Johann Wilhelm Helfer

Scleria is a pantropical genus of annual and perennial herbs and the sixth largest genus in the Cyperaceae family with around 261 species. In this study, we produced preliminary extinction risk assessments for the ~30% of Scleria species that do not yet have a global Red List assessment and followed the Evolutionarily Distinct and Globally Endangered (EDGE2) and Ecologically Distinct and Globally Endangered (EoDGE) protocols to identify evolutionary and ecologically unique Scleria species at greatest risk of extinction and hotspots of rare and endangered species. Our results indicate that 38 of the 78 Scleria species not yet included in the Red List, and 26% of species in the genus, are potentially threatened with extinction. The risk of extinction is not equally distributed across the phylogeny, and the Afrotropics and the Neotropics accumulate most threatened species. Eleven ecoregions mostly from four African (Madagascar, D.R. Congo, Zambia and Tanzania) and two South American (Brazil, Venezuela) countries accumulate almost half of Scleria species and stand out in terms of their sum of EDGE2 scores. Phylogenetic and functional distinctiveness metrics were largely uncorrelated, and the EcoDGE metric mostly points towards South American countries as reservoirs of ecologically distinctive and endangered species: Brazil, Venezuela, Bolivia, Peru, Colombia, Guyana and Dominican Republic. Recent methodological advances in the identification of species at-risk of extinction and the novel EDGE2 framework emerge as powerful tools to identify conservation priorities.

Some plant lineages remain within the same biome over time (biome conservatism), whereas others seem to adapt more easily to new biomes. The c. 398 species (14 genera) of subfamily Cercidoideae (Leguminosae or Fabaceae) are found in many biomes around the world, particularly in the tropical regions of South America, Asia and Africa, and display a variety of growth forms (small trees, shrubs, lianas and herbaceous perennials). Species distribution maps derived from cleaned occurrence records were compiled and compared with existing biome maps and with the literature to assign species to biomes. Rainforest (144 species), succulent (44 species), savanna (36 species), and temperate (10 species) biomes were found to be important in describing the global distribution of Cercidoideae, with many species occurring in more than one biome. Two phylogenetically isolated species-poor temperate ( Cercis ) and succulent ( Adenolobus ) biome lineages are sister to two broadly distributed species-rich tropical clades. Ancestral state reconstructions on a time-calibrated phylogeny suggest biome shifts occurred throughout the evolutionary history of the subfamily, with shifts between the succulent and rainforest biomes, from the rainforest to savanna, from the succulent to savanna biome, and one early occurring shift into (or from) the temperate biome. Of the 26 inferred shifts in biome, three are closely associated with a shift from the ancestral tree/shrub growth form to a liana or herbaceous perennial habit. Only three of the 13 inferred transcontinental dispersal events are associated with biome shifts. Overall, we find that biome shifts tend to occur within the same continent and that dispersals to new continents tend to occur within the same biome, but that nonetheless the biome-conserved and biogeographically structured Cercidoideae have been able to adapt to different environments through time.

Herbarium specimens provide an important and central resource for biodiversity research. Making these records digitally available to end-users represents numerous challenges, in particular, transcribing metadata associated with specimen labels. In this study, we used the citizen science initiative ‘Les Herbonautes’ and the Récolnat network to transcribe specific data from all herbarium specimen labels stored at the Muséum national d’Histoire naturelle in Paris of the large tropical plant family Annonaceae. We compared this database with publicly available global biodiversity repository data and expert checklists. We investigated spatial and taxonomic advances in data availability at the global and country scales. A total of 20 738 specimens were transcribed over the course of more than two years contributing to and significantly extending the previously available specimen and species data for Annonaceae worldwide. We show that several regions, mainly in Africa and South East Asia not covered by online global datasets, are uniquely available in the P herbarium, probably linked to past history of the museum’s botanical exploration. While acknowledging the challenges faced during the transcription of historic specimens by citizen scientists, this study highlights the positive impact of adding records to global datasets both in space and time. This is illustrative for researchers, collection managers, policy makers as well as funders. These datasets will be valuable for numerous future studies in biodiversity research, including ecology, evolution, conservation and climate change science.

AbstractPremiseThe ecological conditions that constrain plants to an environmental niche are assumed to be constant through time. While the fossil record has been used previously to test for niche conservatism of woody flowering plants, additional studies are needed in other plant groups especially since they can provide insight with paleoclimatic reconstructions, high biodiversity in modern terrestrial ecosystems, and significant contributions to agriculture.MethodsWe tested climatic niche conservatism across time by characterizing the climatic niches of living herbaceous ginger plants (Zingiberaceae) and woody dawn redwood (Metasequoia) against paleoniches reconstructed based on fossil distribution data and paleoclimatic models.ResultsDespite few fossil Zingiberaceae occurrences in the latitudinal tropics, unlike living Zingiberaceae, extinct Zingiberaceae likely experienced paratropical conditions in the higher latitudes, especially in the Cretaceous and Paleogene. The living and fossil distributions of Metasequoia largely remain in the upper latitudes of the northern hemisphere. The Zingiberaceae shifted from an initial subtropical climatic paleoniche in the Cretaceous, toward a temperate regime in the late Cenozoic; Metasequoia occupied a more consistent climatic niche over the same time intervals.ConclusionsBecause of the inconsistent climatic niches of Zingiberaceae over geologic time, we are less confident of using them for taxonomic‐based paleoclimatic reconstruction methods like nearest living relative, which assume a consistent climatic niche between extant and extinct relatives; we argue that the consistent climatic niche of Metasequoia is more appropriate for these reconstructions. Niche conservatism cannot be assumed between extant and extinct plants and should be tested further in groups used for paleoclimatic reconstructions.

Considering the global biodiversity crisis and the growing demand for medicinal plants, it is crucial to preserve therapeutically useful herbs. From a conservation management perspective under climate change, identifying areas that enable valuable natural resources to persist in the future is crucial. Machine learning-based models are commonly used to estimate the locations of climate refugia, which are critical for the effective species conservation. The aim of this study was to assess the impact of global warming on the epiphytic medicinal orchid— Bulbophyllum odoratissimum. Given how the long-term survival of plants inhabiting shrubs and trees depends on the availability of suitable phorophyets, in this research potential range changes in reported orchid plant hosts were evaluated. According to conducted analyses, global warming will cause a decline in the coverage of the suitable niches for B. odoratissimum and its main phorophyte. The most significant habitat loss in the case of the studied orchid and Pistacia weinmannifolia will be observed in the southern part of their geographical ranges and some new niches will simultaneously become available for these plants in the northern part. Climate change will significantly increase the overlap of geographical ranges of P. weinmannifolia and the orchid. In the SSP5-8.5 scenario trees will be available for more than 56% of the orchid population. Other analyzed phorophytes, will be available for B. odoratissimum to a very reduced extent, as orchids will only utilize these species as habitats only occasionally. This study provides data on the distribution of climatic refugia of B. odoratissimum under global warming. Moreover, this is the first evaluation of the future geographical ranges for its phorophytes. According to the conducted analyses, only one of the previously reported tree species which are inhabited by B. odoratissimum , P. weinmannifolia, can serve as a phorophyte for this orchid in the future. In this study, the areas designated as suitable for the occurrence of both orchids and their phorophytes should be considered priority conservation areas for the studied medicinal plants.

Premise Cleomaceae is an important model clade for studies of evolutionary processes including genome evolution, floral form diversification, and photosynthetic pathway evolution. Diversification and divergence patterns in Cleomaceae remain tangled as research has been restricted by its worldwide distribution, limited genetic sampling and species coverage, and a lack of definitive fossil calibration points.MethodsWe used target sequence capture and the Angiosperms353 probe set to perform a phylogenetic study of Cleomaceae. We estimated divergence times and biogeographic analyses to explore the origin and diversification of the family. Seed morphology across extant taxa was documented with multifocal image‐stacking techniques and morphological characters were extracted, analyzed, and compared to fossil records.ResultsWe recovered a well‐supported and resolved phylogenetic tree of Cleomaceae generic relationships that includes 236 (~86%) species. We identified 11 principal clades and confidently placed Cleomella as sister to the rest of the family. Our analyses suggested that Cleomaceae and Brassicaceae diverged ~56 mya, and Cleomaceae began to diversify ~53 mya in the Palearctic and Africa. Multiple transatlantic disjunct distributions were identified. Seeds were imaged from 218 (~80%) species in the family and compared to all known fossil species.ConclusionsOur results represent the most comprehensive phylogenetic study of Cleomaceae to date. We identified transatlantic disjunctions and proposed explanations for these patterns, most likely either long‐distance dispersals or contractions in latitudinal distributions caused by climate change over geological timescales. We found that seed morphology varied considerably but mostly mirrored generic relationships.

Submerged macrophytes remediation is a commonly used technique for improving water quality and restoring habitat in aquatic ecosystems. However, the drivers of success in the submerged macrophytes assembly process and their specific impacts on methane emissions are poorly understood. Thus, we conducted a mesocosm experiment to test the growth plasticity and carbon fixation of widespread submerged macrophytes (Vallisneria natans) under different nutrient conditions. A refined dynamic chamber method was utilized to concurrently collect and quantify methane emission fluxes arising from ebullition and diffusion processes. Significant correlations were found between methane flux and variations in the physiological activities of V. nantas by the fluorescence imaging system. Our results show that exceeding tolerance thresholds of ammonia in the water significantly interfered with the photosynthetic systems in submerged leaves and the radial oxygen loss in adventitious roots. The recovery process of V. natans accelerated the consumption of dissolved oxygen, leading to increase in the populations of methanogen (153.3 % increase of mcrA genes) and subsequently elevating CH4 emission fluxes (23.7 %) under high nutrient concentrations. Conversely, V. natans increased the available organic carbon under low nutrient conditions by radial oxygen loss, further increasing CH4 emission fluxes (94.7 %). Quantitative genetic and modeling analyses revealed that plant restoration processes drive ecological niche differentiation of methanogenic and methane oxidation microorganisms, affecting methane release fluxes within the restored area. The speciation process of V. natans is incapable of simultaneously meeting improved water purification and reduced methane emissions goals.

The present study provides an assessment of the distribution of key Non-Timber Forest Product species in India, namely Aegle marmelos (L.) Correa, Buchanania lanzan Spreng., Madhuca longifolia (J. Koenig ex L.) J. F. Macbr., Phyllanthus emblica L. and Terminalia bellirica (Gaertn.) Roxb. The suitable habitat was analyzed under current climate scenarios and subsequently, the future distribution (2050s and 2070s) was mapped under RCP 2.6 and 8.5 scenarios, along with the past distribution (mid-Holocene, ~ 6000 cal year BP) using the MaxEnt species distribution model. The distribution of all species is primarily driven by key bioclimatic factors, including annual precipitation (Bio_12), mean annual temperature (Bio_1), isothermality (Bio_3) and precipitation of the coldest quarter (Bio_19). The results indicate that the present distribution of these species is mainly centred in the Western Ghats regions, Central Highlands, North-eastern India and Siwalik hills. The current study suggests that under the future climate change, the suitable habitat for A. marmelos and T. bellirica is expected to increase while for B. lanzan , M. longifolia and P. emblica , it is projected to decline. A. marmelos and T. bellirica are anticipated to exhibit resilience to future climate changes and are expected to be minimally affected, while B. lanzan , M. longifolia and P. emblica are highly sensitive to high temperature and alteration in rainfall pattern expected under future climate changes. The projections of habitat suitability areas can be used as a valuable foundation for developing conservation and restoration strategies aimed at alleviating the climate change impacts on NTFP species.

Aim Species occurrence data are valuable information that enables one to estimate geographical distributions, characterize niches and their evolution, and guide spatial conservation planning. Rapid increases in species occurrence data stem from increasing digitization and aggregation efforts, and citizen science initiatives. However, persistent quality issues in occurrence data can impact the accuracy of scientific findings, underscoring the importance of filtering erroneous occurrence records in biodiversity analyses.InnovationWe introduce an R package, occTest, that synthesizes a growing open‐source ecosystem of biodiversity cleaning workflows to prepare occurrence data for different modelling applications. It offers a structured set of algorithms to identify potential problems with species occurrence records by employing a hierarchical organization of multiple tests. The workflow has a hierarchical structure organized in testPhases (i.e. cleaning vs. testing) that encompass different testBlocks grouping different testTypes (e.g. environmental outlier detection), which may use different testMethods (e.g. Rosner test, jacknife,etc.). Four different testBlocks characterize potential problems in geographic, environmental, human influence and temporal dimensions. Filtering and plotting functions are incorporated to facilitate the interpretation of tests. We provide examples with different data sources, with default and user‐defined parameters. Compared to other available tools and workflows, occTest offers a comprehensive suite of integrated tests, and allows multiple methods associated with each test to explore consensus among data cleaning methods. It uniquely incorporates both coordinate accuracy analysis and environmental analysis of occurrence records. Furthermore, it provides a hierarchical structure to incorporate future tests yet to be developed.Main conclusionsoccTest will help users understand the quality and quantity of data available before the start of data analysis, while also enabling users to filter data using either predefined rules or custom‐built rules. As a result, occTest can better assess each record's appropriateness for its intended application.

Dense branching and spines are common features of plant species in ecosystems with high mammalian herbivory pressure. While dense branching and spines can inhibit herbivory independently, when combined, they form a powerful defensive cage architecture. However, how cage architecture evolved under mammalian pressure has remained unexplored. Here we show how dense branching and spines emerged during the age of mammalian radiation in the Combretaceae family and diversified in herbivore-driven ecosystems in the tropics. Phylogenetic comparative methods revealed that modern plant architectural strategies defending against large mammals evolved via a stepwise process. First, dense branching emerged under intermediate herbivory pressure, followed by the acquisition of spines that supported higher speciation rates under high herbivory pressure. Our study highlights the adaptive value of dense branching as part of a herbivore defence strategy and identifies large mammal herbivory as a major selective force shaping the whole plant architecture of woody plants. This study explores the evolution of two traits, branching density and spine presence, in the globally distributed plant family Combretaceae. These traits were found to have appeared in a two-step process in response to mammalian herbivory pressure, revealing the importance of large mammals in the evolution of plant architecture diversity.