Predicting genetic biodiversity in salamanders using geographic, climatic, and life history traits

68. Hijmans RJ. raster: Geographic data analysis and modeling. R package version 3.6–26. 2016. https:// cran.r-project.org/web/packages/raster/index.html. 69. Keitt KH, Bivand R. rgdal: Bindings for the Geospatial Data Abstraction Library. R package version 0.2– 5. 2017. https://cran.r-project.org/package=rgdal. 70. Hijmans RJ, Karney C, Williams E, Vennes C. Geosphere: Spherical trigonometry. R package version 1.5–5. 2016. https://cran.r-project.org/package=geosphere. 71. Wickham H. 2011. The Split-Apply-Combine Strategy for Data Analysis. Journal of Statistical Software 40. 72. van Buuren S, Groothuis-Oudshoorn K. 2011. mice: Multivariate Imputation by Chained Equations in R. Journal of Statistical Software 45. 73. Kuhn M. 2008. Building Predictive Models in R Using the caret Package. Journal of Statistical Soft- ware 28. 74. Keesey M. PhyloPic. https://www.phylopic.org. 75. Taiyun Wei, Viliam Simko. 2021. R package ‘corrplot’: Visualization of a Correlation Matrix. (Version 0.92). 76. Hillis DM. 2019. Species Delimitation in Herpetology. Journal of Herpetology 53: 3. 77. Gostel MR, Kress WJ. 2022. The Expanding Role of DNA Barcodes: Indispensable Tools for Ecology, Evolution, and Conservation. Diversity 14: 213. 78. Yiming L, Siqi W, Chaoyuan C, Jiaqi Z, Supen W, Xianglei H, et al. 2021. Latitudinal gradients in genetic diversity and natural selection at a highly adaptive gene in terrestrial mammals. Ecography 44: 206–218. 79. Darrel FR. 2024. Amphibian Species of the World: an Online Reference. Version 6.2 (December 2023).

Electronic Database accessible at https://amphibiansoftheworld.amnh.org/index.php. American Museum of Natural History, New York, USA. 80. Luo A, Ling C, Ho SYW, Zhu C. 2018. Comparison of Methods for Molecular Species Delimitation Across a Range of Speciation Scenarios. Systematic Biology 67: 830–846. https://doi.org/10.1093/ sysbio/syy011 PMID: 29462495 81. Denton RD, Morales AE, Gibbs HL. 2018. Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two ancestral sexual species. Evolution. 72: 1689–1700. PMID: 29926914 82. Liedtke HC, Wiens JJ, Gomez-Mestre I. 2022. The evolution of reproductive modes and life cycles in amphibians. Nature Communications 13: 7039. https://doi.org/10.1038/s41467-022-34474-4 PMID: 36396632 83. Wiens JJ. 2015. Explaining large-scale patterns of vertebrate diversity. Biology Letters 11: 20150506. https://doi.org/10.1098/rsbl.2015.0506 PMID: 26202428 84. Lourenc¸o A, Gonc¸alves J, Carvalho F, Wang IJ, Velo-Anto´ n G. 2019. Comparative landscape genetics reveals the evolution of viviparity reduces genetic connectivity in fire salamanders. Molecular Ecology 28: 4573–4591. https://doi.org/10.1111/mec.15249 PMID: 31541595 85. Burbrink FT, Sara Ruane S. 2021. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. Ichthyology & Herpetology 109: 874–894. 86. Kozak KH, Wiens JJ. 2010. Accelerated rates of climatic-niche evolution underlie rapid species diversifi- cation: Niche evolution and rapid diversification. Ecology Letters 13: 1378–1389.

87. Kuhn M, Johnson K. 2013. Applied Predictive Modeling. New York, NY: Springer New York. 88. Foster J. Provost, Tom Fawcett, Ron Kohavi. 1998. The Case against Accuracy Estimation for Compar- ing Induction Algorithms. Machine learning: proceedings of the fifteenth international conference, Madison, Wisconsin, July 24–27, 1998. San Francisco, Calif: Morgan Kaufmann. 89. Gurevitch J, Koricheva J, Nakagawa S, Stewart G. 2018. Meta-analysis and the science of research synthesis. Nature 555: 175–182. https://doi.org/10.1038/nature25753 PMID: 29517004 90. Wu¨ est RO, Zimmermann NE, Zurell D, Alexander JM, Fritz SA, Hof C, et al. 2020. Macroecology in the age of Big Data–Where to go from here? Journal of Biogeography 47: 1–12. 91. Heberling JM, Miller JT, Noesgaard D, Weingart SB, Schigel D. 2021. Data integration enables global biodiversity synthesis. Proceedings of the National Academy of Sciences 118: e2018093118. https:// doi.org/10.1073/pnas.2018093118 PMID: 33526679 92. Colella JP, Stephens RB, Campbell ML, Kohli BA, Parsons DJ, Mclean BS. 2021. The Open-Specimen Movement. BioScience 71: 405–414. 93. Hardisty AR, Ellwood ER, Nelson G, Zimkus B, Buschbom J, Addink W, et al. 2022. Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet. BioScience 72: 978–987. https://doi.org/10.1093/biosci/biac060 PMID: 36196222 PLOS ONE Predicting hidden lineages in salamanders PLOS ONE | https://doi.org/10.1371/journal.pone.0310932 October 18, 2024 20 / 20