Agricultural production is expanding at rapid rates in the tropics. As a consequence, most tropical forests exist as fragments embedded within a mosaic of agricultural land (Perfecto and Vandermeer 2008). Organisms that inhabit these landscapes must be able to persist within agricultural lands or navigate through them to reach habitable patches (Levins 1969). Therefore, the development of successful conservation strategies requires an understanding of the effect of agricultural production and intensification on population persistence. Agricultural intensification is the transition from traditional production systems (e.g., crop rotation, polycultures) to systems with industrial management practices (e.g., monocultures, use of agrochemicals) (Perfecto et al. 2009). For example, coffee production in Latin America falls along an intensification gradient ranging from rustic polyculture to unshaded monocultures (Moguel and Toledo 1999; Fig. 1a). This has made coffee production a model system for studies of the effects of agricultural intensification on biodiversity. Studies in coffee agroecosystems have shown a decrease in biodiversity as agricultural management intensity increases for many species, such as ants, birds, trees, bees, and bats (Perfecto and Vandermeer 2015). Less is known about the effects that management practices have on the dispersal and gene flow of species in this system.
Recently, with the development of new molecular techniques, indirect measures of dispersal can be used for studies of population connectivity (Manel et al. 2003). Gene flow can decrease with fragmentation, generating population structure within a species and increasing the impact of genetic drift (Frankel and Soulé 1981). With genetic measurements, we can evaluate the negative effects of land use change and fragmentation (e.g., loss of genetic diversity, increased differentiation) (Manel et al. 2003).
This study aims to increase our knowledge about the historical response of tropical terrestrial small mammals to agricultural intensification and forest fragmentation in a coffee agroecosystem. As common members of the animal community, small mammals play important ecological roles (Lidicker 1975), but may be negatively affected by human-driven landscape modifications (Gibson et al. 2013). Heteromys desmarestianus goldmani, a common rodent in southern Mexico, is known to prefer forested environments (Fleming 1983), and consuming and/or dispersing a variety of seeds in tropical forests (Martinez-Gallardo and Sanchez-Cordero 1993). This species, a yearlong breeder (Fleming 1983), has a home range of approximately 100 m2. This is a small home range when compared to other groups of small mammals such as Peromyscus spp., with home ranges averaging 2000 m2 (Scheibe 1984).
We studied the effect of different coffee management practices on the population genetic structure of H. d. goldmani with the goal of addressing the following questions. Can H. d. goldmani persist in a coffee agricultural matrix? If so, what is the nature of the population structure and does it vary between coffee farms and a forest fragment? Because H. d. goldmani is a forest specialist, we expect the species to be present in the forest fragment and within coffee farms that are either close to forest edges or within a coffee matrix of high quality (e.g., low management intensity). Additionally, we expect individuals within the forest fragment to show higher connectivity (i.e., less subpopulation genetic differentiation), than those found within the coffee farms.