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Coffee plantations are divided primarily into shade and sun coffee plantations. Shade plantations are then divided mainly into traditional or rustic plantations. In rustic plantations, the natural rainforest overstory is left and coffee bushes are planted beneath it. In traditional plantations, the coffee bushes are grown beneath a layer of cultivated trees such as Inga (Inga spp), Gliricidia (Gliricidia spp), banana, mango, avocado trees, and other various tree species. In sun coffee plantations, the coffee bushes are generally grown without any form of overtopping vegetation. Rustic shade coffee plantations primarily consist of the pine-oak forests, lowland moist tropical forests, and pre-montane tropical forests found through Latin America. These rustic areas are often fragmented by deforestation and exist in small acreages. Despite being more natural, they may not contain their preexisting biodiversity . In these cases, traditional coffee plantations may offer the next best option for animals.

Although incomparable in diversity to remaining forest fragments, both forms of shade coffee plantations harbor more species, particularly of birds, than sun coffee plantations. Shade coffee plantations have been shown to support migratory and resident species of birds better than agricultural sun coffee plantations. Shade coffee plantations also support some endemic, migratory and resident bird species as well or better than natural forests. This difference in bird populations may be due to the presence of a canopy in a shade plantation rather than the lack of canopy in a sun plantation, and the heavier use of insecticides in sun coffee planations . Coffee plantations planted under a natural (also called “rustic”) canopy seem to contain higher numbers of frugivorous or omnivorous species . In a study in Guatemala, birds were found more often in the canopy layer than in the coffee layer in a shade plantation. Along with containing a higher number of bird species, shade coffee plantations tend to contain more insects, plants, and mammals as well .

One study by Wunderle and Latta showed that some species of birds use, and may prefer, sun plantations while others prefer shade plantations. Shade plantations, however, may be more vital because they contain bird species that are threatened by habitat loss. Sun plantations are preferred by species that are more generalist and are more able to adapt to habitat that has been altered by human activity. Given the rarity of the birds that prefer shade plantations to sun plantations, they are more in danger from coffee modernization.

In another study located in Chiapas, Mexico, rustic and traditional plantations were found to have comparable bird abundances, indicating that traditional and rustic coffee plantations may be of similar usefulness to birds. Overall, shade plantations support not both a high number of bird species as well as high bird densities. The plantations provide food for many types of birds, including frugivores, insectivores, nectarivores, and omnivores. The plantations in this study may not be similar to all shade coffee plantations, however. In the shade plantations studied, the canopy was not heavily trimmed as some shade plantations are. Not all plantations may contain epiphytes, which are important to birds of the genus Euphonia.

Studies also show that rustic shade plantations support different food preferences among birds than traditional shade plantations. In Chiapas, rustic plantations seemed to support more specialized feeders than traditional plantations. Rustic plantations had higher abundances of frugivores, insectivores, and omnivores living in the canopy layer, while traditional plantations only had abundant canopy insectivores and omnivores. The traditional coffee plantations had high overall numbers of nectarivores, while the rustic plantations had abundant frugivore species. Another study in Guatemala found that traditional plantations, particularly one with an Inga spp overstory, had a high prevalence of nectarivorous hummingbirds and Icterid birds.

Shade coffee plantations provide important wintering habitat to temperate and neotropical migratory birds. Many of these birds are potentially endangered, and the coffee plantations coincide with their wintering grounds. If these habitats are converted to modern coffee farming methods, then it will place more pressure upon the already endangered migrants. As well as providing habitat for endangered or threatened birds, the plantations provide some refuge to some endangered animals as well.

Some organizations are starting to become aware of the effects of shade coffee on birds and are working towards more sustainable coffee. There are at least two existing coffee certification programs that work towards promoting shade coffee. The Smithsonian Migratory Bird Center awards a Bird Friendly® certification to coffee plantations. Plantations that are certified as both organic and shade coffee are considered Bird Friendly®. The Smithsonian Migratory Bird Center uses three levels to encourage sustainable coffee. The SMBC works to help importers find Bird Friendly® certified farms. The SMBC also helps roasters find the original coffee farms and the coffee importers that are certified. Lastly, the SMBC works to help coffee drinkers find roasters locally and online. The Rainforest Alliance also certifies coffee farms. Coffee purchasers can find beans that are marked Rainforest Alliance Certified^TM that are from traditional coffee farms. By buying certified coffee beans, then consumers are buying shade grown coffee that will protect wildlife, and may also support small farmers.