Effects of coffee agroecosystem management on the population structure and dispersal of a tropical forest rodent (Heteromys desmarestianus)

Background/Question/Methods

Land-use changes for agricultural production represent the majority of anthropogenic land transformations. The associated loss and fragmentation of natural habitat is considered the main driver of population declines and loss of biodiversity. Understanding the effect of agricultural matrix composition on dispersal of species is essential for the development of successful conservation plans. Our study uses genetic information to address dispersal in fragmented landscapes. We evaluate the genetic structure of a common forest rodent (Heteromys desmarestianus) in forest fragments surrounded by a coffee agricultural matrix in southern Mexico.  We sampled 165 individuals from one forest fragment and 3 coffee farms representing varying management intensity within an area of 10 km². Using microsatellite markers, we assessed the population structure of H. desmarestianusand the effect of management intensity on this genetic structure. We implemented Geneland, a Bayesian clustering program. 

Results/Conclusions

Five genetic clusters were found. One of these clusters included individuals from the forest fragment, low intensity coffee farm and individuals from medium and high intensity coffee farms adjacent to the forest fragment. A second cluster was composed of all other individuals from the medium intensity coffee farm. The individuals from the high intensity farm were assigned to the remaining three clusters, for many individuals we identified mixed cluster membership (i.e., similar probabilities of belonging to different clusters). These results suggest a higher degree of substructuring within the high intensity coffee farm.  We found little influence of isolation-by-distance in genetic structure and similar genetic differentiation between clusters (F_ST).  Together these findings suggest that the coffee agricultural matrix may be permeable enough to facilitate H. desmarestianus dispersal and gene flow, but that the degree of permeability varies with management intensity.