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

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Abstract

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.

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Acknowledgements

We thank Melanie Bucci, Dave Dalton, Sherry Daugherty, Heatherlee Leary, Kara O’Brien, and Chelsey Trejo for field assistance; Suzanne Wilcox and Cristina Francois (Appleton-Whittell Research Ranch of the National Audubon Society) and Ami Pate, Danny Martin, Helen Fitting, and Jessica Garcia (National Park Service) for logistical support; Bob Behrstock, Karen LeMay, Scott Richardson, and Cecil and Carol Schwalbe for hosting capturing sessions at their homes; Christina Brown, Jamison Carey, Adam Leon, and Arielle de la Cruz for collecting fecal samples; Caroline Plecki, Nicolas Katz, and David Woods for assistance with data collection; Elizabeth Bowman, Alison Harrington, Nicole Colón-Carrión, and Shuzo Oita for laboratory support; and Barbara Fransway, Stacy Sotak, and Taylor Edwards of the University of Arizona Genetics Core for guidance in the laboratory. We are grateful to an anonymous reviewer for constructive feedback that helped to improve our manuscript.

Funding

We are grateful for financial support from the National Park Service’s Southwest Border Resource Protection Program, and from the School of Natural Resources and the Environment and School of Plant Sciences at the University of Arizona.

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Authors and Affiliations

  1. School of Natural Resources and the Environment, The University of Arizona, Tucson, AZ, USA

    John-Lee Sky Walker & Robert J. Steidl

  2. Bat Research and Consulting, Tucson, AZ, USA

    Sandy A. Wolf

  3. School of Plant Sciences, The University of Arizona, Tucson, AZ, USA

    Ming-Min Lee & A. Elizabeth Arnold

  4. Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA

    A. Elizabeth Arnold

  5. Bio5 Institute, The University of Arizona, Tucson, AZ, USA

    A. Elizabeth Arnold

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  1. John-Lee Sky Walker
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Contributions

RJS and AEA conceived of the study; JSW, RJS, AEA, and SAW collected samples; JSW and MML collected data; JSW and AEA analyzed data; JSW, AEA, and RJS wrote the manuscript, with input from all authors.

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Correspondence to A. Elizabeth Arnold.

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Walker, JL.S., Steidl, R.J., Wolf, S.A. et al. Improved amplification of fecal DNA supports non-invasive microsatellite genotyping of lesser long-nosed bats (Leptonycteris yerbabuenae). Conservation Genet Resour 16, 159–171 (2024). https://doi.org/10.1007/s12686-023-01344-0

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