Rodent Population Connectivity in Coffee Agroecosystems

Abstract

Humans have been modifying the Earth’s land surface for millennia. In the last 300 years these changes have increase in intensity and spatial extent. In tropical regions these anthropogenic changes are dominated by the expansion of agriculture. This has led the majority of remaining tropical forests to exist as fragments embedded in a matrix of agricultural production. This production varies in type and diversity of crops and management practices, through which organisms must navigating through or surviving within the matrix. For this reason, understanding the effects of these agricultural landscapes on species dispersal is crucial in the development of successful conservation planning. The purpose of this dissertation was to explore the effects of varying coffee production management practices on the population structure and connectivity of tropical rodents. This study was conducted in the coffee growing region of Soconusco and the El Triunfo Biosphere Reserve in Chiapas, Mexico. We used genetic and landscape data to study the population structure and connectivity of two common rodent species, Heteromys desmarestianus goldmani and Peromysucs gymnotis, in this landscape. We found that levels of population connectivity and genetic diversity vary between the two sampled species, which is supported by their differences in ecological specialization. Heteromys in the coffee farms were characterized by subtle genetic structure, which correlates with high management intensity coffee production and high genetic diversity. On the other hand, P. gymnotis individuals showed no signal of population structure and lower degrees of genetic diversity. When comparing H. d. goldmani populations from the continuous forest (El Triunfo Biosphere Reserve) and the coffee production region we found similar levels of genetic diversity, suggesting that high levels of migration and gene flow can be maintained in the coffee agroecosystem. This study highlights the potential of integrating molecular and landscape data to explore population connectivity of elusive species, such as terrestrial small mammals. It also shows the importance of studying the responses to environmental change for species with different levels of ecological specialization within a group, since these responses can vary. Additionally, it identifies coffee production as an important refuge for rodent species within anthropogenic landscapes. This work adds to the growing body of literature in landscape genetics by demonstrating that rodents can show population structure at small scales and that this structure can be driven by landscape factors linked to agricultural management.