Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ (2014) BEAST 2: a software platform for bayesian evolutionary analysis. PLOS Comput Biol 10:e1003537

Boyd A (2002) Morphological analysis of Sky Island populations of Macromeria viridiflora (Boraginaceae). Syst Bot 27:116–126

Brown RP, Yang Z (2011) Rate variation and estimation of divergence times using strict and relaxed clocks. BMC Evol Biol 11(1):271

Chong RA, Mueller RL (2017) Polymorphic duplicate genes and persistent non-coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders. BMC Genom 18:992

Connors LM, Cabe PR (2003) Isolation of dinucleotide microsatellite loci from red-backed salamander (Plethodon cinereus). Mol Ecol Notes 3:131–133

Davis MB (1983) Quaternary history of deciduous forests of eastern North America and Europe. Ann Mo Bot Gard 70:550–563

DeGross DJ (2004) Gene flow and the relationship of Plethodon stormi and P. elongatus assessed with 11 novel microsatellite loci. M.Sc. thesis, Oregon State University

Drummond AJ, Bouckaert RR (2015) Bayesian evolutionary analysis with BEAST. Cambridge University Press, Cambridge

Dyer KA, Jaenike J (2005) Evolutionary dynamics of a spatially structured host-parasite association: Drosophila innubila and male-killing Wolbachia. Evol 59:1518–1528

Excoffier L, Lischer HE (2010) Arlequin Suite Ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567

Frankham R, Ballou JD, Briscoe DA (2009) Introduction to conservation genetics, 2nd edn. Cambridge University Press, Cambridge

Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133(3):693–709

Grant WAS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. J Hered 89:415–426

Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48(2):361–372

Harpending H, Rogers A (2000) Genetic perspectives on human origins and differentiation. Annu Rev Genom Hum Genet 1:361–385

Highton R (1990) Taxonomic treatment of genetically differentiated populations. Herpetologica 46:114–121

Hillis DM, Mable BK, Larson A, Davis SK, EA Zimmer (eds) (1996) Nucleic acids IV: sequencing and cloning. In: Molecular systematics. Sinaeur Associates, Sunderland

Holycross AT, Douglas ME (2007) Geographic isolation, genetic divergence, and ecological non-exchangeability define ESUs in a threatened sky-island rattlesnake. Biol Conserv 134:142–154

Hurvich CM, Tsai CL (1989) Regression and time series model selection in small samples. Biometrika 76(2):297–307

Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120

Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

La Sorte FA, Jetz W (2010) Projected range contractions of montane biodiversity under global warming. Proc R Soc Lond B 277:3401–3410

Larson A (1984) Neontological inferences of evolutionary pattern and process in the salamander family Plethodontidae. Evol Biol 17:119–217

Larson A (1989) The relationship between speciation and morphological evolution. In: Otte D, Endler JA (eds) Speciation and its consequences. Sinauer Associates, Sunderland, pp 579–598

Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452

Liebgold EB, Brodie ED, Cabe PR (2011) Female philopatry and male-biased dispersal in a direct-developing salamander, Plethodon cinereus. Mol Ecol 20:249–257

Lyons MP, Shepard DB, Kozak KH (2016) Determinants of range limits in montane woodland salamanders (Genus Plethodon). Copeia 104:101–110

Maerz JC, Myers EM, Adams DC (2006) Trophic polymorphism in a terrestrial salamander. Evol Ecol Res 8:23

Marsh DM, Page RB, Hanlon TJ, Bareke H, Corritone R, Jetter N, Beckman NG, Gardner K, Seifert DE, Cabe PR (2007) Ecological and genetic evidence that low-order streams inhibit dispersal by red-backed salamanders (Plethodon cinereus). Can J Zool 85:319–327

Marvin GA (2001) Age, growth, and long-term site fidelity in the terrestrial plethodontid salamander Plethodon kentucki. Copeia 2001:108–117

Masta SE (2000) Phylogeography of the jumping spider Habronattus pugillis (Araneae: Salticidae): recent vicariance of sky island populations? Evolution 54:1699–1711

McCormack JE, Peterson AT, Bonaccorso E, Smith TB (2008) Speciation in the highlands of Mexico: genetic and phenotypic divergence in the Mexican jay (Aphelocoma ultramarina). Mol Ecol 17:2505–2521

McCormack JE, Huang H, Knowles LL, Gillespie R, Clague D (2009) Sky islands. Encycl Isl 4:841–843

Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Gateway Computing Environments Workshop (GCE), Ieee, pp 1–8

Moritz C (1994) Defining ‘evolutionarily significant units’ for conservation. Trends Ecol Evol 9:373–375

Moritz C, Patton JL, Conroy CJ, Parra JL, White GC, Beissinger SR (2008) Impact of a century of climate change on small-mammal communities in Yosemite National Park, USA. Science 322:261–264

Mueller RL (2006) Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. Syst Biol 55(2):289–300

Mueller RL, Boore JL (2005) Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Mol Biol Evol 22:2104–2112

Mueller RL, Macey JR, Jaekel M, Wake DB, Boore JL (2004) Morphological homoplasy, life history evolution, and historical biogeography of plethodontid salamanders inferred from complete mitochondrial genomes. Proc Natl Acad Sci USA 101:13820–13825

Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York

Palmer CA, Watts RA, Hastings AP, Houck LD, Arnold SJ (2010) Rapid evolution of plethodontid modulating factor, a hypervariable salamander courtship pheromone, is driven by positive selection. J Mol Evol 70(5):427–440

Palsbøll PJ, Berube M, Allendorf FW (2007) Identification of management units using population genetic data. Trends Ecol Evol 22:11–16

Paradis E (2010) pegas: An R package for population genetics with an integrated–modular approach. Bioinformatics 26:419–420

Parmesan C (2006) Ecological and evolutionary responses to recent climate change. Annu Rev Ecol Evol Syst 37:637–669

Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol notes 6(1):288–295

Petit RJ, Mousadik AE, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conserv Biol 12:844–855

Petranka JW (1998) Salamanders of the United States and Canada. Smithsonian Institution Press, Washington, DC

Polato NR, Gill BA, Shah AA, Gray MM, Casner KL, Barthelet A, … Zamudio KR (2018) Narrow thermal tolerance and low dispersal drive higher speciation in tropical mountains. PNAS 115:12471–12476

Pope MH, Highton R (1980) Geographic genetic variation in the Sacramento Mountain salamander, Aneides hardii. J Herpetol 14:343–346

Posada D (2008) jModelTest: phylogenetic model averaging. Mol Biol Evol 25:1253–1256

R Core Team (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/

Rambaut A (2014) FigTree 1.4. 2 software. Institute of Evolutionary Biology, Univ. Edinburgh

Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA (2018) Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Syst Biol 10:901–904

Ramos-Onsins SE, Rozas J (2002) Statistical properties of new neutrality tests against population growth. Mol Biol Evol 19:2092–2100

Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Heredity 86:248–249

Reilly SB, Wake DB (2015) Cryptic diversity and biogeographical patterns within the black salamander (Aneides flavipunctatus) complex. J Biogeogr 42:280–291

Reilly SB, Marks SB, Jennings WB (2012) Defining evolutionary boundaries across parapatric ecomorphs of Black Salamanders (Aneides flavipunctatus) with conservation implications. Mol Ecol 21:5745–5761

Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9:552–569

Schenekar T, Weiss S (2011) High rate of calculation errors in mismatch distribution analysis results in numerous false inferences of biological importance. Heredity 107:511–512

Sekercioglu CH, Schneider SH, Fay JP, Loarie SR (2008) Climate change, elevational range shifts, and bird extinctions. Conserv Biol 22:140–150

Shen XX, Liang D, Feng YJ, Chen MY, Zhang P (2013) A versatile and highly efficient toolkit including 102 nuclear markers for vertebrate phylogenomics, tested by resolving the higher-level relationships of the Caudata. Mol Biol Evol 30:2235–2248

Shen XX, Liang D, Chen MY, Mao RL, Wake DB, Zhang P (2015) Enlarged multilocus data set provides surprisingly younger time of origin for the Plethodontidae, the largest family of salamanders. Syst Biol 65:66–81

Shepard DB, Burbrink FT (2009) Phylogeographic and demographic effects of Pleistocene climatic fluctuations in a montane salamander, Plethodon fourchensis. Mol Ecol 18:2243–2262

Smith CI, Farrell BD (2005) Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes? Mol Ecol 14:3049–3065

Spatola BN, Peterman WE, Stephens NT, Connette GM, Shepard DB, Kozak KH et al (2013) Development of microsatellite loci for the western slimy salamander (Plethodon albagula) using 454 sequencing. Conserv Genet Resour 5:267–270

Staub NL, Brown CW, Wake DB (1995) Patterns of growth and movements in a population of Ensatina eschscholtzii platensis (Caudata: Plethodontidae) in the Sierra Nevada, California. J Herpetol 29:593–599

Tajima F (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437–460

Tajima F (1989a) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

Tajima F (1989b) The effect of change in population size on DNA polymorphism. Genetics 123:597–601

Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol Ecol 7:381–397

Tennessen JA, Zamudio KR (2008) Genetic differentiation among mountain island populations of the striped plateau lizard, Sceloporus virgatus (Squamata: Phrynosomatidae). Copeia 2008:558–564

Thompson RS, Anderson KH (2000) Biomes of western North America at 18,000, 6000 and 0 14C yr BP reconstructed from pollen and packrat midden data. J Biogeogr 27:555–584

Wake DB, Roth G, Wake MH (1983) On the problem of stasis in organismal evolution. J Theor Biol 101:211–224

Waples RS, Gaggiotti O (2006) INVITED REVIEW: what is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity. Mol Ecol 15:1419–1439

Warshall P (1995) The Madrean sky island archipelago: a planetary overview. Biodiversity and management of the Madrean Archipelago: the sky islands of southwestern United States and Northwestern Mexico. In: DeBano LF (ed) Biodiversity and the management of the Madrean Archipelago: The sky islands of southwestern United States and Northwestern Mexico. DIANE Publishing, Darby, pp 6–18

Watling JI, Braga L (2015) Desiccation resistance explains amphibian distributions in a fragmented tropical forest landscape. Landsc Ecol 30:1449–1459

Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370