Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets

Molecular Phylogenetics and Evolution - Tập 48 - Trang 1027-1040 - 2008
Ze-Long Nie1,2, Jun Wen1,3,4, Hiroshi Azuma5, Yin-Long Qiu6, Hang Sun1, Ying Meng1,7, Wei-Bang Sun1, Elizabeth A. Zimmer3
1Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 132# Lanhei Road, Kunming, Yunnan 650204, PR China
2Graduate School of Chinese Academy of Sciences, Beijing 100039, PR China
3Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC 20013-7012, USA
4Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, PR China
5Department of Botany, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
6Department of Ecology and Evolutionary, University of Michigan, Ann Arbor, MI 48109-1048, USA
7Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, Yunnan 650204, PR China

Tài liệu tham khảo

Archambault, 2004, Phylogenetic utility of the LEAFY/FLORICAULA gene in the Caesalpinioideae (Leguminosae), gene duplication and a novel insertion, Syst. Bot., 29, 609, 10.1600/0363644041744374 Azuma, 2001, Molecular phylogeny of Magnoliaceae, the biogeography of tropical and temperate disjunctions, Am. J. Bot., 88, 2275, 10.2307/3558389 Azuma, 2004, Close relationship between Mexican and Chinese Magnolia (subtropical disjunct of Magnoliaceae) inferred from molecular and floral scent analyses, Acta Phytotaxon. Geobot., 55, 167 Azuma, 2000, Molecular phylogeny of Magnolia based on chloroplast DNA sequence data (trnK intron, psbA–trnH and atpB–rbcL intergenic spacer regions) and floral scent chemistry, 219 Azuma, 1999, Molecular phylogeny of Magnolia (Magnoliaceae) inferred from cpDNA sequences and evolutionary divergence of floral scents, J. Plant Res., 112, 291, 10.1007/PL00013885 Boss, 2002, Association of dwarfism and floral induction with a grape ‘green revolution’ mutation, Nature, 416, 847, 10.1038/416847a Cevallos-Ferriz, 1990, Vegetative remains of the Magnoliaceae from the Princeton chert (Middle Eocene) of British Columbia, Can. J. Bot., 68, 1327, 10.1139/b90-169 Chase, 1993, Phylogenetics of seed plants, an analysis of nucleotide sequences from the plastid gene rbcL, Ann. MO. Bot. Gard., 80, 528, 10.2307/2399846 Chen, 1993, Notes on Magnoliaceae III, the Magnoliaceae of China, Ann. MO. Bot. Gard., 80, 999, 10.2307/2399942 Chun, 1963, Genus speciesque novae Magnoliacearum sinensium, Acta Phytotaxon. Sin., 8, 281 Collinson, 1993, Magnoliophyta (Angiospermae), vol. 2, 809 Cronquist, 1981 Cunningham, 1997, Can three incongruence tests predict when data should be combined?, Mol. Biol. Evol., 14, 733, 10.1093/oxfordjournals.molbev.a025813 Dandy, 1927, The genera of Magnoliaceae, Kew Bul., 7, 264 Dandy, 1971, The classification of the Magnoliaceae, Newsl. Am. Magnolia Soc., 8, 3 Dandy, 1978, Key to subgenera and sections of Magnolia, 27 Dandy, 1978, Revised survey of the genus Magnolia together with Manglietia and Michelia, 29 Degnan, 2006, Discordance of species trees with their most likely gene trees, PLoS Genet., 2, 762, 10.1371/journal.pgen.0020068 Dilcher, 1984, Archaeanthus: an early angiosperm from the Cenomanian of the western interior of North America, Ann. MO. Bot. Gard., 71, 351, 10.2307/2399030 Donoghue, 2004, Patterns in the assembly of temperate forests around the Northern Hemisphere, Philos. Trans. R. Soc. Lond. B Biol. Sci., 359, 1633, 10.1098/rstb.2004.1538 Dorofeev, 1974, Magnoliaceae-Eucommiaceae, vol. 1 Doyle, 1987, A rapid DNA isolation procedure for small quantities of fresh leaf tissue, Phytochem. Bul., 19, 11 Drummond, 2006, Relaxed phylogenetics and dating with confidence, PLoS Biol., 4, 699, 10.1371/journal.pbio.0040088 Drummond, 2007, BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evol. Biol, 7, 214, 10.1186/1471-2148-7-214 Edwards, 2000, Gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies, Evolution, 54, 1839 Farris, 1994, Testing significance of incongruence, Cladistics, 10, 315, 10.1111/j.1096-0031.1994.tb00181.x Felsenstein, 1988, Phylogenies from molecular sequences, inference and reliability, Ann. Rev. Genet., 22, 521, 10.1146/annurev.ge.22.120188.002513 Figlar, 1993, Stone Magnolias, Arnoldia, 53, 2 Figlar, R.B., 2006. Taxonomy topics - a new classification for Magnolia. In: Royal Horticultural Society (Ed.), Rhododendrons with Camellias and Magnolias. MPG Books Ltd., Bodmin, Cornwall, pp. 69–82. Figlar, 2004, Notes on Magnoliaceae IV, Blumea, 49, 87, 10.3767/000651904X486214 Friis, 1997, Fossil history of magnoliid angiosperms, 121 Friis, 2006, Cretaceous angiosperm flowers: innovation and evolution in plant reproduction, Palaeogeogr. Palaeoclimatol. Palaeoecol., 232, 251, 10.1016/j.palaeo.2005.07.006 Frodin, 1996 Frumin, 1996, Liriodendroid seeds from the Late Cretaceous of Kazakhstan and North Carolina, USA, Rev. Palaeobot. Palynol., 94, 39, 10.1016/0034-6667(95)00136-0 Frumin, 1999, Magnoliid reproductive organs from the Cenomanian-Turonian of north-western Kazakhstan: Magnoliaceae and Illiciaceae, Plant Syst. Evol., 216, 265, 10.1007/BF01084403 Gong, 2001, The cross compatibility of Magnoliaceae, Acta Bot. Yunnan, 23, 339 Graham, 1999 Graham, 2000, Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms, Am. J. Bot., 87, 1712, 10.2307/2656749 Hall, 1999, BioEdit, a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucl. Acids. Symp. Ser., 41, 95 Hipp, 2004, Congruence versus phylogenetic accuracy, Revisiting the incongruence length difference test, Syst. Biol., 53, 81, 10.1080/10635150490264752 Ho, 2005, Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation, Mol. Biol. Evol., 22, 1355, 10.1093/molbev/msi125 Hoot, 2001, The utility of nuclear ITS, a LEAFY homolog intron, and chloroplast atpB–rbcL spacer region data in phylogenetic analyses and species delimitation in Isoetes, Am. Fern J., 91, 166, 10.1640/0002-8444(2001)091[0166:TUONIA]2.0.CO;2 Huelsenbeck, 2001, MRBAYES, Bayesian inference of phylogenetic trees, Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754 Ickert-Bond, 2007, Comparative infructescence morphology in Altingia (Altingiaceae) and discordance between morphological and molecular phylogenies, Am. J. Bot., 94, 1094, 10.3732/ajb.94.7.1094 Ji, 2006, Phylogeny and classification of Paris (Melanthiaceae) inferred from DNA sequence data, Ann. Bot., 98, 245, 10.1093/aob/mcl095 Jobes, 1998, Molecular systematics of the Magnoliaceae: a review of recent molecular studies, 59 Kim, 2001, Phylogenetic relationships in family Magnoliaceae inferred from ndhF sequences, Am. J. Bot., 88, 717, 10.2307/2657073 Kim, 2004, DNA sequences from Miocene fossils, an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae), Am. J. Bot., 91, 615, 10.3732/ajb.91.4.615 Kolukisaoglu, 1995, Divergence of the phytochrome gene family predates angiosperm evolution and suggests that Selaginella and Equisetum arose prior to Psilotum, J. Mol. Evol., 41, 329, 10.1007/BF01215179 Law, 1984, A preliminary study on the taxonomy of the family Magnoliaceae, Acta Phytotaxon. Sin., 22, 80 Law, Y.W., 1996. Magnoliaceae. In: Flora Reipublicae Popularis Sinicae, vol. 30, Issue No. 1, Science Press, Beijing, pp. 82–269. Law, 2004 Li, 2003, Phylogenetic relationships in Magnoliaceae subfam. Magnolioideae, a morphological cladistic analysis, Plant Syst. Evol., 242, 33, 10.1007/s00606-003-0055-5 Liang, 2007, Development of a BAC library resource for yellow poplar (Liriodendron tulipifera) and the identification of genomic regions associated with flower development and lignin biosynthesis, Tree Genet. Genomics, 3, 215, 10.1007/s11295-006-0057-x Liu, 1995, The origin, evolution and phytogeography of Magnoliaceae, J. Trop. Subtrop. Bot., 3, 1 Liu, 1996, Catalogue of Cenozoic megafossil plants in China, Palaeontogr. Abt. B Paläophytol., 238, 141 Lourens, 2005, Astronomical pacing of late Palaeocene to early Eocene global warming events, Nature, 435, 1083, 10.1038/nature03814 Maddison, 1997, Gene trees in species trees, Syst. Biol., 46, 523, 10.1093/sysbio/46.3.523 Mai, 1995 Manabe, 1997, The structure and function of phytochrome A, the roles of the entire molecule and of its various parts, J. Plant Res., 110, 109, 10.1007/BF02506850 Manchester, 1999, Biogeographical relationships of North American Tertiary floras, Ann. Mo. Bot. Gard., 86, 472, 10.2307/2666183 Mathews, 2003, Adaptive evolution in the photosensory domain of phytochrome A in early angiosperms, Mol. Biol. Evol., 20, 1087, 10.1093/molbev/msg123 Mathews, 1999, The root of angiosperm phylogeny inferred from duplicate phytochrome genes, Science, 268, 947, 10.1126/science.286.5441.947 Mathews, 1995, Evolution of the phytochrome gene family and its utility for phylogenetic analyses of angiosperms, Ann. Mo. Bot. Gard., 82, 296, 10.2307/2399882 Mathews, 1996, The phytochrome gene family in grasses (Poaceae), a phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms, Mol. Biol. Evol., 13, 1141, 10.1093/oxfordjournals.molbev.a025677 McCartan, 1990, Late Tertiary floral assemblage from upland gravel deposits of the southern Maryland Coastal plain, Geology, 18, 311, 10.1130/0091-7613(1990)018<0311:LTFAFU>2.3.CO;2 Milne, 2006, Northern hemisphere plant disjunctions, a window on Tertiary land bridges and climate change?, Ann. Bot., 98, 465, 10.1093/aob/mcl148 Milne, 2002, The origin and evolution of tertiary relict floras, Adv. Bot. Res., 38, 281, 10.1016/S0065-2296(02)38033-9 Muller, 1981, Fossil pollen records of extant angiosperms, Bot. Rev., 47, 1, 10.1007/BF02860537 Nie, 2005, Monophyly of Kelloggia Torrey ex Benth. (Rubiaceae) and evolution of its intercontinental disjunction between western North America and eastern Asia, Am. J. Bot., 92, 642, 10.3732/ajb.92.4.642 Nooteboom, 1985, Notes on Magnoliaceae, with a revision of Pachylarnax and Elmerrillia and the Malesian species of Manglietia and Michelia, Blumea, 31, 65 Nooteboom, 1993, Magnoliaceae, vol. II, 391 Nooteboom, 1998, The tropical Magnoliaceae and their classification, 71 Parkinson, 1999, Multigene analyses identify the three earliest lineages of extant flowering plants, Curr. Biol., 9, 1485, 10.1016/S0960-9822(00)80119-0 Parks, 1983, Genetic divergence within the genus Liriodendron (Magnoliaceae), Ann. Mo. Bot. Gard., 70, 658, 10.2307/2398983 Parks, 1994, The significance of allozyme variation and introgression in the Liriodendron tulipifera complex (Magnoliaceae), Am. J. Bot., 81, 878, 10.2307/2445769 Parks, 1990, Molecular divergence between Asian and North American species of Liriodendron (Magnoliaceae) with implications for interpretation of fossil floras, Am. J. Bot., 77, 1243, 10.2307/2444585 Peigler, 1989, Fossil Magnoliaceae, a review of literature, Magnolia (J. Magnolia Soc.), 25, 1 Peng, 1999, ‘Green revolution’ genes encode mutant gibberellin response modulators, Nature, 400, 256, 10.1038/22307 Pérez-Losada, 2004, Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches, Syst. Biol., 53, 244, 10.1080/10635150490423458 Posada, 2004, Model selection and model averaging in phylogenetics, advantages of the AIC and Bayesian approaches over likelihood ratio tests, Syst. Biol., 53, 793, 10.1080/10635150490522304 Posada, 1998, Modeltest, testing the model of DNA substitution, Bioinformatics, 14, 817, 10.1093/bioinformatics/14.9.817 Qiu, 1993, Molecular phylogenetics of the Magnoliidae, cladistic analyses of nucleotide sequences of the plastid gene rbcL, Ann. Mo. Bot. Gard., 80, 587, 10.2307/2399848 Qiu, 1995, A chloroplast DNA phylogenetic study of the eastern Asia–eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae), Am. J. Bot., 82, 1582, 10.2307/2446187 Qiu, 1995, Molecular divergence in the eastern Asia eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae), Am. J. Bot., 82, 1589, 10.2307/2446188 Qiu, 1999, The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes, Nature, 402, 404, 10.1038/46536 Qiu, 1994, Disparity of allozyme variation levels in three Magnolia (Magnoliaceae) species from the southeastern United States, Am. J. Bot., 81, 1300, 10.2307/2445406 Rambaut, A., Drummond, A.J., 2004. Tracer v1.3, Available from http://evolve.zoo.ox.ac.uk/software.html. Reeves, 2001, Molecular systematics of Iridaceae: evidence from four plastid DNA regions, Am. J. Bot., 88, 2074, 10.2307/3558433 Rember, W.C., 1991. Stratigraphy and paleobotany of Miocene Lake sediments near Clarkia, Idaho. Ph.D. dissertation, University of Idaho, Moscow, Idaho, USA. Renner, 2005, Relaxed molecular clocks for dating historical plant dispersal events, Trends Plant Sci., 10, 550, 10.1016/j.tplants.2005.09.010 Rieseberg, 1991, Phylogenetic consequences of cytoplasmic gene flow in plants, Evol. Trends, P1. 5, 65 Roger, 2006, The origin and diversification of eukaryotes, problems with molecular phylogenetics and molecular clock estimation, Philos. Trans. R. Soc. Lond. B Biol. Sci., 361, 1039, 10.1098/rstb.2006.1845 Sanderson, 2002, Estimating absolute rates of molecular evolution and divergence times, a penalized likelihood approach, Mol. Biol. Evol., 19, 101, 10.1093/oxfordjournals.molbev.a003974 Sanderson, 2003, r8s: Inferring absolute rates of molecular evolution and divergence dates in the absence of a molecular clock, Bioinformatics, 19, 301, 10.1093/bioinformatics/19.2.301 Setoguchi, 2000, Intersectional gene flow between insular endemics of Ilex (Aquifoliaceae) on the Bonin Islands and the Ryukyu Islands, Am. J. Bot., 87, 793, 10.2307/2656887 Sheahan, 2000, Phylogenetic relationships within Zygophyllaceae based on DNA sequences of three plastid regions, with special emphasis on Zygophylloideae, Syst. Bot., 25, 371, 10.2307/2666648 Shi, 2000, Phylogenetic relationships of Magnoliaceae inferred from cpDNA matK sequences, Theor. Appl. Genet., 101, 925, 10.1007/s001220051563 Shimodaira, 1999, Multiple comparisons of log-likelihoods with applications to phylogenetic inference, Mol. Biol. Evol., 16, 1114, 10.1093/oxfordjournals.molbev.a026201 Silverstone, 1998, The Arabidopsis RGA gene encodes a transcriptional regulator repressing the gibberellin signal transduction pathway, Plant Cell, 10, 155, 10.1105/tpc.10.2.155 Small, 2004, Use of nuclear genes for phylogeny reconstruction in plants, Aust. Syst. Bot., 17, 145, 10.1071/SB03015 Soltis, 1996, Discordance between ITS and chloroplast topologies in the Boykinia group (Saxifragaceae), Syst. Bot., 21, 169, 10.2307/2419746 Soltis, 1995, Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae): evidence of chloroplast capture and paraphyly, Evolution, 49, 727, 10.2307/2410326 Soltis, 1999, Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology, Nature, 402, 402, 10.1038/46528 Sun, 2004, A new proposal on generic division of the Chinese Magnoliaceae, Acta Bot. Yunnan, 26, 139 Swofford, D.L. 2003. PAUP* 4.0b10 Phylogenetic Analysis using Parsimony (*and other Methods), Version 4.0b10. Sinauer Associates Sunderland, Massachusetts. Takhtajan, 1969 Tanai, 1972, Tertiary history of vegetation in Japan, 235 Tao, 1992, Two angiosperm reproductive organs from the Early Cretaceous of China, Acta Phytotaxon. Sin., 30, 423 Templeton, 1983, Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes, Evolution, 37, 221, 10.2307/2408332 Thompson, 1997, The CLUSTAL X windows interface, flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucl. Acids Res., 25, 4876, 10.1093/nar/25.24.4876 Thorne, 1993, Magnoliaceae, 27 Thornsberry, 2001, Dwarf8 polymorphisms associate with variation in flowering time, Nat. Genet., 28, 286, 10.1038/90135 Tiffney, 1977, Fruits and seeds of the Brandon Lignite, Magnoliaceae, Bot. J. Linnean Soc., 75, 299, 10.1111/j.1095-8339.1977.tb01491.x Tralau, 1963, Asiatic dicotyledonous affinities in the Cainozoic flora of Europe, Kungliga Svenska Vetenskapsakademiens Handlingar, 9, 1 Ueda, 2000, Molecular phylogeny of the Magnoliaceae, 205 Vázquez-garcia, 1994, Magnolia (Magnoliaceae) in Mexico and Central America, a synopsis, Brittonia, 46, 1, 10.2307/2807454 Wagner, 1987, Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids, PNAS, 84, 2097, 10.1073/pnas.84.7.2097 Walther, 1999, Die Tertiärflora von Kleinsaubernitz bei Bautzen, Palaeontogr. Abt. B Paläophytol., 249, 63 Wang, 2006, The utility of matK gene in the phylogenetic analysis of the genus Magnolia, Acta Phytotaxon. Sin., 44, 135, 10.1360/aps040013 Wen, 1999, Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants, Ann. Rev. Ecol. Syst., 30, 421, 10.1146/annurev.ecolsys.30.1.421 Wen, 2001, Evolution of eastern Asian-Eastern North American biogeographic disjunctions, a few additional issues, Int. J. Plant Sci., 162, S117, 10.1086/322940 Wen, 2007, Phylogeny of Vitaceae based on the nuclear GAI1 gene sequences, Can. J. Bot., 85, 731, 10.1139/B07-071 Wendel, 1998, Phylogenetic incongruence: window into genome history and speciation, 265 White, 1997, An 18 million year record of vegetation and climate change in northwestern Canada and Alaska, tectonic and global climatic correlates, Palaeogeogr. Palaeoclimatol. Palaeoecol., 130, 293, 10.1016/S0031-0182(96)00146-0 Wiens, 1998, Combining data sets with different phylogenetic histories, Syst. Biol., 47, 568, 10.1080/106351598260581 Wikström, 2001, Evolution of the angiosperms, calibrating the family tree, Philos. Trans. R. Soc. Lond. B Biol. Sci., 268, 2211, 10.1098/rspb.2001.1782 Wolfe, 1969, Neogene floristic and vegetational history of the Pacific Northwest, Madroño, 20, 83 Wolfe, 1972, An interpretation of Alaskan tertiary floras, 201 Wolfe, 1975, Some aspects of plant geography of the Northern Hemisphere during the late Cretaceous and Tertiary, Ann. Mo. Bot. Gard., 62, 264, 10.2307/2395198 Wolfe, J.A., 1977. Paleogene Floras from the Gulf of Alaska Region. US. Geological Survey, professional 997, 1–108. Wolfe, J.A., 1985. Distribution of major vegetational types during the Tertiary: the carbon cycle and atmospheric CO2 natural variations archean to present; Proceedings of the Chapman Conference on Natural Variations in Carbon Dioxide and the Carbon Cycle, Tarpon Springs, FL, January 9–13, 1984 (A86-39426 18–46). American Geophysical Union, Washington, DC, pp. 357–375. Wolfe, 1987, Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast and nuclear DNAs, PNAS, 84, 9054, 10.1073/pnas.84.24.9054 Xu, 2006, Comparative floral anatomy and ontogeny in Magnoliaceae, Plant Syst. Evol., 258, 1, 10.1007/s00606-005-0361-1 Yi, 2007, Phylogeny of Rhus (Anacardiaceae) based on sequences of nuclear Nia-i3 intron and chloroplast trnC-trnD, Syst. Bot., 32, 379, 10.1600/036364407781179635 Yoo, 2002, Discordance of chloroplast and nuclear ribosomal DNA in Osmorhiza (Apiaceae), Am. J. Bot., 89, 966, 10.3732/ajb.89.6.966 Zachos, 2001, Trends, rhythms, and aberrations in global climate 65 Ma to present, Science, 292, 686, 10.1126/science.1059412 Zhang, 2001, Fossil records of Magnoliaceae, Acta Palaeontol. Sin., 40, 433 Zwickl, D.J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.