Improved amplification of fecal DNA supports non-invasive microsatellite genotyping of lesser long-nosed bats (Leptonycteris yerbabuenae)

Feces of animals that forage on nectar and fruit, including many species of bats, often contain DNA that is low in quality and quantity. We developed an approach based on DNA from feces gathered passively to generate microsatellite data for individual lesser long-nosed bats (Leptonycteris yerbabuenae), which are important pollinators for columnar cacti and agave across much of Mexico and in the southwestern U.S. We collected feces from roosts near the U.S-Mexico border and developed a two-step amplification approach to characterize five highly polymorphic microsatellite loci from fecal DNA. Addition of a multiplex PCR step improved amplification success and conserved DNA extracts with a minimal increase in cost. In our initial screening of 433 samples, five focal loci distinguished individuals reliably, with a probability of identity (i.e., the probability of two unrelated individuals having the same microsatellite profile by chance) of 7.5E-09. Repeated analyses revealed a genotyping error rate < 2%. We explore the benefits and limits of our approach for population studies of lesser long-nosed bats and other nectivorous and frugivorous species that provide key ecosystem services and are often of conservation concern.