| [1] | Pinto G, Mahler DL, Harmon LJ, Losos JB (2008) Testing the island effect in adaptive radiation: rates and patterns of morphological diversification in Caribbean and mainland Anolis lizards. P R Soc B 275(1652): 2749–2757.
|
| [2] | Givnish TJ (2010) Ecology of plant speciation. Taxon 59(5): 1326–1366.
|
| [3] | Slatkin M (1977) Gene flow and genetic drift in a species subject to frequent local extinctions. Theor Popul Biol 12(3): 253–262.
|
| [4] | Chiang TY, Schaal BA (2006) Phylogeography of plants in Taiwan and the Ryukyu archipelago. Taxon 55(1): 31–41.
|
| [5] | Hsieh TH (2002) Composition, endemism and phytogeographical affinities of the Taiwan flora. Taiwania 47(4): 298–310.
|
| [6] | Schluter D (1996) Ecological causes of adaptive radiation. Am Nat 148: S40–S64.
|
| [7] | Rainey PB, Travisano M (1998) Adaptive radiation in a heterogeneous environment. Nature 394(6688): 69–72.
|
| [8] | Gittenberger E (1991) What about non-adaptive radiation? Biol J Linn Soc 43(4): 263–272.
|
| [9] | Lin TP (2001) Allozyme variations in Michelia formosana (Kanehira) Masamune (Magnoliaceae), and the inference of a glacial refugium in Taiwan. Theor Appl Genet 102(2–3): 450–457.
|
| [10] | Huang SSF, Hwang SY, Lin TP (2002) Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and east Asia. Mol Ecol 11(11): 2349–2358.
|
| [11] | Hwang SY, Lin TP, Ma CS, Lin CL, Chung JD, et al. (2003) Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation. Mol Ecol 12(10): 2689–2695.
|
| [12] | Cheng YP, Hwang SY, Lin TP (2005) Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae). Mol Ecol 14(7): 2075–2085.
|
| [13] | Cheng YP, Hwang SY, Chiou WL, Lin TP (2006) Allozyme variation of populations of Castanopsis carlesii (Fagaceae) revealing the diversity centres and areas of the greatest divergence in Taiwan. Ann Bot-London 98(3): 601–608.
|
| [14] | Lee YJ, Hwang SY, Ho KC, Lin TP (2006) Source populations of Quercus glauca in the last glacial age in taiwan revealed by nuclear microsatellite markers. Journal of Heredity 97(3): 261–269.
|
| [15] | Wu SH, Hwang CY, Lin TP, Chung JD, Cheng YP, et al. (2006) Contrasting phylogeographical patterns of two closely related species, Machilus thunbergii and Machilus kusanoi (Lauraceae), in Taiwan. J Biogeogr 33(5): 936–947.
|
| [16] | Hewitt G (2000) The genetic legacy of the Quaternary ice ages. Nature 405(6789): 907–913.
|
| [17] | Carstens BC, Knowles LL (2007) Shifting distributions and speciation: species divergence during rapid climate change. Mol Ecol 16(3): 619–627.
|
| [18] | Wagstaff SJ, Hickerson L, Spangler R, Reeves PA, Olmstead RG (1998) Phylogeny in Labiatae s.l., inferred from cpDNA sequences. Plant Syst Evol 209(3–4): 265–274.
|
| [19] | Janicsak G, Veres K, Kakasy AZ, Mathe I (2006) Study of the oleanolic and ursolic acid contents of some species of the Lamiaceae. Biochem Syst Ecol 34(5): 392–396.
|
| [20] | Vidal F, Vidal JC, Gadelha AP, Lopes CS, Coelho MG, et al. (2007) Giardia lamblia: the effects of extracts and fractions from Mentha x piperita Lin. (Lamiaceae) on trophozoites. Exp Parasitol 115(1): 25–31.
|
| [21] | Charami MT, Lazari D, Karioti A, Skaltsa H, Hadjipavlou-Litina D, et al. (2008) Antioxidant and antiinflammatory activities of Sideritis perfoliata subsp. perfoliata (Lamiaceae). Phytother Res 22(4): 450–454.
|
| [22] | Schmiderer C, Grassi P, Novak J, Weber M, Franz C (2008) Diversity of essential oil glands of clary sage (Salvia sclarea L., Lamiaceae). Plant Biol 10(4): 433–440.
|
| [23] | Lukas B, Schmiderer C, Franz C, Novak J (2009) Composition of essential oil compounds from different Syrian populations of Origanum syriacum L. (Lamiaceae). J Agr Food Chem 57(4): 1362–1365.
|
| [24] | Sun M (1999) Cleistogamy in Scutellaria indica (Labiatae): effective mating system and population genetic structure. Mol Ecol 8(8): 1285–1295.
|
| [25] | Denda T (2002) Cleistogamy in Scutellaria rubropunctata Hayata (Labiatae) from the Ryukyu Archipelago. Biol Mag Okinawa 40: 7–14.
|
| [26] | Olmstead RG (1990) Biological and historical factors influencing genetic diversity in the Scutellaria angustifolia complex (Labiatae). Evolution 44(1): 54–70.
|
| [27] | Williams PA (1992) Ecology of the endangered herb Scutellaria novae-zelandiae. New Zeal J Ecol 16(2): 127–135.
|
| [28] | Cruzan MB (2001) Population size and fragmentation thresholds for the maintenance of genetic diversity in the herbaceous endemic Scutellaria montana (Lamiaceae). Evolution 55(8): 1569–1580.
|
| [29] | Paton AJ (1990) A global taxonomic investigation of Scutellaria (Labiatae). Kew Bull 45(3): 399–450.
|
| [30] | Hsieh TH, Huang TC (1995) Notes on the Flora of Taiwan (20) – Scutellaria (Lamiaceae) in Taiwan. Taiwania 40(1): 35–56.
|
| [31] | Hsieh TH, Huang TC (1997) Notes on the Flora of Taiwan (29) – Scutellaria austrotaiwanensis Hsieh & Huang sp. nov. (Lamiaceae) from Taiwan. Taiwania 42(2): 109–116.
|
| [32] | Huang TC, Hsieh TH, Cheng WT (1998) Lamiaceae. In: Huang T-C, Boufford DE, Hsieh C-F, Lowry PPI, Ohashi H, et al.., editors. Flora of Taiwan, 2nd edition. Taipei, Taiwan, R.O.C.: Editorial Committee of the Flora of Taiwan, Department of Botany, National Taiwan University. 432–543.
|
| [33] | Huang TC, Hsiao A, Wu MJ (2003) Note on the flora of Taiwan (35) –Scutellaria taipeiensis T.-C. Huang, A. Hsiao et M.-J. Wu sp. nov. (Laminaceae). Taiwania 48(2): 129–137.
|
| [34] | Li XW, Hedge IC (1994) Scutellaria Linnaeus, Lamiaceae Lindley. St. Louis, MO and Cambridge, MA: Missouri Botanical Garden and Harvard University Herbaria. 75–103. Available: http://www.efloras.org. Accessed 2008 Feb 22.
|
| [35] | Yamazaki T (1992) A revision of Scutellaria in Taiwan. J Jap Bot 67(6): 315–319.
|
| [36] | Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19: 11–15.
|
| [37] | Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24): 4876–4882.
|
| [38] | Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95–98.
|
| [39] | Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10): 2731–2739.
|
| [40] | Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12): 1572–1574.
|
| [41] | Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214.
|
| [42] | Wolfe KH, Li WH, Sharp PM (1987) Rates of Nucleotide Substitution Vary Greatly among Plant Mitochondrial, Chloroplast, and Nuclear DNAs. P Natl Acad Sci USA 84(24): 9054–9058.
|
| [43] | Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17(10): 1483–1498.
|
| [44] | Rambaut A, Drummond AJ (2003) Tracer ver. 1.4.1. Edinburgh: Institute of Evolutionary Biology, University of Edinburgh. Available: http://tree.bio.ed.ac.uk/software/tracer？/. Accessed 2012 Nov 5.
|
| [45] | Rambaut A (2008) FigTree ver. 1.3.1. Edinburgh: Institute of Evolutionary Biology, University of Edinburgh. Available: http://tree.bio.ed.ac.uk/software/FigTre？e/. Accessed 2012 Nov 5.
|
| [46] | Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51(3): 492–508.
|
| [47] | Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29(2): 170–179.
|
| [48] | Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16(8): 1114–1116.
|
| [49] | Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17(12): 1246–1247.
|
| [50] | Shimodaira H (2004) Approximately unbiased tests of regions using multistep-multiscale bootstrap resampling. Ann Stat 32(6): 2616–2641.
|
| [51] | Rozas J, Sanchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19(18): 2496–2497.
|
| [52] | Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123(3): 585–595.
|
| [53] | Fulford GR, Roberts MG, Heesterbeek JA (2002) The metapopulation dynamics of an infectious disease: tuberculosis in possums. Theor Popul Biol 61(1): 15–29.
|
| [54] | Yu Y, Harris AJ, He XJ (2011) RASP (Reconstruct Ancestral State in Phylogenies) 2.0 beta. Available: http://mnh.scu.edu.cn/soft/blog/RASP. Accessed 2012 Nov 5.
|
| [55] | Moore BR, Chan KMA, Donoghue MJ (2004) Detecting diversification rate variation in supertrees. In: Bininda-Emonds ORP, editor. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Dordrecht, The Netherlands: Kluwer Academic. 487–533.
|
| [56] | Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20(2): 289–290.
|
| [57] | Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10(3): 564–567.
|
| [58] | Excoffier L (2004) Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model. Mol Ecol 13(4): 853–864.
|
| [59] | Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47–50.
|
| [60] | Harpending HC (1994) Signature of ancient population-growth in a low-resolution mitochondrial DNA mismatch distribution. Hum Biol 66(4): 591–600.
|
| [61] | Esselstyn JA, Timm RM, Brown RM (2009) Do geological or climatic processes drive speciation in dynamic archipelagos? The tempo and mode of diversification in Southeast Asian shrews. Evolution 63(10): 2595–2610.
|
| [62] | Hosoda T, Sato JJ, Lin LK, Chen YJ, Harada M, et al. (2011) Phylogenetic history of mustelid fauna in Taiwan inferred from mitochondrial genetic loci. Can J Zool 89(6): 559–569.
|
| [63] | Wang CF, Hsieh CH, Lee SC, Wang HY (2011) Systematics and phylogeography of the Taiwanese endemic minnow Candidia barbatus (Pisces: Cyprinidae) based on DNA sequence, allozymic, and morphological analyses. Zool J Linn Soc-Lond 161(3): 613–632.
|
| [64] | Huang JP, Lin CP (2011) Lineage-specific late pleistocene expansion of an endemic subtropical gossamer-wing damselfly, Euphaea formosa, in Taiwan. BMC Evol Biol 11: 94.
|
| [65] | Nakamura K, Denda T, Kokubugata G, Suwa R, Yang TYA, et al. (2010) Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands, the Ryukyu Archipelago, Japan. J Biogeogr 37(10): 1907–1918.
|
| [66] | Simpson GG (1953) The Major Features of Evolution. New York: Columbia University Press.
|
| [67] | Glor RE (2010) Phylogenetic insights on adaptive radiation. Annu Rev Ecol Evol Syst 41: 251–270.
|
| [68] | McGlone MS, Duncan RP, Heenan PB (2001) Endemism, species selection and the origin and distribution of the vascular plant flora of New Zealand. J Biogeogr 28(2): 199–216.
|
| [69] | Martin-Bravo S, Valcarcel V, Vargas P, Luceno M (2010) Geographical speciation related to Pleistocene range shifts in the western Mediterranean mountains (Reseda sect. Glaucoreseda, Resedaceae). Taxon 59(2): 466–482.
|
| [70] | Middleton B (2000) Hydrochory, seed banks, and regeneration dynamics along the landscape boundaries of a forested wetland. Plant Ecol 146(2): 169–184.
|
| [71] | Huang ZY, Yu HS (2003) Morphology and geologic implications of Penghu Channel off southwest Taiwan. Terr Atmos Ocean Sci 14(4): 469–485.
|
| [72] | Shih HT, Fang SH, Ng PKL (2007) Phylogeny of the freshwater crab genus Somanniathelphusa Bott (Decapoda : Parathelphusidae) from Taiwan and the coastal regions of China, with notes on their biogeography. Invertebr Syst 21(1): 29–37.
|
| [73] | Shih HT, Cai Y (2007) Two new species of the land-locked freshwater shrimps genus, Neocaridina Kubo, 1938 (Decapoda : Caridea : Atyidae), from Taiwan, with notes on speciation on the island. Zool Stud 46(6): 680–694.
|
| [74] | Levin DA (2005) Niche shifts: The primary driver of novelty within angiosperm genera. Syst Bot 30(1): 9–15.
|
| [75] | Liew PM, Kuo CM, Huang SY, Tseng MH (1998) Vegetation change and terrestrial carbon storage in eastern Asia during the Last Glacial Maximum as indicated by a new pollen record from central Taiwan. Global Planet Change 17: 85–94.
|
| [76] | Wei KY (2002) Environmental changes during the late Quaternary in Taiwan and adjacent seas: an overview of recent results of the past decade (1990–2000). West Pac Earth Sci 2: 149–160.
|
| [77] | Hudson RR (1990) Gene genealogies and the coalescent process. In: Futuyma DJ, Antonovics J, editors. Oxford Survey of Evolutionary Biology. New York: Oxford University Press. 1–44.
|
| [78] | Vilaca ST, Santos FR (2010) Biogeographic history of the species complex Basileuterus culicivorus (Ayes, Parulidae) in the Neotropics. Mol Phylogenet Evol 57(2): 585–597.
|
| [79] | Boggs SJ, Wang W-C, Lewis FS, Chen J-C (1979) Sediment properties and water characteristics of the Taiwan shelf and Slope. Acta Oceanographica Taiwanica 10: 10–49.
|
