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Reconciliation ecology is the science of accommodating wild species within human-modified or -occupied landscapes. It holds that protecting wilderness, though necessary, is not enough to preserve biodiversity given the large area required for a diverse range of species to survive in the long term. It acknowledges the overwhelming impact anthropogenic change has had on most natural habitats, and seeks to modify human habitats to make them more hospitable to a wide variety of species, allowing humans and wild species to share the same ranges. It takes steps to preserve species diversity in a rapidly-changing world facing a mass extinction the likes of which has rarely been seen in Earth's history. Because the earth has already been modified so dramatically, reconciliation ecology seeks to re-modify the landscape in a manner designed to accommodate species and ecosystem conservation alongside other human needs. It has applications for disappearing ecosystems (for example, by maintaining natural disturbance regimes and creating wetlands and backyard habitats), and for disappearing species (for example, by creating appropriate nestboxes for birds or ponds for toads). Furthermore, it suggests how management practices on landscapes primarily used for production or human habitation might be modified to better accommodate species and ecosystem needs (for example, in agriculture, encouraging a natural suite of pollinators, applying integrated pest management, and maintaining important resources for cattle and bird species). The concept has been popularized by the ecologist Michael Rosenzweig in his book Win-Win Ecology.

Human Domination of Ecosystems
Human alteration of the planet is widespread and severe: no ecosystem is free of human influence, and humans transform landscapes through various processes including agriculture, residential and commercial development, and resource extraction including grazing, timbering, and mining. Estimates of human domination of the ice-free, terrestrial landscape range from 40% to 95%, depending on one’s definition of ‘dominated’ in terms of alteration of species composition and ecosystem processes. Humans also modify ocean habitats: a large percentage of the human population lives on a coast, coastal wetland destruction is common and nutrient input and unsustainable fisheries modify ocean food webs and productivity. Even biogeochemical cycles are altered: humans have modified the carbon cycle by releasing substantial quantities of CO2 and other gases into the atmosphere through fossil fuel combustion and other industrial and agricultural processes, the nitrogen cycle is manipulated through the intentional and unintentional fixation of N2 into terrestrial systems by fertilizer inputs and industrial emissions, historical water flows have been dammed and diverted as a result of humans using more than half the world's fresh water, and humans also represent the largest planetary source for atmospheric sulfur, heavy metals, synthetic organic chemicals (including insecticides and CFCs ), and other toxins. Loss of biodiversity is occurring at an extraordinary rates: human activity is culpable for vastly accelerating rates of species extinctions by perhaps 100 to 1000 times over natural background levels, and this may be even faster for certain groups. Humans can drive species to extinction through habitat destruction, as well as overharvesting or direct competition for space or resources. Humans have also facilitated unprecedented rates of species movement to areas where they had never historically occurred, causing harmful species invasions such that invading species are present almost everywhere, and many of these invasions are chronic and irreversible. Many of these factors are additive or multiplicative, making it clear that human domination of the planet, through habitation or activities, has created a universal rapidly changing environment. With so much of the earth's surface occupied and/or altered, reconciliation ecology can provide guidance on maximizing species diversity in these landscapes.

Foundations in Ecological Theory
Reconciliation ecology is guided by, and can help contribute to, some of the big questions in ecological theory.

Species-Area Relationships
How can human domination of increasing amount of land area impact species persistence, and what can be done to mitigate these impacts? Frank Preston developed the idea of species-area relationships, which is the relationship between the area of a habitat and the number of species found within that area. He divided this relationship into two types: contiguous or mainland species-area relationships, and discontiguous or island species-area relationships. MacArthur and Wilson further developed the idea of discontiguous species-area relationships (SPARs) with their paper on island biogeography that seeks to explain patterns of species richness. They showed that immigration and extinction rates can explain species richness on islands and on archipelagos. SPARs are governed by the power function $$S = cA^z$$ where S is the number of species, A is area, c is a constant (number of species in the smallest sampling area) and z is the slope of the species area relationship in log-log space. Island or discontiguous SPARs are based on the equation S=A^0.3, but species-area relationships for very large contiguous areas—those including different biogeographic provinces or continents—behave differently from species-area relationships for islands or smaller contiguous areas. These interprovincial SPARs are governed by the equation S=A. SPARs help ecologists realize that the small areas humans often set aside for other species are too small to protect many of these species indefinitely. In order to maintain many such species, immigrants from a source area with a healthy population of the species would be required. (see Source–sink dynamics) These source populations do not exist in areas where the entire matrix is developed. The interprovincial SPAR equation, which is the appropriate one to use for many human-dominated landscapes, reveals that the % of species preserved in a steady state is equal to the % preserved land. Thus, saving 20% of Earth's surface, a generous estimate for the amount of land likely to be conserved or restored, will save only 20% of wild species without the use of reconciliation ecology on the remaining 80%. The first species to be lost are often endemics, species restricted to specialized habitats that cannot persist elsewhere, when these specialist habitats are completely destroyed. Sink species restricted to habitats in which deaths outweigh births are often lost rapidly as well. Especially without source habitats, and with the human-dominated matrix often preventing immigration from those sources that remain, populations within nature reserves face increasing future threats from demographic stochasticity, climate change-induced changes in habitat, and new parasites and diseases. Since the area of most natural reserves is so small, speciation rate will be depressed and losses will not be replaced. Thus, using reserves alone, most species alive today would be doomed to extinction. To counter this trend, reconciliation ecology emphasizes efforts to functionally increase the area available to species, allowing for their persistence. This might be achieved by targeting matrix habitat immediately adjacent to existing reserves and improving habitat structure and function in human landscapes as much as possible. Some ecological models that incorporate the quality of the surrounding matrix and edge effects into species-area predictions suggest that improvements in matrix quality and reduction of edge effect severity can allow additional species to persist in core reserved habitats. These results allow for optimism that additional species can be conserved with the use of reconciliation ecology, aiding managers in making conservation decisions under the new reconciliation ecology paradigm.

Community Ecology
What processes govern how many species can persist in the same habitat, and how can habitats therefore be managed to promote species diversity? Reconciliation ecology has to understand and contribute to community ecology in order to save multiple species in the same habitat. Plots of local (alpha) vs. regional (gamma) species diversities generally results in a straight line, leading some ecologists to believe that species in a local area are random assemblies from a regional pool, which could mean that an understanding of species interactions may not be of paramount importance for explaining diversity patterns. However, research has shown that species distributions are usually determined by SPARs, abiotic factors, species interactions, and niche theory. Also, it is possible that competition from other species is currently excluding many species from areas in which they could otherwise persist; observing current species distributions does not reveal these effects, which are often evident only after competitors are removed. Reconciliation ecology must determine what variables are responsible for niche division in an ecosystem in order to create a habitat in which different species and guilds can persist. This typically requires preservation of heterogeneity of resources, spatial habitat variation, and processes that vary over time. However, it can be difficult to ascertain how to make a new environment hospitable to native species, especially as species may not have achieved their optimal phenotype in human environments. Also, the small size of reserves and limitations on what can be accomplished in the surrounding matrix can make habitat management challenging. Nevertheless, increasing habitat heterogeneity has proved successful in some instances; for instance, building artificial oyster reefs in the Chesapeake Bay have proven effective at bolstering struggling native oyster populations. Finally, an understanding of the degree to which top-down versus bottom-up effects regulate the species of interest can be important for reconciliation ecology and can be informed by reconciliation efforts. For example, experiments in oil palm plantations can measure the impacts of insectivorous birds on the health of oil palms to determine how strong their effect is, and see whether insect populations are controlled by bottom-up productivity or by top-down predation. These findings would suggest strategies to conserve as many insect and bird species as possible while maximizing oil palm production.

Beyond Natural History
How can understanding of species' natural history aid their effective conservation in human-dominated ecosystems? Humans often conduct activities that allow for the incorporation of other species, whether as a byproduct or as a result of a focus on nature. Traditional natural history can only inform how best to do this to a certain degree, because landscapes have been changed so dramatically. However, there is much more to learn through direct study of species' ecology in human-dominated ecosystems, through what is known as focused natural history. Rosenzweig cites four examples: shrikes (Laniidae) thrived in altered landscapes when wooden fence post perches allowed them easy access to pouncing on prey, but inhospitable steel fence posts contributed to their decline. Replacing steel fenceposts with wood fenceposts reverses the shrikes' decline and allows humans to determine the reasons for the distribution and abundance of shrikes. Additionally, cirl bunting (Emberiza cirlus) thrived on farms when fields alternated between harvests and hay, but declined where farmers began to plant winter grain crops, natterjack toads (Bufo calamatus) declined when reductions in sheep grazing ceased to alter ponds to their preferred shape and depth, and longleaf pine (Pinus palustris) declined in the southeastern United States when lack of wildfires prevented its return after timbering. Thus, applying focused natural history in human-dominated landscapes can contribute to conservation efforts.

Existence in Fragmented and Degraded Landscapes
How can the detrimental effects of habitat fragmentation on species best be mitigated? Fragmentation and urbanization of landscapes are known to contribute to losses in native species diversity and the persistence of invasive species. However, urbanization is occurring at an unstoppable rate, and it is thus critical to understand how populations of native species can be maintained in this landscape. Studies of butterfly richness in forest reserves, vegetation fragments, and urban parks have shown that connectedness between fragments and similarity of anthropogenic habitats to natural forested ones are the most factors important in determining the survival of forest-dependent butterfly populations. In order for reconciliation ecology to be effective, urban parks should contain a diversity of host plants (in order to maintain coevolutionary relationships) and should be as close as possible to a forest in order to maximize conservation value. Future research must focus on more detailed strategies to maintain diversity in urban landscapes.

Urban Management Techniques
Of all human habitats, urban habitats are the most sharply distinct from natural habitats because they have undergone dramatic changes in resource availability, stress intensity, and disturbance regimes from human impacts. Despite the apparent novelty of urban habitats, they can often represent analogues to natural habitats, although their colonization by native species may be limited by barriers to dispersal or environmental factors. An example of a habitat analogue is a stone wall that resembles a natural cliff, which can be colonized by the once-endangered peregrine falcon, or an urban soil resembling a rock-based ecosystem, where cyanobacterial crusts are responsible for primary productivity. However, in either of these cases, the analogous habitat is located patchily within a novel ecosystem, making immigration unlikely. This means that urban habitats have similar species-area relationships to islands. In order to create urban habitat sufficiently analogous to natural habitats with potential value for biodiversity, it may be necessary to alter microhabitat conditions in order to reduce habitat homogenization. Many urban features can be managed or altered to support several species, particularly if colonization is facilitated. For instance, creating green roofs in Switzerland and the U.K. resulted in the roofs being colonized by endangered orchid and spider species, and drilling holes in quarry faces supports climbing vegetation. Mammal species such as foxes and bats can be supported by increasing connectivity between suitable habitats. Urban systems can also minimize impact on native species by maintaining open spaces in neighborhood planning, by replacing impervious surfaces with porous pavements, green roofs, and infiltration basins, and by including natural features such as wetlands or prairies. All of these measures have the added positive effect of increasing contact and accessibility between people and biodiversity that may help improve attitudes toward conservation, as well as increasing human health and well-being.

Oil Palm Harvests
The oil palm (Elaeis guineensis) is one of the most important and rapidly expanding tropical crops, so lucrative because it is used in many diverse products throughout the world. Unfortunately, oil-palm agriculture is one of the main drivers of forest conversion in southeast Asia and is devastating for native biodiversity, perhaps even more so than logging. However, attempts are being made to foster the sustainability of this industry. As a monoculture, oil palm is subject to potentially devastating attacks from insect pests. Many companies are attempting an integrated pest management approach which encourages the planting of species that support predators and parasitoids of these insect pests, as well as an active native bird community. Experiments have shown that a functioning bird community, especially at higher densities, can serve to reduce insect herbivory on oil palms, promoting increased crop yields and profits. Thus, oil palm plantation managers can participate in reconciliation ecology by promoting local vegetation that is beneficial to insectivorous birds, including maintaining ground plants that serve as nesting sites, thereby protecting natural communities. Additionally, steps such as maintaining riparian buffer zones or natural forest patches can help to slow the loss of biodiversity within oil palm plantation landscapes. By engaging in these environmentally-friendly practices, fewer chemicals and less effort are required to maintain both plantation productivity and ecosystem services.

Agro-environmental schemes
Agro-environment schemes can mitigate agricultural impacts and protect biodiversity, while maintaining products and profit. In agroforestry systems, trees or shrubs are intentionally used within agricultural systems, or non-timber forest products are cultured in forest settings. For instance, agroforestry can integrate trees and shrubs with crops or livestock, allowing for the protection of native tree species and/or other native species that benefit from their presence. Agroforestry with crops or cattle under shade trees can protect many forest species, and maintenance of older trees with higher basal area benefits the ecosystem the most, helping to protect and improve soil conditions. Cocoa or coffee plantations have the greatest benefit to native biodiversity when they include reintroduced native tree species, including medicinal and edible plants which may also give financial benefit to indigenous farmers. The understory can also be managed with reconciliation ecology: allowing weeds to grow among crops (minimizing labor and preventing the invasion of noxious weed species) and leaving fallowlands alongside farmed areas can enhance understory plant richness with associated benefits for native insects and birds compared to other agricultural practices. Additionally, where additional forest land must be converted to agriculture, strategically selecting land that has low levels of native understory diversity can help to minimize impacts. Fortunately, in at least some landscapes, native plant diversity may be lowest where overall ecosystem productivity is highest, due to the phenomenon of good competitors being able to outcompete other co-occurring species in favorable conditions.

Freshwater Conservation
Freshwater makes up only 0.01% of water on Earth, yet supports 6% of all species. This natural resource is being affected more strongly by human activities than even terrestrial systems, threatening biodiversity. Freshwater species face six main threats: global environmental change (nitrogen deposition, global warming , etc), overexploitation (predominantly of vertebrate species), water pollution (toxins, nutrients, other chemicals) , flow modification (levees, water storage, dams) , habitat destruction and degradation, and invasive species. Declining water quality negatively impacts human populations as well: clean water that is not contaminated with toxins or diseases is needed for agriculture, drinking, and transport. Using reconciliation ecology to mimic or restore natural flow regimes is critical for maintenance of human populations as well as biodiversity. For example, structures such as fish ladders reconcile migrating diadromous fishes with river flow modifications (e.g. dams). Although little work has been done on freshwater reconciliation ecology, a new movement called Integrated Water Resources Management seeks to reconcile the needs of humans and freshwater ecosystems through holistic management.