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

22. Blanchet S, Prunier JG, De Kort H. 2017. Time to Go Bigger: Emerging Patterns in Macrogenetics. Trends in Genetics 33: 579–580. https://doi.org/10.1016/j.tig.2017.06.007 PMID: 28720482 23. Leigh DM, van Rees CB, Millette KL, Breed MF, Schmidt C, Bertola LD, et al. 2021. Opportunities and challenges of macrogenetic studies. Nature Reviews Genetics 22: 791–807. https://doi.org/10.1038/ s41576-021-00394-0 PMID: 34408318 24. Miraldo A, Li S, Borregaard MK, Flo´rez-Rodrı´guez A, Gopalakrishnan S, Rizvanovic M, et al. 2016. An Anthropocene map of genetic diversity. Science 353: 1532–1535. https://doi.org/10.1126/science. aaf4381 PMID: 27708102 25. Millette KL, Fugère V, Debyser C, Greiner A, Chain FJJ, Gonzalez A. 2020. No consistent effects of humans on animal genetic diversity worldwide (A Mooers, Ed.). Ecology Letters 23: 55–67. 26. Carstens BC, Morales AE, Field K, Pelletier TA. 2018. A global analysis of bats using automated com- parative phylogeography uncovers a surprising impact of Pleistocene glaciation. Journal of Biogeogra- phy 45: 1795–1805. 27. Baranzelli MC, Cosacov A, Sede SM, Nicola MV, Se´ rsic AN. 2022. Anthropocene refugia in Patagonia: A macrogenetic approach to safeguarding the biodiversity of flowering plants. Biological Conservation 268: 109492. 28. Gratton P, Marta S, Bocksberger G, Winter M, Keil P, Trucchi E, et al. 2017. Which Latitudinal Gradients for Genetic Diversity? Trends in Ecology & Evolution 32: 724–726. https://doi.org/10.1016/j.tree.2017. 07.007 PMID: 28807398

29. Pelletier TA, Carstens BC. 2018. Geographical range size and latitude predict population genetic struc- ture in a global survey. Biology Letters 14: 20170566. https://doi.org/10.1098/rsbl.2017.0566 PMID: 29343561 30. Barrow LN, Fonseca EM, Thompson CEP, Carstens BC. 2021. Predicting amphibian intraspecific genetic diversity with machine learning: Challenges and prospects for integrating traits, geography, and genetic data, Molecular Ecology Resources 21: 2718–2831. 31. Fonseca EM, Pelletier TA, Decker SK, Parsons DJ, Carstens BC. 2023. Pleistocene glaciations caused the latitudinal gradient of within-species genetic diversity, Evolution Letters 7: 331–338. https://doi.org/ 10.1093/evlett/qrad030 PMID: 37829497 32. Pelletier TA, Carstens BC, Tank DC, Sullivan J, Espı´ndola A. 2018. Predicting plant conservation priori- ties on a global scale. Proceedings of the National Academy of Sciences 115: 13027–13032. https:// doi.org/10.1073/pnas.1804098115 PMID: 30509998 33. Raposo MA, Kirwan GM, Lourenc¸o ACC, Sobral G, Bockmann FA, Stopiglia R. 2021. On the notions of taxonomic ‘impediment’, ‘gap’, ‘inflation’ and ‘anarchy’, and their effects on the field of conservation. Systematics and Biodiversity 19: 296–311. 34. Breiman L. 2001. Random Forests. Machine Learning 45: 5–32. 35. Parsons DJ, Pelletier TA, Wieringa JG, Duckett DJ, Bryan C. Carstens. 2022. Analysis of biodiversity data suggests that mammal species are hidden in predictable places. Proceedings of the National Academy of Sciences 119: e2103400119. https://doi.org/10.1073/pnas.2103400119 PMID: 35344422

36. Smith BT, Seeholzer GF, Harvey MG, Cuervo AM, Brumfield RT. 2017. A latitudinal phylogeographic diversity gradient in birds. PLOS Biology 15: e1002610. 37. Amador L, Arroyo-Torres I, Lisa N. Barrow LN. 2023. Machine learning and phylogenetic models iden- tify predictors of genetic variation in Neotropical amphibians. bioRxiv. 38. Pelletier TA, Parsons DJ, Decker SK, Crouch S, Franz E, Ohrstrom J, et al. 2022. PhylogatR: Phylogeo- graphic data aggregation and repurposing. Molecular Ecology Resources 22: 2830–2842. https://doi. org/10.1111/1755-0998.13673 PMID: 35748425 39. Ba´ nki, O., Roskov, Y., Do¨ ring, M., Ower, G., Vandepitte, L., Hobern, D., et al. 2022. Catalogue of Life Checklist (Y. Roskov, Ed.; Version 2022-05-20). 40. Pelletier TA, Duffield DA, DeGrauw EA. 2011. Rangewide Phylogeography of the Western Red-Backed Salamander (Plethodon vehiculum). Northwestern Naturalist 92: 200–210. 41. Pelletier TA, Crisafulli C, Wagner S, Zellmer AJ, Carstens BC. 2015. Historical Species Distribution Models Predict Species Limits in Western Plethodon Salamanders. Systematic Biology 64: 909–925. https://doi.org/10.1093/sysbio/syu090 PMID: 25414176 42. Pelletier TA, Carstens BC. 2016. Comparing range evolution in two western Plethodon salamanders: glacial refugia, competition, ecological niches, and spatial sorting. Journal of Biogeography 43: 2237– 2249. 43. Jones KS, Weisrock DW. 2018. Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders. Evolution 72: 2378–2393. https://doi.org/10.1111/evo.

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