An operational definition of the biome for global change research

CITATION: Conradi, T. et al. 2020. An operational definition of the biome for global change research. New Phytologist, 227:1294–1306, doi:10.1111/nph.16580.The original publication is available at https://nph.onlinelibrary.wiley.comBiomes are constructs for organising knowledge on the structure and functioning of the world’s ecosystems, and serve as useful units for monitoring how the biosphere responds to anthropogenic drivers, including climate change. The current practice of delimiting biomes relies on expert knowledge. Recent studies have questioned the value of such biome maps for comparative ecology and global-change research, partly due to their subjective origin. Here we propose a flexible method for developing biome maps objectively. The method uses range modelling of several thousands of plant species to reveal spatial attractors for different growth-form assemblages that define biomes. The workflow is illustrated using distribution data from 23 500 African plant species. In an example application, we create a biome map for Africa and use the fitted species models to project biome shifts. In a second example, we map gradients of growth-form suitability that can be used to identify sites for comparative ecology. This method provides a flexible framework that (1) allows a range of biome types to be defined according to user needs and (2) enables projections of biome changes that emerge purely from the individualistic responses of plant species to environmental changes.Publisher's versio

Functional traits explain the Hutchinsonian niches of plant species

CITATION: Martina, T. et al. 2019. Functional traits explain the Hutchinsonian niches of plant species. Global Ecology and Biogeography, 29(3):534–54. doi:10.1111/geb.13048The original publication is available at https://onlinelibrary.wiley.com/journal/14668238Aim: The Hutchinsonian niche is a foundational concept in ecology and evolutionary biology that describes fundamental characteristics of any species: the global maximum population growth rate (rmax); the niche optimum (the environment for which rmax is reached); and the niche width (the environmental range for which intrinsic population growth rates are positive). We examine whether these characteristics are related to inter- and intraspecific variation in functional traits. Location: Cape Floristic Region, South Africa. Time period: Present day. Major taxa studied: Twenty-six plant species (Proteaceae). Methods: We measured leaf, plant-architectural and seed traits across species geographical ranges. We then examined how species-mean traits are related to demographically derived niche characteristics of rmax, in addition to niche optima and widths in five environmental dimensions, and how intraspecific trait variation is related to niche widths. Results: Interspecific trait variation generally exceeded range-wide intraspecific trait variation. Species-mean trait values were associated with variation in rmax (R2 = 0.27) but were more strongly related to niche optima (mean R2 = 0.56). These relationships generally matched trait–environment associations described in the literature. Both species-mean traits and intraspecific trait variability were strongly related to niche widths (R2 = 0.66 and 0.59, respectively). Moreover, niche widths increased with intraspecific trait variability. Overall, the different niche characteristics were associated with few, largely non-overlapping sets of traits. Main conclusions: Our study relating functional traits to Hutchinsonian niches demonstrates that key demographic properties of species relate to few traits with relatively strong effects. Our results further support the hypothesis that intraspecific trait variation increases species niche widths. Given that niche characteristics were related to distinct sets of traits, different aspects of environmental change might affect axes of trait variation independently. Trait-based studies of Hutchinsonian niches thus yield important insights into the mechanisms shaping functional biodiversity, which should reinforce the role of traits in functional biogeography.https://onlinelibrary.wiley.com/doi/10.1111/geb.13048Publishers versio

An operational definition of the biome for global change research

CITATION: Conradi, T. et al. 2020. An operational definition of the biome for global change research. New Phytologist, 227:1294–1306, doi:10.1111/nph.16580.The original publication is available at https://nph.onlinelibrary.wiley.comBiomes are constructs for organising knowledge on the structure and functioning of the world’s ecosystems, and serve as useful units for monitoring how the biosphere responds to anthropogenic drivers, including climate change. The current practice of delimiting biomes relies on expert knowledge. Recent studies have questioned the value of such biome maps for comparative ecology and global-change research, partly due to their subjective origin. Here we propose a flexible method for developing biome maps objectively. The method uses range modelling of several thousands of plant species to reveal spatial attractors for different growth-form assemblages that define biomes. The workflow is illustrated using distribution data from 23 500 African plant species. In an example application, we create a biome map for Africa and use the fitted species models to project biome shifts. In a second example, we map gradients of growth-form suitability that can be used to identify sites for comparative ecology. This method provides a flexible framework that (1) allows a range of biome types to be defined according to user needs and (2) enables projections of biome changes that emerge purely from the individualistic responses of plant species to environmental changes.Publisher's versio

A novel phylogenetic regionalization of phytogeographical zones of southern Africa reveals their hidden evolutionary affinities

AIM : Although existing bioregional classification schemes often consider the compositional affinities within regional biotas, they do not typically incorporate phylogenetic information explicitly. Because phylogeny captures information on the evolutionary history of taxa, it provides a powerful tool for delineating biogeographical boundaries and for establishing relationships among them. Here, we present the first vegetation delineation of the woody flora of southern Africa based upon evolutionary relationships. LOCATION : Southern Africa. METHODS : We used a published time-calibrated phylogenetic tree for 1400 woody plant species along with their geographical distributions and a metric of phylogenetic beta diversity to generate a phylogenetic delineation of the woody vegetation of southern Africa. We then explored environmental correlates of phylogenetic turnover between them, and the evolutionary distinctiveness of the taxa within them. RESULTS : We identified 15 phylogenetically distinct biogeographical units, here referred to as phyloregions. The largest phyloregion broadly overlaps with Savanna vegetation, while the phyloregion overlapping with the south-western portion of the Fynbos biome is the most evolutionarily distinct. Potential evapotranspiration and mean annual temperature differ significantly among phyloregions and correlate with patterns of phylogenetic beta diversity between them. Our phylogeny-based delimitation of southern Africa’s woody vegetation broadly matches currently recognized phytogeographical classifications, but also highlights parts of the Namib Karoo and Greater Limpopo Transfrontier Park as distinct, but previously under-recognized biogeographical units. MAIN CONCLUSIONS : Our analysis provides new insights into the structure and phylogenetic relationships among the woody flora of southern Africa. We show that evolutionary affinities differentiate phyloregions closely resembling existing vegetation classifications, yet also identify ‘cryptic’ phyloregions that are as evolutionarily distinct as some of the recognized African vegetation types.Government of Canada through Genome Canada and the Ontario Genomics Institute (2008-OGI-ICI-03), the International Development Research Centre (IDRC) Canada, the University of Johannesburg and the South African National Research Foundation (NRF).http://onlinelibrary.wiley.com/doi/10.1111/jbi.126192017-01-31hb201

Priority questions for biodiversity conservation in the Mediterranean biome: Heterogeneous perspectives across continents and stakeholders

International audienceThe identification of research questions with high relevance for biodiversity conservation is an important step towards designing more effective policies and management actions, and to better allocate funding among alternative conservation options. However, the identification of priority questions may be influenced by regional differences in biodiversity threats and social contexts, and to variations in the perceptions and interests of different stakeholders. Here we describe the results of a prioritization exercise involving six types of stakeholders from the Mediterranean biome, which includes several biodiversity hotspots spread across five regions of the planet (Europe, Africa, North and South America, and Australia). We found great heterogeneity across regions and stakeholder types in the priority topics identified and disagreement among the priorities of research scientists and other stakeholders. However, governance, climate change, and public participation issues were key topics in most regions. We conclude that the identification of research priorities should be targeted in a way that integrates the spectrum of stakeholder interests, potential funding sources and regional needs, and that further development of interdisciplinary studies is required. The key questions identified here provide a basis to identify priorities for research funding aligned with biodiversity conservation needs in this biome

Stochastic Species Turnover and Stable Coexistence in a Species-Rich, Fire-Prone Plant Community

Understanding the mechanisms that maintain diversity is important for managing ecosystems for species persistence. Here we used a long-term data set to understand mechanisms of coexistence at the local and regional scales in the Cape Floristic Region, a global hotspot of plant diversity. We used a dataset comprising 81 monitoring sites, sampled in 1966 and again in 1996, and containing 422 species for which growth form, regeneration mode, dispersal distance and abundances at both the local (site) and meta-community scales are known. We found that species presence and abundance were stable at the meta-community scale over the 30 year period but highly unstable at the local scale, and were not influenced by species' biological attributes. Moreover, rare species were no more likely to go extinct at the local scale than common species, and that alpha diversity in local communities was strongly influenced by habitat. We conclude that stochastic environmental fluctuations associated with recurrent fire buffer populations from extinction, thereby ensuring stable coexistence at the meta-community scale by creating a “neutral-like” pattern maintained by niche-differentiation

Forest restoration or propaganda? The need for Transparency and Openness Promotion (TOP) scores to uphold research integrity

In a time of environmental crisis and ‘fake news’, there are calls for scientists to engage in public debate or advocacy. Some are wary, fearing that revealing subjective views poses a risk to scientific credibility or erodes trust in scholarly publishing. Others are less concerned, seeing it as their duty to society or an opportunity to boost their profile. Ideally, we need better checks and balances that allow scientists to contribute to public discourse without fear of compromising the credibility of their science, while avoiding subjective views influencing the outcomes of peer-reviewed research. For better or worse, scientists have personal views. The question is not whether they should be condoned or condemned, but how they should be managed in the context of scholarly publishing to maximise benefits and minimise negative outcomes. Using the recent contention around global tree ‘restoration’ potential as an example, I propose we score journals and articles based on the Transparency and Openness Promotion (TOP) guidelines and associated criteria. A high TOP score means readers have sufficient access to information to assess the objectivity and credibility of scientific publications and their authors. I show that current practice provides very little access to information, and readers are essentially being asked to have faith in the scholarly publication system. We must do better. Significance: Science is predicated upon objectivity, yet readers are rarely given enough information to assess the objectivity, and thus integrity, of peer-reviewed research. To address this issue, a scoring system is proposed, which is based on the principles of transparency and openness. Improving transparency and openness in scholarly publishing is essential for allowing readers to assess the objectivity of published research and researchers, growing public trust, and allowing researchers to engage in public debates without fear of loss of scientific credibility

Forest restoration or propaganda? The need for Transparency and Openness Promotion (TOP) scores to uphold research integrity

In a time of environmental crisis and ‘fake news’, there are calls for scientists to engage in public debate or advocacy. Some are wary, fearing that revealing subjective views poses a risk to scientific credibility or erodes trust in scholarly publishing. Others are less concerned, seeing it as their duty to society or an opportunity to boost their profile. Ideally, we need better checks and balances that allow scientists to contribute to public discourse without fear of compromising the credibility of their science, while avoiding subjective views influencing the outcomes of peer-reviewed research. For better or worse, scientists have personal views. The question is not whether they should be condoned or condemned, but how they should be managed in the context of scholarly publishing to maximise benefits and minimise negative outcomes. Using the recent contention around global tree ‘restoration’ potential as an example, I propose we score journals and articles based on the Transparency and Openness Promotion (TOP) guidelines and associated criteria. A high TOP score means readers have sufficient access to information to assess the objectivity and credibility of scientific publications and their authors. I show that current practice provides very little access to information, and readers are essentially being asked to have faith in the scholarly publication system. We must do better. Significance: Science is predicated upon objectivity, yet readers are rarely given enough information to assess the objectivity, and thus integrity, of peer-reviewed research. To address this issue, a scoring system is proposed, which is based on the principles of transparency and openness. Improving transparency and openness in scholarly publishing is essential for allowing readers to assess the objectivity of published research and researchers, growing public trust, and allowing researchers to engage in public debates without fear of loss of scientific credibility

Monitoring the critically endangered Clanwilliam cedar with freely available Google Earth imagery

Monitoring of species and populations is essential for biodiversity observation and reporting at local, national and global scales, but can be an exceedingly difficult task for many, if not most, species. We tested the viability of using Google Earth™ imagery to manually map and monitor all individuals of the critically endangered Clanwilliam cedar, Widdringtonia wallichii Endl. ex Carrière, across its global native distribution; the remote and rugged Cederberg mountains. Comparison with sampling from field surveys reveals this to be a highly efficient and effective method for mapping healthy adult tree localities, but it fails to detect small or unhealthy individuals with green canopies <4 m2, or discern the number of individuals in clumps. This approach is clearly viable as a monitoring tool for this species and, with the rapid progress being made in machine learning approaches and satellite technology, will only become easier and more feasible for a greater number of species in the near future. Sadly, our field surveys revealed that the number of trees that have recently died (dead leaves still present) outnumbered live trees by a ratio of 2:1

Identifying research questions for the conservation of the Cape Floristic Region

We conducted a survey among people working in the nature conservation community in an implementation, research or policy capacity to identify research questions that they felt were important for ensuring the conservation of the Cape Floristic Region. Following an inductive process, 361 submitted questions were narrowed to 34 questions in seven themes: (1) effective conservation management; (2) detecting and understanding change: monitoring, indicators and thresholds; (3) improving governance and action for effective conservation; (4) making the case that biodiversity supports critical ecosystem services; (5) making biodiversity a shared concern; (6) securing sustainable funding for biodiversity conservation; and (7) prioritising research. The final questions were evaluated against the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services Conceptual Framework to test whether the questions addressed elements identified by this Framework as those essential to ensure that conservation contributes to a positive future for the Cape Floristic Region. We found that all elements in this Framework received attention from the collective group of questions. This finding suggests that the conservation community we approached recognises implicitly that research in multiple disciplines as well as interdisciplinary approaches are required to address societal, governance and biological issues in a changing environment in order to secure the conservation of the Cape Floristic Region. Because the majority of people responding to this survey had a background in the natural sciences, a challenge to tackling some of the questions lies in developing integrative approaches that will accommodate different disciplines and their epistemologies. Significance: We present a hierarchical compendium of research questions to generate the knowledge required to conserve the Cape Floristic Region as a social-ecological system. The conservation community of the Cape Floristic Region collectively recognises that effective conservation management needs to be supported by knowledge of ecosystems, factors that impact them and context appropriate conservation approaches. In addition, knowledge to develop effective governance and institutions, sustainable funding and broader societal participation in conservation are also identified. The questions reflect the elements and linkages of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services Conceptual Framework, suggesting that the questions presented follow global prerogatives for developing a sustainable future. The range and complexity of knowledge gaps presented suggest the need for a broader research agenda that includes the social sciences and humanities to address conservation in the Cape Floristic Region. Open data set:&nbsp; https://doi.org/10.6084/m9.figshare.7484903.v