Using genetics to reveal how coffee agriculture affects a forest dwelling rodent

Otero Jiménez B, Li K, Tucker PK. 2020. Landscape drivers of connectivity for a forest rodent in a coffee agroecosystem. Landsc Ecol. 35(5):1249–1261. doi:10.1007/s10980-020-00999-6. [accessed 2020 Jul 30].

Featured Image: Coffee grown in Chiapas Mexico, image by pxfuel

A patchwork of forests 

A growing concern for conservation biologists is how tropical forests are being replaced by human development. In many cases, this results in a patchwork of forest cover and varying levels of human development. This process can lead to loss of wildlife and also make it hard for species to move from one area to another. Agricultural land use is growing more abundant and interrupting many forest systems at a global scale. Because of this it is important to understand how agricultural landscapes can impact wildlife.

Conserving biodiversity in agriculturally productive landscapes 

Revealing what features of agriculture benefit and/or impact species is necessary for writing conservation plans that will ensure sustainable agriculture. This has led Dr. Beatriz Otero Jiménez to focus her research on disentangling the complex relationship of agricultural landscapes and the species that inhabit them. In particular, Dr. Otero Jiménez wanted to reveal which features of agricultural habitat function as barriers or conduits for species movement. Genetic analyses of DNA samples have become an important tool to answer that question. These analyses work by evaluating how similar the genes of individuals are in association to the type of landscapes that separate them. For example, you might find that individuals tend to have more genetic similarity in forested landscapes where animals can more freely move, than in landscapes where they are separated by pasture. Then you would contrast those values to what the genetic similarity would be when just explained by distance (that is the further away individuals are the less likely they are to be related). With this information,  it is possible to characterize the resistance of the landscape to genetic mixing (gene flow).

Preserving genetic diversity has become an important part of conservation plans. Animals that cannot move through their habitat will tend to have less gene flow. This means that for a given area the relatedness of individuals will be high. This can result in the accumulation of bad genetic mutations which can slowly make species more vulnerable to extinction. 

Coffee plantations & biodiversity 

Traditionally agricultural practices are viewed in direct opposition to biodiversity conservation. However, by studying how agricultural landscapes specifically impact species, policy can be redirected towards more sustainable agricultural practices. In her study, Dr. Otero Jiménez evaluated different agricultural practices for coffee plantations in the montane region of Soconusco in Chiapas, Mexico. These coffee farms vary in intensity of departure from natural forest cover. The low intensity coffee farms have native shade trees and understory trees. Medium intensity farms typically are commercial polyculture (grow several species of plants) along with coffee. High intensity coffee farms typically have trees that are heavily pruned to increase sun exposure to the coffee and often use synthetic fertilizers, herbicides and pesticides (Figure 1).  

Figure 1: Panel a shows the management intensity of coffee plantations. More intense plantations have fewer trees and tend to use synthetic fertilizers and pesticides. Panel b shows the location of the study sites in the montante region of Chiapas, Mexico. (Figure from Otero Jiménez et al 2020)

Our small protagonist 

Dr. Otero Jiménez and her team studied the small rodent Goldman’s spiny pocket mouse (Heteromys desmarestianus goldmanii). This rodent lives in Mexico and Guatemala and is an important seed disperser in forest habitats. For their study, the scientists trapped rodents along coffee plantations (Figure 2) and collected DNA samples from ear tissue.

Figure 2: Sampling sites for the small rodent. Top panel shows roads and trails colored in red and the bottom panel shows streams colored in blue. In both panels forest areas are colored in green, and farm management intensity in shades of grey with lighter shading corresponding to increasing management intensity.  (Figure from Otero Jiménez et al., 2020)

Is the forest on the other side just as green? 

Dr. Otero Jiménez and her team found some interesting insights about how coffee plantations affected the small rodent. Surprisingly, slope and not forest cover was one of the most important variables associated with gene flow. Even more surprising, intermediate slopes were better conduits for gene flow than completely flat slopes. Perhaps because flat slopes were dominated by coffee plantations and tended to have less forest cover. Similarly, intermediate forest cover (50%-75%) were better bridges to genetic mixing for the species. With these results, Dr. Otero Jiménez and her team show the importance of maintaining tree cover in farms (especially native tree cover) since the trees can allow movement through these developed landscapes. Having these natural corridors will allow the species to maintain a healthy genetic mixing and avoid increasing relatedness. On the other hand, high intensity sun coffee farms negatively affect this species. If no natural corridors are available to the rodent this could impact their ability to move to other areas and lead to inbreeding. Hopefully these results can be applied by local conservation planners to shifts towards more sustainable coffee farm practices. 

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Kevin Aviles Rodriguez

I am in the process of completing my PhD in Ecology and Evolutionary Biology at the University of Massachusetts in Boston. I am interested in human environmental changes as natural experiments to test hypothesis about the evolution of animals. Specifically, I study small lizards known as anoles and how living near human households impacts their ecology and behavior. I love fieldwork because often it takes me away from the cold and towards the sunny beachy islands that I love the most.

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