Biological diversity should be viewed through the lens of genetic diversity, overall species diversity, and on a broader scale, ecosystem diversity. Small populations have very low genetic diversity, and have high probabilities of extinction. Ecologists use various types of population viability analyses to predict the probability of extinction. Field ecologists collect population data on survival of young and fecundity of females to construct life tables that help with making projections of future population growth. Immigration of individuals from nearby populations can maintain population viability and species diversity. Metapopulations are most viable when they are large and well-connected to numerous subpopulations, so they experience high immigration rates. Humans have caused the decline or extinction of many populations and species by degrading or destroying habitats, by fragmenting habitats, by overexploiting species, and indirectly by introducing non-native (invasive) species to a novel environment. Habitat destruction, habitat fragmentation, and direct exploitation of a naturally small population threaten the viability of the newly discovered Tapanuli orangutans.

Facilitative interactions include mutualisms, in which both species benefit, and commensalisms, in which only one species benefits and the second species is unaffected by the interaction. The commercially important pollination mutualism between honeybees and plants is under assault by a mysterious emerging disease, CCD. Mutualistic species play critical roles in biological communities, including coral and their algal symbionts that are the foundations of coral reef communities, and the mycorrhizal association between plant roots and their fungal symbionts that is essential for most plant communities. A facilitative interaction can benefit species either directly, or indirectly by its effect on another species. There is usually some cost to each mutualistic species; thus, mutualism is most likely to evolve if the benefits exceed the costs, and if each species can ensure that its mutualistic partner provides the appropriate benefit. Facilitation may be more common in stressful environments, where the benefits of facilitation are greater than they might be in more benign environments. Some facilitative interactions, such as the interaction between the great spotted cuckoo and the carrion crow, are beneficial under some conditions and detrimental under other conditions.

Using data from direct observations, experimental mesocosms, field experiments, and complex computer models, the IPCC has made a very strong case supporting the hypothesis that human behavior is leading to rapid and substantial climate change. One important anthropogenic effect is changes to the carbon cycle, primarily greater CO2 export into the atmosphere from industrial activity. In recent years, both oceans and terrestrial sources have taken up some of this excess CO2, but ocean uptake is particularly problematic, because it leads to acidification. There are many other important greenhouse gases that influence Earth’s surface temperatures, including methane, nitrous oxide, ozone, and a diverse group of halocarbons. Though less abundant, these gases have a much greater global warming potential than CO2, on a per molecule basis. Many effects of greenhouse gases on global climate are complex; for example, a particular halocarbon can increase and decrease surface temperatures via different mechanisms. There are many different types of climate models that use the movement of the atmosphere around Earth, and the interaction of the atmosphere with the oceans and with biological processes, to project future climate. Though there are quantitative differences between the projections of each model, these models all project a much warmer and wetter global climate over the next century, with northern latitudes experiencing the greatest impact of climate change.

The tremendous biological diversity of some plant communities may be a reflection of the variety of direct and indirect interactions that plants have with predators, competitors, and mutualists. Ecologists have several ways of measuring biological diversity; some diversity indices, such as the Shannon index, integrate species richness and evenness. Alpha diversity measures species richness within an area, beta diversity measures species turnover, while gamma diversity is the combined species richness of all communities under consideration. Biotic and abiotic factors can influence community diversity directly and indirectly. For example, in southwest Finland, host plant abundance directly and positively influenced lepidopteran species abundance. In the African savanna, herbivorous mammals indirectly and negatively affected bird diversity by consuming trees and reducing the abundance of insects that served as food for the birds. Abiotic factors influencing community diversity include the type of habitat, geological heterogeneity, nutrient levels, and the type and intensity of disturbance. Ecologists predict that diverse communities will be more stable than less diverse communities, but that the populations of species in diverse communities will be less stable.

The distribution and abundance of species is limited by the availability of nutrients and energy. Adding limiting nutrients to an ecosystem can increase the abundance of some species and may have far-reaching effects on ecosystem functioning. Conversion of light energy into chemical energy by photosynthesis is the primary method by which energy enters an ecosystem. Three different processes of carbon fixation have evolved: C3, C4, and CAM. Each process has costs and benefits that are environment-dependent, but scientists are still evaluating these. Heterotrophs get energy by consuming autotrophs and other heterotrophs. Herbivores, carnivores, omnivores, detritivores, and decomposers are the major classifications of heterotrophs and combined with autotrophs make up the organisms within a biological community. There are numerous morphological, physiological, and behavioral adaptations associated with each type of feeding. Species distribution is influenced by how the ratio of nutrients available to species affects their physiological and ecological processes. It is also influenced by the presence of predators and adaptations of prey species that reduce their probability of being eaten. Some defenses may be induced by the presence of predators.