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Previous work found that tree turnover, biomass, and large liana densities increased in mature tropical forests in the late 20th century, indicating a concerted shift in forest ecological processes. However, the findings have proved controversial. Here, regional-scale patterns of tree turnover are characterized, using improved datasets available for Amazonia that span the last twenty-five years. The main findings include: trees at least 10 cm in diameter recruit and die twice as fast on the richer soils of western Amazonia compared to trees on the poorer soils of eastern Amazonia; turnover rates have increased throughout Amazonia over the last two decades; mortality and recruitment rates have tended to increase in every region and environmental zone; recruitment rates consistently exceed mortality rates; and increases in recruitment and mortality rates are greatest in western Amazonia. These patterns and trends are not caused by obvious artefacts in the data or the analyses, and cannot be directly driven by a mortality driver such as increased drought because the biomass in these forests has simultaneously increased. Apparently, therefore, widespread environmental changes are stimulating the growth and productivity of Amazon forests.

Salt marshes dominate the intertidal zone in temperate latitudes and present some unique features pertaining to measurement of primary production. Several destructive harvest and non-destructive methods for quantifying salt marsh production are described. Allometric methods that account for stem turnover are the recommended approach. Field and laboratory procedures illustrating the recommended protocol are detailed using examples from LTER sites.

Although there is a common perception that deserts support few species, some deserts have high local diversity, largely because organisms are able to exploit patches of high productivity. This chapter differentiates between local species richness (also called α diversity), β diversity, which is also known as species turnover or the change in species among sites, and γ diversity, which is regional species diversity. Productivity-diversity relationships have been well studied in some deserts and have helped us understand the factors controlling ecosystem function at a large spatial scale. Studies of convergence of desert communities and consideration of the similarity of desert communities with neighbouring mesic communities are some of the best elucidated of this genre. The chapter also considers the major differences and similarities among desert taxa in the various deserts of the world, to draw inferences on the major biogeographic patterns.

This chapter discusses the colonization and extinction events and species turnover. It shows how, in the face of ongoing colonization and extinction events, cumulative species numbers on islands increase while the number of residents at any one time remains nearly constant. The chapter also examines the parameters that affect species turnover and cumulative species counts. Species turnover can be measured within islands over time, and also between islands over space. The chapter also discusses the distance decay phenomenon, which means that nearby islands may share more plant species than islands which are far apart, and that species turnover may increase with the distance between the islands being compared.

Measurements of daily energy expenditure and water turnover showed that energy expenditure in cheetahs was not significantly greater than expected, but water turnover was low. There were no sex differences in daily energy expenditure, but when hunting along riverbeds cheetahs used more energy than when hunting in the dunes, probably because they moved further in the riverbeds. There were no differences in daily energy expenditure between females in different stages of reproduction. Energy expended chasing prey differed; small prey being least costly and large species most costly. Analyses of prey chases using both GPS and accelerometer loggers revealed that there were two phases; an initial rapid acceleration to catch up with the prey, followed by a slowing phase as cheetahs followed twists and turns of the prey as the distance between them closed. A visualization of five phases recorded from accelerometer data during a successful steenbok hunt is presented.

Urban development modifies natural habitats by replacing their fundamental components with new ones, causing a loss of biodiversity. However, we know little about urbanization effects on birds in tropical areas of the world. We studied the bird communities of forest habitats and in the city of Morelia, in a region of western Mexico. Bird-species richness was negatively related to urbanization, while bird abundance was positively related to it. Richness was also positively related to tree foliage and herbaceous cover and negatively affected by human activity. Bird abundances were positively related to building and herbaceous height. Although we did not find significant relationships between bird diversity and income, residential areas with the highest bird-species richness corresponded to high-income areas.

Species are units for understanding the evolution of diversity over large geographical scales and long timescales. This chapter investigates the processes causing proliferation and demise of species diversity within lineages and regions. Phylogenetic approaches have focused on documenting speciation and extinction rates, but mechanistic theory explaining variation in rates is scarce. Diversity patterns are better explained by geographical and ecological opportunity than by correlates of speciation and extinction rates per se. The neutral theory of biodiversity provides a framework that can be adapted to predict diversity patterns in terms of limits due to competition for space and resources, and species turnover (which cannot be detected directly from phylogenetic trees). These theories bring macroevolutionary and microevolutionary theories closer together. In particular, diversity patterns are the outcome of individual selection and dispersal playing out over long timescales. Some of the processes influencing species patterns can also structure diversity at higher taxonomic levels.

This chapter examines how phylogenetic diversity changes across spatial and temporal gradients. Spatial ecophylogenetic patterns can reveal how different processes shape ecological communities. Metacommunity ecology reinvigorated the search for general mechanisms that create diversity and structural differences among communities, and by using phylogenetic patterns we can understand how shared traits and evolution inform community differences. The chapter first considers phylobetadiversity as a measure of phylogenetic turnover before discussing two types of phylobetadiversity metrics, diversity partitioning and pairwise distances. It also analyzes the influence of spatial scale on phylogenetic patterns, focusing on the scale dependency of phylogenetic patterns, and concludes with an overview of phylogenetic diversity–area relationships.

This chapter focuses on the aerobic oxidation of organic material by microbes. Microbes account for about 50 per cent of primary production in the biosphere, but they probably account for more than 50 per cent of organic material oxidization and respiration (oxygen use). The traditional role of microbes is to degrade organic material and to release plant nutrients such as phosphate and ammonium as well as carbon dioxide. Microbes are responsible for about half of soil respiration while size fractionation experiments show that bacteria are responsible for about half of respiration in aquatic habitats. In soils, both fungi and bacteria are important, with relative abundances and activity varying with soil type. In contrast, fungi are not common in the oceans and lakes, where they are out-competed by bacteria with their small cell size. Dead organic material – detritus – used by microbes comes from dead plants and waste products from herbivores. This, and associated microbes, can be eaten by many eukaryotic organisms, forming a detritus food web. These large organisms also break up detritus to small pieces, creating more surface area on which microbes can act. Microbes in turn need to use extracellular enzymes to hydrolyze large molecular weight compounds, which releases small compounds that can be transported into cells. Photochemical reactions are also important in the degradation of certain compounds. Some compounds are very difficult to degrade and are thousands of years old.

A topic extensively debated is whether sciences that focus on historical entities are somehow fundamentally different from those sciences that are not concerned with the history of the entities they study. This duality has been treated when authors have discussed the difference between contingent and nomothetic approaches, between historical and functional approaches, and between pattern and process based approaches The history of thought on these concepts will be considered here, with special emphasis placed on writings in macroevolutionary theory and phylogenetics. A central focus will be documenting how these “dualities” should not be viewed as truly distinct. Furthermore, it is argued that repeated analysis of contingent histories is the key to discovering the nomothetic principles that exist in the history of life. This is in fact a central tenet of the hierarchical view of evolution.

Modern macroevolutionary theory can be viewed as an expansion of the Modern Synthesis involving the interpretation of patterns and processes above the organizational level of organisms packaged in local populations, including modes and processes of speciation and the emergence and development of clades. New interpretations of the fossil record (punctuated equilibria, species selection, regional and global mass extinctions and recoveries) are the empirical and conceptual building blocks in this theoretical expansion. But as in most microevolutionary thinking, macroevolutionary theory has rarely placed ecologic processes on equal footing with evolutionary processes: ecology is seen as the stage, backdrop or product of adaptive evolution; all the important action actually involves evolutionary transformations. Several new movements in macroevolutionary theory (Turnover Pulse Hypothesis, Coordinated Stasis, the Sloshing Bucket Model), however, require attention to be focused on patterns of stability and reorganization/replacement of large ecologic systems in order to understand patterns of evolutionary stasis and turnover (invasion/abandonment, extinction, bouts of adaptive speciation) recorded in the fossil record. Connecting macroevolutionary patterns to macroecologic dynamics (the Theory of Macroevolutionary Consonance) could lead on to discovery of further conceptual connections and a more complete explication of large-scale patterns in the history of life.

This chapter examines ecosystem changes through time and the processes that control these changes. Metacommunity theory predicts many of the spatial and temporal patterns of taxa in regional ecosystems and can be useful for inferring processes of structure and turnover if properly scaled to the fossil record. The fossil record provides a unique perspective that must be reconciled with ecological perspectives. The integration of metacommunity theory with an analysis of environmental distributions of taxa and taxonomic turnover in regional ecosystems, based on a sequence stratigraphic framework, is ripe for future work. Integrating properly scaled metacommunity models with the fossil record should provide a better synthesis of how ecosystems change. Stratigraphic paleobiology will play a key role in this synthesis by providing the data needed to test model predictions.

The aerobic oxidation of organic material by microbes is the focus of this chapter. Microbes account for about 50% of primary production in the biosphere, but they probably account for more than 50% of organic material oxidization and respiration (oxygen use). The traditional role of microbes is to degrade organic material and to release plant nutrients such as phosphate and ammonium as well as carbon dioxide. Microbes are responsible for more than half of soil respiration, while size fractionation experiments show that bacteria are also responsible for about half of respiration in aquatic habitats. In soils, both fungi and bacteria are important, with relative abundances and activity varying with soil type. In contrast, fungi are not common in the oceans and lakes, where they are out-competed by bacteria with their small cell size. Dead organic material, detritus, used by microbes, comes from dead plants and waste products from herbivores. It and associated microbes can be eaten by many eukaryotic organisms, forming a detritus food web. These large organisms also break up detritus into small pieces, creating more surface area on which microbes can act. Microbes in turn need to use extracellular enzymes to hydrolyze large molecular weight compounds, which releases small compounds that can be transported into cells. Fungi and bacteria use a different mechanism, “oxidative decomposition,” to degrade lignin. Organic compounds that are otherwise easily degraded (“labile”) may resist decomposition if absorbed to surfaces or surrounded by refractory organic material. Addition of labile compounds can stimulate or “prime” the degradation of other organic material. Microbes also produce organic compounds, some eventually resisting degradation for thousands of years, and contributing substantially to soil organic material in terrestrial environments and dissolved organic material in aquatic ones. The relationship between community diversity and a biochemical process depends on the metabolic redundancy among members of the microbial community. This redundancy may provide “ecological insurance” and ensure the continuation of key biogeochemical processes when environmental conditions change.