Alcala N, Goudet J, Vuilleumier S (2014) On the transition of genetic differentiation from isolation to panmixia: what we can learn from GST and D. Theor Popul Biol 93:75–84
Barton NH (1996) Natural selection and random genetic drift as causes of evolution on islands. Philos Trans R Soc Lond B Biol Sci 351:785–795
Bellemain E, Ricklefs RE (2008) Are islands the end of the colonization road? Trends Ecol Evol 23:461–468
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B-Methodol 57:289–300
Bolger A, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120
Bouckaert R (2010) DensiTree: making sense of sets of phylogenetic trees. Bioinformatics 26:1372–1373
Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D et al. (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Comput Biol 10:e1003537
Bryant D, Moulton V (2004) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21:255–265
Bryant D, Bouckaert R, Felsenstein J, Rosenberg NA, RoyChoudhury A (2012) Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Mol Biol Evol 29:1917–1932
Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140
Chapin III FS, Matson PA, Vitousek PM (2002) Principles of terrestrial ecosystem ecology. Springer, New York
Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B et al. (2009) The last glacial maximum. Science 325:710–714
DeChaine EG, Martin AP (2005) Marked genetic divergence among sky island populations of Sedum lanceolatum (Crassulaceae) in the Rocky Mountains. Am J Bot 92:477–486
Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
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 10:564–567
Foote AD, Morin PA (2016) Genome-wide SNP data suggest complex ancestry of sympatric North Pacific killer whale ecotypes. Heredity 117:316–325
Frankham R (1997) Do island populations have less genetic variation than mainland populations? Heredity 78:311–327
Frichot E, François O (2015) LEA: an R package for landscape and ecological association studies. Methods Ecol Evol 6:925–929
Frichot E, Mathieu F, Trouillon T, Bouchard G, François O (2014) Fast and efficient estimation of individual ancestry coefficients. Genetics 196:973–983
Frichot E, Schoville SD, Bouchard G, François O (2013) Testing for associations between loci and environmental gradients using latent factor mixed models. Mol Biol Evol 30:1687–1699
Frichot E, Schoville SD, De Villemereuil P, Gaggiotti OE, François O (2015) Detecting adaptive evolution based on association with ecological gradients: orientation matters! Heredity 115:22–28
Funk WC, Lovich RE, Hohenlohe PA, Hofman CA, Morrison SA, Sillett TS et al. (2016) Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Mol Ecol 25:2176–2194
Garot E, Joët T, Combes M, Severac D, Lashermes P (2019) Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island. N Phytol 224:974–986
Gillespie R (2004) Community assembly through adaptive radiation in Hawaiian spiders. Science 303:356–359
Hamabata T, Kinoshita G, Kurita K, Cao PL, Ito M, Murata J et al. (2019) Endangered island endemic plants have vulnerable genomes. Commun Biol 2:244
Hedrick PW (2005) A standardized genetic differentiation measure. Evolution 59:1633–1638
Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267
Izuno A, Kitayama K, Onoda Y, Tsujii Y, Hatakeyama M, Nagano AJ et al. (2017) The population genomic signature of environmental association and gene flow in an ecologically divergent tree species Metrosideros polymorpha (Myrtaceae). Mol Ecol 26:1515–1532
James JE, Lanfear R, Eyre-Walker A (2016) Molecular evolutionary consequences of island colonization. Genome Biol Evol 8:1876–1888
Juan C, Emerson BC, Oromı́ P, Hewitt GM (2000) Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands. Trends Ecol Evol 15:104–109
Kamijo T, Hashiba K (2003) Island ecosystem and vegetation dynamics before and after the 2000-year eruption on Miyake-jima Island, Japan, with implications for conservation of the island’s ecosystem. Glob Environ Res 7:69–78
Kier G, Kreft H, Lee TM, Jetz W, Ibisch PL, Nowicki C et al. (2009) A global assessment of endemism and species richness across island and mainland regions. Proc Natl Acad Sci USA 106:9322–9327
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 17:1483–1498
Liu X, Fu YX (2015) Exploring population size changes using SNP frequency spectra. Nat Genet 47:555–559
MacArthur RH, Wilson EO (1963) An equilibrium theory of insular zoogeography. Evolution 17:373–387
Maekawa F (1949) Makinoesia and its bearing to Oriental Asiatic flora. J Jpn Bot 24:91–96. in Japanese
McGlaughlin ME, Wallace LE, Wheeler GL, Bresowar G, Riley L, Britten NR et al. (2014) Do the island biogeography predictions of MacArthur and Wilson hold when examining genetic diversity on the near mainland California Channel Islands? Examples from endemic Acmispon (Fabaceae). Bot J Linn Soc 174:289–304
Ministry of the Environment of Japan (2019) Threatened wildlife of Japan – red list 2019. http://www.env.go.jp/press/106383.html
Murray M, Thompson W (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4326
Nakamura K, Denda T, Kokubugata G, Suwa R, Yang TYA, Peng C-I et al. (2010) Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands, the Ryukyu Archipelago, Japan. J Biogeogr 37:1907–1918
Nei M, Tajima F, Tateno Y (1983) Accuracy of estimated phylogenetic trees from molecular data. J Mol Evol 19:153–170
Ossowski S, Schneeberger K, Lucas-Lledó JI, Warthmann N, Clark RM, Shaw RG et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327:92–94
Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135
Petit JR, Jouzel J, Raynaud D, Barkov NI, Barnola J-M, Basile I et al. (1999) Climate and atmospheric history of the past 420,000 years from the Vostok ice core, Antarctica. Nature 399:429–436
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575
R Development Core Team (2019) R: a language and environment for statistical computing. https://www.R-project.org/
Rellstab C, Gugerli F, Eckert AJ, Hancock AM, Holderegger R (2015) A practical guide to environmental association analysis in landscape genomics. Mol Ecol 24:4348–4370
Stervander M, Illera JC, Kvist L, Barbosa P, Keehnen NP, Pruisscher P et al. (2015) Disentangling the complex evolutionary history of the Western Palearctic blue tits (Cyanistes spp.) – Phylogenomic analyses suggest radiation by multiple colonization events and subsequent isolation. Mol Ecol 24:2477–2494
Stuessy TF, Takayama K, López-Sepúlveda P, Crawford DJ (2014) Interpretation of patterns of genetic variation in endemic plant species of oceanic islands. Bot J Linn Soc 174:276–288
Sundqvist L, Keenan K, Zackrisson M, Prodöhl P, Kleinhans D (2016) Directional genetic differentiation and relative migration. Ecol Evol 6:3461–3475
Taira A, Saito S, Aoike K, Morita S, Tokuyama H, Suyehiro K et al. (1998) Nature and growth rate of the northern Izu-Bonin (Ogasawara) arc crust and their implications for continental crust formation. Isl Arc 7:395–407
Takahashi H (1971) Fossa Magna element plants. Res Reports Kanagawa Prefect Museum. Nat Hist 2:2–59. in Japanese
Takahashi H, Katsuyama T (1992) Natural hybrids between Rhododendron tsusiophyllum and R. kaempferi var. macrogemma (Ericaceae). Bull Kanagawa Prefect. Museum 21:59–71. in Japanese
Takezaki N, Nei M, Tamura K (2010) POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 27:747–752
Tanaka N (1999) Plant communities in Mt. Tenjo, Koudzu Island, Tokyo. Actinia 12:147–158. in Japanese
Vaxevanidou Z, González-Martínez SC, Climent J, Gil L (2006) Tree populations bordering on extinction: a case study in the endemic Canary Island pine. Biol Conserv 129:451–460
Velo-Antón G, Zamudio K, Cordero-Rivera A (2012) Genetic drift and rapid evolution of viviparity in insular fire salamanders (Salamandra salamandra). Heredity 108:410–418
Wagner DB, Furnier GR, Saghai-Maroof MA, Williams SM, Dancik BP, Allard RW (1987) Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids. Proc Natl Acad Sci USA 84:2097–2100
Warren BH, Simberloff D, Ricklefs RE, Aguilée R, Condamine FL, Gravel D et al. (2015) Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson. Ecol Lett 18:200–217
Weigelt P, Jetz W, Kreft H (2013) Bioclimatic and physical characterization of the world’s islands. Proc Natl Acad Sci USA 110:15307–15312
Yamada T, Maki M (2012) Impact of geographical isolation on genetic differentiation in insular and mainland populations of Weigela coraeensis (Caprifoliaceae) on Honshu and the Izu Islands. J Biogeogr 39:901–917
Yamamoto S, Kikuchi T, Yamagiwa Y, Handa T (2017) Genetic diversity of Lilium auratum var. platyphyllum endemic to the Izu archipelago and its relationship to a nearby population of L. auratum var. auratum by morphological and SSR analysis. Hortic J 86:379–388
Yoichi W, Minamitani T, Oh S-H, Nagano AJ, Abe H, Yukawa T (2019) New taxa of Rhododendron tschonoskii alliance (Ericaceae) from East Asia. PhytoKeys 134:97–114
Source: Ecology - nature.com
