GlobalUsefulNativeTrees, a database documenting 14,014 tree species, supports synergies between biodiversity recovery and local livelihoods in landscape restoration.

Tree planting has the potential to improve the livelihoods of millions of people as well as to support environmental services such as biodiversity conservation. Planting however needs to be executed wisely if benefits are to be achieved. We have developed the GlobalUsefulNativeTrees (GlobUNT) database to directly support the principles advocated by the 'golden rules for reforestation', including planting tree mixtures that maximize the benefits to local livelihoods and the diversity of native trees. Developed primarily by combining data from GlobalTreeSearch with the World Checklist of Useful Plant Species (WCUPS), GlobUNT includes 14,014 tree species that can be filtered for ten major use categories, across 242 countries and territories. The 14,014 species represent roughly a quarter of the tree species from GlobalTreeSearch and a third of the plant species from WCUPS. GlobUNT includes over 8000 species used as materials (9261 species; 68.4% of the total in WCUPS for that use category) or medicines (8283; 31.1%), over 2000 species with environmental uses (3317; 36.9%), used as human food (3310; 47.0%) or fuel (2162; 85.5%), over 1000 species used as gene sources (1552; 29.8%), animal food (1494; 33.7%), social uses (1396; 53.8%) or poisons (1109; 36.8%), and 712 species (68.4%) as insect food.

TreeGOER: A database with globally observed environmental ranges for 48,129 tree species.

The TreeGOER (Tree Globally Observed Environmental Ranges) database provides information for most known tree species of their environmental ranges for 38 bioclimatic, eight soil and three topographic variables. It is based on species distribution modelling analyses of more than 44 million occurrences. The database can be accessed from https://doi.org/10.5281/zenodo.7922927. Statistics that include 5% and 95% quantiles were estimated for a cleaned and taxonomically standardized occurrence data set with different methods of outlier detection, with estimates for roughly 45% of species being based on 20 or more observation records. Where sufficient representative observations are available, the ranges provide useful preliminary estimates of suitable conditions particularly for lesser-known species under climate change. Inferred core bioclimatic ranges of species along global temperature and moisture index gradients and across continents follow the known global distribution of tree diversity such as its highest levels in moist tropical forests and the 'odd man out' pattern of lower levels in Africa. To demonstrate how global analyses for large numbers of tree species can easily be done in R with TreeGOER, here I present two case studies. The first case study investigated latitudinal trends of tree vulnerability and compared these with previous results obtained for urban trees. The second case study focused on tropical areas, compared trends in different longitudinal zones and investigated patterns for the moisture index. TreeGOER is expected to benefit researchers conducting biogeographical and climate change research for a wide range of tree species at a variety of spatial and temporal scales.

Forgotten food crops in sub-Saharan Africa for healthy diets in a changing climate.

As climate changes in sub-Saharan Africa (SSA), Africa's "forgotten" food crops offer a wide range of options to diversify major staple production as a key measure toward achieving zero hunger and healthy diets. So far, however, these forgotten food crops have been neglected in SSA's climate-change adaptation strategies. Here, we quantified their capacity to adapt cropping systems of SSA's major staples of maize, rice, cassava, and yams to changing climates for the four subregions of West, Central, East, and Southern Africa. We used climate-niche modeling to explore their potential for crop diversification or the replacement of these major staples by 2070, and assessed the possible effects on micronutrient supply. Our results indicated that approximately 10% of the present production locations of these four major staples in SSA may experience novel climate conditions in 2070, ranging from a high of almost 18% in West Africa to a low of less than 1% in Southern Africa. From an initial candidate panel of 138 African forgotten food crops embracing leafy vegetables, other vegetables, fruits, cereals, pulses, seeds and nuts, and roots and tubers, we selected those that contributed most to covering projected future and contemporary climate conditions of the major staples' production locations. A prioritized shortlist of 58 forgotten food crops, able to complement each other in micronutrient provision, was determined, which covered over 95% of assessed production locations. The integration of these prioritized forgotten food crops in SSA's cropping systems will support the "double-win" of more climate-resilient and nutrient-sensitive food production in the region.

AlleleShift: an R package to predict and visualize population-level changes in allele frequencies in response to climate change.

BACKGROUND: At any particular location, frequencies of alleles that are associated with adaptive traits are expected to change in future climates through local adaption and migration, including assisted migration (human-implemented when climate change is more rapid than natural migration rates). Making the assumption that the baseline frequencies of alleles across environmental gradients can act as a predictor of patterns in changed climates (typically future but possibly paleo-climates), a methodology is provided by AlleleShift of predicting changes in allele frequencies at the population level. METHODS: The prediction procedure involves a first calibration and prediction step through redundancy analysis (RDA), and a second calibration and prediction step through a generalized additive model (GAM) with a binomial family. As such, the procedure is fundamentally different to an alternative approach recently proposed to predict changes in allele frequencies from canonical correspondence analysis (CCA). The RDA step is based on the Euclidean distance that is also the typical distance used in Analysis of Molecular Variance (AMOVA). Because the RDA step or CCA approach sometimes predict negative allele frequencies, the GAM step ensures that allele frequencies are in the range of 0 to 1. RESULTS: AlleleShift provides data sets with predicted frequencies and several visualization methods to depict the predicted shifts in allele frequencies from baseline to changed climates. These visualizations include 'dot plot' graphics (function shift.dot.ggplot), pie diagrams (shift.pie.ggplot), moon diagrams (shift.moon.ggplot), 'waffle' diagrams (shift.waffle.ggplot) and smoothed surface diagrams of allele frequencies of baseline or future patterns in geographical space (shift.surf.ggplot). As these visualizations were generated through the ggplot2 package, methods of generating animations for a climate change time series are straightforward, as shown in the documentation of AlleleShift and in the supplemental videos. AVAILABILITY: AlleleShift is available as an open-source R package from https://cran.r-project.org/package=AlleleShift and https://github.com/RoelandKindt/AlleleShift. Genetic input data is expected to be in the adegenet::genpop format, which can be generated from the adegenet::genind format. Climate data is available from various resources such as WorldClim and Envirem.

WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data.

PREMISE: The standardization of plant names is a critical step in various fields of biology, including biodiversity, biogeography, and vegetation research. The WorldFlora package is introduced here to help achieve this goal by matching lists of plant names with a static copy from World Flora Online (WFO), an ongoing global effort to complete an online flora of all known vascular plants and bryophytes by 2020. METHODS AND RESULTS: Based on direct and fuzzy matching, WorldFlora inserts matching cases from the WFO to a submitted data set containing taxonomic names. The results and success rates for selecting the expected best single matches are presented for four data sets, including two data sets used in recent comparisons of software tools for correcting taxon names. CONCLUSIONS: WorldFlora offers a straightforward pipeline for semi-automatic plant name checking. For the four data sets, the success rate of credible matches ranged from 94.7% to 99.9%.

Mapping tree species vulnerability to multiple threats as a guide to restoration and conservation of tropical dry forests.

Understanding the vulnerability of tree species to anthropogenic threats is important for the efficient planning of restoration and conservation efforts. We quantified and compared the effects of future climate change and four current threats (fire, habitat conversion, overgrazing and overexploitation) on the 50 most common tree species of the tropical dry forests of northwestern Peru and southern Ecuador. We used an ensemble modelling approach to predict species distribution ranges, employed freely accessible spatial datasets to map threat exposures, and developed a trait-based scoring approach to estimate species-specific sensitivities, using differentiated trait weights in accordance with their expected importance in determining species sensitivities to specific threats. Species-specific vulnerability maps were constructed from the product of the exposure maps and the sensitivity estimates. We found that all 50 species face considerable threats, with an average of 46% of species' distribution ranges displaying high or very high vulnerability to at least one of the five threats. Our results suggest that current levels of habitat conversion, overexploitation and overgrazing pose larger threats to most of the studied species than climate change. We present a spatially explicit planning strategy for species-specific restoration and conservation actions, proposing management interventions to focus on (a) in situ conservation of tree populations and seed collection for tree planting activities in areas with low vulnerability to climate change and current threats; (b) ex situ conservation or translocation of populations in areas with high climate change vulnerability; and (c) active planting or assisted regeneration in areas under high current threat vulnerability but low climate change vulnerability, provided that interventions are in place to lower threat pressure. We provide an online, user-friendly tool to visualize both the vulnerability maps and the maps indicating priority restoration and conservation actions.

The future of coffee and cocoa agroforestry in a warmer Mesoamerica.

Climate change threatens coffee production and the livelihoods of thousands of families in Mesoamerica that depend on it. Replacing coffee with cocoa and integrating trees in combined agroforestry systems to ameliorate abiotic stress are among the proposed alternatives to overcome this challenge. These two alternatives do not consider the vulnerability of cocoa and tree species commonly used in agroforestry plantations to future climate conditions. We assessed the suitability of these alternatives by identifying the potential changes in the distribution of coffee, cocoa and the 100 most common agroforestry trees found in Mesoamerica. Here we show that cocoa could potentially become an alternative in most of coffee vulnerable areas. Agroforestry with currently preferred tree species is highly vulnerable to future climate change. Transforming agroforestry systems by changing tree species composition may be the best approach to adapt most of the coffee and cocoa production areas. Our results stress the urgency for land use planning considering climate change effects and to assess new combinations of agroforestry species in coffee and cocoa plantations in Mesoamerica.

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition.

Especially in low-income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low-input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop 'rewildings'.

Spatially explicit multi-threat assessment of food tree species in Burkina Faso: A fine-scale approach.

Over the last decades agroforestry parklands in Burkina Faso have come under increasing demographic as well as climatic pressures, which are threatening indigenous tree species that contribute substantially to income generation and nutrition in rural households. Analyzing the threats as well as the species vulnerability to them is fundamental for priority setting in conservation planning. Guided by literature and local experts we selected 16 important food tree species (Acacia macrostachya, Acacia senegal, Adansonia digitata, Annona senegalensis, Balanites aegyptiaca, Bombax costatum, Boscia senegalensis, Detarium microcarpum, Lannea microcarpa, Parkia biglobosa, Sclerocarya birrea, Strychnos spinosa, Tamarindus indica, Vitellaria paradoxa, Ximenia americana, Ziziphus mauritiana) and six key threats to them (overexploitation, overgrazing, fire, cotton production, mining and climate change). We developed a species-specific and spatially explicit approach combining freely accessible datasets, species distribution models (SDMs), climate models and expert survey results to predict, at fine scale, where these threats are likely to have the greatest impact. We find that all species face serious threats throughout much of their distribution in Burkina Faso and that climate change is predicted to be the most prevalent threat in the long term, whereas overexploitation and cotton production are the most important short-term threats. Tree populations growing in areas designated as 'highly threatened' due to climate change should be used as seed sources for ex situ conservation and planting in areas where future climate is predicting suitable habitats. Assisted regeneration is suggested for populations in areas where suitable habitat under future climate conditions coincides with high threat levels due to short-term threats. In the case of Vitellaria paradoxa, we suggest collecting seed along the northern margins of its distribution and considering assisted regeneration in the central part where the current threat level is high due to overexploitation. In the same way, population-specific recommendations can be derived from the individual and combined threat maps of the other 15 food tree species. The approach can be easily transferred to other countries and can be used to analyze general and species specific threats at finer and more local as well as at broader (continental) scales in order to plan more selective and efficient conservation actions in time. The concept can be applied anywhere as long as appropriate spatial data are available as well as knowledgeable experts.

An Ecoregion-Based Approach to Protecting Half the Terrestrial Realm.

We assess progress toward the protection of 50% of the terrestrial biosphere to address the species-extinction crisis and conserve a global ecological heritage for future generations. Using a map of Earth's 846 terrestrial ecoregions, we show that 98 ecoregions (12%) exceed Half Protected; 313 ecoregions (37%) fall short of Half Protected but have sufficient unaltered habitat remaining to reach the target; and 207 ecoregions (24%) are in peril, where an average of only 4% of natural habitat remains. We propose a Global Deal for Nature-a companion to the Paris Climate Deal-to promote increased habitat protection and restoration, national- and ecoregion-scale conservation strategies, and the empowerment of indigenous peoples to protect their sovereign lands. The goal of such an accord would be to protect half the terrestrial realm by 2050 to halt the extinction crisis while sustaining human livelihoods.

Suitability Analysis and Projected Climate Change Impact on Banana and Coffee Production Zones in Nepal.

The Government of Nepal has identified opportunities in agricultural commercialization, responding to a growing internal demand and expansion of export markets to reduce the immense trade deficit. Several cash crops, including coffee and bananas, have been identified in the recently approved Agriculture Development Strategy. Both of these crops have encouraged smallholder farmers to convert their subsistence farming practices to more commercial cultivation. Identification of suitable agro-ecological zones and understanding climate-related issues are important for improved production and livelihoods of smallholder farmers. Here, the suitability of coffee and banana crops is analyzed for different agro-ecological zones represented by Global Environmental Stratification (GEnS). Future shifts in these suitability zones are also predicted. Plantation sites in Nepal were geo-referenced and used as input in species distribution modelling. The multi-model ensemble model suggests that climate change will reduce the suitable growing area for coffee by about 72% across the selected emission scenarios from now to 2050. Impacts are low for banana growing, with a reduction in suitability by about 16% by 2050. Bananas show a lot of potential for playing an important role in Nepal as a sustainable crop in the context of climate change, as this study indicates that the amount of area suited to banana growing will grow by 40% by 2050. Based on our analysis we recommend possible new locations for coffee plantations and one method for mitigating climate change-related problems on existing plantations. These findings are expected to support planning and policy dialogue for mitigation and support better informed and scientifically based decision-making relating to these two crops.

Environmental gap analysis to prioritize conservation efforts in eastern Africa.

Countries in eastern Africa have set aside significant proportions of their land for protection. But are these areas representative of the diverse range of species and habitats found in the region? And do conservation efforts include areas where the state of biodiversity is likely to deteriorate without further interventions? Various studies have addressed these questions at global and continental scales. However, meaningful conservation decisions are required at finer geographical scales. To operate more effectively at the national level, finer scale baseline data on species and on higher levels of biological organization such as the eco-regions are required, among other factors. Here we adopted a recently developed high-resolution potential natural vegetation (PNV) map for eastern Africa as a baseline to more effectively identify conservation priorities. We examined how well different potential natural vegetations (PNVs) are represented in the protected area (PA) network of eastern Africa and used a multivariate environmental similarity index to evaluate biases in PA versus PNV coverage. We additionally overlaid data of anthropogenic factors that potentially influence the natural vegetation to assess the level of threat to different PNVs. Our results indicate substantial differences in the conservation status of PNVs. In addition, particular PNVs in which biodiversity protection and ecological functions are at risk due to human influences are revealed. The data and approach presented here provide a step forward in developing more transparent and better informed translation from global priorities to regional or national implementation in eastern Africa, and are valid for other geographic regions.

tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.