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Discontinuities in an organism's environment causing population fragmentation. Habitat fragmentation describes the emergence of discontinuities (fragmentation) in an organism's preferred environment (habitat), causing population fragmentation and ecosystem decay. Causes of habitat fragmentation include geological processes that slowly alter the layout of the physical environment (suspected of being one of the major causes of speciation

In scientific literature, there is some debate whether the term "habitat fragmentation" applies in cases of habitat loss, or whether the term primarily applies to the phenomenon of habitat being cut into smaller pieces without significant reduction in habitat area. Scientists who use the stricter definition of "habitat fragmentation" per se For example, From research the results show that the impact of deer herbivory on forest plant communities can be observed at the landscape level at the Rondeau Provincial park for the period of 1955 1978 After intensive clearing, the separate fragments tend to be very small islands isolated from each other by cropland, pasture, pavement, or even barren land. The latter is often the result of slash and burn farming in tropical forests. In the wheat belt of central western New South Wales, Australia, 90% of the native vegetation has been cleared and over 99% of the tall grass prairie of North America has been cleared, resulting in extreme habitat fragmentation.

There are two types of processes that can lead to habitat fragmentation. There are exogenous processes and endogenous processes. Endogenous is a process that develops as a part of species biology so they typically include changes in biology, behavior, and interactions within or between species. Endogenous threats can result in changes to breeding patterns or migration patterns and are often triggered by exogenous processes. Exogenous processes are independent of species biology and can include habitat degradation, habitat subdivision or habitat isolation. These processes can have a substantial impact on endogenous processes by fundamentally altering species behavior. Habitat subdivision or isolation can lead to changes in dispersal or movement of species including changes to seasonal migration. These changes can lead to a decrease in a density of species, increased competition or even increased predation.

One of the major ways that habitat fragmentation affects biodiversity is by reducing the amount of suitable habitat available for organisms. Habitat fragmentation often involves both habitat destruction and the subdivision of previously continuous habitat. Plants and other sessile organisms are disproportionately affected by some types of habitat fragmentation because they cannot respond quickly to the altered spatial configuration of the habitat. Habitat fragmentation consistently reduces biodiversity by 13 to 75% and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. This underscores the severe and lasting ecological impacts of fragmentation, which could be highlighted in the sections discussing the consequences of fragmentation. Habitat loss, which can occur through the process of habitat fragmentation, is considered to be the greatest threat to species. But, the effect of the configuration of habitat patches within the landscape, independent of the effect of the amount of habitat within the landscape (referred to as fragmentation per se), has been suggested to be small. A review of empirical studies found that, of the 381 reported significant effect of habitat fragmentation per se on species occurrences, abundances or diversity in the scientific literature, 76% were positive whereas 24% were negative. Despite these results, the scientific literature tends to emphasize negative effects more than positive effects. Positive effects of habitat fragmentation per se imply that several small patches of habitat can have higher conservation value than a single large patch of equivalent size. Area is the primary determinant of the number of species in a fragment and the relative contributions of demographic and genetic processes to the risk of global population extinction depend on habitat configuration, stochastic environmental variation and species features. Minor fluctuations in climate, resources, or other factors that would be unremarkable and quickly corrected in large populations can be catastrophic in small, isolated populations. Thus fragmentation of habitat is an important cause of species extinction. Additionally, habitat fragmentation leads to edge effects. Microclimatic changes in light, temperature, and wind can alter the ecology around the fragment, and in the interior and exterior portions of the fragment. Fires become more likely in the area as humidity drops and temperature and wind levels rise. Exotic and pest species may establish themselves easily in such disturbed environments, and the proximity of domestic animals often upsets the natural ecology. Also, habitat along the edge of a fragment has a different climate and favours different species from the interior habitat. Small fragments are therefore unfavourable for species that require interior habitat. The percentage preservation of contiguous habitats is closely related to both genetic and species biodiversity preservation. Generally a 10% remnant contiguous habitat will result in a 50% biodiversity loss. Much of the remaining terrestrial wildlife habitat in many third world countries has experienced fragmentation through the development of urban expansion such as roads interfering with habitat loss. Aquatic species’ habitats have been fragmented by dams and water diversions. These fragments of habitat may not be large or connected enough to support species that need a large territory where they can find mates and food. The loss and fragmentation of habitats makes it difficult for migratory species to find places to rest and feed along their migration routes. The existence of viable habitat is critical to the survival of any species, and in many cases, the fragmentation of any remaining habitat can lead to difficult decisions for conservation biologists. Given a limited amount of resources available for conservation is it preferable to protect the existing isolated patches of habitat or to buy back land to get the largest possible contiguous piece of land. In rare cases, a conservation reliant species may gain some measure of disease protection by being distributed in isolated habitats, and when controlled for overall habitat loss some studies have shown a positive relationship between species richness and fragmentation; this phenomenon has been called the habitat amount hypothesis, though the validity of this claim has been disputed. The ongoing debate of what size fragments are most relevant for conservation is often referred to as SLOSS (Single Large or Several Small). Habitat loss in a biodiversity hotspot can result in a localized extinction crisis, generally speaking habitat loss in a hotspot location can be a good indicator or predictor of the number of threatened and extinct endemic species. One solution to the problem of habitat fragmentation is to link the fragments by preserving or planting corridors of native vegetation. In some cases, a bridge or underpass may be enough to join two fragments. This has the potential to mitigate the problem of isolation but not the loss of interior habitat. Wildlife corridors can help animals to move and occupy new areas when food sources or other natural resources are lacking in their core habitat, and animals can find new mates in neighbouring regions so that genetic diversity can increase. Species that relocate seasonally can do so more safely and effectively when it does not interfere with human development barriers. Due to the continuous expansion of urban landscapes, current research is looking at green roofs being possible vectors of habitat corridors. A recent study has found that green roofs are beneficial in connecting the habitats of arthropods, specifically bees and weevils. Another mitigation measure is the enlargement of small remnants to increase the amount of interior habitat. This may be impractical since developed land is often more expensive and could require significant time and effort to restore. The best solution is generally dependent on the particular species or ecosystem that is being considered. More mobile species, like most birds, do not need connected habitat while some smaller animals, like rodents, may be more exposed to predation in open land. These questions generally fall under the headings of metapopulations island biogeography.

As the remaining habitat patches are smaller, they tend to support smaller populations of fewer species. Small populations are at an increased risk of a variety of genetic consequences that influence their long term survival. Remnant populations often contain only a subset of the genetic diversity found in the previously continuous habitat. In these cases, processes that act upon underlying genetic diversity, such as adaptation, have a smaller pool of fitness maintaining alleles to survive in the face of environmental change. However, in some scenarios, where subsets of genetic diversity are partitioned among multiple habitat fragments, almost all original genetic diversity can be maintained despite each individual fragment displaying a reduced subset of diversity.

Gene flow occurs when individuals of the same species exchange genetic information through reproduction. Populations can maintain genetic diversity through migration. When a habitat becomes fragmented and reduced in area, gene flow and migration are typically reduced. Fewer individuals will migrate into the remaining fragments, and small disconnected populations that may have once been part of a single large population will become reproductively isolated. Scientific evidence that gene flow is reduced due to fragmentation depends on the study species. While trees that have long range pollination and dispersal mechanisms may not experience reduced gene flow following fragmentation, most species are at risk of reduced gene flow following habitat fragmentation. Inbreeding depression is associated with conservation risks, like local extinction.

Small populations are more susceptible to genetic drift. Genetic drift is random changes to the genetic makeup of populations and leads to reductions in genetic diversity. The smaller the population is, the more likely genetic drift will be a driving force of evolution rather than natural selection. Because genetic drift is a random process, it does not allow species to become more adapted to their environment. Habitat fragmentation is associated with increases to genetic drift in small populations which can have negative consequences for the genetic diversity of the populations.

In order for populations to evolve in response to natural selection, they must be large enough that natural selection is a stronger evolutionary force than genetic drift. Recent studies on the impacts of habitat fragmentation on adaptation in some plant species have suggested that organisms in fragmented landscapes may be able to adapt to fragmentation. However, there are also many cases where fragmentation reduces adaptation capacity because of small population size.

Habitat fragmentation due to anthropogenic activities has been shown to greatly affect the predator prey dynamics of many species by altering the number of species and the members of those species. The way in which fragmentation changes and re shapes these interactions can occur in many different forms. Most prey species have patches of land that are a refuge from their predators, allowing them the safety to reproduce and raise their young. Human introduced structures such as roads and pipelines alter these areas by facilitating predator activity in these refuges, increasing predator prey overlap. These features have allowed their natural predators, the wolf, and the black bear to more efficiently travel over landscapes and between patches of land. Occasionally it is used as a threat signal to signify an impending attack on territory. A large song repertoire can enhance a male's ability to survive and reproduce as he has a greater ability to defend his territory from other males, and a larger number of males in the species means a larger variety of songs being transmitted. Although there are some species which are able to survive these kinds of harsh conditions, such as, cutting down wood in the forests for pulp and paper industries, there are animals which can survive this change but some that cannot. An example includes, varying aquatic insects are able to identify appropriate ponds to lay their eggs with the aid of polarized light to guide them, however, due to ecosystem modifications caused by humans they are led onto artificial structures which emit artificial light which are induced by dry asphalt dry roads for an example.

While habitat fragmentation is often associated with its effects on large plant and animal populations and biodiversity, due to the interconnectedness of ecosystems there are also significant effects that it has on the microbiota of an environment. Increased fragmentation has been linked to reduced populations and diversity of fungi responsible for decomposition, as well as the insects they are host to. This has been linked to simplified food webs in highly fragmented areas compared to old growth forests. Furthermore, edge effects have been shown to result in significantly varied microenvironments compared to interior forest due to variations in light availability, presence of wind, changes in precipitation, and overall moisture content of leaf litter. These microenvironments are often not conducive to overall forest health as they enable generalist species to thrive at the expense of specialists that depend on specific environments. For example, the mutualistic relationship between Mesogyne insignis and Megachile. A study has found greater pollination and increased fruit production of M. insignis in unfragmented forests verses fragmented forests. As for an example of an antagonistic relationship of nest predation, a study found that there is no increase in nest predation on fragmented forests thus not supporting the edge effect hypothesis.

Habitat fragmentation has profound effects on ecosystem services, impacting nutrient retention, species richness, and local biophysical conditions. Fragmentation mediated processes cause generalizable responses at the population, community, and ecosystem levels, resulting in decreased nutrient retention. Furthermore, habitat fragmentation alters relationships between biodiversity and ecosystem functioning across multiple scales, affecting both the local loss of biodiversity and the local loss of function. Moreover, fragmentation can change the microclimate at both local and regional scales, influencing biodiversity through interactions with anthropogenic climate change. Overall, habitat fragmentation significantly disrupts ecosystem services by altering nutrient retention, biodiversity, and ecosystem functioning at various spatial and temporal scales.

Two approaches are typically used to understand habitat fragmentation and its ecological impacts.

The species oriented approach focuses specifically on individual species and how they each respond to their environment and habitat changes with in it. This approach can be limited because it does only focus on individual species and does not allow for a broad view of the impacts of habitat fragmentation across species.

The pattern oriented approach is based on land cover and its patterning in correlation with species occurrences. One model of study for landscape patterning is the patch matrix corridor model developed by Richard Forman The pattern oriented approach focuses on land cover defined by human means and activities. This model has stemmed from island biogeography and tries to infer causal relationships between the defined landscapes and the occurrence of species or groups of species within them. The approach has limitations in its collective assumptions across species or landscapes which may not account for variations amongst them.

The other model is the variegation model. Variegated landscapes retain much of their natural vegetation but are intermixed with gradients of modified habitat This model of habitat fragmentation typically applies to landscapes that are modified by agriculture. In contrast to the fragmentation model that is denoted by isolated patches of habitat surrounded by unsuitable landscape environments, the variegation model applies to landscapes modified by agriculture where small patches of habitat remain near the remnant original habitat. In between these patches are a matrix of grassland that is often modified versions of the original habitat. These areas do not present as much of a barrier to native species.