Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)
Tóm tắt
Từ khóa
Tài liệu tham khảo
APG III, 2009, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III, Bot. J. Linn. Soc., 161, 105, 10.1111/j.1095-8339.2009.00996.x
Bamboo Phylogeny Group, 2012, An updated tribal and subtribal classification for the Bambusoideae (Poaceae), Proceedings of the 9th World Bamboo Congress, 3
Barrett, 2013, Plastid genomes and deep relationships among the commelinid monocot angiosperms, Cladistics, 29, 65, 10.1111/j.1096-0031.2012.00418.x
Bergsten, 2005, A review of long-branch attraction, Cladistics, 21, 163, 10.1111/j.1096-0031.2005.00059.x
Birky, 1983, An approach to population and evolutionary genetic theory for genes in mitochondria and chloroplasts, and some results, Genetics, 103, 513, 10.1093/genetics/103.3.513
Bouchenak-Khelladi, 2008, Large multi-gene phylogenetic trees of the grasses (Poaceae): progress towards complete tribal and generic level sampling, Mol. Phylogenet. Evol., 47, 488, 10.1016/j.ympev.2008.01.035
Bouchenak-Khelladi, 2010, Biogeography of the grasses (Poaceae): a phylogenetic approach to reveal evolutionary history in geographical space and ecological time, Bot. J. Linn. Soc., 162, 543, 10.1111/j.1095-8339.2010.01041.x
Brandley, 2005, Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards, Syst. Biol., 54, 373, 10.1080/10635150590946808
Brown, 2007, The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics, Syst. Biol., 56, 643, 10.1080/10635150701546249
Burke, 2012, Plastome sequences of two new world bamboos-Arundinaria giganteaandCryptochloa strictiflora(Poaceae)-extended phylogenomic understanding of Bambusoideae, Am. J. Bot., 99, 1951, 10.3732/ajb.1200365
Burlerigh, 2011, Genome-scale phylogenetics: inferring the plant Tree of Life from 18,896 gene trees, Syst. Biol., 60, 117, 10.1093/sysbio/syq072
Bystriakova, 2003, Bamboo biodiversity: information for planning conservation and management in the Asia-Pacific region
Chen, 2003, Chromosome atlas of various bamboo species, Chromosome atlas of major economic plants genome in China IV
Christin, 2008, Oligocene CO2decline promoted C4photosynthesis in grasses, Curr. Biol., 18, 37, 10.1016/j.cub.2007.11.058
Christin, 2008, Evolutionary switch and genetic convergence onrbcLfollowing the evolution of C4photosynthesis, Mol. Biol. Evol., 25, 2361, 10.1093/molbev/msn178
Delsuc, 2005, Phylogenomics and the reconstruction of the tree of life, Nat. Rev. Genet., 6, 361, 10.1038/nrg1603
Doyle, 1987, A rapid DNA isolation procedure for small quantities of fresh leaf tissue, Phytochem. Bull., 19, 11
Drummond, 2012, Multiple continental radiations and correlates of diversification inLupinus(Leguminosae): testing for key innovation with incomplete taxon sampling, Syst. Biol., 61, 443, 10.1093/sysbio/syr126
Felsenstein, 1978, Cases in which parsimony or compatibility methods will be positively misleading, Syst. Zool., 27, 401, 10.2307/2412923
Flynn, 2005, Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships, Syst. Biol., 54, 317, 10.1080/10635150590923326
Fu, 2001, Chinese moso bamboo: its importance, Bamboo, 22, 5
Guo, 2001, Genetic variation and evolution of the alpine bamboos (Poaceae: Bambusoideae) using DNA sequence data, J. Plant Res., 114, 315, 10.1007/PL00013993
Guo, 2004, Phylogenetics of theThamnocalamusgroup and its allies (Gramineae: Bambusoideae): inference from the sequence of GBSSI gene and ITS spacer, Mol. Phylogenet. Evol., 30, 1, 10.1016/S1055-7903(03)00161-1
Hackett, 2008, A phylogenomic study of birds reveals their evolutionary history, Science, 320, 1763, 10.1126/science.1157704
Hedtke, 2006, Resolution of phylogenetic conflict in large data sets by increased taxon sampling, Syst. Biol., 55, 522, 10.1080/10635150600697358
Hodkinson, 2010, Phylogenetic analyses of plastid and nuclear DNA sequences indicate a rapid late Miocene radiation of the temperate bamboo tribe Arundinarieae (Poaceae, Bambusoideae), Plant Ecol. Divers., 3, 109, 10.1080/17550874.2010.521524
Huelsenbeck, 1998, Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved? Syst, Biol., 47, 519
Huson, 2006, Application of phylogenetic networks in evolutionary studies, Mol. Biol. Evol., 23, 254, 10.1093/molbev/msj030
Jansen, 2007, Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns, Proc. Natl Acad. Sci. U. S. A., 104, 19369, 10.1073/pnas.0709121104
Janzen, 1976, Why bamboos wait so long to flower, Ann. Rev. Ecol. Syst., 7, 347, 10.1146/annurev.es.07.110176.002023
Jeffroy, 2006, Phylogenomics: the beginning of incongruence?, Trends Genet, 22, 225, 10.1016/j.tig.2006.02.003
Jian, 2008, Resolving an ancient, rapid radiation in Saxifragales, Syst. Biol., 57, 38, 10.1080/10635150801888871
Katoh, 2005, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res., 33, 511, 10.1093/nar/gki198
Kelchner, 2013, Higher level phylogenetic relationships within the bamboos (Poaceae: Bambusoideae) based on five plastid markers, Mol. Phylogenet. Evol., 67, 404, 10.1016/j.ympev.2013.02.005
Kennedy, 2005, Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks, Syst. Biol., 54, 620, 10.1080/106351591007462
Lanfear, 2012, PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses, Mol. Biol. Evol., 29, 1695, 10.1093/molbev/mss020
Lerner, 2011, Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers, Curr. Biol., 21, 1838, 10.1016/j.cub.2011.09.039
Li, 2008, Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci, Syst. Biol., 57, 519, 10.1080/10635150802206883
Li, 1999, Taxonomy and biogeography of the Bambuseae (Gramineae: Bambusoideae), Bamboo—conservation, diversity, ecogeography, germplasm, resource utilization and taxonomy. Proceeding of training course cum workshop, Kunming and Xishuangbanna, Yunnan, China, 14
Li, 2006, Bambuseae in Flora of China
Li, 2010, De novo assembly of human genomes with massively parallel short read sequencing, Genome Res., 20, 265, 10.1101/gr.097261.109
Marshall, 2010, Cryptic failure if partitioned Bayesian phylogenetic analyses: lost in the land of long trees, Syst. Biol., 59, 108, 10.1093/sysbio/syp080
McClure, 1973, The Bamboos: a fresh perspective
Moore, 2007, Using plastid genome-scale data to resolve enigmatic relationships among the basal angiosperms, Proc. Natl Acad. Sci. U. S. A., 104, 19363, 10.1073/pnas.0708072104
Moore, 2010, Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots, Proc. Natl Acad. Sci. U. S. A., 107, 4623, 10.1073/pnas.0907801107
Moyle, 2012, Phylogeny and biogeography of the core babblers (Aves: Timaliidae), Syst. Biol., 61, 631, 10.1093/sysbio/sys027
Nylander, 2004, Bayesian phylogenetic analysis of combined data, Syst. Biol., 53, 47, 10.1080/10635150490264699
Nylander, 2008, AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics, Bioinformatics, 24, 581, 10.1093/bioinformatics/btm388
Ohrnberger, 1999, The bamboos of the world: annotated nomenclature and literature of the species and the higher and lower taxa
Palmer, 1985, Comparative organization of chloroplast genomes, Annu. Rev. Genet., 19, 325, 10.1146/annurev.ge.19.120185.001545
Parks, 2009, Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes, BMC Biol., 7, 84, 10.1186/1741-7007-7-84
Peng, 2008, Highly heterogeneous generic delimitation within the temperate bamboo clade (Poaceae: Bambusoideae): evidence from GBSSI and ITS sequences, Taxon, 57, 799, 10.1002/tax.573011
Philippe, 2011, Resolving difficult phylogenetic questions: why more sequences are not enough, PLoS Biol., 9, e1000602, 10.1371/journal.pbio.1000602
Posada, 2004, Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion 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
Rambaut, 1997, Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Comput. Appl. Biosci., 13, 235
Ronquist, 2003, MRBAYES 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180
Rosenberg, 2001, Incomplete taxon sampling is not a problem for phylogenetic inference, Proc. Natl Acad. Sci. U. S. A., 98, 10751, 10.1073/pnas.191248498
Ruiz-Sanchez, 2011, Biogeography and divergence time estimates of woody bamboos: insights in the evolution of neotropical bamboos, Bol. Soc. Bot. Mex., 88, 67
Schnitzler, 2011, Causes of plant diversification in the cape biodiversity hotspot of South Africa, Syst. Biol., 60, 343, 10.1093/sysbio/syr006
Shimodaira, 2002, An approximately unbiased test of phylogenetic tree selection, Syst. Biol., 51, 492, 10.1080/10635150290069913
Shimodaira, 2001, CONSEL: for assessing the confidence of phylogenetic tree selection, Bioinformatics, 17, 1246, 10.1093/bioinformatics/17.12.1246
Stamatakis, 2006, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, 22, 2688, 10.1093/bioinformatics/btl446
Stapleton, 2013, BergbambosandOldeanianew genera of African bamboos (Poaceae, Bambusoideae), PhytoKeys, 25, 87, 10.3897/phytokeys.25.6026
Sungkaew, 2009, Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s, J. Plant Res., 122, 95, 10.1007/s10265-008-0192-6
Swofford, 2002, PAUP*. Phylogenetic analysis using parsimony (* and other methods), version 4
Tamura, 2007, MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0, Mol. Biol. Evol., 24, 1596, 10.1093/molbev/msm092
Triplett, 2010, Phylogeny of the temperate bamboos (Poaceae: Bambusoideae: Bambuseae) with an emphasis onArundinariaand allies, Syst. Bot., 35, 102, 10.1600/036364410790862678
Valente, 2010, Unparalleled rates of species diversification in Europe, Proc. R. Soc. B, 277, 1489, 10.1098/rspb.2009.2163
Ward, 2010, Phylogeny and biogeography of Dolichoderine ants: effects of data partitioning and relict taxa on historical inference, Syst. Biol., 59, 342, 10.1093/sysbio/syq012
Waterway, 2009, Phylogeny, species richness, and ecological specialization in Cyperaceae tribe Cariceae, Bot. Rev., 75, 138, 10.1007/s12229-008-9024-6
Whitfield, 2007, Deciphering ancient rapid radiations, Trends Ecol. Evol., 22, 258, 10.1016/j.tree.2007.01.012
Wiens, 2005, Hylid frog phylogeny and sampling strategies for speciose clades, Syst. Biol., 54, 719, 10.1080/10635150500234625
Wiens, 2008, Branch length, support, and congruence: testing the phylogenomic approach with 20 nuclear loci in snakes, Syst. Biol., 57, 420, 10.1080/10635150802166053
Wu, 2009, Complete nucleotide sequence ofDendrocalamus latiflorusandBambusa oldhamiichloroplast genomes, Tree Physiol., 29, 847, 10.1093/treephys/tpp015
Wu, 2012, The phylogeny of the BEP clade in grasses revisited: evidence from the whole-genome sequences of chloroplast, Mol. Phylogenet. Evol., 62, 573, 10.1016/j.ympev.2011.10.019
Wyman, 2004, Automatic annotation of organellar genomes with DOGMA, Bioinformatics, 20, 3252, 10.1093/bioinformatics/bth352
Xi, 2012, Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales, Proc. Natl Acad. Sci. U. S. A., 109, 17519, 10.1073/pnas.1205818109
Yang, 2013, The monophyly ofChimonocalamusand conflicting gene trees in Arundinarieae (Poaceae: Bambusoideae) inferred from four plastid and two nuclear markers, Mol. Phylogenet. Evol., 68, 340, 10.1016/j.ympev.2013.04.002
Yang, 2014, Highly effective sequencing whole chloroplast genomes of angiosperms by nine novel universal primer pairs, Mol. Ecol. Resour., 14, 1024, 10.1111/1755-0998.12251
Zeng, 2010, Large multi-locus plastid phylogeny of the tribe Arundinarieae (Poaceae: Bambusoideae) reveals ten major lineages and low rate of molecular divergence, Mol. Phylogenet. Evol., 56, 821, 10.1016/j.ympev.2010.03.041
Zhang, 2011, High-throughput sequencing of six bamboo chloroplast genomes: phylogenetic implications for temperate woody bamboos (Poaceae: Bambusoideae), PLoS One, 6, e20596, 10.1371/journal.pone.0020596
Zhang, 2012, Complex evolution in Arundinarieae (Poaceae: Bambusoideae): incongruence between plastid and nuclear GBSSI gene phylogenies, Mol. Phylogenet. Evol., 63, 777, 10.1016/j.ympev.2012.02.023
Zhou, 2012, Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the Laurasiatherian mammals, Syst. Biol., 61, 150, 10.1093/sysbio/syr089