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Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers

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Abstract

Genetic data are increasingly being used in conservation planning for declining species. We sampled both the ecological and distributional limits of the foothill yellow-legged frog, Rana boylii to characterize mitochondrial DNA (mtDNA) variation in this declining, riverine amphibian. We evaluated 1525 base pairs (bp) of cytochrome b and ND2 fragments for 77 individuals from 34 localities using phylogenetic and population genetic analyses. We constructed gene trees using maximum likelihood and Bayesian inference, and quantified genetic variance (using AMOVA and partial Mantel tests) within and among hydrologic regions and river basins. Several moderately supported, geographically-cohesive mtDNA clades were recovered for R. boylii. While genetic variation was low among populations in the largest, most inclusive clade, samples from localities at the edges of the geographic range demonstrated substantial genetic divergence from each other and from more central populations. Hydrologic regions and river basins, which represent likely dispersal corridors for R. boylii, accounted for significant levels of genetic variation. These results suggest that both rivers and larger hydrologic and geographic regions should be used in conservation planning for R. boylii.

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Acknowledgments

We are indebted to M. Fujita, T. Engstrom, T. Near, D. Starkey, and J. Abramyan for their help with laboratory techniques and analyses, and the Shaffer Lab (University of California, Davis) for discussion and input on data analysis. L. Clark, D. Chester, A. Fesnock, K. Freel, P. Johnson, P. Kleeman, T. Murphey, G. Rotta, T. Sutfin, T. Tharalson, J. Uyehara, M. van Hattem, and S. Yarnell provided information on sampling localities and/or accompanied AJL in the field and helped with collecting. A. Borisenko, C. Rombough, M. Stephens, R. Grasso, K. Mathews, and L. Vance contributed tissue samples. Funding was provided by U.C. Davis Graduate Group in Ecology and U.C. Davis Center for Biosystematics (to AJL) and CALFED Bay-Delta Program, UC Davis Agricultural Experimental Station, and the NSF (#0817042) (to HBS). T. Beebee, S. Greco, and P. Moyle provided reviews and guidance on earlier drafts of this manuscript. Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.S. government.

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Authors and Affiliations

  1. Department of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA, 95616, USA

    Amy J. Lind, Phillip Q. Spinks & H. Bradley Shaffer

  2. USDA Forest Service, Pacific Southwest Research Station, Sierra Nevada Research Center, 1735 Research Park Drive, Davis, CA, 95618, USA

    Amy J. Lind

  3. U.S. Geological Survey, Western Ecological Research Center, Point Reyes National Seashore, Point Reyes, CA, 94956, USA

    Gary M. Fellers

  4. Center for Population Biology, University of California, One Shields Avenue, Davis, CA, 95616, USA

    H. Bradley Shaffer

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  1. Amy J. Lind
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Correspondence to Amy J. Lind.

Appendix

Appendix

See Table 5 and Fig. 3.

Table 5 Locality information for R. boylii and outgroup samples
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Lind, A.J., Spinks, P.Q., Fellers, G.M. et al. Rangewide phylogeography and landscape genetics of the Western U.S. endemic frog Rana boylii (Ranidae): implications for the conservation of frogs and rivers. Conserv Genet 12, 269–284 (2011). https://doi.org/10.1007/s10592-010-0138-0

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