Forests and Societies

Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand the molecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification. Genomes and transcriptomes of five distinct lineages of African cichlids, a textbook example of adaptive radiation, have been sequenced and analysed to reveal that many types of molecular changes contributed to rapid evolution, and that standing variation accumulated during periods of relaxed selection may have primed subsequent diversification. The 2,000 or so species of cichlid fish, to be found in the lakes and rivers of Africa's Rift Valley, provide the classic example of adaptive radiations. This large-scale international collaboration has sequenced and analysed the genomes and transcriptomes of five distinct lineages of African cichlids. The data reveal an excess of gene duplications in comparison to other fish species. There is an abundance of non-coding element divergence; accelerated coding sequence evolution; expression divergence associated with transposable element insertions in orthologous gene pairs; and regulation by novel miRNAs. Sequencing data from sixty individuals from six closely related Lake Victoria species point to rapid cichlid speciation associated with genome-wide diversifying selection on coding and regulatory variants, and imply that ancient periods of relaxed purifying selection enabled the accumulation of standing variation, which may have been important in facilitating diversification.

Mapping aboveground forest biomass is central for assessing the global carbon balance. However, current large-scale maps show strong disparities, despite good validation statistics of their underlying models. Here, we attribute this contradiction to a flaw in the validation methods, which ignore spatial autocorrelation (SAC) in data, leading to overoptimistic assessment of model predictive power. To illustrate this issue, we reproduce the approach of large-scale mapping studies using a massive forest inventory dataset of 11.8 million trees in central Africa to train and validate a random forest model based on multispectral and environmental variables. A standard nonspatial validation method suggests that the model predicts more than half of the forest biomass variation, while spatial validation methods accounting for SAC reveal quasi-null predictive power. This study underscores how a common practice in big data mapping studies shows an apparent high predictive power, even when predictors have poor relationships with the ecological variable of interest, thus possibly leading to erroneous maps and interpretations.

Accurate characterization of tropical moist forest changes is needed to support conservation policies and to quantify their contribution to global carbon fluxes more effectively. We document, at pantropical scale, the extent and changes (degradation, deforestation, and recovery) of these forests over the past three decades. We estimate that 17% of tropical moist forests have disappeared since 1990 with a remaining area of 1071 million hectares in 2019, from which 10% are degraded. Our study underlines the importance of the degradation process in these ecosystems, in particular, as a precursor of deforestation, and in the recent increase in tropical moist forest disturbances (natural and anthropogenic degradation or deforestation). Without a reduction of the present disturbance rates, undisturbed forests will disappear entirely in large tropical humid regions by 2050. Our study suggests that reinforcing actions are needed to prevent the initial degradation that leads to forest clearance in 45% of the cases.

Abstract Most of the planet's diversity is concentrated in the tropics, which includes many regions undergoing rapid climate change. Yet, while climate‐induced biodiversity changes are widely documented elsewhere, few studies have addressed this issue for lowland tropical ecosystems. Here we investigate whether the floristic and functional composition of intact lowland Amazonian forests have been changing by evaluating records from 106 long‐term inventory plots spanning 30 years. We analyse three traits that have been hypothesized to respond to different environmental drivers (increase in moisture stress and atmospheric CO 2 concentrations): maximum tree size, biogeographic water‐deficit affiliation and wood density. Tree communities have become increasingly dominated by large‐statured taxa, but to date there has been no detectable change in mean wood density or water deficit affiliation at the community level, despite most forest plots having experienced an intensification of the dry season. However, among newly recruited trees, dry‐affiliated genera have become more abundant, while the mortality of wet‐affiliated genera has increased in those plots where the dry season has intensified most. Thus, a slow shift to a more dry‐affiliated Amazonia is underway, with changes in compositional dynamics (recruits and mortality) consistent with climate‐change drivers, but yet to significantly impact whole‐community composition. The Amazon observational record suggests that the increase in atmospheric CO 2 is driving a shift within tree communities to large‐statured species and that climate changes to date will impact forest composition, but long generation times of tropical trees mean that biodiversity change is lagging behind climate change.

Tropical forests disappear rapidly because of deforestation, yet they have the potential to regrow naturally on abandoned lands. We analyze how 12 forest attributes recover during secondary succession and how their recovery is interrelated using 77 sites across the tropics. Tropical forests are highly resilient to low-intensity land use; after 20 years, forest attributes attain 78% (33 to 100%) of their old-growth values. Recovery to 90% of old-growth values is fastest for soil (<1 decade) and plant functioning (<2.5 decades), intermediate for structure and species diversity (2.5 to 6 decades), and slowest for biomass and species composition (>12 decades). Network analysis shows three independent clusters of attribute recovery, related to structure, species diversity, and species composition. Secondary forests should be embraced as a low-cost, natural solution for ecosystem restoration, climate change mitigation, and biodiversity conservation.

For agronomic, environmental, and economic reasons, the need for spatialized information about agricultural practices is expected to rapidly increase. In this context, we reviewed the literature on remote sensing for mapping cropping practices. The reviewed studies were grouped into three categories of practices: crop succession (crop rotation and fallowing), cropping pattern (single tree crop planting pattern, sequential cropping, and intercropping/agroforestry), and cropping techniques (irrigation, soil tillage, harvest and post-harvest practices, crop varieties, and agro-ecological infrastructures). We observed that the majority of the studies were exploratory investigations, tested on a local scale with a high dependence on ground data, and used only one type of remote sensing sensor. Furthermore, to be correctly implemented, most of the methods relied heavily on local knowledge on the management practices, the environment, and the biological material. These limitations point to future research directions, such as the use of land stratification, multi-sensor data combination, and expert knowledge-driven methods. Finally, the new spatial technologies, and particularly the Sentinel constellation, are expected to improve the monitoring of cropping practices in the challenging context of food security and better management of agro-environmental issues.

Quinoa (Chenopodium quinoa Willd.) was first domesticated in Andean countries over 7000 years ago. Following the Spanish conquest, quinoa was rejected as "Indian food." After centuries of neglect, the potential of quinoa was rediscovered during the second half of the 20th century. Since then, the number of countries importing quinoa increased, with new producers appearing on the map and quinoa now being cultivated in areas outside the Andean countries. The geographical increase in distribution of quinoa has highlighted the difficulty of access to quality seed, which is a key factor for testing the crop outside the Andes. In this context, research partnerships have helped promote the exchange of quinoa germplasm and have allowed trials to be undertaken in non-traditional areas of cultivation. The number of countries growing the crop has increased rapidly from eight in 1980, to 40 in 2010, and to 75 in 2014. A further 20 countries have sown quinoa for the first time in 2015. In this paper, we analyze this trend and discuss the limits of quinoa's expansion. As commercial production of quinoa is expected to develop, changes in international regulatory frameworks on genetic resources are needed in order to facilitate plant breeding for the most adaptive varieties for each region.

Abstract Forests are a substantial terrestrial carbon sink, but anthropogenic changes in land use and climate have considerably reduced the scale of this system 1 . Remote-sensing estimates to quantify carbon losses from global forests 2–5 are characterized by considerable uncertainty and we lack a comprehensive ground-sourced evaluation to benchmark these estimates. Here we combine several ground-sourced 6 and satellite-derived approaches 2,7,8 to evaluate the scale of the global forest carbon potential outside agricultural and urban lands. Despite regional variation, the predictions demonstrated remarkable consistency at a global scale, with only a 12% difference between the ground-sourced and satellite-derived estimates. At present, global forest carbon storage is markedly under the natural potential, with a total deficit of 226 Gt (model range = 151–363 Gt) in areas with low human footprint. Most (61%, 139 Gt C) of this potential is in areas with existing forests, in which ecosystem protection can allow forests to recover to maturity. The remaining 39% (87 Gt C) of potential lies in regions in which forests have been removed or fragmented. Although forests cannot be a substitute for emissions reductions, our results support the idea 2,3,9 that the conservation, restoration and sustainable management of diverse forests offer valuable contributions to meeting global climate and biodiversity targets.

Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity.

The island of Madagascar has a unique biodiversity, mainly located in the tropical forests of the island. This biodiversity is highly threatened by anthropogenic deforestation. Existing historical forest maps at national level are scattered and have substantial gaps which prevent an exhaustive assessment of long-term deforestation trends in Madagascar. In this study, we combined historical national forest cover maps (covering the period 1953-2000) with a recent global annual tree cover loss dataset (2001-2014) to look at six decades of deforestation and forest fragmentation in Madagascar (from 1953 to 2014). We produced new forest cover maps at 30 m resolution for the year 1990 and annually from 2000 to 2014 over the full territory of Madagascar. We estimated that Madagascar has lost 44% of its natural forest cover over the period 1953-2014 (including 37% over the period 1973-2014). Natural forests cover 8.9 Mha in 2014 (15% of the national territory) and include 4.4 Mha (50%) of moist forests, 2.6 Mha (29%) of dry forests, 1.7 Mha of spiny forests (19%) and 177 000 ha (2%) of mangroves. Since 2005, the annual deforestation rate has progressively increased in Madagascar to reach 99 000 ha/yr during 2010-2014 (corresponding to a rate of 1.1%/yr). Around half of the forest (46%) is now located at less than 100 m from the forest edge. Our approach could be replicated to other developing countries with tropical forest. Accurate forest cover change maps can be used to assess the effectiveness of past and current conservation programs and implement new strategies for the future. In particular, forest maps and estimates can be used in the REDD+ framework which aims at "Reducing Emissions from Deforestation and forest Degradation" and for optimizing the current protected area network.

Anthropogenic activities profoundly impact soil organic carbon (SOC), affecting its contribution to ecosystem services such as climate regulation. Here, we conducted a thorough review of the impacts of land-use change, land management, and climate change on SOC. Using second-order meta-analysis, we synthesized findings from 230 first-order meta-analyses comprising over 25,000 primary studies. We show that (i) land conversion for crop production leads to high SOC loss, that can be partially restored through land management practices, particularly by introducing trees and incorporating exogenous carbon in the form of biochar or organic amendments, (ii) land management practices that are implemented in forests generally result in depletion of SOC, and (iii) indirect effects of climate change, such as through wildfires, have a greater impact on SOC than direct climate change effects (e.g., from rising temperatures). The findings of our study provide strong evidence to assist decision-makers in safeguarding SOC stocks and promoting land management practices for SOC restoration. Furthermore, they serve as a crucial research roadmap, identifying areas that require attention to fill the knowledge gaps concerning the factors driving changes in SOC.

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view.

The sensitivity of tropical forest carbon to climate is a key uncertainty in predicting global climate change. Although short-term drying and warming are known to affect forests, it is unknown if such effects translate into long-term responses. Here, we analyze 590 permanent plots measured across the tropics to derive the equilibrium climate controls on forest carbon. Maximum temperature is the most important predictor of aboveground biomass (-9.1 megagrams of carbon per hectare per degree Celsius), primarily by reducing woody productivity, and has a greater impact per °C in the hottest forests (>32.2°C). Our results nevertheless reveal greater thermal resilience than observations of short-term variation imply. To realize the long-term climate adaptation potential of tropical forests requires both protecting them and stabilizing Earth's climate.

Environmental factors affect the sex ratio of many gonochoristic fish species. They can either determine sex or influence sex differentiation. Temperature is the most common environmental cue affecting sex but density, pH and hypoxia have also been shown to influence the sex ratio of fish species from very divergent orders. Differential growth or developmental rate is suggested to influence sex differentiation in sea bass. Studies in most fish species used domestic strains reared under controlled conditions. In tilapia and sea bass, domestic stocks and field-collected populations showed similar patterns of thermosensitivity under controlled conditions. Genetic variability of thermosensitivity is seen between populations but also between families within the same population. Furthermore, in the Nile tilapia progeny testing of wild male breeders has strongly suggested the existence of XX males in 2 different natural populations. Tilapia and Atlantic silverside studies have shown that temperature sensitivity is a heritable trait which can respond to directional (tilapia) or frequency dependent selection. In tilapia, transitional forms within a genetic sex determination (GSD) and environmental sex determination (ESD) continuum seem to exist. Temperature regulates the expression of the ovarian-aromatase cyp19a1 which is consistently inhibited in temperature masculinized gonads. Foxl2 is suppressed before cyp19a1. Recent in vitro studies have shown that foxl2 activates cyp19a1, suggesting that temperature acts directly on foxl2 or further upstream. Dmrt1 up-regulation is correlated with temperature-induced male phenotypes. Temperature through apoptosis or germ cell proliferation could be a critical threshold for male or female sex differentiation.

The Routledge Handbook of Research Methods for Social-Ecological Systems provides a synthetic guide to the range of methods that can be employed in social-ecological systems (SES) research.\nThe book is primarily targeted at graduate students, lecturers and researchers working on SES, and has been written in a style that is accessible to readers entering the field from a variety of different disciplinary backgrounds. Each chapter discusses the types of SES questions to which the particular methods are suited and the potential resources and skills required for their implementation, and provides practical examples of the application of the methods. In addition, the book contains a conceptual and practical introduction to SES research, a discussion of key gaps and frontiers in SES research methods, and a glossary of key terms in SES research. Contributions from 97 different authors, situated at SES research hubs in 16 countries around the world, including South Africa, Sweden, Germany and Australia, bring a wealth of expertise and experience to this book.\nThe first book to provide a guide and introduction specifically focused on methods for studying SES, this book will be of great interest to students and scholars of sustainability science, environmental management, global environmental change studies and environmental governance. The book will also be of interest to upper-level undergraduates and professionals working at the science–policy interface in the environmental arena.

International audience

Ce guide de terrain est la synthèse de plus de quinze années de pratique en aménagement forestier dans le cadre des actions entreprises par le Cirad. Cette expérience a été mise à profit pour combler un manque de documentation sur la flore des zones sèches d'Afrique de l'Ouest. Les 1300 photographies en couleurs des fleurs, des fruits, des feuilles et de l'écorce facilitent l'identification de chacune des 360 espèces ligneuses présentées. Parce que l'arbre participe à l'équilibre des paysages et remplit nombre de fonctions et de services, un inventaire actualisé des usages traditionnels des différentes parties de la plante, en pharmacopée, en nutrition humaine ou animale et dans la vie quotidienne, est aussi proposé. Les clés de reconnaissance, comme les fiches descriptives, sont accessibles aux non-spécialistes de la botanique, qu'ils soient techniciens de la forêt, de l'agriculture ou de l'élevage, enseignants ou étudiants. Ce guide constitue un ouvrage de référence pour toute personne appelée à connaître la flore arbustive et forestière de la région.

Summary Concerns over the ecological impacts of high African elephant Loxodonta africana densities suggest that it may be necessary to control their numbers locally, although the best management approach is still widely debated. Artificial water supply is believed to be a major cause of local overabundance, and could be used as a potential tool to regulate elephant distribution and impact across landscapes, but its effect on elephants at the population scale has never been studied. We assessed how dry‐season surface‐water availability constrained the distribution of an entire elephant population, using aerial and waterhole census data from Hwange National Park, Zimbabwe. The study was initiated in 1986, when the population was released from culling. We studied how artificial waterholes, holding water throughout the dry season, and vegetation production, estimated from a normalized difference vegetation index (NDVI), influenced the long‐term distribution of elephant densities. We also investigated how the elephant distribution responded to changes in population density and annual rainfall, a driver of surface‐water availability. Long‐term dry‐season elephant densities across the park tended to increase with vegetation production, and increased asymptotically with the density of artificial waterholes. Since the culling stopped, dry‐season elephant densities have increased in most areas of the park, except in areas of low vegetation production and low water availability. Interannual fluctuations in elephant distribution are linked to rainfall variability through its effect on surface‐water availability. During dry years elephants concentrated in areas where artificial pumping maintained surface‐water availability during the dry season. During dry years elephant numbers at waterholes increased because of reduced surface‐water availability, and elephants were distributed more evenly across waterholes, although active waterholes were unevenly distributed across the park. Synthesis and applications . Surface‐water availability drives the distribution and abundance of elephants within Hwange National Park, and therefore appears to be at the heart of the trade‐off between elephant conservation and the extent of their impact on ecosystems. Artificial manipulation of surface water is one of the tools available for the management of elephant populations and should not be overlooked when considering options for controlling elephant numbers in places where they are considered to be overabundant.

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.

National audience