SEARCH

SEARCH BY CITATION

References

  • Akeroyd JR. 1993. Aquilegia. In: Tutin TG, Heywood VH, Burges NA, Valentine DH, Walters SM, Webb DA, eds. Flora Europaea I: Psilotaceae to Platanaceae. Cambridge, UK: Cambridge University Press, 287290.
  • Anderson CL, Bremer K, Friis EM. 2005. Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points. American Journal of Botany 92: 17371748.
  • Arakaki M, Christin P-A, Nyffeler R, Lendel A, Eggli U, Ogburn RM, Spriggs E, Moore MJ, Edwards EJ. 2011. Contemporaneous and recent radiations of the world's major succulent plant lineages. Proceedings of the National Academy of Sciences, USA 108: 83798384.
  • Bastida JM, Alcantara JM, Rey PJ, Vargas P, Herrera CM. 2010. Extended phylogeny of Aquilegia: the biogeographical and ecological patterns of two simultaneous but contrasting radiations. Plant Systematics and Evolution 284: 171185.
  • Bell CD, Soltis DE, Soltis PS. 2010. The age and diversification of the angiosperms re-revisited. American Journal of Botany 97: 12961303.
  • Birky CW, Maruyama T, Fuerst P. 1983. An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results. Genetics 103: 513527.
  • Bulavkina AA. 1937. Aquilegia. In: Komarov VL, ed. Flora of the USSR, vol. VII: Ranales and Rhoeadales. Moscow, Russia: Botanicheskii Institut Akademii Nauk USSR, 6978.
  • Bybee SM, Bracken-Grissom H, Haynes BD, Hermansen RA, Byers RL, Clement MJ, Udall JA, Wilcox ER, Crandall KA. 2011. Targeted Amplicon Sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. Genome Biology and Evolution 3: 13121323.
  • Comes HP, Kadereit JW. 2003. Spatial and temporal patterns in the evolution of the flora of the European Alpine System. Taxon 52: 451462.
  • Cronn RC, Wendel J. 2004. Cryptic trysts, genomic mergers, and plant speciation. New Phytologist 161: 133142.
  • De Bodt S, Maere S, Van de Peer Y. 2005. Genome duplication and the origin of angiosperms. Trends in Ecology & Evolution 20: 591597.
  • De Queiroz K. 2007. Species concepts and species delimitation. Systematic Biology 56: 879886.
  • DeBry RW, Olmstead RG. 2000. A simulation study of reduced tree-search effort in bootstrap resampling analysis. Systematic Biology 49: 171179.
  • Dobson M, Kawamura Y. 1998. Origin of the Japanese land mammal fauna: allocation of extant species to historically-based categories. Quaternary Research 37: 385395.
  • Drummond AJ, Ashton B, Buxton S, Cheung M, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R et al. 2011. Geneious v5.3 created by Biomatters. [WWW document] URL http://www.geneious.com/ [accessed on 28 June 2011].
  • Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7: 214.
  • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 17921797.
  • Erixon P, Oxelman B. 2008. Reticulate or tree-like chloroplast DNA evolution in Sileneae (Caryophyllaceae)? Molecular Phylogenetics and Evolution 48: 313325.
  • Faircloth BC, McCormack JE, Crawford NG, Harvey MG, Brumfield RT, Glenn TC. 2012. Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales. Systematic Biology 61: 717726.
  • Fang G-C, Blackmon BP, Henry DC, Staton ME, Saski CA, Hodges SA, Tomkins JP, Luo H. 2010. Genomic tools development for Aquilegia: construction of a BAC-based physical map. BMC Genomics 11: 621.
  • Fishbein M, Hibsch-Jetter C, Soltis DE, Hufford L. 2001. Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation. Systematic Biology 50: 817847.
  • Franzke A, Hurka H, Janssen D, Neuffer B, Friesen N, Markov M, Mummenhoff K. 2004. Molecular signals for late Tertiary/early Quaternary range splits of an Eurasian steppe plant: Clausia aprica (Brassicaceae). Molecular Ecology 13: 27892795.
  • Gao L, Su Y-J, Wang T. 2010. Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects. Journal of Systematics and Evolution 48: 7793.
  • Gladenkov AY, Oleinik AE, Marincovich L, Barinov KB. 2002. A refined age for the earliest opening of Bering Strait. Palaeogeography Palaeoclimatology Palaeoecology 183: 321328.
  • Grant V. 1993. Origin of floral isolation between ornithophilous and sphingophilous plant species. Proceedings of the National Academy of Sciences, USA 90: 77297733.
  • Grant V. 1994. Historical development of ornithophily in the western North American flora. Proceedings of the National Academy of Sciences, USA 91: 1040710411.
  • Grassi F, Minuto L, Casazza G, Labra M, Sala F. 2009. Haplotype richness in refugial areas: phylogeographical structure of Saxifraga callosa. Journal of Plant Research 122: 377387.
  • Griffin PC, Robin C, Hoffmann AA. 2011. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biology 9: 19.
  • Hodges SA. 1997. Floral nectar spurs and diversification. International Journal of Plant Sciences 158: S81S88.
  • Hodges SA, Arnold ML. 1994. Columbines: a geographically widespread species flock. Proceedings of the National Academy of Sciences, USA 91: 51295132.
  • Hodges SA, Arnold ML. 1995. Spurring plant diversification: are floral nectar spurs a key innovation? Proceedings of the Royal Society of London, Series B 262: 343348.
  • Hodges SA, Derieg NJ. 2009. Adaptive radiations: from field to genomic studies. Proceedings of the National Academy of Sciences, USA 106(Suppl 1): 99479954.
  • Hodges SA, Fulton M, Yang JY, Whittall JB. 2004. Verne Grant and evolutionary studies of Aquilegia. New Phytologist 161: 113120.
  • Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23: 254267.
  • Jeffory O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: the beginning of incongruence? Trends in Genetics 22: 225231.
  • Jian S, Soltis PS, Gitzendanner MA, Moore MJ, Li R, Hendry TA, Qiu Y-L, Dhingra A, Bell CD, Soltis DE. 2008. Resolving an ancient, rapid radiation in Saxifragales. Systematic Biology 57: 3857.
  • Kadereit JW, Licht W, Uhink CH. 2008. Asian relationships of the flora of the European Alps. Plant Ecology & Diversity 1: 171179.
  • Kay KM, Whittall JB, Hodges SA. 2006. A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evolutionary Biology 6: 36.
  • Kelchner SA. 2000. The evolution of non-coding chloroplast DNA and its application in plant systematics. Annals of the Missouri Botanical Garden 87: 482498.
  • Kramer EM. 2009. Aquilegia: a new model for plant development, ecology, and evolution. Annual Review of Plant Biology 60: 261277.
  • Kramer EM, Hodges SA. 2010. Aquilegia as a model system for the evolution and ecology of petals. Philosophical Transactions of the Royal Society of London, Series B 365: 477490.
  • Kramer EM, Holappa L, Gould B, Jaramillo MA, Setnikov D, Santiago PM. 2007. Elaboration of B gene function to include the identity of novel floral organs in the lower eudicot Aquilegia. The Plant Cell 19: 750766.
  • Kuneš P, Pelánková B, Chytrý M, Jankovská V, Pokorný P, Petr L. 2008. Interpretation of the last-glacial vegetation of eastern-central Europe using modern analogues from southern Siberia. Journal of Biogeography 35: 22232236.
  • Lam H-M, Xu X, Liu X, Chen W, Yang G, Wong F-L, Li M-W, He W, Qin N, Wang B et al. 2010. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nature Genetics 42: 10531059.
  • Lemmon AR, Emme SA, Lemmon EM. 2012. Anchored hybrid enrichment for massively high-throughput phylogenomics. Systematic Biology 61: 727744.
  • Lin CP, Huang JP, Wu CS, Hsu CY, Chaw SM. 2010. Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Genome Biology and Evolution 2: 504517.
  • Liu J-Q, Gao T-G, Chen Z-D, Lu A-M. 2002. Molecular phylogeny and biogeography of the Qinghai–Tibet Plateau endemic Nannoglottis (Asteraceae). Molecular Phylogenetics and Evolution 23: 307325.
  • Maddison W. 1997. Gene trees in species trees. Systematic Biology 46: 523536.
  • Maddison WP, Maddison DR. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75. [WWW document] URL http://mesquiteproject.org [accessed on 2 August 2011].
  • Mai DH, Walter H. 1978. Die floren der Haselbacher Serie im Weisselster-Becken (Bezirk Leipzig, DDR). Abhandlungen des Staatliches Museums fur Minerologie und Geologie zu Dresden 28: 1200.
  • Mallet J. 1995. A species definition for the modern synthesis. Trends in Ecology & Evolution 10: 294299.
  • Massey SE, Churbanov A, Rastogi S, Liberles DA. 2008. Characterizing positive and negative selection and their phylogenetic effects. Gene 418: 2226.
  • Médail F, Diadema K. 2009. Glacial refugia influence plant diversity patterns in the Mediterranean Basin. Journal of Biogeography 36: 13331345.
  • Metzker ML. 2010. Sequencing technologies – the next generation. Nature Reviews Genetics 11: 3146.
  • Meyer M, Stenzel U, Hofreiter M. 2008. Parallel tagged sequencing on the 454 platform. Nature Protocols 3: 267278.
  • Miller KG, Kominz MA, Browning JV, Wright JD, Mountain GS, Katz ME, Sugarman PJ, Cramer BS, Christie-Blick N, Pekar SF. 2005. The Phanerozoic record of global sea-level change. Science 310: 12931298.
  • Mort ME, Archibald JK, Randle CP, Levsen ND, O'Leary TR, Topalov K, Wiegand CM, Crawford DJ. 2007. Inferring phylogeny at low taxonomic levels: utility of rapidly evolving cpDNA and nuclear ITS loci. American Journal of Botany 94: 173183.
  • Muller J. 1981. Fossil pollen records of extant angiosperms. Botanical Review 47: 1140.
  • Munz P. 1946. Aquilegia: the cultivated and wild columbines. Gentes Herbarum 7: 1150.
  • Neuffer B, Oyuntsetseg B, Schamsran Z, Friesen N, Hurka H. 2003. Contribution to the knowledge of the Flora of the Mongolian Altai. Feddes Repertorium 114: 358371.
  • Njuguna W, Liston A, Cronn RC, Ashman T-L, Bassil N. 2013. Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. Molecular Phylogenetics and Evolution 66: 1729.
  • Nylander JAA, Olsson U, Alström P, Sanmartín I. 2008a. Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Systematic Biology 57: 257268.
  • Nylander JAA, Wilgenbusch JC, Warren DL, Swofford DL. 2008b. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581583.
  • Ozenda P. 2009. On the genesis of the plant population in the Alps: new or critical aspects. Comptes Rendus Biologies 332: 10921103.
  • Parks M, Cronn RC, Liston A. 2009. Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biology 7: 84.
  • Parks M, Cronn RC, Liston A. 2012. Separating the wheat from the chaff: mitigating the effects of noise in a plastome phylogenomic data set from Pinus L. (Pinaceae). BMC Evolutionary Biology 12: 100.
  • Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C. 2003. Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300: 15631565.
  • Pignatti S. 2013. Flora d'Italia, 2nd edn. Bologna, Italy: Edagricole.
  • Pleijel F, Jondelius U, Norlinder E, Nygren A, Oxelman B, Schander C, Sundberg P, Thollesson M. 2008. Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies. Molecular Phylogenetics and Evolution 48: 369371.
  • Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Systematic Biology 53: 793808.
  • Posada D, Crandall KA. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817818.
  • Prazmo W. 1965. Cytogenetic studies on the genus Aquilegia. III. Inheritance of the traits distinguishing different complexes in the genus. Aquilegia 34: 403437.
  • Qiu Y-X, Fu C-X, Comes HP. 2011. Plant molecular phylogeography in China and adjacent regions: tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora. Molecular Phylogenetics and Evolution 59: 225244.
  • Rambaut A, Drummond AJ. 2007. Tracer v.1.4. [WWW document] URL http://tree.bio.ed.ac.uk/software/tracer/ [accessed on 12 April 2011].
  • Rannala B, Yang Z. 2008. Phylogenetic inference using whole genomes. Annual Review of genomics and Human Genetics 9: 217231.
  • Rechinger KH. 1992 Aquilegia. In: Rechinger KH, ed. Flora Iranica, vol 171: Ranunculaceae. Akademische Druck - u. Verlagsansstalt: Graz, Austria, 1118.
  • Ree RH, Moore BR, Webb CO, Donoghue MJ. 2005. A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution 59: 22992311.
  • Ree RH, Smith SA. 2008. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology 57: 414.
  • Reeves PA, Richards CM. 2009. Accurate inference of subtle population structure (and other genetic discontinuities) using principal coordinates. PLoS ONE 4: e4269.
  • Reeves PA, Richards CM. 2011. Species delimitation under the general lineage concept: an empirical example using wild North American hops (Cannabaceae: Humulus lupulus). Systematic Biology 60: 4559.
  • Rodriguez-de la Rosa RA, Cevallos-Ferriz SRS, Silva-Pineda A. 1998. Paleobiological implications of Campanian coprolites. Palaeogeography Palaeoclimatology Palaeoecology 142: 231254.
  • Ronquist F. 1997. Dispersal-vicariance analysis: a new approach to the quantification of historical biogeography. Systematic Biology 46: 195203.
  • Ronquist F. 2001. DIVA 1.2. [WWW document] URL ftp.uu.se or ftp.systbot.uu.se. [accessed on 21 January 2012].
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 15721574.
  • Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL. 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92: 142166.
  • Shaw J, Lickey EB, Schilling EE, Small RL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany 94: 275288.
  • Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51: 492508.
  • Shimodaira H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 11141116.
  • Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17: 12461247.
  • Simmons M, Ochoterena H. 2000. Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369381.
  • Staats M, Cuenca A, Richardson JE, Ginkel RV-V, Petersen G, Seberg O, Bakker FT. 2011. DNA damage in plant herbarium tissue. PLoS ONE 6: e28448.
  • Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22: 26882690.
  • Steele PR, Hertweck KL, Mayfield D, McKain MR, Leebens-Mack J, Pires JC. 2012. Quality and quantity of data recovered from massively parallel sequencing: examples in Asparagales and Poaceae. American Journal of Botany 99: 330348.
  • Steele PR, Pires JC. 2011. Biodiversity assessment: state-of-the-art techniques in phylogenomics and species identification. American Journal of Botany 98: 415425.
  • Strand AE, Milligan BG, Pruitt CM. 1996. Are populations islands? Analysis of chloroplast DNA variation in Aquilegia. Evolution 66: 1729.
  • Straub SCK, Parks M, Weitemier K, Fishbein M, Cronn RC, Liston A. 2012. Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. American Journal of Botany 99: 349364.
  • Swofford D. 2002. PAUP*: phylogenetic analysis using parsimony (* and Other Methods). Version 4.0 b10. Sunderland, MA, USA: Sinauer Associates.
  • Takahata N, Slatkin M. 1984. Mitochondrial gene flow. Proceedings of the National Academy of Sciences, USA 81: 17641767.
  • Taylor RJ. 1967. Interspecific hybridization and its evolutionary significance in the genus Aquilegia. Brittonia 19: 374390.
  • Tsitrone A, Kirkpatrick M, Levin DA. 2003. A model for chloroplast capture. Evolution 57: 17761782.
  • Turner TL, Bourne EC, Von Wettberg EJ, Hu TT, Nuzhdin SV. 2010. Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils. Nature Genetics 42: 260263.
  • Voelckel C, Borevitz JO, Kramer EM, Hodges SA. 2010. Within and between whorls: comparative transcriptional profiling of Aquilegia and Arabidopsis. PLoS ONE 5: e9735.
  • Wang H, Moore MJ, Soltis PS, Bell CD, Brockington SF, Alexandre R, Davis CC, Latvis M, Manchester SR, Soltis DE. 2009a. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proceedings of the National Academy of Sciences, USA 106: 38533858.
  • Wang W, Lu A-M, Ren Y, Endress ME, Chen Z-D. 2009b. Phylogeny and classification of Ranunculales: evidence from four molecular loci and morphological data. Perspectives in Plant Ecology Evolution and Systematics 11: 81110.
  • Weber W. 2003. The Middle Asian Element in the Southern Rocky Mountain Flora of the western United States: a critical biogeographical review. Journal of Biogeography 30: 649685.
  • Wendel JF, Doyle JJ. 1998. Phylogenetic incongruence: window into genome history and molecular evolution. In: Soltis DE, Soltis PS, Doyle JJ, eds. Molecular systematics of plants II: DNA sequencing. Dordrecht, the Netherlands: Kluwer Academic Publisher, 265296.
  • Whitfield JB, Kjer KM. 2008. Ancient rapid radiations of insects: challenges for phylogenetic analysis. Annual Review of Entomology 53: 26.
  • Whittall JB, Hodges SA. 2007. Pollinator shifts drive increasingly long nectar spurs in columbine flowers. Nature 447: 706709.
  • Wikstrom N, Savolainen V, Chase MW. 2001. Evolution of the angiosperms: calibrating the family tree. Proceedings of the Royal Society of London, Series B 268: 22112220.
  • Wortley AH, Rudall PJ, Harris DJ, Scotland RW. 2005. How much data are needed to resolve a difficult phylogeny? Case study in Lamiales. Systematic Biology 54: 697709.
  • Yang Z. 2002. Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci. Genetics 162: 18111823.
  • Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 15861591.
  • Zhang Y-J, Ma P-F, Li D-Z. 2011. High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae). PLoS ONE 6: e20596.