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This chapter discusses the niche concept. One of the earliest applications of the niche theory in quantitative ecology addressed the seemingly simple question of the extent to which the niches of two species can overlap and allow co-occurrence or coexistence of the species. This question grew out of the then recent development of the notions of limiting similarity and niche packing, according to which coexistence among species with similar resource requirements was assumed to be promoted through minimization of niche overlap through divergence in habitat utilization patterns or character displacement. The answer is highly relevant in the context of climate change, or of any environmental change in general. Fluctuation in abiotic conditions such as mean annual temperature may be seen as just as important, if not more so, to the persistence or maintenance of the degree of niche overlap that is tolerable for co-occurring species as the trend in abiotic conditions itself.

This chapter illustrates the addition of niche construction to evolutionary theory, focusing primarily on the EvoDevo relationship. It elaborates the concept of niche inheritance to illustrate how the various candidate inheritance systems correspond to different components of niche inheritance and considers the principal subcomponents of niche inheritance. The chapter shows that the niche construction theory (NCT) links evolution to ecosystem-level ecology. It suggests that niche construction contributes to the “evo-devo” relationship by improving the contributions of prior evolution to the subsequent development of individual organisms, and by allowing plastic, niche-constructing developing organisms to influence the subsequent evolution of populations.

Evolutionary biogeography lies at the intersection between two sets of highly dynamic processes. One set dictates the physical environment, in which changes in size, isolation, and overall suitability for supporting life, tend to occur in cycles of different frequencies. The second set of processes shapes the ecological and evolutionary trajectories of organisms that inhabit the physical environment. The chapter reviews some of the major biogeographic patterns, and summarize theories that have been developed to account for the different patterns, including vicariance, dispersal, island biogeography, ecophylogenetics, niche theory, and neutral theory. The chapter develops propositions for a synthetic theory of biogeography that integrates the dynamic nature of geographic space with the spatial and temporal dynamics of biodiversity. Specifically, it outlines how geological and climatological cycles lead to periods of isolation and fusion of organisms inhabiting a given area, with associated effects speciation and extinction. A synthetic theory of biogeography requires cross-domain consideration of how the cyclical nature of change in the physical environment affects the ecological and evolutionary processes of different taxa and at different scales of space and time.

This chapter, which discusses problems on genetic erosion and offers a theoretical framework to improve understanding of genetic erosion, suggests two ecological models that might serve to generate more robust crop ecology. Modern niche theory and metapopulation analysis offer numerous insights and advantages to efforts to understand genetic erosion. A shared insight is that general population processes, such as genetic erosion, are affected by environmental heterogeneity. Modern niche theory and metapopulation analysis provide a middle ground between general theory and site specificity. The chapter discusses how the application of formal population models to crops presents daunting challenges—to define key variables and specify functional relationships. The need to include both biological and social variables and functional relationships is particularly difficult to satisfy.

This chapter, which discusses the similarities and differences between the classical and contemporary approaches to the niche, begins with comparisons between consumer–resource and Lotka–Volterra models. It then describes a revised niche framework that seeks to clarify and resurrect the niche concept in a more quantifiable and biologically meaningful way than the previously loosely associated ideas of the niche. The niche framework is used to illuminate a series of issues from conventional niche theory.

Impact assessments increasingly rely on models to project the potential impacts of climate change on species distributions. Ecological niche models have become established as an efficient and widely used method for interpolating (and sometimes extrapolating) species’ distributions. They use statistical and machine-learning approaches to relate species’ observations to environmental predictor variables and identify the main environmental determinants of species’ ranges. Based on this estimated species–environment relationship, the species’ potential distribution can be mapped in space (and time). In this chapter, we explain the concept and underlying assumptions of ecological niche models, describe the basic modelling steps using the silvereye (Zosterops lateralis) as a simple real-world example, identify potential sources of uncertainty in underlying data and in the model, and discuss potential limitations as well as latest developments and future perspectives of ecological niche models in a global change context.

Our next major question is, how can we characterize the sediment as a habitat for biota? Marine sediments range from coarse gravels in areas subjected to much wave and current action, to muds typical of low-energy estuarine areas and to fine silts and clays in deep-sea sediments. The settling velocity of those particles and the ability of any particle to be re-suspended, moved, and redeposited depends on the prevailing hydrographic regime (e.g. see Open University 2002). The latter will in turn influence the transport of a species´ dispersal stages, especially larvae which will then be allowed to settle following metamorphosis under the appropriate hydrographic conditions (defined as hydrographic concentration). Hence the presence of fine sediments will indicate the depositing/accreting areas which may also be suitable for passively settling organisms. Clearly the particle size is of major importance in characterizing sediments, although sediments can also be categorized by their origin (fluvial, biogenic, cosmogenic, etc.) and their material (quartz, carbonates, clays, etc.) (Open University 2002). On a typical sandy beach the coarsest particles lie at the top of the beach and grade down to the finest sediments at the waterline. The top of the beach is dry and there is much windblown sand, since coarse sands drain rapidly, whereas at the lower end of the beach the sediments are wet, with frequent standing pools. Coarse sediment is found at the top of the shore because as the waves break on the beach the heaviest particles sediment out first. Finer particles remain in suspension longer and are carried seaward on the wave backwash. Beaches change their slope over the seasons, being steeper in winter and shallower in summer. A greater degree of wave energy will produce steeper beaches, as particles are pushed up the beach and so may be stored there, whereas gentle waves produce shallow, sloping beaches. Waves hitting the shore obliquely will create sediment movement as longshore drift. Subtidally, waves are important in distributing and affecting sediments down to depths of 100 m, but the effect decreases exponentially with depth and so the dominant subtidal influences on sediment transport are currents.

Understanding the processes involved in generating distribution patterns of carnivorous plants requires investigation at multiple scales. Carnivorous plants typically occur in warm or hot and humid or wet climates in subtropical to tropical regions of all continents. Carnivorous plants tend to grow in wet, open, and nutrient-poor habitats. Most carnivorous plants are less tolerant of dry soils than are non-carnivorous plants. The reasons why many carnivorous plants are absent from habitats with nutrient-rich soils remain unclear, but the roles of competition and soil anoxia warrant greater attention. Reduced competition from woody plants (e.g., following fires) contributes to neutral coexistence of carnivorous and noncarnivorous herbs, and there is no evidence to date in support of nutrient-niche partitioning. More studies of interspecific competition are needed to understand better the distribution patterns and drivers of species coexistence of carnivorous and noncarnivorous plants.

As the oceans cover 70% of the earth’s surface, marine sediments constitute the second largest habitat on earth, after the ocean water column, and yet we still know more about the dark side of the moon than about the biota of this vast habitat. The primary aim of this book is to give an overview of the biota of marine sediments from an ecological perspective—we will talk of the benthos, literally the plants and animals at the bottom of the sea, but we will also use the term to include those organisms living on the intertidal sediments, the sands and muds of the shore. Given that most of that area is below the zone where light penetrates, the photic zone, the area is dominated by the animals and so we will concentrate on this component. Many of the early studies of marine sediments were taxonomic, describing new species. One of the pioneers was Carl von Linnaeus (1707–1778), the great Swedish biologist who developed the Linnaean classification system for organisms that is still used today (but under threat from some molecular biologists who argue that the Linnaean system is outdated and propose a new system called Phylocode). Linnaeus described hundreds of marine species, many of which come from marine sediments. The British marine biologist Edward Forbes was a pioneer who invented the dredge to sample marine animals that lived below the tidemarks. Forbes showed that there were fewer species as the sampled depth increased and believed that the great pressures at depths meant that no animals would be found deeper than 600 m. This was disproved by Michael Sars who in 1869 used a dredge to sample the benthos at 600 m depth off the Lofoten islands in Norway. Sars found 335 species and in fact was the first to show that the deep sea (off the continental shelf) had high numbers of species. Following these pioneering studies, one of the earliest systematic studies of marine sediments was the HMS Challenger expedition of 1872–1876, the first global expedition. The reports of the expedition were extensive but were mostly descriptive, relating to taxonomy and general natural history.

In this chapter the primary emphasis is on spatial scales of disturbances, and we will follow on from our earlier discussions on the mechanisms of competition and predation and the controversy over their importance in controlling species richness. Huston (1994) realized that the effects of competition, predation, and general physical disturbance were similar in that individuals were removed from the assemblage. We now show that there is a need to link these aspects with the tolerances of individual species, for example to determine in which of these cases the organisms are absent because the conditions now fall outside the optimal tolerance ranges. Thus we discuss disturbance as a general phenomenon which includes the effects of any processes that lead to a reduction in numbers of individuals and/or biomass. Disturbance includes physical disturbance as well as biological processes such as the effects of competition and predation on assemblages. The spatial scales covered range from micrometres to many hundreds of kilometres for the effects of bottom trawling, which is now considered to be one of the most serious and damaging threats to sediment habitats and assemblages. Disturbance effects caused by trawling and by pollution are considered in the following chapters. First, it is necessary to consider scale since many new insights have developed in the past few years of research. In the past couple of decades a new branch of ecology, landscape ecology, has developed, devoted to considering patterns over large areas, and a terminology of spatial scales has been defined. Grain is the first level of spatial resolution; it relates to the individual data unit and can be described as fine-grained to coarse-grained. Extent refers to the overall size of the study area. A map of 100 km2 and one of 100 000 km2 differ in extent by a factor of 1000. Grain and extent are illustrated in Fig. 6.1. A third component is lag, which is the betweensample distance. Figure 6.2 summarizes temporal and spatial scales of disturbances (modified from Zajac et al. 1998). The figure shows the main types of disturbances affecting soft-sediment systems, and separates them into natural and anthropogenic effects (see also Chapter 11, which indicates some of the management responses to these effects).