Phylogeny and biogeography of Primula sect. Armerina: implications for plant evolution under climate change and the uplift of the Qinghai-Tibet Plateau

[1]  W. Thuiller,et al.  Replicated radiations of the alpine genus Androsace (Primulaceae) driven by range expansion and convergent key innovations , 2013, Journal of biogeography.

[2]  C. Graham,et al.  Evolutionary and Ecological Causes of the Latitudinal Diversity Gradient in Hylid Frogs: Treefrog Trees Unearth the Roots of High Tropical Diversity , 2006, The American Naturalist.

[3]  S. Woodell.  NATURAL HYBRIDIZATION IN BRITAIN BETWEEN P RIMULA VULGARIS HUDS. (THE PRIMROSE) AND P. ELAT/OR (L.) HILL (THE OXLIP) , 1969 .

[4]  Susan Kelley,et al.  Flora of China , 2008 .

[5]  Flora of Tibet , 1934, Nature.

[6]  M. Lascoux,et al.  Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci. , 2010, Molecular biology and evolution.

[7]  S. Kelso.  Taxonomy of Primula sects. Aleuritia and Armerina in North America , 1991 .

[8]  O. Gascuel,et al.  Estimating maximum likelihood phylogenies with PhyML. , 2009, Methods in molecular biology.

[9]  D. Pearl,et al.  Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. , 2007, Systematic biology.

[10]  T. Stadler,et al.  Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity , 2010, Science.

[11]  N. Mouquet,et al.  Biodiversity and Climate Change: Integrating Evolutionary and Ecological Responses of Species and Communities , 2010 .

[12]  Loren H. Rieseberg,et al.  Hybrid Origins of Plant Species , 1997 .

[13]  David R. Anderson,et al.  Model selection and multimodel inference : a practical information-theoretic approach , 2003 .

[14]  Jianquan Liu,et al.  Molecular phylogeny and biogeography of Gentiana sect. Cruciata (Gentianaceae) based on four chloroplast DNA datasets , 2009 .

[15]  Dianmo Li,et al.  Study on biogeographical divisions of China , 2004, Biodiversity & Conservation.

[16]  Jianquan Liu,et al.  Out of the Qinghai-Tibet Plateau: evidence for the origin and dispersal of Eurasian temperate plants from a phylogeographic study of Hippophaë rhamnoides (Elaeagnaceae). , 2012, The New phytologist.

[17]  J. Doyle,et al.  Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy , 1992 .

[18]  Xingjin He,et al.  S-DIVA (Statistical Dispersal-Vicariance Analysis): A tool for inferring biogeographic histories. , 2010, Molecular phylogenetics and evolution.

[19]  U. Grossniklaus,et al.  Genomic origin and organization of the allopolyploid Primula egaliksensis investigated by in situ hybridization. , 2008, Annals of botany.

[20]  De‐Zhu Li,et al.  Incongruence between Nuclear and Chloroplast DNA Phylogenies in Pedicularis Section Cyathophora (Orobanchaceae) , 2013, PloS one.

[21]  W. Rice,et al.  LABORATORY EXPERIMENTS ON SPECIATION: WHAT HAVE WE LEARNED IN 40 YEARS? , 1993, Evolution; international journal of organic evolution.

[22]  Jerry A. Coyne,et al.  Genetics and speciation , 1992, Nature.

[23]  G. A. Horridge,et al.  Animal species and evolution. , 1964 .

[24]  A. Czaja.  Paläokarpologische Untersuchungen von Taphozönosen des Unter- und Mittelmiozäns aus dem Braunkohlentagebau Berzdorf/Oberlausitz (Sachsen) , 2003 .

[25]  Kazutaka Katoh,et al.  Recent developments in the MAFFT multiple sequence alignment program , 2008, Briefings Bioinform..

[26]  S. Jähnig,et al.  The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas , 2015, Biological reviews of the Cambridge Philosophical Society.

[27]  N. Alvarez,et al.  RECONSTRUCTING THE ORIGINS OF HIGH‐ALPINE NICHES AND CUSHION LIFE FORM IN THE GENUS ANDROSACE S.L. (PRIMULACEAE) , 2012, Evolution; international journal of organic evolution.

[28]  S. Kelso.  The genus Primula as a model for evolution in the Alaskan flora , 1992 .

[29]  N. Oguge,et al.  The role of dispersal and vicariance in the Pleistocene history of an East African mountain rodent, Praomys delectorum , 2014 .

[30]  P. Schönswetter,et al.  Vicariance and dispersal in the alpine perennial Bupleurum stellatum L. (Apiaceae) , 2005 .

[31]  L. Excoffier,et al.  Gene flow and species delimitation. , 2009, Trends in ecology & evolution.

[32]  D. Dawson,et al.  Hybridization but No Evidence for Backcrossing and Introgression in a Sympatric Population of Great Reed Warblers and Clamorous Reed Warblers , 2012, PloS one.

[33]  Patricia A. McLenachan,et al.  A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting , 2009, The American Naturalist.

[34]  N. Salamin,et al.  Scale‐dependent adaptive evolution and morphological convergence to climatic niche in Californian eriogonoids (Polygonaceae) , 2014 .

[35]  F. Lei,et al.  Phylogeography of regional fauna on the Tibetan Plateau: A review , 2009 .

[36]  Jianquan Liu,et al.  Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals. , 2010, The New phytologist.

[37]  Hang Sun,et al.  Evolutionary history and underlying adaptation of alpine plants on the Qinghai–Tibet Plateau , 2014 .

[38]  G. Hewitt.  Genetic consequences of climatic oscillations in the Quaternary. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[39]  Jianquan Liu,et al.  Pliocene intraspecific divergence and Plio‐Pleistocene range expansions within Picea likiangensis (Lijiang spruce), a dominant forest tree of the Qinghai‐Tibet Plateau , 2013, Molecular ecology.

[40]  Ramón Doallo,et al.  CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics , 2012, Nature Methods.

[41]  P. Hollingsworth,et al.  Rapid Diversification of a Species-Rich Genus of Neotropical Rain Forest Trees , 2001, Science.

[42]  M. Donoghue,et al.  Historical biogeography, ecology and species richness. , 2004, Trends in ecology & evolution.

[43]  Nicolas Salamin,et al.  Linking Life-History Traits, Ecology, and Niche Breadth Evolution in North American Eriogonoids (Polygonaceae) , 2013, The American Naturalist.

[44]  J. Wiens,et al.  Niche Conservatism Drives Elevational Diversity Patterns in Appalachian Salamanders , 2010, The American Naturalist.

[45]  C. Graham,et al.  Niche Conservatism: Integrating Evolution, Ecology, and Conservation Biology , 2005 .

[46]  Gaurav Vaidya,et al.  SequenceMatrix: concatenation software for the fast assembly of multi‐gene datasets with character set and codon information , 2011, Cladistics : the international journal of the Willi Hennig Society.

[47]  J. Wiens.  The niche, biogeography and species interactions , 2011, Philosophical Transactions of the Royal Society B: Biological Sciences.

[48]  Walter Krämer,et al.  Review of Modern applied statistics with S, 4th ed. by W.N. Venables and B.D. Ripley. Springer-Verlag 2002 , 2003 .

[49]  P. Schönswetter,et al.  Complex biogeographic patterns in Androsace (Primulaceae) and related genera: evidence from phylogenetic analyses of nuclear internal transcribed spacer and plastid trnL-F sequences. , 2004, Systematic biology.

[50]  Weibang Sun,et al.  Evidence for natural hybridization between Primula beesiana and P. bulleyana, two heterostylous primroses in NW Yunnan, China , 2014 .

[51]  R. Abbott,et al.  Genetic divergence, range expansion and possible homoploid hybrid speciation among pine species in Northeast China , 2011, Heredity.

[52]  M. Higgie,et al.  Reinforcement drives rapid allopatric speciation , 2005, Nature.

[53]  E. Conti,et al.  Disentangling reticulate evolution in an arctic-alpine polyploid complex. , 2009, Systematic biology.

[54]  B. Burchfiel,et al.  The Geological Evolution of the Tibetan Plateau , 2008, Science.

[55]  T. Kawecki.  Adaptation to Marginal Habitats , 2008 .

[56]  E. Conti,et al.  Polyploid evolution and Pleistocene glacial cycles: A case study from the alpine primrose Primula marginata (Primulaceae) , 2012, BMC Evolutionary Biology.

[57]  P. Stephens,et al.  Bridging the gap between community ecology and historical biogeography: niche conservatism and community structure in emydid turtles , 2009, Molecular ecology.

[58]  Noah A Rosenberg,et al.  Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.

[59]  Jianquan Liu,et al.  Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai-Tibetan Plateau and adjacent regions , 2010, BMC Evolutionary Biology.

[60]  黄万 波计宏祥.  DISCOVERY OF HIPPARION FAUNA IN XIZANG , 1979 .

[61]  E. Conti,et al.  Phylogenetic analysis of Primula section Primula reveals rampant non-monophyly among morphologically distinct species. , 2012, Molecular phylogenetics and evolution.

[62]  G. Nieto Feliner,et al.  Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae). , 2003, Molecular phylogenetics and evolution.

[63]  Jianquan Liu,et al.  Molecular phylogeny and biogeography of the Qinghai-Tibet Plateau endemic Nannoglottis (Asteraceae). , 2002, Molecular phylogenetics and evolution.

[64]  C. Nowak,et al.  Intraspecific range dynamics and niche evolution in Candidula land snail species , 2007 .

[65]  Jianquan Liu,et al.  Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex (Asteraceae) triggered by uplift of the Qinghai-Tibetan Plateau. , 2006, Molecular phylogenetics and evolution.

[66]  T. Harrison,et al.  Raising Tibet , 1992, Science.

[67]  Chun-Xia Zeng,et al.  Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies. , 2012, Molecular phylogenetics and evolution.

[68]  Patrick J. McIntyre,et al.  Evolution and Ecology of Species Range Limits , 2009 .

[69]  Margaret E K Evans,et al.  Climate, Niche Evolution, and Diversification of the “Bird‐Cage” Evening Primroses (Oenothera, Sections Anogra and Kleinia) , 2008, The American Naturalist.

[70]  Shuzhen Peng,et al.  Onset of Asian desertification by 22 Myr ago inferred from loess deposits in China , 2002, Nature.

[71]  E. Conti,et al.  Heterostyly accelerates diversification via reduced extinction in primroses , 2014, Proceedings of the Royal Society B: Biological Sciences.

[72]  Hang Sun,et al.  Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau , 2014, Front. Genet..

[73]  P. Ericson,et al.  Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset , 2011, BMC Evolutionary Biology.

[74]  Hang Sun,et al.  Phylogenetic and biogeographic analyses of the Sino-Himalayan endemic genus Cyananthus (Campanulaceae) and implications for the evolution of its sexual system. , 2013, Molecular phylogenetics and evolution.

[75]  Christina Gloeckner,et al.  Modern Applied Statistics With S , 2003 .

[76]  E. Conti,et al.  Evolution of biogeographic patterns, ploidy levels, and breeding systems in a diploid-polyploid species complex of Primula. , 2006, The New phytologist.

[77]  A. Angert.  The niche, limits to species' distributions, and spatiotemporal variation in demography across the elevation ranges of two monkeyflowers , 2009, Proceedings of the National Academy of Sciences.

[78]  Hang Sun,et al.  Molecular phylogeny and biogeography of three closely related genera, Soroseris, Stebbinsia, and Syncalathium (Asteraceae, Cichorieae), endemic to the Tibetan Plateau, SW China , 2011 .

[79]  Jianquan Liu,et al.  Rapid radiation of Rheum (Polygonaceae) and parallel evolution of morphological traits. , 2012, Molecular phylogenetics and evolution.

[80]  Jianquan Liu,et al.  Phylogenetic origins of the Himalayan endemic Dolomiaea, Diplazoptilon and Xanthopappus (Asteraceae: Cardueae) based on three DNA regions. , 2007, Annals of botany.

[81]  G. Marion,et al.  Species' Range: Adaptation in Space and Time , 2009, The American Naturalist.

[82]  De‐Zhu Li,et al.  Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants , 2011, Proceedings of the National Academy of Sciences.

[83]  J. Aguilar,et al.  Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae). , 1999, Systematic biology.

[84]  Libing Zhang,et al.  Distribution of living Cupressaceae reflects the breakup of Pangea , 2012, Proceedings of the National Academy of Sciences.

[85]  Jianquan Liu,et al.  MOLECULAR AND MORPHOLOGICAL EVIDENCE FOR NATURAL HYBRIDIZATION BETWEEN PRIMULA SECUNDIFLORA FRANCHET AND P. POISSONII FRANCHET (PRIMULACEAE) , 2009 .

[86]  B. O’Meara,et al.  MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN–UHLENBECK MODEL OF ADAPTIVE EVOLUTION , 2012, Evolution; international journal of organic evolution.

[87]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[88]  C. Simon,et al.  Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). , 2006, Systematic biology.

[89]  J. L. Parra,et al.  Very high resolution interpolated climate surfaces for global land areas , 2005 .

[90]  R. Poudel,et al.  Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot. , 2013, The New phytologist.

[91]  E. Conti,et al.  Are any primroses (Primula) primitively monomorphic? , 2006, The New phytologist.

[92]  P. Valdes,et al.  Constant elevation of southern Tibet over the past 15 million years , 2003, Nature.

[93]  V. Sánchez‐Cordero,et al.  Conservatism of ecological niches in evolutionary time , 1999, Science.

[94]  J. Aguilar,et al.  Additive polymorphisms and reticulation in an ITS phylogeny of thrifts (Armeria, Plumbaginaceae) , 2003 .

[95]  Y. Yu,et al.  RASP (Reconstruct Ancestral State in Phylogenies): a tool for historical biogeography. , 2015, Molecular phylogenetics and evolution.

[96]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[97]  I. Pen,et al.  Geographical patterns of adaptation within a species’ range: interactions between drift and gene flow , 2006, Journal of evolutionary biology.

[98]  M. Gandolfo,et al.  Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales). , 2012, Systematic biology.