Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

[1]  Ling Zhang,et al.  Molecular phylogeny and inflorescence evolution of Prunus (Rosaceae) based on RAD-seq and genome skimming analyses , 2023, Plant diversity.

[2]  Zhen Wei,et al.  Phylogeny of Trigonotis in China—with a special reference to its nutlet morphology and plastid genome , 2023, Plant diversity.

[3]  J. Landis,et al.  Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: new insights from plastid phylogenomics , 2022, Annals of botany.

[4]  Andan Zhu,et al.  Phylogenetic Analysis of Wild Species and the Maternal Origin of Cultivars in the Genus Lilium Using 114 Plastid Genomes , 2022, Frontiers in Plant Science.

[5]  Jiong Cai,et al.  Phylogeny, Age, and Evolution of Tribe Lilieae (Liliaceae) Based on Whole Plastid Genomes , 2022, Frontiers in Plant Science.

[6]  Xingjin He,et al.  Backbone phylogeny and evolution of Apioideae (Apiaceae): New insights from phylogenomic analyses of plastome data. , 2021, Molecular phylogenetics and evolution.

[7]  M. Engel,et al.  The mid-Miocene Zhangpu biota reveals an outstandingly rich rainforest biome in East Asia , 2021, Science Advances.

[8]  P. Valdes,et al.  Orographic evolution of northern Tibet shaped vegetation and plant diversity in eastern Asia , 2021, Science Advances.

[9]  J. Landis,et al.  Plastome phylogenomics of Cephalotaxus (Cephalotaxaceae) and allied genera , 2020, Annals of botany.

[10]  P. Valdes,et al.  The topographic evolution of the Tibetan Region as revealed by palaeontology , 2020, Palaeobiodiversity and Palaeoenvironments.

[11]  R. Spicer,et al.  Cenozoic topography, monsoons and biodiversity conservation within the Tibetan Region: An evolving story , 2020, Plant diversity.

[12]  Matthew A. Gitzendanner,et al.  Recent accelerated diversification in rosids occurred outside the tropics , 2020, Nature Communications.

[13]  Gregory W. Stull,et al.  Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages. , 2020, American journal of botany.

[14]  M. Chase,et al.  Implications of plastome evolution in the true lilies (monocot order Liliales). , 2020, Molecular phylogenetics and evolution.

[15]  Jung Sung Kim,et al.  New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome Sequences , 2019, Plants.

[16]  Yan Yu,et al.  RASP 4: ancestral state reconstruction tool for multiple genes and characters. , 2019, Molecular biology and evolution.

[17]  A. C. Seijmonsbergen,et al.  Origins of global mountain plant biodiversity: Testing the ‘mountain‐geobiodiversity hypothesis’ , 2019, Journal of Biogeography.

[18]  C. dePamphilis,et al.  GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes , 2019, bioRxiv.

[19]  M. Chase,et al.  Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae) , 2019, BMC Plant Biology.

[20]  Haiyang Liu,et al.  Chloroplast phylogenomic analysis provides insights into the evolution of the largest eukaryotic genome holder, Paris japonica (Melanthiaceae) , 2019, BMC Plant Biology.

[21]  Matthew A. Gitzendanner,et al.  Origin of angiosperms and the puzzle of the Jurassic gap , 2019, Nature Plants.

[22]  Patricia P. Chan,et al.  tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes , 2019, bioRxiv.

[23]  Hang Sun,et al.  Pollination in Lilium sargentiae (Liliaceae) and the first confirmation of long‐tongued hawkmoths as a pollinator niche in Asia , 2019 .

[24]  W. Kress,et al.  Resolving the rapid plant radiation of early diverging lineages in the tropical Zingiberales: Pushing the limits of genomic data. , 2018, Molecular phylogenetics and evolution.

[25]  Li-Qin Yang,et al.  Molecular phylogenetics and historical biogeography of the tribe Lilieae (Liliaceae): bi-directional dispersal between biodiversity hotspots in Eurasia. , 2018, Annals of botany.

[26]  Emmanuel Paradis,et al.  ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R , 2018, Bioinform..

[27]  Joo-Hwan Kim,et al.  Updated molecular phylogenetic analysis, dating and biogeographical history of the lily family (Liliaceae: Liliales) , 2018, Botanical Journal of the Linnean Society.

[28]  Diego F. Morales-Briones,et al.  Phylogenomic analyses reveal a deep history of hybridization and polyploidy in the Neotropical genus Lachemilla (Rosaceae). , 2018, The New phytologist.

[29]  M. Suchard,et al.  Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7 , 2018, Systematic biology.

[30]  S. Clemens,et al.  Late Miocene climate cooling and intensification of southeast Asian winter monsoon , 2018, Nature Communications.

[31]  Michael R McKain,et al.  Practical considerations for plant phylogenomics , 2018, Applications in plant sciences.

[32]  Daniel L. Ayres,et al.  Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10 , 2018, Virus evolution.

[33]  Bin Wang,et al.  The global monsoon across time scales: Mechanisms and outstanding issues , 2017 .

[34]  I. Choi,et al.  Chloroplast genomes of Lilium lancifolium, L. amabile, L. callosum, and L. philadelphicum: Molecular characterization and their use in phylogenetic analysis in the genus Lilium and other allied genera in the order Liliales , 2017, PloS one.

[35]  R. Spicer.  Tibet, the Himalaya, Asian monsoons and biodiversity – In what ways are they related? , 2017, Plant diversity.

[36]  T. Hsu,et al.  Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae) , 2017, PloS one.

[37]  Xiuhai Zhang,et al.  Complete chloroplast genome sequences of Lilium: insights into evolutionary dynamics and phylogenetic analyses , 2017, Scientific Reports.

[38]  Matthew W. Pennell,et al.  Speciation gradients and the distribution of biodiversity , 2017, Nature.

[39]  Axel Fischer,et al.  GeSeq – versatile and accurate annotation of organelle genomes , 2017, Nucleic Acids Res..

[40]  Richard H. Ree,et al.  Uplift-driven diversification in the Hengduan Mountains, a temperate biodiversity hotspot , 2017, Proceedings of the National Academy of Sciences.

[41]  Xiaojuan Li,et al.  Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae) , 2016, Front. Plant Sci..

[42]  T. Herbert,et al.  Late Miocene global cooling and the rise of modern ecosystems , 2016 .

[43]  Yundong Gao,et al.  Accommodating Nomocharis in Lilium (Liliaceae) , 2016 .

[44]  J. Mandel,et al.  Ancestral Gene Flow and Parallel Organellar Genome Capture Result in Extreme Phylogenomic Discord in a Lineage of Angiosperms , 2016, Systematic biology.

[45]  Olga Chernomor,et al.  Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices , 2016, Systematic biology.

[46]  Alejandro Ordonez,et al.  The influence of paleoclimate on present-day patterns in biodiversity and ecosystems , 2015 .

[47]  D. Schluter.  Speciation, Ecological Opportunity, and Latitude , 2015, The American Naturalist.

[48]  David C. Tank,et al.  Oligocene niche shift, Miocene diversification – cold tolerance and accelerated speciation rates in the St. John’s Worts (Hypericum, Hypericaceae) , 2015, BMC Evolutionary Biology.

[49]  G. Shi,et al.  A tropical forest of the middle Miocene of Fujian (SE China) reveals Sino-Indian biogeographic affinities , 2015 .

[50]  Justin Zobel,et al.  Bandage: interactive visualization of de novo genome assemblies , 2015, bioRxiv.

[51]  T. Gianfagna,et al.  Chemistry and biological activity of steroidal glycosides from the Lilium genus. , 2015, Natural product reports.

[52]  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.

[53]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[54]  Daniel L. Rabosky,et al.  BAMMtools: an R package for the analysis of evolutionary dynamics on phylogenetic trees , 2014 .

[55]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[56]  Shuang Li,et al.  Molecular phylogeny and genetic variation in the genus Lilium native to China based on the internal transcribed spacer sequences of nuclear ribosomal DNA , 2014, Journal of Plant Research.

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

[58]  Yundong Gao,et al.  Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q-T plateau and the Hengduan Mountains. , 2013, Molecular phylogenetics and evolution.

[59]  B. Dong,et al.  Influence of the Tibetan Plateau uplift on the Asian monsoon-arid environment evolution , 2013 .

[60]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[61]  V. Mosbrugger,et al.  Vegetation and climatic changes of SW China in response to the uplift of Tibetan Plateau , 2012 .

[62]  Shane S. Sturrock,et al.  Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data , 2012, Bioinform..

[63]  R. Ohlemüller.  Running Out of Climate Space , 2011, Science.

[64]  Lesley T Lancaster,et al.  Phylogenetic inference of reciprocal effects between geographic range evolution and diversification. , 2011, Systematic biology.

[65]  V. Mosbrugger,et al.  Quantitative reconstruction of Miocene climate patterns and evolution in Southern China based on plant fossils , 2011 .

[66]  Zhekun Zhou,et al.  Quantitative reconstruction of the Late Miocene monsoon climates of southwest China: A case study of the Lincang flora from Yunnan Province , 2011 .

[67]  H. Philippe,et al.  Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough , 2011, PLoS biology.

[68]  A. Graham.  A Natural History of the New World: The Ecology and Evolution of Plants in the Americas , 2010 .

[69]  J. G. Burleigh,et al.  Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots , 2010, Proceedings of the National Academy of Sciences.

[70]  D. Schluter,et al.  Evidence for Ecological Speciation and Its Alternative , 2022 .

[71]  M. Huber,et al.  Simulation of the Middle Miocene Climate Optimum , 2009 .

[72]  H. Linder.  Plant species radiations: where, when, why? , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[73]  Gerald R. Dickens,et al.  An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics , 2008, Nature.

[74]  James Leebens-Mack,et al.  Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns , 2007, Proceedings of the National Academy of Sciences.

[75]  Pamela S Soltis,et al.  Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms , 2007, Proceedings of the National Academy of Sciences.

[76]  A. Ashworth,et al.  Major middle Miocene global climate change: Evidence from East Antarctica and the Transantarctic Mountains , 2007 .

[77]  Anchun Li,et al.  Development of the East Asian monsoon: Mineralogical and sedimentologic records in the northern South China Sea since 20 Ma , 2007 .

[78]  P. Lockhart,et al.  Deciphering ancient rapid radiations. , 2007, Trends in ecology & evolution.

[79]  James H. Brown,et al.  Kinetic effects of temperature on rates of genetic divergence and speciation. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[80]  Zheng Du,et al.  Uplifting of Tibetan Plateau with Its Environmental Effects , 2006 .

[81]  Pinxian Wang,et al.  How old is the Asian monsoon system?—Palaeobotanical records from China , 2005 .

[82]  S. Carroll,et al.  More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. , 2005, Molecular biology and evolution.

[83]  D. Posada,et al.  Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. , 2004, Systematic biology.

[84]  F. Blattner,et al.  Mauve: multiple alignment of conserved genomic sequence with rearrangements. , 2004, Genome research.

[85]  M. Collinson,et al.  Eocene–Oligocene mammalian faunal turnover in the Hampshire Basin, UK: calibration to the global time scale and the major cooling event , 2004, Journal of the Geological Society.

[86]  H. Qian.  A comparison of the taxonomic richness of temperate plants in East Asia and North America. , 2002, American journal of botany.

[87]  A. Oleinik,et al.  A refined age for the earliest opening of Bering Strait , 2002 .

[88]  M. Donoghue,et al.  Phylogenetic Patterns in Northern Hemisphere Plant Geography , 2001, International Journal of Plant Sciences.

[89]  Sudhir Kumar,et al.  Incomplete taxon sampling is not a problem for phylogenetic inference , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[90]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[91]  J. Kutzbach,et al.  Evolution of Asian monsoons and phased uplift of the Himalaya–Tibetan plateau since Late Miocene times , 2001, Nature.

[92]  L. Sloan,et al.  Trends, Rhythms, and Aberrations in Global Climate 65 Ma to Present , 2001, Science.

[93]  H. Qian,et al.  A Comparison of Generic Endemism of Vascular Plants between East Asia and North America , 2001, International Journal of Plant Sciences.

[94]  R. Ricklefs,et al.  Large-scale processes and the Asian bias in species diversity of temperate plants , 2000, Nature.

[95]  P. Pearson,et al.  Atmospheric carbon dioxide concentrations over the past 60 million years , 2000, Nature.

[96]  T. Nagamine,et al.  A Molecular Phylogeny of Lilium in the Internal Transcribed Spacer Region of Nuclear Ribosomal DNA , 1999, Journal of Molecular Evolution.

[97]  D. Soltis,et al.  Discordance Between ITS and Chloroplast Topologies in the Boykinia Group (Saxifragaceae) , 1996 .

[98]  D. Soltis,et al.  DISCORDANCE BETWEEN NUCLEAR AND CHLOROPLAST PHYLOGENIES IN THE HEUCHERA GROUP (SAXIFRAGACEAE) , 1995, Evolution; international journal of organic evolution.

[99]  B. Flower,et al.  The middle Miocene climatic transition: East Antarctic ice sheet development, deep ocean circulation and global carbon cycling , 1994 .

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

[101]  Huayu Lu,et al.  Evolution of the monsoon and dry climate in East Asia during late Cenozoic: A review , 2013, Science China Earth Sciences.

[102]  A. Harris,et al.  A new species in the genus Nomocharis Franchet (Liliaceae): evidence that brings the genus Nomocharis into Lilium , 2011, Plant Systematics and Evolution.

[103]  J. Lei,et al.  Collection and evaluation of the genus Lilium resources in Northeast China , 2010, Genetic Resources and Crop Evolution.

[104]  A. Liston,et al.  Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes , 2009 .

[105]  J. Townsend,et al.  Phylogenomics , 2008, Methods in Molecular Biology™.

[106]  Wu Xue-wei.  Distribution Situation and Suggestion on Protecting Wild Lilies in Yunnan Province , 2006 .

[107]  David Posada,et al.  MODELTEST: testing the model of DNA substitution , 1998, Bioinform..

[108]  B. Tiffney.  The Eocene North Atlantic land bridge: its importance in Tertiary and modern phytogeography of the northern hemisphere , 1985 .

[109]  E. Pahlich,et al.  A rapid DNA isolation procedure for small quantities of fresh leaf tissue , 1980 .