Diversity 2013, 5, 657-679; doi:10.3390/d5030657 OPEN ACCESS diversity ISSN 1424-2818 www.mdpi.com/journal/diversity Article Genetic Diversity of Black Salamanders (Aneides flavipunctatus) across Watersheds in the Klamath Mountains Sean B. Reilly 1,*, Mitchell F. Mulks 2, Jason M. Reilly 3, W. Bryan Jennings 4, and David B. Wake 1 1 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA 94720-3160, USA; E-Mail:
[email protected] 2 Department of Ecology and Evolutionary Biology, University of California, 1156 High Street, Santa Cruz, CA 95064, USA; E-Mail:
[email protected] 3 Bureau of Land Management, Medford Interagency Office, Medford, OR 97504, USA; E-Mail:
[email protected] 4 Museu Nacional, Departamento de Vertebrados, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, RJ 20940-040, Brazil; E-Mail:
[email protected] * Author to whom correspondence should be addressed; E-Mail:
[email protected]; Tel.: +1-510-642-3567; Fax: +1-510-643-8238. Received: 31 May 2013; in revised form: 2 August 2013 / Accepted: 8 August 2013 / Published: 29 August 2013 Abstract: Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prior ecological results, which suggest that Black Salamanders avoid high elevations such as the ridges that separate watersheds. Our mitochondrial results revealed two major lineages, one in the Sacramento River watershed, and another containing the Klamath, Smith, and Rogue River watersheds.