1469-8137/asset/NPH_left.gif?v=1&s=08bb9ae88048d5716b3d3495e7b2fcfe48536ab2)
Full paper
You have full text access to this OnlineOpen article
Pleistocene climatic oscillations and the speciation history of an alpine endemic and a widespread arctic-alpine plant
Article first published online: 13 FEB 2012
DOI: 10.1111/j.1469-8137.2012.04061.x
© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust
Additional Information
How to Cite
Ikeda, H., Carlsen, T., Fujii, N., Brochmann, C. and Setoguchi, H. (2012), Pleistocene climatic oscillations and the speciation history of an alpine endemic and a widespread arctic-alpine plant. New Phytologist, 194: 583–594. doi: 10.1111/j.1469-8137.2012.04061.x
Publication History
- Issue published online: 19 MAR 2012
- Article first published online: 13 FEB 2012
- Received: 16 November 2011, Accepted: 27 December 2011
References
- . 2000. Phylogeography: the history and formation of species. Cambridge, MA, USA: Harvard University Press.
- , , , , . 2010. Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proceedings of the National Academy of Sciences, USA, 107: 18724–18728.
- , . 2009. Learning about modes of speciation by computational approaches. Evolution 63: 2547–2562.
- , , . 2010. ABC as a flexible framework to estimate demography over space and time: some cons, many pros. Molecular Ecology 19: 2609–2625.
- , . 1999. Sex and genes in the flora of Svalbard – implications for conservation biology and climate change. Det Norske Videnskaps-Akademi. I. Matematisk-Naturvitenskapelig Klasse, Skrifter, Ny Serie 38: 33–72.
- , , , , . 2009. Biogeography and phylogeny of Cardamine (Brassicaceae). Annals of the Missouri Botanical Garden 96: 215–236.
- , , . 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657–1659.
- , . 2004. Speciation. Sunderland, MA, USA: Sinauer associates.
- , . 2004. Cryptic trysts, genomic mergers, and plant speciation. New Phytologist 161: 133–142.
- , , , . 2008. The hidden side of invasions: massive introgression by local genes. Evolution 62: 1908–1920.
- , , . 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 9: 2611–2620.
- , , . 2003. Inference of population structure: extensions to linked loci and correlated allele frequencies. Genetics 164: 1567–1587.
- , , . 2007. A Markov Chain Monte Carlo approach for joint inference of population structure and inbreeding rates from multilocus genotype data. Genetics 176: 1635–1651.
- , . 2004. The Pleistocene and Holocene Epochs. In: Gradstein FM, Ogg JG, Smith AG, eds. A geologic time scale. London, UK: Cambridge University Press, 441–452.
- . 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907–913.
- , . 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila psudoobscura and D. persimilis. Genetics 167: 747–760.
- , . 2007. Integration within the Felsenstein equation for improvaed Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, USA 104: 2785–2790.
- , . 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147–164.
- , , . 1987. A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153–159.
- , . 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754–755.
- , . 1986. Atlas of North European vascular plants north of the tropic of Cancer II. Kőnigstein, Germany: Koeltz Scientific Books.
- , , . 2009a. Application of the isolation with migration model demonstrates the Pleistocene origin of geographic differentiation in Cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant. Molecular Biology and Evolution 26: 2207–2216.
- , , . 2009b. Molecular evolution of phytochromes in Cardamine nipponica (Brassicaceae) suggests the involvement of PHYE in local adaptation. Genetics 182: 603–614.
- , , , . 2006. Refugia of Potentilla matsumurae (Rosaceae) located at high mountains in the Japanese archipelago. Molecular Ecology 15: 3731–3740.
- , , , . 2008. Consistent geographic structure among multiple nuclear sequences and cpDNA polymorphisms of Cardamine nipponica Franch. et Savat. (Brassicaceae). Molecular Ecology 17: 3178–3188.
- , . 2007. Phylogeography and refugia of the Japanese endemic alpine plant Phyllodoce nipponica Makino (Ericaceae). Journal of Biogeography 34: 169–176.
- , , . 2011. Molecular evolution of cryptochrome genes and the evolutionary manner of photoreceptor genes in Cardamine nipponica (Brassicaceae). Journal of Plant Research 124: 85–92.
- , . 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801–1806.
- , , . 2004. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology 4: 18.
- , , , . 2010. Disjunct distribution of chloroplast DNA haplotypes in the understory perennial Veratrum album ssp. oxysepalum (Melanthiaceae) in Japan as a result of ancient introgression. New Phytologist 188: 879–891.
- . 1999. Brassicaceae 8. Cardamine. In: Satake Y, Ohwi J, Kitamura S, Watari S, Tominari T, eds. Wild Flowers of Japan I. Tokyo, Japan: Heibonsha, 130–132.
- , , . 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Molecular Biology and Evolution 17: 1483–1498.
- , , . 2003. Differential cycles of range contraction and expansion in European high mountain plants during the Late Quaternary, insights from Pritzelago alpine (L.) O. Kuntze (Brassicaceae). Molecular Ecology 12: 931–949.
- , , . 2005. Online database of the chromosome numbers of the genus Cardamine (Brassicaceae). Biologia (Bratislava) 60: 473–476.
- , , , , , , , , , et al. 2002. Primers for 22 candidate genes for ecological adaptations in Brassicaceae. Molecular Ecology Notes 2: 258–262.
- , . 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.
- . 2008. BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics 24: 2542–2543.
- , , , . 2008. Estimating species trees using multiple-allele DNA sequence data. Evolution 62: 2080–2091.
- . 1987. Molecular Evolutionary Genetics. New York, NY, USA: Columbia University Press.
- , . 2001. Distinguishing migration from isolation: a Markov Chain Monte Carlo approach. Genetics 158: 885–896.
- , , , , , , , . 2010. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92–94.
- , , , , , , , , , et al. 2011. The genetic ghost of an invasion past: colonization and extinction revealed by historical hybridization in Senecio. Molecular Ecology 21: 369–387.
- , . 2009. Gene flow and species delimitation. Trends in Ecology and Evolution 24: 386–393.
- , . 2010. Divergence with gene flow: models and data. Annual Review of Ecology, Evolution, and Systematics 41: 215–230.
- , , . 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945–959.
- , . 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574.
- . 1982. The New Alpine Flora of Japan in color, vol 1. Osaka, Japan: Hoikusha.
- . 1983. The New Alpine Flora of Japan in color, vol 2. Osaka, Japan: Hoikusha.
- , , , . 2008. Polyploid speciation did not confer instant reproductive isolation in Capesella (Brassicaceae). Molecular Biology and Evolution 25: 1472–1481.
- , , . 2005. Genealogical footprints of speciation processes in wild tomatoes: demography and evidence for historical gene flow. Evolution 59: 1268–1279.
- , . 2008. Molecular demographi history of the annual sunflowers Helianthus annuus and H. petiolaris—large effective population sizes and rates of long-term gene flow. Evolution 62: 1936–1950.
- , . 2010. How robust are “Isolation with Migration” analyses to violations of the IM model? A simulation study Molecular Biology and Evolution 27: 297–310.
- . 1989. Statistical method for testing neutral mutation hypothesis by DNA polymorphisms. Genetics 123: 585–595.
- , , , , . 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 25: 4876–4882.
- , , . 2001. Asymmetrical crossing barriers in angiosperms. Proceedings of the Royal Society of London Series B 268: 861–867.
- , . 2006. Brassicaceae: chromosome number index and database on CD-Rom. Plant Systematic and Evolution 259: 237–248.
- , , . 1989. Rates of synonymous substitution in plant nuclear genes. Journal of Molecular Evolution 29: 208–211.
- , . 2010. Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara). Molecular Ecology 19: 2439–2454.