Cultivation of crops close to their wild relatives may jeopardise the integrity of wild genetic resources. Detecting cultivars among wild plants is necessary to characterise crop-wild gene flow, but can be challenging if cultivars and wild plants are phenotypically highly similar. Genomics tools can be used instead, but the selection of diagnostic loci for cultivar identification can be difficult if the wild and cultivated genepools are closely related. In Ethiopia, Arabica coffee cultivars resistant to coffee berry disease (CBD) occur near wild Coffea arabica plants and local landraces. However, the abundance and distribution of these cultivars across coffee sites remains unclear. Here, we present a new module of the SMAP package called SMAP relatedness pairwise to characterise pairwise genetic relationships between individuals based on haplotype calls and to identify diagnostic loci that distinguish (sets of) individuals from each other. Next, we estimate the relative abundance of CBD-resistant cultivars across 60 Ethiopian Arabica coffee sites using a genome-wide fingerprinting approach. We confirm the presence of these cultivars in around 75% of the coffee sites with a high agreement between a field survey and our DNA fingerprinting approach. At least 20 out of 60 sites with supposedly wild C. arabica individuals contain signatures of the cultivated genepool. Overall, we conclude that CBD-resistant cultivars are widespread in Ethiopian coffee sites. The development of SMAP relatedness pairwise opens opportunities to assess the distribution of coffee cultivars in other regions in Ethiopia and to apply similar screenings near wild relatives from other crops.

As the climate is changing, species respond by changing their distributions and abundances. The effects of climate are not only direct, but also occur via changes in biotic interactions, such as competition. Yet, the role of competition in mediating the effects of climate is still largely unclear. To examine how climate influences species performance, directly and via competition with other species, we transplanted two moss species differing in climate niches, alone and together at 59 sites along a climate gradient. Growth was monitored over three growing seasons. In the absence of competition, both species performed better under warmer conditions. Yet, when transplanted together, a warmer climate had negative effects on the northern moss, while the effects remained positive for the southern species. The negative effect of a cold climate on the southern species was larger when both species were transplanted together. Over three growing seasons, the southern species almost outcompeted the northern in warmer climates. Our results illustrate how competitive interactions can modify, and even reverse, the direct effects of climate on organism performance. A broader implication of our results is that species interactions can have important effects on how environmental and climate change influence performance and abundance.

1. Understorey biodiversity is increasingly impacted by extreme climate events. Retention forestry, which involves preserving small patches of live and dead trees from preharvest forests within clearcuts, can help mitigate these extremes by creating more favourable microclimates than traditional clearcutting practices. Despite their importance in buffering climate extremes, it remains unclear whether, and to what extent, the microclimates in retention patches enhance the growth response and recovery of the understorey after extreme droughts in boreal managed forests.
2. We retrospectively investigated the annual growth response from 2016 to 2022 of the mat-forming understorey moss Hylocomium splendens, in relation to micro- and macroclimate, including an extreme drought in 2018, in retention patches relative to clearcuts and mature forests, across 130 plots distributed across 30 forest sites in a boreal landscape in Sweden.
3. The 2018 summer drought reduced the annual growth rates of H. splendens. Clearcuts experienced the greatest climatic impact from the 2018 drought and exhibited the lowest growth rates, followed by retention patches, while mature forests maintained the highest growth rates. This pattern persisted subsequent two post-drought years. Closer alignment of below-canopy temperature and vapour pressure deficits (VPDs) with those of mature forests enhanced moss growth in retention patches, bringing it closer to the levels observed in mature forests.
4. In clearcuts and mature forests, where variation in forest canopy and microclimate was minimal, biological legacies did not influence annual moss growth. In retention patches, however, a greater basal area of large living trees and the presence of standing deadwood contributed to higher canopy closure, which reduced microclimate VPDs and increased H. splendens growth. Increasing volumes of lying deadwood positively contributed to H. splendens growth, likely by creating favourable microhabitats and microclimates near the logs.
5. Synthesis and applications. This study demonstrates that drought reduced the growth of mat-forming understorey H. splendens in boreal forest ecosystems, but drought effects in clearcuts are mitigated in retention patches. By preserving large living trees, standing and lying deadwood, retention patches can be further optimized. Foresters and policymakers can use these findings to minimize the impact of drought after clearcutting on understorey biodiversity and functionality.

Societal Impact Statement: Arabica coffee grows in the forests and woodlands of Ethiopia. These Arabica coffee populations contain a reservoir of the highest genetic variation of this species, which is extremely valuable from a biodiversity conservation and coffee breeding point of view. Knowledge about the distribution of these populations, including how and to what extent they have been managed by local communities now and in the past, is limited. We reveal insights into the history, distribution, and management of Arabica coffee populations in the remaining forests of Ethiopia, which is essential for developing effective conservation policies for this globally important resource. Summary: To guide conservation of forest biodiversity in a broad sense, we need to understand the landscape-level variation in current and historical management practices of agroforestry systems. We collected data on coffee management practices across a large forested landscape in Ethiopia within Arabica coffee's indigenous distribution, using interviews in 11 villages and field surveys and interviews at 78 coffee sites in the forest. There was a gradient in coffee density (higher), liana cover (lower), and canopy cover (lower) from sites with high management intensity to sites without management. Recently, management intensity has increased in the forest edges. Interviews suggest that substantial areas of currently unmanaged coffee forests are a legacy of reforestation of abandoned (semi-) open landscapes in the late 19th century. Despite a dynamic history of coffee cultivation across these areas, the conservation of forest biodiversity, including unmanaged populations of genetically diverse Arabica coffee, should be a priority, given the few such remaining areas in Ethiopia and elsewhere in the world.

Extreme droughts are globally increasing in frequency and severity. Most research on drought in forests focuses on the response of trees, while less is known about the impacts of drought on forest understory species and how these effects are moderated by the local environment. We assessed the impacts of a 45-day experimental summer drought on the performance of six boreal forest understory plants, using a transplant experiment with rainout shelters replicated across 25 sites. We recorded growth, vitality and reproduction immediately, 2 months, and 1 year after the simulated drought, and examined how differences in ambient soil moisture and canopy cover among sites influenced the effects of drought on the performance of each species. Drought negatively affected the growth and/or vitality of all species, but the effects were stronger and more persistent in the bryophytes than in the vascular plants. The two species associated with older forests, the moss Hylocomiastrum umbratum and the orchid Goodyera repens, suffered larger effects than the more generalist species included in the experiment. The drought reduced reproductive output in the moss Hylocomium splendens in the next growing season, but increased reproduction in the graminoid Luzula pilosa. Higher ambient soil moisture reduced some negative effects of drought on vascular plants. Both denser canopy cover and higher soil moisture alleviated drought effects on bryophytes, likely through alleviating cellular damage. Our experiment shows that boreal understory species can be adversely affected by drought and that effects might be stronger for bryophytes and species associated with older forests. Our results indicate that the effects of drought can vary over small spatial scales and that forest landscapes can be actively managed to alleviate drought effects on boreal forest biodiversity. For example, by managing the tree canopy and protecting hydrological networks.

Increasing temperatures and shifting precipitation patterns have major consequences for smallholder farmers, especially in the Global South. Our study examined spatial patterns and climatic drivers of farmers' perceptions of climate change, and how these perceptions translated into adaptation actions. We interviewed 56 farmers in southwestern Ethiopia and analyzed ERA5-Land reanalysis climate data from 1971 to 2020. The majority of farmers perceived the recorded temperature increase as well as a decrease and shift in the timing of rainfall. Perceived climate change varied with local climate factors and not with the rate of climate change itself. Farmers' adaptation practices showed associations with local temperature, but not with farmers’ perceptions of climate change. Our findings highlight that even if farmers perceive climate change, perceptions are most common in areas where climate action is already urgent, and perceptions may not translate into adaptation. Thus, targeted and timely information and extension programs are crucial.

Climate is assumed to strongly influence species distribution and abundance. Although the performance of many organisms is influenced by the climate in their immediate proximity, the climate data used to model their distributions often have a coarse spatial resolution. This is problematic because the local climate experienced by individuals might deviate substantially from the regional average. This problem is likely to be particularly important for sessile organisms like plants and in environments where small-scale variation in climate is large. To quantify the effect of local temperature on vital rates and population growth rates, we used temperature values measured at the local scale (in situ logger measures) and integral projection models with demographic data from 37 populations of the forest herb Lathyrus vernus across a wide latitudinal gradient in Sweden. To assess how the spatial resolution of temperature data influences assessments of climate effects, we compared effects from models using local data with models using regionally aggregated temperature data at several spatial resolutions (≥1 km). Using local temperature data, we found that spring frost reduced the asymptotic population growth rate in the first of two annual transitions and influenced survival in both transitions. Only one of the four regional estimates showed a similar negative effect of spring frost on population growth rate. Our results for a perennial forest herb show that analyses using regionally aggregated data often fail to identify the effects of climate on population dynamics. This emphasizes the importance of using organism-relevant estimates of climate when examining effects on individual performance and population dynamics, as well as when modeling species distributions. For sessile organisms that experience the environment over small spatial scales, this will require climate data at high spatial resolutions. 

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.

1. 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.
2. 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.
3. 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.
4. 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.

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.