarily translate into reduced pest levels. Instead, direct effects of management on pest levels may be more important than bottom-up or top-down mediated effects.
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10.
  • Getachew, Merkebu, et al. (författare)
  • Within and among farm variability of coffee quality of smallholders in southwest Ethiopia
  • 2023
  • Ingår i: Agroforestry Systems. - : Springer Science and Business Media LLC. - 0167-4366 .- 1572-9680. ; 97:5, s. 883-905
  • Tidskriftsartikel (refereegranskat)abstract
    • The biophysical drivers that affect coffee quality vary within and among farms. Quantifying their relative importance is crucial for making informed decisions concerning farm management, marketability and profit for coffee farmers. The present study was designed to quantify the relative importance of biophysical variables affecting coffee bean quality within and among coffee farms and to evaluate a near infrared spectroscopy-based model to predict coffee quality. Twelve coffee plants growing under low, intermediate and dense shade were studied in twelve coffee farms across an elevational gradient (1470–2325 m asl) in Ethiopia. We found large within farm variability, demonstrating that conditions varying at the coffee plant-level are of large importance for physical attributes and cupping scores of green coffee beans. Overall, elevation appeared to be the key biophysical variable influencing all the measured coffee bean quality attributes at the farm level while canopy cover appeared to be the most important biophysical variable driving the above-mentioned coffee bean quality attributes at the coffee plant level. The biophysical variables driving coffee quality (total preliminary and specialty quality) were the same as those driving variations in the near-infrared spectroscopy data, which supports future use of this technology to assess green bean coffee quality. Most importantly, our findings show that random forest is computationally fast and robust to noise, besides having comparable prediction accuracy. Hence, it is a useful machine learning tool for regression studies and has potential for modeling linear and nonlinear multivariate calibrations. The study also confirmed that near-infrared spectroscopic-based predictions can be applied as a supplementary approach for coffee cup quality evaluations.
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  • Hailu, Beyene Zewdie, 1983- (författare)
  • Fungal disease dynamics, genetic variation and biodiversity-yield relationships : — a study along a gradient of coffee management in southwestern Ethiopia
  • 2020
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Intensification of agricultural systems is a major threat to the associated biodiversity and could also affect the dynamics of pests and pathogens. One such system that is currently under an intensification trajectory is the production of Arabica coffee. In this thesis, I studied the relationships between fungal diseases and their natural enemies, the genetic variation in coffee, coffee yield and associated biodiversity along a coffee management gradient in southwestern Ethiopia.The specific goals of this thesis were to investigate variation in fungal diseases on coffee and their natural enemies along a gradient of management (I, II), how genetic variation in coffee among sites relate to variation in incidence of the fungal diseases (III), and to investigate the trade-offs in biodiversity-yield relationships along the gradient of coffee management (IV). To answer these questions, I selected 60 sites along a gradient of management that ranged from coffee naturally growing in only little disturbed forests to intensively managed plantations. I used both observational studies and molecular approaches.In paper I, I examined if the severity of the four major fungal diseases on coffee varied along the gradient and assessed the main drivers of variation in disease severity. I found that two of the fungal diseases were more severe in the intensively managed coffee sites, while the other two were more severe in the less intensively managed sites. Altitude was the main driver for the diseases, but related in a different way to the different diseases. In paper II, I examined the temporal dynamics in coffee leaf rust-hyperparasite interaction, the biocontrol potential of the hyperparasite and environmental drivers for the two species for three consecutive years during the dry and wet seasons. I found that the rust was more common during the dry season and in managed sites while the hyperparasite was common during the wet season and in sites that were less managed. My results also revealed that higher hyperparasite incidence during the wet season resulted in a lower growth rate of the rust during the subsequent dry season. In paper III, I investigated if genetic composition and diversity of coffee sites relate to the incidence of the fungal diseases assessed. I found that genetic composition of the coffee stands was linked to the incidence of the four fungal diseases, but genetic diversity among the coffee sites did not relate to the incidence of the diseases. In paper IV, I examined biodiversity-yield trade-offs and shape of the relationships between biodiversity and yield along the gradient of management. I found a steep, concave shape initial decline in biodiversity values as coffee yield increased to a certain level, after which a further increase in yield did not have much effect on biodiversity values.In conclusion, I found different drivers for the different diseases and for the parasite-hyperparasite interaction. It is difficult to achieve a single management approach that can suit the different pathogen species investigated. High genetic diversity among coffee sites did not reduce disease pressure. While the more complex, less managed sites provide high biodiversity values, and could potentially serve as habitats for natural pest control and in situ conservation for coffee genetic diversity, the yield gap compared to more intensively managed sites was very high. To optimize coffee management and conservation of biodiversity in these landscapes, there is a need to develop strategies whereby the smallholder farmers who depend on coffee and the forest as the main source of livelihood can benefit through for example coffee certification schemes that can pay premium prices for biodiversity-friendly coffee management.
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  • Hailu, Beyene Zewdie, et al. (författare)
  • Patterns and drivers of fungal disease communities on Arabica coffee along a management gradient
  • 2020
  • Ingår i: Basic and Applied Ecology. - : Elsevier BV. - 1439-1791 .- 1618-0089. ; 47, s. 95-106
  • Tidskriftsartikel (refereegranskat)abstract
    • Plants, including those managed by humans, are often attacked by multiple diseases. Yet, most studies focus on single diseases, even if the disease dynamics of multiple species is more interesting from a farmers’ perspective. Moreover, most studies are from single management systems, although it is valuable to understand how diseases are distributed across broad management gradients, especially in cases where less intensive management also provides biodiversity values in the landscape. To understand the spatial dynamics and drivers of diseases across such a broad management gradient, we assessed the four major fungal diseases on Arabica coffee (Coffea arabica) at 60 sites in southwestern Ethiopia along a gradient from only little managed wild coffee in the forest understory to intensively managed coffee plantations. We found that environmental and management factors related to disease incidence and severity differed strongly among the four fungal diseases. Coffee leaf rust (Hemileia vastatrix) and Armillaria root rot (Armillaria mellea) were more severe in intensively managed sites, whereas coffee berry disease (Colletotrichum kahawae) and wilt disease (Gibberella xylarioides) were more severe in less managed sites. Among sites, incidence and severity of the four fungal diseases poorly correlated with each other. Within sites, however, shrubs that were severely attacked by coffee leaf rust also had high levels of berry disease symptoms. A better understanding of disease dynamics is important for providing management recommendations that benefit smallholder farmers, but also to evaluate possibilities for maintaining biodiversity values in the landscape related to shade cover complexity and wild coffee genetic variation.
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  • Hylander, Kristoffer, 1970-, et al. (författare)
  • Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world
  • 2024
  • Ingår i: Communications Biology. - 2399-3642. ; 7
  • Forskningsöversikt (refereegranskat)abstract
    • The reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.
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  • Koelemeijer, Irena A., et al. (författare)
  • Management intensity and landscape configuration affect the potential for woody plant regeneration in coffee agroforestry
  • 2021
  • Ingår i: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 313
  • Tidskriftsartikel (refereegranskat)abstract
    • With the current deforestation rates in tropical ecosystems, optimizing biodiversity in managed systems has become fundamental for conservation. Agroforestry has been suggested to conserve biodiversity and buffer deforestation rates, while also sustaining local livelihoods. While many studies have focused on the relation between local management intensity and biodiversity, processes at the landscape scale are often overlooked and remain a knowledge gap. In this study we identified drivers behind woody plant regeneration in coffee agroforestry on both local and landscape scale. We used univariate-, multivariate- and structural equation models to relate seedling species richness, diversity, density, community composition and height to local management intensity and location in the landscape of 60 coffee agroforestry sites in southwestern Ethiopia. Local management intensity, which simplifies and reduces canopy cover, negatively impacted species richness, diversity and density, presumably due to altered microclimatic conditions and a reduction in local seed sources. Seedling height was also reduced by management intensity, including slashing frequency and canopy cover. On the landscape scale, species richness and diversity of seedlings was higher at sites adjacent to continuous forests where seed sources are abundant, and declined with distance to the forest. In particular, late successional species were negatively affected, whereas common shade tree species and pioneers occurred as seedlings throughout the landscape and in more managed systems. This suggests that dispersal limitation is detrimental for the regeneration of late successional species, especially in agroforestry systems where the standing woody plant diversity is largely reduced. Our results indicate that natural regeneration of woody plants still occurs in coffee agroforestry systems, primarily when the canopy structure is dense and diverse and/or when sites are located nearby continuous forests. Management intensification and deforestation will limit the potential for many woody plant species to regenerate in coffee agroforestry sites, by altering the local microclimate, reducing local seed sources and disrupting seed dispersal from the surrounding landscape. This will likely result in a positive feedback loop, as a reduction in woody plant regeneration reduces future seed sources. We therefore stress that both a local and a landscape perspective should be incorporated in conservation and restoration approaches.
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  • Nurihun, Biruk Ayalew, 1983-, et al. (författare)
  • Impact of climate and management on coffee berry disease and yield in coffee's native range
  • 2024
  • Ingår i: Basic and Applied Ecology. - 1439-1791 .- 1618-0089. ; 76, s. 25-34
  • Tidskriftsartikel (refereegranskat)abstract
    • Climate change might increase plant diseases, reduce crop yields and threaten the livelihoods of millions of smallholder farmers globally. It is thus important to understand the relationships between climate, disease levels and yield to improve management strategies for sustainable agroforestry in a changing climate. One of the major threats to coffee production in Africa is the coffee berry disease (Colletotrichum kahawae). To investigate the effects of climatic and management variables on coffee berry disease (CBD) incidence and yield, we recorded minimum and maximum temperature and relative humidity, as well as CBD and yield, along a broad environmental and management gradient in southwestern Ethiopia during two consecutive years. CBD was affected by several climatic and management variables. For example, CBD incidence increased with minimum temperature during the fruit expansion stage, and decreased with minimum temperature during the endosperm filling stage. CBD incidence was negatively affected by the proportion of resistant cultivars, whereas the coffee structure index (pruning) had no effect on disease incidence. Coffee yield decreased with increasing minimum temperature during the flowering period in 2018 and maximum temperature during the fruit developmental period in 2019. Coffee yield was negatively affected by canopy cover and positively affected by the coffee structure index in both years. Our findings highlight that CBD and yield were affected by different climatic and management variables. Yet, managing for low disease levels and high yield is practically difficult due to season -dependent effects of several climatic variables. One way to break the correlation of climatic variables between seasons might be to take advantage of differences among shade trees in the presence or timing of leaf drop. To reduce CBD incidence, using resistant cultivars is an effective strategy, but this might threaten the wild coffee genetic reservoir.
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  • Nurihun, Biruk Ayalew, 1983-, et al. (författare)
  • Impact of climate on a host-hyperparasite interaction on Arabica coffee in its native range
  • 2024
  • Ingår i: Journal of Applied Ecology. - 0021-8901 .- 1365-2664. ; 61:3, s. 538-550
  • Tidskriftsartikel (refereegranskat)abstract
    • Natural enemies of plant pathogens might play an important role in controlling plant disease levels in natural and agricultural systems. Yet, plant pathogen–natural enemy interactions might be sensitive to climatic changes. Understanding the relationship between climate, plant pathogens and their natural enemies is thus important for developing climate-resilient, sustainable agriculture.To this aim, we recorded shade cover, daily minimum and maximum temperature, relative humidity, coffee leaf rust and its hyperparasite at 58 sites in southwestern Ethiopia during the dry and wet season for 2 years.Coffee leaf rust severity was positively related to the maximum temperature. Hyperparasite severity was higher when the minimum temperature was low (i.e. in places with cold night temperatures). While canopy cover did not have a direct effect on rust severity, it reduced rust severity indirectly by lowering the maximum temperature. Canopy cover had a direct positive effect on the hyperparasite severity during one surveying period.Synthesis and applications. Our findings highlight that coffee leaf rust and its hyperparasite are both affected by shade cover and temperature, but in different ways. On the one hand, these niche differences lead to the worrying prediction that levels of coffee leaf rust will increase, and its hyperparasite will decrease, with climate change. On the other hand, these niche differences between coffee leaf rust and its hyperparasite provide opportunities to develop strategies to manage the environment (such as shade cover and microclimate) in such a way that the rust is disfavoured and the hyperparasite is favoured.
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17.
  • Nurihun, Biruk Ayalew, et al. (författare)
  • The impact of shade tree species identity on coffee pests and diseases
  • 2022
  • Ingår i: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 340
  • Tidskriftsartikel (refereegranskat)abstract
    • The multifunctional role of shade trees for conservation of biodiversity and ecosystem services in natural forests and agroforests is well documented, yet we lack insights into the impact of shade tree species identity on pest and disease dynamics on agroforestry crops such as coffee and cacao, and its implications for management. We conducted two surveys on the impact of shade tree species identity and canopy cover on pests, diseases and a fungal hyperparasite on Arabica coffee in southwestern Ethiopia, which is one of the areas of origin of Arabica coffee. One survey was in a commercial plantation, and the other along a management gradient from only little managed coffee growing in the natural forest to intensively managed commercial plantations. To link these findings to current shade tree selection criteria, we complemented these surveys by interviews with farmers and managers. Shade tree species identity left a weak imprint on insect pest levels, and insect pests levels differed strongly in the strength and direction of their response to canopy cover. In contrast to the insect pests, the incidence of coffee leaf rust and its hyperparasite, as well as coffee berry disease, differed among shade tree species, with particularly high levels of coffee leaf rust and the hyperparasite underneath the canopy of the shade trees Acacia abyssinica and Croton macrostachyus, and coffee berry disease underneath the canopy of Acacia abyssinica and Polyscias fulva. Smallholder farmers used many criteria for selecting shade trees, such as leaf traits and competition for soil moisture, but low priority is given to the effect of shade tree species identity on pests and diseases. Our findings help to understand spatial variation in pest and disease dynamics in natural forests and agroforests, and may inform the selection of shade tree species by coffee producers and thereby contribute to ecologically-informed pest and disease management. Importantly, our finding highlight the potential for using tree identity for the sustainable management of pests and diseases, with relevance for global agroforestry systems.
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  • Shimales, Tamiru, et al. (författare)
  • Management intensity affects insect pests and natural pest control on Arabica coffee in its native range
  • 2023
  • Ingår i: Journal of Applied Ecology. - 0021-8901 .- 1365-2664. ; 60:5, s. 911-922
  • Tidskriftsartikel (refereegranskat)abstract
    • 1. Agroforestry systems provide opportunities to reduce the trade -off between agricultural production and biodiversity, for example by enhancing a diverse community of species potentially acting as natural pest control agents. While management of agroforestry systems is intensifying across the globe, we lack insights into the impact of management intensity on pest levels and natural pest control, especially along broad management gradients and as compared with nat- ural forests.2. We assessed the impact of management intensity on major insect pests (the coffee blotch miner, the serpentine leaf miner, the coffee leaf skeletonizer and damage by other free-feeding herbivores) and natural pest control by parasitoid wasps across sixty sites in the centre of origin of Arabica coffee in southwestern Ethiopia. Within this region, coffee is growing along a broad management gradi- ent ranging from little or no management in the natural forest to intensively man- aged commercial plantations.3. In the wet season, pest levels were largely similar in the natural forest, semi-forest and semi-plantation systems, whereas pests reached outbreak densities in the most intensively managed plantation system. In contrast, management intensity did not significantly affect pest levels in the dry season. The insect pests differed in their seasonal dynamics, consistently declined with elevation and were largely unaffected by shade levels. Parasitism rate of the coffee blotch miner was lower, and the parasitoid community was distinct, in the most intensively managed plan- tation system.4. Synthesis and applications : Our findings support the hypothesis that the weaker top -down control by parasitoids in the intensively managed plantation sites leads to higher pest levels, and that - at least for some pest species - there is a threshold in the effect of management intensity on pest levels and natural pest control. It is important to consider such non-linear relationships to maintain or enhance the sustainability of agroforestry systems during management intensification. Overall, our findings highlight that ecological knowledge of natural pest control can be used to intensify production to improve the livelihood of smallholder farmers without jeopardizing natural pest control but only up to a certain point where it starts to deteriorate.
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19.
  • Stüber, Moritz, et al. (författare)
  • Multi-scale mosaics in top-down pest control by ants from natural coffee forests to plantations
  • 2021
  • Ingår i: Ecology. - : Wiley. - 0012-9658 .- 1939-9170. ; 102:7
  • Tidskriftsartikel (refereegranskat)abstract
    • While top-down control plays an important role in shaping both natural and agricultural food webs, we lack insights into how top-down control effects vary across spatial scales. We used a multi-scale survey of top-down control of coffee pests and diseases by arboreal ants to examine if colony location creates a small-scale mosaic in top-down control around trees and if the strength of that control varies between sites at the landscape scale. We investigated pest and disease levels on coffee shrubs at different distances from shade trees with and without a Crematogaster spp. ant colony in 59 sites along a coffee management intensity gradient in southwestern Ethiopia. Within sites, ants significantly suppressed herbivory and coffee leaf rust at distances less than 10 m from nesting trees. Top-down control varied between sites, with stronger top-down control of free-feeding herbivory near ant colonies at sites with lower management intensity and stronger top-down control of a skeletonizer at sites with higher canopy cover. We conclude that the strength of top-down control by ants is highly heterogeneous across spatial scales, as a consequence of the biology of the predator at the small scale and herbivore density or changes in herbivore–ant interactions at the landscape scale.
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20.
  • Zewdie, Beyene, 1983-, et al. (författare)
  • Genetic composition and diversity of Arabica coffee in the crop’s centre of origin and its impact on four major fungal diseases
  • 2023
  • Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 32:10, s. 2484-2503
  • Tidskriftsartikel (refereegranskat)abstract
    • Conventional wisdom states that genetic variation reduces disease levels in plant populations. Nevertheless, crop species have been subject to a gradual loss of genetic variation through selection for specific traits during breeding, thereby increasing their vulnerability to biotic stresses such as pathogens. We explored how genetic variation in Arabica coffee sites in southwestern Ethiopia was related to the incidence of four major fungal diseases. Sixty sites were selected along a gradient of management intensity, ranging from nearly wild to intensively managed coffee stands. We used genotyping-by-sequencing of pooled leaf samples (pool-GBS) derived from 16 individual coffee shrubs in each of the 60 sites to assess the variation in genetic composition (multivariate: reference allele frequency) and genetic diversity (univariate: mean expected heterozygosity) between sites. We found that genetic composition had a clear spatial pattern and that genetic diversity was higher in less managed sites. The incidence of the four fungal diseases was related to the genetic composition of the coffee stands, but in a specific way for each disease. In contrast, genetic diversity was only related to the within-site variation of coffee berry disease, but not to the mean incidence of any of the four diseases across sites. Given that fungal diseases are major challenges of Arabica coffee in its native range, our findings that genetic composition of coffee sites impacted the major fungal diseases may serve as baseline information to study the molecular basis of disease resistance in coffee. Overall, our study illustrates the need to consider both host genetic composition and genetic diversity when investigating the genetic basis for variation in disease levels. 
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21.
  • Zewdie, Beyene, 1983-, et al. (författare)
  • Plant biodiversity declines with increasing coffee yield in Ethiopia's coffee agroforests
  • 2022
  • Ingår i: Journal of Applied Ecology. - : Wiley. - 0021-8901 .- 1365-2664. ; 59:5, s. 1198-1208
  • Tidskriftsartikel (refereegranskat)abstract
    • Tropical agroforestry systems provide farmers with resources for their livelihoods, but are also well-recognized as refuges for biodiversity. However, the relationship between yield and biodiversity might be negative in these systems, reflecting a potential trade-off between managing for increased yield or biodiversity. The potential for synergies will depend partly on the shape of the biodiversity–yield relationship, where a concave relationship suggests a faster decline in biodiversity with increasing yields than a linear or convex shape.We studied the relationship between biodiversity (plant species richness and composition) and coffee yield along a gradient of management in south-western Ethiopia, coffee's native range. We inventoried species richness and community compoasition of woody plants, herbaceous plants and bryophytes at 60 sites. We also measured coffee management-related variables and assessed coffee yield for 3 consecutive years at each site.Species richness of woody plants had a concave relationship with coffee yield, that is, tree richness declined fast initially before levelling out at higher yields, whereas there was no relationship between coffee yield and species richness of herbaceous plants or bryophytes. Species composition of woody plants, herbaceous plants and bryophytes all had a concave relationship with coffee yield.From a methodological perspective, we found that multi-year data on yield were necessary to reliably assess the relationship between biodiversity and yield, and that the number of coffee shrubs or coffee dominance were poor proxies for yield when trying to capture the biodiversity–yield relationship.Synthesis and applications. The concave relationship between biodiversity components (species richness and composition) and yield suggests that there is a strong conflict between the goals of increasing production and conserving biodiversity. However, it is important to recognize that this pattern is largely driven by the very low-yielding sites in natural forests. Here, even minor intensification of coffee management seems to rapidly erode biodiversity. Along the rest of the productivity gradient, there was generally no negative relationship between yield and biodiversity, implying opportunities for developing strategies for increasing yields without biodiversity loss.
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22.
  • Zewdie, Beyene, et al. (författare)
  • Temporal dynamics and biocontrol potential of a hyperparasite on coffee leaf rust across a landscape in Arabica coffee's native range
  • 2021
  • Ingår i: Agriculture, Ecosystems & Environment. - : Elsevier BV. - 0167-8809 .- 1873-2305. ; 311
  • Tidskriftsartikel (refereegranskat)abstract
    • Agroforestry systems can provide habitats for a rich biodiversity including multitrophic interactions, which presents opportunities to develop natural pest control. Shade coffee systems in several coffee growing areas of the world host such unique habitats where pests and their natural enemies interact. One of the major global challenges for coffee production, coffee leaf rust caused by the fungal pathogen Hemileia vastatrix is attacked by the fungal hyperparasite, Lecanicillium lecanii. However, we lack insights in the dynamics and biocontrol potential of the hyperparasite on coffee leaf rust from landscapes in Arabica coffee's native range. To understand the temporal dynamics across landscapes and environmental drivers of the rust and hyperparasite, and the potential for biocontrol of the rust by the hyperparasite, we studied the rust and hyperparasite during the dry and wet seasons for three consecutive years at 60 sites across a gradient of coffee management in southwestern Ethiopia. We found that coffee leaf rust was more severe during the dry season, whereas the hyperparasite was more severe during the wet season in two out of three years. The rust growth rate from the wet to the dry season transition was negatively related to the hyperparasite index during the wet season, implying a potential top-down control. Coffee leaf rust was generally more severe at lower altitudes in the dry season, whereas the hyperparasite was more severe at high altitude. The rust incidence increased with management intensity, while the hyperparasite was more common under less intensive management. This study could be interesting in that it represents a landscape where Arabica coffee originated and the rust and hyperparasite might have a long co-evolutionary history. Our findings highlight the potential of the hyperparasite to suppress the rust's growth rate from the wet to dry season transition when the rust severity could otherwise be at its peak. We show that less intensively managed landscapes with dense shade levels are likely to increase hyperparasite abundance and result in an improved top-down control of the rust. However, more detailed knowledge is needed on the interaction of these species to assess its importance for reducing rust induced yield losses or the risk of rust outbreaks.
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23.
  • Zignol, Francesco, et al. (författare)
  • The understory microclimate in agroforestry now and in the future-a case study of Arabica coffee in its native range
  • 2023
  • Ingår i: Agricultural and Forest Meteorology. - 0168-1923 .- 1873-2240. ; 340
  • Tidskriftsartikel (refereegranskat)abstract
    • Climate change is having a major impact on crop production and food security worldwide, and particularly so for smallholder farmers. As agroforestry is common with smallholder farmers, it is important to not only model the macroclimate, but also the microclimate that crops experience below the canopies. However, there are few highresolution spatiotemporal climate projections for forest understories, because of constraints related to the lack of i) development of models for downscaling global climate projections, ii) high-resolution gridded datasets of environmental factors influencing microclimate, and iii) spatially replicated in-situ microclimate measurements. We focused on a landscape in southwestern Ethiopia where Arabica coffee originated, and, in the present day, is commonly grown as a shade crop. We first examined the relative contribution of in-situ field measurements vs. GIS-derived estimates of vegetation and topographic features in explaining in-situ microclimate. Second, we used a statistical downscaling approach to obtain past and future microclimate maps at 30-meter spatial resolution for the part of the landscape that is covered by trees. Predictive models using in-situ variables performed equal to models with GIS variables, indicating that remote sensing data might substitute for in-situ field measurements. Vegetation and topographic features were both important in explaining microclimatic variation. Our spatiotemporal projections of the microclimate indicate that coffee farming might have to relocate to higher altitudes due to increasing temperatures, that vegetation might buffer the macroclimate at middle altitudes to some extent, and that decreasing trends in relative humidity at the beginning of the wet season might become problematic for coffee production. Taken together, our findings demonstrate that we can rely on remote sensing data to create microclimate maps in landscapes where in-situ field measurements are challenging, and we suggest how these microclimate projections can be used as a tool to promote climate-resilient agriculture at the local and landscape levels.
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