Bank, C., Bürger, R., & Hermisson, J. (2012). The limits to parapatric speciation: Dobzhansky–Muller incompatibilities in a continent–island model. Genetics, 191(3), 845-863.
Bazin, E., Glémin, S., & Galtier, N. (2006). Population size does not influence mitochondrial genetic diversity in animals. Science, 312(5773), 570-572.
Bech, N., Boissier, J., Drovetski, S., & Novoa, C. (2009). Population genetic structure of rock ptarmigan in the ‘sky islands’ of French Pyrenees: implications for conservation. Animal Conservation, 12(2), 138-146.
Campbell‐Staton, S., Edwards, S., & Losos, J. (2016). Climate‐mediated adaptation after mainland colonization of an ancestrally subtropical island lizard, Anolis carolinensis. Journal of Evolutionary Biology, 29(11), 2168-2180.
Cariou, M., Duret, L., & Charlat, S. (2013). Is RAD‐seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecology and Evolution, 3(4), 846-852.
Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22(11), 3124-3140.
Catchen, J. M., Amores, A., Hohenlohe, P., Cresko, W., & Postlethwait, J. H. (2011). Stacks: building and genotyping loci de novo from short-read sequences. Genes, Genomes, Genetics, 1(3), 171-182.
De Queiroz, K. (2007). Species concepts and species delimitation. Systematic Biology, 56(6), 879-886.
Earl, D. A. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359-361.
Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611-2620.
Feder, J. L., Egan, S. P., & Nosil, P. (2012). The genomics of speciation-with-gene-flow. Trends in genetics, 28(7), 342-350.
Fick, S. E., & Hijmans, R. J. (2017). WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas. International Journal of Climatology, 37(12), 4302-4315.
Fischer, M. C., Foll, M., Excoffier, L., & Heckel, G. (2011). Enhanced AFLP genome scans detect local adaptation in high‐altitude populations of a small rodent (Microtus arvalis). Molecular Ecology, 20(7), 1450-1462.
Foll, M., Fischer, M. C., Heckel, G., & Excoffier, L. J. M. e. (2010). Estimating population structure from AFLP amplification intensity. Molecular Ecology, 19(21), 4638-4647.
Foll, M., & Gaggiotti, O. J. G. (2008). A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180(2), 977-993.
Freedman, A. H., Gronau, I., Schweizer, R. M., Ortega-Del Vecchyo, D., Han, E., Silva, P. M., . . . Lorente-Galdos, B. (2014). Genome sequencing highlights the dynamic early history of dogs. PLoS genetics, 10(1), e1004016.
Goslee, S. C., & Urban, D. L. (2007). The ecodist package for dissimilarity-based analysis of ecological data. Journal of Statistical Software, 22(7), 1-19.
Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G., & Siepel, A. (2011). Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics, 43(10), 1031.
He, K., & Jiang, X. (2014). Sky islands of southwest China. I: an overview of phylogeographic patterns. Chinese Science Bulletin, 59(7), 585-597.
Heald, W. F. (1951). Sky islands of Arizona. Natural History, 60(56-63), 95-96.
Hijmans, R. J., Williams, E., Vennes, C., & Hijmans, M. R. J. (2017). Package ‘geosphere’. Spherical Trigonometry. v.
Huang, S.-P., Hsu, Y., & Tu, M.-C. (2006). Thermal tolerance and altitudinal distribution of two Sphenomorphus lizards in Taiwan. Journal of Thermal Biology, 31(5), 378-385.
Huang, W.-S. (1998). Sexual size dimorphism and microhabitat use of two sympartric lizards, Sphenomorphus taiwanensis and Takydromus hsuehshanensis, from the central highlands of Taiwan. Zoological Studies, 37, 302-308.
Jakobsson, M., & Rosenberg, N. A. (2007). CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14), 1801-1806.
Jombart, T. (2008). adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics, 24(11), 1403-1405.
Jombart, T., Devillard, S., & Balloux, F. (2010). Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC genetics, 11(1), 94.
Kanno, Y., Vokoun, J. C., & Letcher, B. H. (2011). Fine‐scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks. Molecular Ecology, 20(18), 3711-3729.
Knaus, B. J., & Grünwald, N. J. (2017). vcfr: a package to manipulate and visualize
variant call format data in R. Molecular Ecology Resources, 17(1), 44-53.
Knowles, L. L. (2001). Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshopprers. Molecular Ecology, 10(3), 691-701.
Leaché, A. D., Banbury, B. L., Felsenstein, J., De Oca, A. N.-M., & Stamatakis, A. (2015). Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Systematic Biology, 64(6), 1032-1047.
Lewis, P. O. (2001). A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50(6), 913-925.
McRae, B. H. (2006). Isolation by resistance. Evolution, 60(8), 1551-1561.
Pérez‐Alquicira, J., Molina‐Freaner, F., Piñero, D., Weller, S., Martínez‐Meyer, E., Rozas, J., & Domínguez, C. (2010). The role of historical factors and natural selection in the evolution of breeding systems of Oxalis alpina in the Sonoran desert ‘Sky Islands’. Journal of Evolutionary Biology, 23(10), 2163-2175.
Paris, J. R., Stevens, J. R., & Catchen, J. M. (2017). Lost in parameter space: a road map for stacks. Methods in Ecology Evolution, 8(10), 1360-1373.
Peterman, W. E. (2018). ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms. Methods in Ecology and Evolution, 9(6), 1638-1647.
Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS one, 7(5), e37135.
Phillips, S. J., Dudík, M., & Schapire, R. E. (2004). A maximum entropy approach to species distribution modeling. Paper presented at the Proceedings of the twenty-first international conference on Machine learning.
Pritchard, J. K., Stephens, M., & Donnelly, P. (2000). Inference of population structure using multilocus genotype data. Genetics, 155(2), 945-959.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., . . . Daly, M. J. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. The American journal of human genetics, 81(3), 559-575.
Rambaut, A., Suchard, M., Xie, D., & Drummond, A. (2014). Tracer v1. 6. Computer program and documentation distributed by the author. In.
RODRÍGUEZ‐RAMILO, S. T., & Wang, J. (2012). The effect of close relatives on unsupervised Bayesian clustering algorithms in population genetic structure analysis. Molecular Ecology Resources, 12(5), 873-884.
Rosenberg, N. A. (2004). DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes, 4(1), 137-138.
Sexton, J. P., Hangartner, S. B., & Hoffmann, A. A. (2014). Genetic isolation by environment or distance: which pattern of gene flow is most common? Evolution, 68(1), 1-15.
Shepard, D. B., & Burbrink, F. T. (2008). Lineage diversification and historical demography of a sky island salamander, Plethodon ouachitae, from the Interior Highlands. Molecular Ecology, 17(24), 5315-5335.
Stamatakis, A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312-1313.
Steinbauer MJ, Field R, Grytnes JA, Trigas P, Ah-Peng C, Attorre F, Birks HJB, Borges PAV, Cardoso P, Chou CH, De Sanctis M, de Sequeira MM, Duarte MC, Elias RB, Fernández-Palacios JM, Gabriel R, Gereau RE, Gillespie RG, Greimler J, Harter DEV, Huang TJ, Irl SDH, Jeanmonod D, Jentsch A, Jump AS, Kueffer C, Nogué S, Otto R, Price J, Romeiras MM, Strasberg D, Stuessy T, Svenning JC, Vetaas OR, Beierkuhnlein C (2016). Topography‐driven isolation, speciation and a global increase of endemism with elevation. Global Ecology and Biogeography, 25(9), 1097-1107.
Tennessen, J. A., & Zamudio, K. R. (2008). Genetic differentiation among mountain island populations of the striped plateau lizard, Sceloporus virgatus (Squamata: Phrynosomatidae). Copeia, 2008(3), 558-564.
Tingley, R., Thompson, M. B., Hartley, S., & Chapple, D. G. (2016). Patterns of niche filling and expansion across the invaded ranges of an Australian lizard. Ecography, 39(3), 270-280.
Venables, W., & Ripley, B. (2002). Statistics Complements to Modern Applied Statistics with S (fourth ed.). New York: Springer.
Wang, I. J., & Bradburd, G. S. (2014). Isolation by environment. Molecular Ecology, 23(23), 5649-5662.
Wright, S. (1943). Isolation by distance. Genetics, 28(2), 114.
Wu, S.-P., Huang, C.-C., Tsai, C.-L., Lin, T.-E., Jhang, J.-J., & Wu, S.-H. (2016). Systematic revision of the Taiwanese genus Kurixalus members with a description of two new endemic species (Anura, Rhacophoridae). ZooKeys(557), 121.
You, C. W., Poyarkov Jr, N. A., & Lin, S. M. (2015). Diversity of the snail‐eating snakes Pareas (Serpentes, Pareatidae) from Taiwan. Zoologica Scripta, 44(4), 349-361.
郭瓊華. (2001). 臺灣蜓蜥族群遺傳結構之研究. 國立台灣師範大學碩士論文.