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Modern Applied Statistics With S

The most unique feature of Earth is the existence of life, and the most extraordinary feature of life is its diversity. Approximately 9 million types of plants, animals, protists and fungi inhabit the Earth. So, too, do 7 billion people. Two decades ago, at the first Earth Summit, the vast majority of the world's nations declared that human actions were dismantling the Earth's ecosystems, eliminating genes, species and biological traits at an alarming rate. This observation led to the question of how such loss of biological diversity will alter the functioning of ecosystems and their ability to provide society with the goods and services needed to prosper.

/pdf/biodiversity-loss-and-its-impact-on-humanity-2d0fgc88mg.pdf

Biodiversity loss and its impact on humanity

Species distribution models (SDMs) are numerical tools that combine observations of species occurrence or abundance with environmental estimates. They are used to gain ecological and evolutionary insights and to predict distributions across landscapes, sometimes requiring extrapolation in space and time. SDMs are now widely used across terrestrial, freshwater, and marine realms. Differences in methods between disciplines reflect both differences in species mobility and in “established use.” Model realism and robustness is influenced by selection of relevant predictors and modeling method, consideration of scale, how the interplay between environmental and geographic factors is handled, and the extent of extrapolation. Current linkages between SDM practice and ecological theory are often weak, hindering progress. Remaining challenges include: improvement of methods for modeling presence-only data and for model selection and evaluation; accounting for biotic interactions; and assessing model uncertainty.

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Species Distribution Models: Ecological Explanation and Prediction Across Space and Time

Modelling strategies for predicting the potential impacts of climate change on the natural distribution of species have often focused on the characterization of a species’ bioclimate envelope. A number of recent critiques have questioned the validity of this approach by pointing to the many factors other than climate that play an important part in determining species distributions and the dynamics of distribution changes. Such factors include biotic interactions, evolutionary change and dispersal ability. This paper reviews and evaluates criticisms of bioclimate envelope models and discusses the implications of these criticisms for the different modelling strategies employed. It is proposed that, although the complexity of the natural system presents fundamental limits to predictive modelling, the bioclimate envelope approach can provide a useful first approximation as to the potentially dramatic impact of climate change on biodiversity. However, it is stressed that the spatial scale at which these models are applied is of fundamental importance, and that model results should not be interpreted without due consideration of the limitations involved. A hierarchical modelling framework is proposed through which some of these limitations can be addressed within a broader, scale-dependent

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Predicting the impacts of climate change on the distribution of species: are bioclimate envelope models useful?

There is growing recognition that classifying terrestrial plant species on the basis of their function (into 'functional types') rather than their higher taxonomic identity, is a promising way forward for tackling important ecological questions at the scale of ecosystems, landscapes or biomes. These questions include those on vegetation responses to and vegetation effects on, environmental changes (e.g. changes in climate, atmospheric chemistry, land use or other disturbances). There is also growing consensus about a shortlist of plant traits that should underlie such functional plant classifications, because they have strong predictive power of important ecosystem responses to environmental change and/or they themselves have strong impacts on ecosystem processes. The most favoured traits are those that are also relatively easy and inexpensive to measure for large numbers of plant species. Large international research efforts, promoted by the IGBP–GCTE Programme, are underway to screen predominant plant species in various ecosystems and biomes worldwide for such traits. This paper provides an international methodological protocol aimed at standardising this research effort, based on consensus among a broad group of scientists in this field. It features a practical handbook with step-by-step recipes, with relatively brief information about the ecological context, for 28 functional traits recognised as critical for tackling large-scale ecological questions.

/pdf/a-handbook-of-protocols-for-standardised-and-easy-2uo4112zhh.pdf

A handbook of protocols for standardised and easy measurement of plant functional traits worldwide

Aboveground and belowground biomass compartments of vegetation fulfil different functions and they are coupled by complex interactions. These compartments exchange water, carbon and nutrients and the belowground biomass compartment has the capacity to buffer vegetation dynamics when aboveground biomass is removed by disturbances such as herbivory or fire. However, despite their importance, root-shoot interactions are often ignored in more heuristic vegetation models. Here, we present a simple two-compartment grassland model that couples aboveground and belowground biomass. In this model, the growth of belowground biomass is influenced by aboveground biomass and the growth of aboveground biomass is influenced by belowground biomass. We used the model to explore how the dynamics of a grassland ecosystem are influenced by fire and grazing. We show that the grassland system is most persistent at intermediate levels of aboveground-belowground coupling. In this situation, the system can sustain more extreme fire or grazing regimes than in the case of strong coupling. In contrast, the productivity of the system is maximised at high levels of coupling. Our analysis suggests that the yield of a grassland ecosystem is maximised when coupling is strong, however, the intensity of disturbance that can be sustained increases dramatically when coupling is intermediate. Hence, the model predicts that intermediate coupling should be selected for as it maximises the chances of persistence in disturbance driven ecosystems.

/pdf/intermediate-coupling-between-aboveground-and-belowground-qhy5si7x9u.pdf

Intermediate coupling between aboveground and belowground biomass maximises the persistence of grasslands.

C3 plants can increase nutrient uptake by increasing transpiration, which promotes the flow of water with dissolved nutrients towards the roots. However, it is not clear if this mechanism of nutrient acquisition, termed ‘mass flow’, also operates in C4 plants. This is an important question, as differences in mass flow capacity may affect competitive interactions between C3 and C4 species. To test if mass flow can be induced in C4 species, we conducted an experiment in a semiarid seasonal savanna in South Africa. We grew six C4 grasses in nutrient-poor sand and supplied no nutrients, nutrients to the roots or nutrients spatially separated from the roots. We measured the rates of photosynthesis and transpiration, water-use efficiency (WUE), nitrogen gain and biomass. For all species biomass, N gain, photosynthesis and transpiration were lowest in the treatment without any nutrient additions. Responses to different nutrient positioning varied among species from no effect on N gain to a 50% reduction when nutrients were spatially separated. The ability to access spatially separated nutrients showed a nonsignificant positive relationship with both the response of transpiration and the response of WUE to spatial nutrient separation. This indicates that nutrient acquisition is not regulated by decreasing WUE in C4 grasses. Overall, our study suggests that under elevated CO2, when evaporative demand is lower, C4 species may be at a competitive disadvantage to C3 species when it comes to nutrient acquisition.

Effects of nutrient supply on carbon and water economies of C4 grasses.

A flexible use of the crassulacean acid metabolism (CAM) has been hypothesised to represent an intermediate stage along a C3 to full CAM evolutionary continuum, when relative contributions of C3 vs CAM metabolism are co-determined by evolutionary history and prevailing environmental constraints. However, evidence for such eco-evolutionary interdependencies is lacking. We studied these interdependencies for the leaf-succulent genus Drosanthemum (Aizoaceae, Southern African Succulent Karoo) by testing for relationships between leaf δ13 C diagnostic for CAM dependence (i.e. contribution of C3 and CAM to net carbon gain), and climatic variables related to temperature and precipitation and their temporal variation. We further quantified the effects of shared phylogenetic ancestry on CAM dependence and its relation to climate. CAM dependence is predicted by rainfall and its temporal variation, with high predictive power of rainfall constancy (temporal entropy). The predictive power of rainfall seasonality and temperature-related variables was negligible. Evolutionary history of the tested clades significantly affected the relationship between rainfall constancy and CAM dependence. We argue that higher CAM dependence might provide an adaptive advantage in increasingly unpredictable rainfall environments when the anatomic exaptation (succulence) is already present. These observations might shed light on the evolution of full CAM.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17250

The eco-evolutionary significance of rainfall constancy for facultative CAM photosynthesis.

Diversification processes underpin the patterns of species diversity 1 that fascinate biologists. Two competing hypotheses disagree about the effect of competition on these processes. The bounded hypothesis suggests that species diversity is limited (bounded) by competition between species for finite niche space, while the unbounded hypothesis proposes that evolution and ecological opportunity associated with speciation, render competition unimportant. We use phylogenetically structured niche modelling, to show that processes consistent with both these diversification models have driven species accumulation in conifers. In agreement with the bounded hypothesis, niche competition constrained diversification, and in line with the unbounded hypothesis, niche evolution and partitioning promoted diversification. We then analyse niche traits to show that these diversification enhancing and inhibiting processes can occur simultaneously on different niche dimensions. Together these results suggests a new hypothesis for lineage diversification based on the multi-dimensional nature of ecological niches that accommodates both bounded and unbounded diversification processes.

/pdf/the-dimensions-of-species-diversity-1ss53krzi7.pdf

Steven I. Higgins

Papers

Intermediate coupling between aboveground and belowground biomass maximises the persistence of grasslands.

Effects of nutrient supply on carbon and water economies of C4 grasses.

The eco-evolutionary significance of rainfall constancy for facultative CAM photosynthesis.

The dimensions of species diversity

Data from: Defining functional biomes and monitoring their change globally