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Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20382-20387. doi: 10.1073/pnas.1908289116. Epub 2019 Sep 23.

Cryptic diversity of a widespread global pathogen reveals expanded threats to amphibian conservation.

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Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720.
Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720.
Department of Biology, San Francisco State University, San Francisco, CA 94132.
Department of Pathology, Bacteriology and Avian Diseases, Ghent University, 9820 Merelbeke, Belgium.
Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington DC 20560.
Department of Herpetology, California Academy of Sciences, San Francisco, CA 94118.
Florida Museum of Natural History, University of Florida, Gainesville, FL 32601.
Department of Biology, University of Massachusetts Boston, Boston, MA 02125.
Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Cientificas (CSIC), 28006 Madrid, Spain.
Research Unit of Biodiversity, CSIC-Universidad de Oviedo-Gobierno del Principado de Asturias, E-33600 Mieres, Spain.
Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106.
University of Kansas Biodiversity Institute, University of Kansas, Lawrence, KS 66045.
Department of Ecology and Evolution, University of Kansas, Lawrence, KS 66045.
Department of Biological Sciences, Florida International University, Miami, FL 33199.
School of Environment and Sciences, Griffith University, Gold Coast, QLD 4215, Australia.
Department of Evolution and Ecology, University of California, Davis, CA 95616.
School of Life Sciences, University of Nevada, Las Vegas, NV 89154.
Department of Oceanography, University of Hawai'i at Manoa, Honolulu, HI 96822.
Institute of Parasitology, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic.
Sierra Nevada Aquatic Research Laboratory, University of California, Mammoth Lakes, CA 93546.
Department of Biodiversity Conservation, El Colegio de la Frontera Sur, San Cristobal de las Casas, Chiapas 29290, México.
Department of Ecology and Evolution, University of Arizona, Tucson, AZ 85721.
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260.
Environmental Sciences Graduate Program, Oregon State University, Corvallis, OR 97331.
Unidad de Genómica Avanzada (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato CP36824, México.
Reptile, Amphibian and Fish Conservation, 6525 ED Nijmegen, The Netherlands.
Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, Hanoi, Vietnam.
Department of Biology, University of Nevada, Reno, NV 89557.
One Health Research Group, The University of Melbourne, Werribee, VIC 3030, Australia.
College of Forestry, Southwest Forestry University, Kunming 650224, Yunnan, China.
Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720;


Biodiversity loss is one major outcome of human-mediated ecosystem disturbance. One way that humans have triggered wildlife declines is by transporting disease-causing agents to remote areas of the world. Amphibians have been hit particularly hard by disease due in part to a globally distributed pathogenic chytrid fungus (Batrachochytrium dendrobatidis [Bd]). Prior research has revealed important insights into the biology and distribution of Bd; however, there are still many outstanding questions in this system. Although we know that there are multiple divergent lineages of Bd that differ in pathogenicity, we know little about how these lineages are distributed around the world and where lineages may be coming into contact. Here, we implement a custom genotyping method for a global set of Bd samples. This method is optimized to amplify and sequence degraded DNA from noninvasive skin swab samples. We describe a divergent lineage of Bd, which we call BdASIA3, that appears to be widespread in Southeast Asia. This lineage co-occurs with the global panzootic lineage (BdGPL) in multiple localities. Additionally, we shed light on the global distribution of BdGPL and highlight the expanded range of another lineage, BdCAPE. Finally, we argue that more monitoring needs to take place where Bd lineages are coming into contact and where we know little about Bd lineage diversity. Monitoring need not use expensive or difficult field techniques but can use archived swab samples to further explore the history-and predict the future impacts-of this devastating pathogen.


Batrachochytrium dendrobatidis; amphibian; conservation; genetic monitoring

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