Examining patterns of coexistence in the Cape genus Tetraria (Cyperaceae) from a phylogenetic perspective : tracing the history of community assembly processes

The coexistence of species is fundamentally important in maintaining high species diversity in a defined area, and is partly responsible for the remarkable diversity of the Cape Floristic Region. The ecological attributes that determine the community assembly processes of competitive interactions and ecological sorting are subject to phylogenetic constraint and niche conservatism, suggesting that patterns of coexistence should be phylogenetically structured. This study compares patterns of coexistence against phylogenetic and ecological divergence in the genus Tetraria (Cyperaceae), and related sedges in the tribe Schoeneae, at different spatial and phylogenetic scales in multiple communities across the Cape Fynbos Biome. The investigation is based on coexistence data inferred from plot data from 13 phytosociological studies, ecological distances based on plant functional traits, and phylogenetic distances based on a molecular phylogeny of the species in question. Species coexisting in plots are significantly less related than expected on the basis of chance, and plots of phylogenetic distance against coexistence show triangular relationships, implying coexistence between closely related species is restricted, but that coexistence levels between more distantly related species may vary greatly. Quantification of these triangular relationships was problematic due to the small sample sizes and the low power of the nonparametric tests used. The pattern is more pronounced when a closely related subset of the species was used in a separate analysis, suggesting that phylogenetic scale is important. Coexisting species are significantly more closely related at the study than at the plot scale, implying relaxation of the effects of competitive interactions at coarser spatial scales. Significant positive correlation between ecological and phylogenetic divergence implies that phylogenetic constraint and niche conservatism has a strong effect on the ecological attributes of the study species. These results provide support for the hypothesis that the patterns of coexistence among species' in the genus Tetraria, and related sedges in the tribe Schoeneae, are influenced by phylogenetic constraint and niche conservatism on ecological attributes

Branch junction constriction and hydraulic limitation in two species in the Cape Proteaceae : a mechanism explaining the trade-off between longevity and degree of ramification in the Cape Proteaceae

The purpose of this study was to establish if hydraulic limitation and branch junction constriction explain the trade-off between longevity and increased ramification in species of the Cape Proteaceae. This was done by establishing if branch nodes are regions of greater resistance to xylem sap flow in the study species; attempting to quantify nodal resistance for a plant as a whole; and by determining if there is any evidence for hydraulic limitation or compensation in Leucadendron laureolum (Lam.) Fourc. and Leucospermum oleifolium (Berg.) R. Br. individuals. The extent of branch junction constriction was established by comparing the ratio of the xylem sap flow rates of adjacent branch segments of equal length. The ratio of a proximal intemodal to a distal intemodal segment was compared against the ratio of a proximal intemodal segment to a distal node. Branch nodes were found to create significant resistance to xylem sap flow rates in both species (p < .005 for L. laureolum, and p < .05 for L. oleifolium). Total nodal resistance in L. laureolum was modelled as equivalent extra branch length, and as loss of sap flow rate. Equivalent extra branch length increased exponentially with increased branching order, and increased much faster in more ramified plants. Loss of flow rate increased linearly with increased branching order and was unaffected by differences in ramification. This was because the nodes in more ramified plants had smaller basal sapwood areas, and the resistance imposed by nodes decreased with decreased basal sapwood area. As more ramified plants tend to branch earlier, and/or with greater temporal frequency, they will still accumulate greater nodal hydraulic resistance faster than less ramified plants, and thus may be limited to smaller size and younger maximum age. Branch specific conductivities (kₛ), leaf specific conductivities (LSC) and transpiration rates were investigated in higher (11 nodes) and lower (10 nodes) order branches of L. laureolum. All were found to be significantly lower in higher order branches (11 nodes), which can be related to greater nodal resistance to sap flow limiting the amount of water available to the area of developing xylem, causing the vessels to have narrower diameters. There was no significant difference in leaf to sapwood area ratios (Aₗ/As) between the two branching orders. Previous studies have suggested that changes in Aₗ/Aₛratios occur to compensate for hydraulic limitation. Reductions in Aₗ/Aₛin plants with greater hydraulic restriction allow LSC values, and thus transpiration rates, to stay as high as plants with less hydraulic restriction. As there was no such compensation, LSC values, and thus transpiration rates, were much lower in branches of higher order. Transpiration rate is a good indication of rates of photosynthesis. Lower transpiration rate in higher order branches is thus a good indication of hydraulic limitation on rates of photosynthesis with increased branching order. Hydraulic resistance in nodes thus imposes an important limitation on size and/or age of L. laureolum individuals, and explains the apparent trade-off between longevity and degree of ramification in the Cape Proteaceae

Tracking socioeconomic vulnerability using network analysis: insights from an avian influenza outbreak in an ostrich production network

BACKGROUND: The focus of management in many complex systems is shifting towards facilitation, adaptation, building resilience, and reducing vulnerability. Resilience management requires the development and application of general heuristics and methods for tracking changes in both resilience and vulnerability. We explored the emergence of vulnerability in the South African domestic ostrich industry, an animal production system which typically involves 3-4 movements of each bird during its lifetime. This system has experienced several disease outbreaks, and the aim of this study was to investigate whether these movements have contributed to the vulnerability of this system to large disease outbreaks. METHODOLOGY/PRINCIPAL FINDINGS: The ostrich production system requires numerous movements of birds between different farm types associated with growth (i.e. Hatchery to juvenile rearing farm to adult rearing farm). We used 5 years of movement records between 2005 and 2011 prior to an outbreak of Highly Pathogenic Avian Influenza (H5N2). These data were analyzed using a network analysis in which the farms were represented as nodes and the movements of birds as links. We tested the hypothesis that increasing economic efficiency in the domestic ostrich industry in South Africa made the system more vulnerable to outbreak of Highly Pathogenic Avian Influenza (H5N2). Our results indicated that as time progressed, the network became increasingly vulnerable to pathogen outbreaks. The farms that became infected during the outbreak displayed network qualities, such as significantly higher connectivity and centrality, which predisposed them to be more vulnerable to disease outbreak. Conclusions/Significance Taken in the context of previous research, our results provide strong support for the application of network analysis to track vulnerability, while also providing useful practical implications for system monitoring and management

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