Ecology, the study of interactions among organisms and their surroundings, can be approached on multiple scales ranging from the organism to the biosphere (Fig. 1), with unique processes governing interactions and dynamics at each scale. Individual organisms interact with their environment in many ways, including feeding, movement, and respiration. Populations are groups of individuals of a single species living in a local area, and population ecology relates to the dynamics of population size, density, and demographic structure. Communities consist of the populations living and interacting in an area; community ecologists study interactions within communities and their effects on the abundance, diversity, and distribution of species and populations. Ecosystems consist of communities of organisms plus their chemical and physical environment, and ecosystems are typically studied in terms of the movement of energy and nutrients among organisms and the environment. The biosphere encompasses all ecosystems (Fig. 1).

Changes in nutrient cycles and energy fluxes (i.e., ecosystem dynamics) likely drove numerous trends and disruptions in the history of life. Advances in geochemistry offer great insights into paleoecosystem function, as does an understanding of the biogeochemical roles played by ancient organisms. A theoretical ecospace that describes the chemical exchanges between organisms and their environments is presented. Previous descriptions of ecospace principally described spatial and physical aspects of ecology; the new ecospace description broadens the concept to encompass a wider range of ecological processes that control abundance and diversity of fossil organisms. Organisms require materials from the environment for generating energy and building tissues, and these factors are broken down, ultimately specifying particular substances acquired from the environment. Different organisms require specific substances in different amounts depending on factors such as physiology, environmental conditions, etc.; thus, physiological ecospace describes an organism's sensitivity to ecosystem/earth system perturbations and trends. Several examples relating to organisms' requirements for skeletal minerals are reviewed, and a new analysis of extinction selectivity related to ocean acidification is presented. Selective extinction of heavily calcified metazoa is demonstrated to have occurred at least eight times during the Phanerozoic, including the early Cambrian, Frasnian (Late Devonian), and Aptian (Early Cretaceous). Multidimensional structure of ecospace occupation (e.g., correlations among ecological traits) strongly controls the effects of an extinction such that the same kill mechanism applied at different times will affect the ecological composition of the biosphere in a variety of ways.

Energy and nutrients are the fundamental currencies of ecology and changes in energy and nutrient availability are thought to have played an important role in the long-term development of marine ecosystems. However, meaningfully quantifying when, where, and how such changes have occurred has been a difficult and longstanding problem. Here, some of the various lines of evidence that have been brought to bear on this issue in the past two decades are reviewed, particularly those based on the fossil record of benthic invertebrates. This paper focuses on abundance, body size, and metabolism, three distinct but closely interrelated aspects of ecosystem structure that control (or are controlled by) energy fluxes. Each of these is subject to biases and inherent uncertainties that present significant challenges for making inferences from the fossil record, but when carefully controlling for environmental, taphonomic, and methodological variations there are robust trends that can be discerned above the noise. Integrating these different types of data in a single quantitative framework presents additional complications, but coherent patterns emerge from some such analyses. Accurate quantification of energetic trends in the fossil record is difficult but is a worthwhile goal because of its potential to illuminate the energetic dimension of major diversifications, extinctions, and secular ecological-evolutionary trends and link them more directly to their Earth Systems context.

Stromatolite shapes, sizes, and spacings are products of microbial processes and interactions with topography, sedimentation, and flow. Laboratory experiments and studies of modern microbial mats and sediments can help reconstruct processes that shaped some typical stromatolite forms and some atypical microbially influenced sediments from Neoproterozoic cap carbonates. Studies of modern, cohesive microbial mats indicate that microbialaminite facies in the lower Rasthof Formation (Cryogenian) formed in the presence of very low flow and were not deformed by strong waves or currents. Giant wave ripples, corrugated stromatolites, and tube-hosting stromatolites in basal Ediacaran cap carbonates record interactions between microbes, flow, and evolving bedforms. Preferential cementation in and close to the giant ripple crests is attributed to interactions between flow and local topography. These interactions pumped alkaline porewaters into ripple crests and helped nucleate elongated stromatolites. The similar textures of giant wave ripples and elongated, corrugated, and tube-hosting stromatolites suggest growth in the presence of organic-rich, rounded particles and microbial mats, and in flow regimes that permitted mat growth. These hypotheses can be tested by experiments and models that investigate lithification and the macroscopic morphology of microbial mats as a function of the flow regime, preexisting topography, redox-stratification in sediments, and delivery of organic-rich particles. The widespread microbially influenced textures in Cryogenian microbialaminites and basal Ediacaran cap dolostones record a strong reliance of carbonate deposition on the presence of organic nuclei, supporting carbonate accumulation rates comparable to those in modern reefs. Therefore, the unusual macroscopic morphologies of microbially influenced facies in Neoproterozoic cap carbonates may not reflect oceans that were greatly oversaturated with respect to carbonate minerals.

Not all organisms have an equal chance of entering the fossil record. Previo—us attempts to quantify this percentage suggest that for megascopic marine organisms (megafauna), ∼30% would be predicted to leave no identifiable fossils. Here, that exercise is repeated for marine macrofauna, for which ∼80% are predicted to leave no identifiable fossils. The percentage will be far higher for meiofauna, the numerically most dominant marine animals. The organisms which are often most abundant in marine sediments, such as small polychaetes and nematodes, have essentially no fossil record. Yet such organisms are ecologically important in the modern oceans, and almost certainly were in ancient environments as well, so it is useful to consider the roles they play in different ecosystems. Insight into the evolution and paleoecology of these groups can be gained by using molecular divergence estimates to infer temporal origins combined with modern distributional and ecological data. As a case study, this approach is applied to the small and soft-bodied early animal fauna living under low levels of atmospheric oxygen that likely characterized the Precambrian.

The Big Five mass-extinction events are characterized by dramatic changes in primary producers. Initial disturbance to primary producers is usually followed by a succession of pioneers that represent qualitative and quantitative changes in standing crops of land plants and/or phytoplankton. On land, a transient collapse of arborescent (tree-bearing) vegetation and the rapid spread of a pioneer vegetation dominated by ferns and fern allies characterizes the Permian/Triassic (P/T), Triassic/Jurassic (T/J), and Cretaceous/Paleogene (K/Pg) mass-extinction events. The availability of low-quality food, such as herbaceous low-growing plants, likely played a role in triggering secondary extinctions of herbivores (reptiles, insects). Furthermore, malformation of acritarchs, pollen, and spores during the end-Ordovician, end-Devonian, P/T and T/J extinctions also suggests primary producers were of lesser quality. More importantly, changes in vegetation drove important increases in weathering and erosion leading to elevated nutrient transfer from the continents to the oceans. In the marine realm, the end-Ordovician, end-Devonian, end-Permian, and end-Triassic extinction events are all followed by periods of high primary production, which is reflected in the widespread deposition of black shales. Due to their small size, low nutritional quality, and possible toxicity, the abundance of picoplankton, such as prasinophytes, acritarchs, as well as bacterioplankton (cyanobacteria and green sulfur bacteria) may have been additional factors in delaying ecosystem recovery.

Mass extinctions shape the history of life and can be used to inform understanding of the current biodiversity crisis. In this paper, a general introduction is provided to the methods used to investigate the ecosystem effects of mass extinctions (Part I) and to explore major patterns and outstanding research questions in the field (Part II). The five largest mass extinctions of the Phanerozoic had profoundly different effects on the structure and function of ecosystems, although the causes of these differences are currently unclear. Outstanding questions and knowledge gaps are identified that need to be addressed if the fossil record is to be used as a means of informing the dynamics of future biodiversity loss and ecosystem change.

Leaf-compression fossils with insect feeding traces are unique in providing rich, direct evidence of two levels in a fossil food web. Plant-insect associations dominate terrestrial trophic interactions, emphasizing the need to understand their ecological and evolutionary history. This paper first discusses methods of recognizing insect herbivore damage on fossil leaves and quantifying fossil insect herbivory. By conducting an unbiased insect damage census, damage frequency (percent of leaves with insect feeding damage), percent of leaf surface area removed by insects, and damage diversity (the number of discrete damage morphotypes, or DTs, found on a fossil flora or individual host plant) can all be measured. Three examples of responses of past plant-insect trophic interactions to environmental stresses are examined. In the first case study, late Oligocene fossil floras from Ethiopia document forest response to local perturbation and key characteristics to recognize disturbance in the plant fossil record. The second case study considers the terrestrial ecosystem response to the catastrophic global perturbation at the Cretaceous–Paleogene boundary. In the third case study, the impact of past global warming events—including the Paleocene–Eocene Thermal Maximum—on insect herbivory is discussed. Productive avenues for further research include: insect damage studies conducted outside the North American Cretaceous and Paleogene, actualistic and taphonomic studies of insect herbivory, and tighter collaboration across paleobotany, paleoentomology, botany, and entomology.

Mathematical models of fluid flow thorough plant stems permit quantitative assessment of plant ecology using anatomy alone, allowing extinct and extant plants to be measured against one another. Through this process, a series of patterns and observations about plant ecology and evolution can be made. First, many plants evolved high rates of water transport through the evolution of a diverse suite of anatomical adaptations over the last four hundred million years. Second, adaptations to increase hydraulic supply to leaves tend to precede, in evolutionary time, adaptations to increase the safety margin of plant water transport. Third, anatomical breakthroughs in water transport function tend to occur in step with ecological breakthroughs, including the appearance of leaves during the Devonian, the evolution of high leaf areas in early seed plants during the Carboniferous, and the early radiation of flowering plants during the Cretaceous. Quantitative assessment of plant function not only opens up the plant fossil record to ecological comparison, but also provides data that can be used to model fluxes and dynamics of past ecosystems that are rooted in individual plant anatomy.