Phylogeny of Lamiidae

American Journal of Botany

Volumn 101, Issue 2, 2014, Pages 287-299

  Refulio Rodriguez, Nancy F ^a   Olmstead, Richard G ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Boraginales; Chloroplast; Garryales; Gentianales; Lamiales; Lamiidae; Mitochondrial; Solanales

Indexed keywords

PLANT DNA;

ANGIOSPERM; ARTICLE; BAYES THEOREM; BORAGINALES; CHLOROPLAST; DNA SEQUENCE; GARRYALES; GENETICS; GENTIANALES; LAMIALES; LAMIIDAE; MITOCHONDRIAL; MITOCHONDRION; MOLECULAR EVOLUTION; PHYLOGENY; PLASTID; SOLANALES;

BORAGINALES; CHLOROPLAST; GARRYALES; GENTIANALES; LAMIALES; LAMIIDAE; MITOCHONDRIAL; SOLANALES;

ANGIOSPERMS; BAYES THEOREM; DNA, PLANT; EVOLUTION, MOLECULAR; MITOCHONDRIA; PHYLOGENY; PLASTIDS; SEQUENCE ANALYSIS, DNA;

EID: 84893927462     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1300394     Document Type: Article

References (100)

1. Albach DC, Y Kun, J Søren rosendal, and, L Hong-Qing. 2009. Phy-logenetic placement of Triaenophora (formerly Scrophulariaceae) with some implications for the phylogeny of Lamiales. Taxon 58: 749-756.
2. Albach, D. C., H. M. Meudt and B Oxelman. 2005. Piecing together the "new" Plantaginaceae. American Journal of Botany 92: 297-315.
3. Albach D. C., P. S. Soltis, D. E. Soltis and R. G. Olmstead. 2001. Phylogenetic analysis of asterids based on sequences of four genes. Annals of the Missouri Botanical Garden 88: 163-212.
4. Angiosperm Phylogeny Group. 1998. An ordinal classification of the families of flowering plants. Annals of the Missouri Botanical Garden 85: 531-553.
5. Angiosperm Phylogeny Group. 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnean Society 141: 399-436.
6. Angiosperm Phylogeny Group. 2009. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161: 105-121.
7. Backlund, M., B. Oxelman and B Bremer. 2000. Phylogenetic relationships within the Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae. American Journal of Botany 87: 1029-1043.
8. Beardsley PM and R. G. Olmstead. 2002. Redefining Phrymaceae: The placement of Mimulus, tribe Mimuleae, and Phryma, character evolution and biogeography. American Journal of Botany 89: 1093-1102.
9. Bendiksby M, L Thorbek, A.C. Scheen, C Lindqvist and O Ryding 2011. An updated phylogeny and classification of Lamiaceae subfamily Lamioideae. Taxon 60: 471-484.
10. Bennett, J. R., and S Mathews. 2006. Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. American Journal of Botany 93: 1039-1051.
11. Bremer B, K Bremer, N Heidari, P Erixon, R.G. Olmstead, A.A. Anderberg, M Källersjö and E Barkhordarian. 2002. Phylogenetics of asterids based on 3 coding and 3 noncoding chloro-plast DNA markers and the utility of non-coding DNA at higher taxo-nomic levels. Molecular Phylogenetics and Evolution 24: 274-301.
12. Cantino, P. D. 1992. Evidence for a polyphyletic origin of the Labiatae. Annals of the Missouri Botanical Garden 79: 361-379.
13. Cantino, P. D. 1992. Toward a phylogenetic classification of the Labiatae. In R. M. Harley and T. Reynolds [eds.], Advances in Labiate science, 27-37. Royal Botanic Gardens, Kew, Richmond, U.K.
14. Cantino, P. D., J. A. Doyle, S. W. Graham, W. S. Judd, R. G. Olmstead, D. E. Soltis, PS Soltis and M. J. Donoghue. 2007. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56: 822-846.
15. Catalán, M. P., E. A. Kellogg and R. G. Olmstead. 1997. Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndh F gene sequences. Molecular Phylogenetics and Evolution 8: 150-166.
16. Chase, M. W., D. E. Soltis, R. G. Olmstead, D Morgan, D. H. Les B. D. Mishler, M. R. Duvall et al. 1993. Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden 80: 528-580.
17. Cohen, J. I. 2013. A phylogenetic analysis of morphological and molecular characters of Boraginaceae: evolutionary relationships, taxonomy, and patterns of character evolution. Cladistics (early access): http://onlinelibrary.wiley.com/doi/10.1111/cla.12036/full
18. Cronquist, A. 1981. An Integrated System of Classification of Flowering Plants. Columbia University Press, New York.
19. DeBry, R. W., and R. G. Olmstead. 2000. A simulation study of reduced tree-search effort in bootstrap resampling analysis. Systematic Biology 49: 171-179.
20. Diane N, H Förther and H. H. Hilger. 2002. A systematic analysis of Heliotropium, Tournefortia, and allied taxa of the Heliotropiaceae (Boraginales) based on ITS1 sequences and morphological data. American Journal of Botany 89: 287-295.
21. Douady, C. J., F. Delsuc, Y Boucher, W. F. Doolittle and E. J. P. Douzery. 2003. Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Molecular Biology and Evolution 20: 248-254.
22. Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin Botanical Society of America 19: 11-15.
23. Drummond A and A Rambaut. 2007. BEAST: Bayesian evolutionary analysis sampling trees. BMC Evolutionary Biology 7: 214.
24. Ferguson, D. 1999. Phylogenetic analysis and relationships in Hydrophyllaceae based on ndh F sequence data. Systematic Botany 23: 253-268.
25. Frasier, C. L. 2009. Evolution and systematics of the angiosperm order Gentianales with an in-depth focus on Loganiaceae and its species-rich and toxic genus Strychnos. Ph.D. dissertation, Rutgers University, New Brunswick, New Jersey, USA.
26. González F, J Betancur, O. Maurin, J. V. Freudenstein and M. W. Chase. 2007. Metteniusaceae, an early-diverging family in the lamiid clade. Taxon 56: 795-800.
27. Gottschling M., and H. H. Hilger. 2001. Phylogenetic analysis and character evolution of Ehretia and Bourreria (Ehretiaceae, Boraginales) and their allies based on ITS1 sequences. Botanische Jahrbücher für Systematik 123: 249-268.
28. Gottschling, M., H. H. Hilger, M Wolf and N Diane. 2001. Secondary structure of the ITS1 transcript and its application in a reconstruction of the phylogeny of Boraginales. Plant Biology 3: 629-636.
29. Gottschling M, JS Miller, M Weigend and H. H. Hilger. 2005. Congruence of a phylogeny of Cordiaceae (Boraginales) inferred from ITS1 sequence data with morphology, ecology, and biogeogra-phy. Annals of the Missouri Botanical Garden 92: 425-437.
30. Hilger, H. H., and N Diane. 2003. A systematic analysis of Heliotro-piaceae (Boraginales) based on trnL and ITS1 sequence data. Botanische Jahrbücher für Systematik 125: 19-51.
31. Hilu, K.W., T. Borsch, K Müller, D.E. Soltis, PS Soltis, V Savolainen, M. W. Chase et al. 2003. Angiosperm phylogeny based on matK sequence information. American Journal of Botany 90: 1758-1776.
32. Huelsenbeck, J. P., and F Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England) 17: 754-755.
33. Huson, D.H., D.C. Richter, C Rausch, T Dezulian, M Franz and R Rupp. 2007. Dendroscope: An interactive viewer for large phyloge-netic trees. BMC Bioinformatics 8: 460.
34. Jiao Z and J Li. 2007. Phylogeny of intercontinental disjunct Gelsemiaceae inferred from chloroplast and nuclear DNA sequences. Systematic Botany 32: 617-627.
35. Jobson, R. W., J. Playford, K. M. Cameron and V. A. Albert. 2003. Molecular phylogenetics of Lentibulariaceae inferred from plastid rps16 intron and trnL-F DNA sequences: Implications for character evolution and biogeography. Systematic Botany 28: 157-171.
36. rd Ed. Sinauer, Sunderland, Massachusetts, USA.
37. Judd, W. S., and R. G. Olmstead. 2004. A survey of tricolpate (eu-dicot) phylogenetic relationships. American Journal of Botany 91: 1627-1644.
38. Kårehed, J. 2001. Multiple origin of the tropical forest tree family Icacinaceae. American Journal of Botany 88: 2259-2274.
39. Katoh K and H Toh. 2008. Recent developments in the MAFFT multiple sequence alignment program. Briefings in Bioinformatics 9: 286-298.
40. Kornhall P and B Bremer. 2004. New circumscription of the tribe Limoselleae (Scrophulariaceae) that includes the taxa of the tribe Manuleeae. Botanical Journal of the Linnean Society 146: 453-467.
41. Kornhall P, N Heidari, and, B Bremer.2001. SelagineaeandManuleeae, two tribes or one? Phylogenetic studies in the Scrophulariaceae. Plant Systematics and Evolution 228: 199-218.
42. Lens F, J Kårehed, P Baas, S Jansen, D Rabaey, S Huysmans, T Hamann and E Smets. 2008. The wood anatomy of the polyphyletic Icaci-naceae s.l., and their relationships within asterids. Taxon 57: 525-552.
43. Luebert F, G Brokamp, J Wen, M Weigend and H. H. Hilger. 2011. Phylogenetic relationships and morphological diversity in Neotropical Heliotropium (Heliotropiaceae). Taxon 60: 663-680.
44. Luebert, F., and J Wen. 2008. Phylogenetic analysis and evolutionary diversification of Heliotropium sect. Cochranea (Heliotropiaceae) in the Atacama Desert. Systematic Botany 33: 390-402.
45. Marx H. E., N. O'Leary, Y.W. Yuan, P Lu-Irving, D. C. Tank, M Múlgura and R. G. Olmstead. 2010. A molecular phylogeny and classification of Verbenaceae. American Journal of Botany 97: 1647-1663.
46. McDade LA, TF Daniel, C.A. Kiel and, A.J. Borg. 2013. Phylogenetic placement, delimitation, and relationships among genera of the enigmatic Nelsonioideae (Lamiales: Acanthaceae). Taxon 61: 637-651.
47. McDade L. A., S. E. Masta, ML Moody and E Waters. 2000. Phylogenetic relationships among Acanthaceae: evidence from two genomes. Systematic Botany 25: 106-121.
48. Morgan, D. R., and D. E. Soltis. 1993. Phylogenetic relationships among members of Saxifragaceae sensu lato based on rbcL sequence data. Annals of the Missouri Botanical Garden 80: 631-660.
49. Müller K, T Borsch, L Legendre, S Porembski, I Thiesen and W Barthlott. 2004. Evolution of carnivory in Lentibulariaceae and the Lamiales. Plant Biology 6: 477-490.
50. Nazaire M and L Hufford. 2012. A broad phylogenetic analysis of Boraginaceae: implications for the relationships of Mertensia. Systematic Botany 37: 758-783.
51. Oliver, J. C. 2013. Microevolutionary processes generate phylogenomic discordance at ancient divergences. Evolution 67: 1823-1830.
52. Olmstead, R. G. 2012 [onward] A synoptical classification of Lamiales vers. 2.4. Website http://depts.washington.edu/phylo/Classification. pdf [last accessed on 21 October, 2013]
53. Olmstead, R. G. 2013. Phylogeny and biogeography in Solanaceae, Verbenaceae, and Bignoniaceae: a comparision of continental and intercontinental diversification patterns. Botanical Journal of the Linnean Society 171: 80-102.
54. Olmstead R, GB Bremer, K. M. Scott and JD Palmer. 1993. Apar-simony analysis of the Asteridae sensu lato based on rbcL sequences. Annals of the Missouri Botanical Garden 80: 700-722.
55. Olmstead, R. G., C. W. Depamphilis, A. D. Wolfe, N. D. Young, W. J. Elisons and P. A. Reeves. 2001. Disintegration of the Scrophulariaceae. American Journal of Botany 88: 348-361.
56. Olmstead, R. G., and F. Ferguson. 2001. A molecular phylogeny of the Boraginaceae-Hydrophyllaceae. Botany 2001 Abstracts. Botanical Society of America http://www.2001.botanyconference.org/botany 2001c.pdf (accessed 30 Dec, 2013).
57. Olmstead, R. G., K. J. Kim, R. K. Jansen and S. J. Wagstaff. 2000. The phylogeny of the Asteridae sensu lato based on chloroplast ndhF gene sequences. Molecular Phylogenetics and Evolution 16: 96-112.
58. Olmstead, R. G., H. J. Michaels, K Scott and J. D. Palmer. 1992. Monophyly of the Asteridae and identification of their major lineages inferred from DNA sequences of rbcL. Annals of the Missouri Botanical Garden 79: 249-265.
59. Olmstead R. G., M. L. Zjhra, L. G. Lohmann, S. O. Grose and A. J. Eckert. 2009. A molecular phylogeny and classification of Bignon-iaceae. American Journal of Botany 96: 1731-1743.
60. Oxelman, B., M. Backlund and B Bremer. 1999. Relationships of the Buddlejaceae s. l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF and rbcL sequence data. Systematic Botany 24: 164-182.
61. Oxelman, B., P. Kornhall, R. G. Olmstead and B Bremer. 2005. Further disintegration of the Scrophulariaceae. Taxon 54: 411-425.
62. Perret M, A Chautems, A Onofre de Araujo and N Salamin. 2013. Temporal and spatial origin of Gesneriaceae in the New World inferred from plastid DNA sequences. Botanical Journal of the Linnean Society 171: 61-79.
63. Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253-1256.
64. Rahmanzadeh R, K Müller, E Fischer, D Bartels and T Borsch 2005. The Linderniaceae and Gratiolaceae are further lineages distinct from the Scrophulariaceae (Lamiales). Plant Biology 7: 67-78.
65. Rambaut, A. 1996-2002. Se-Al: Sequence alignment editor, version 2.0.a11, Website http://tree.bio.ed.ac.uk/software/.
66. Rambaut A and A. J. Drummond. 2003-2007. Tracer, version 1.4, MCMC trace analysis package. Website http://tree.bio.ed.ac.uk/ software/tracer/.
67. Reveal, J. L. 2011. Summary of recent systems of angiosperm classification. Kew Bulletin 66: 5-48.
68. Ronquist F and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phy-logenetic inference under mixed models. Bioinformatics (Oxford, England) 19: 1572-1574.
69. Ronquist, F., J. P. Huelsenbeck and P Van Der Mark. 2005. MrBayes 3.1 manual. http://mrbayes.csit.fsu.edu/mb3.1_manual.pdf
70. Schäferhoff B, A Fleishmann, E Fischer, D.C. Albach, T Borsch, G Heubl and K. F. Müller. 2010. Towards resolving Lamiales relationships: insights from rapidly evolving chloroplast sequences. BMC Evolutionary Biology 10: 352.
71. Shimodaira, H. 2002. An Approximately Unbiased Test of Phylogenetic Tree Selection. Systematic Biology 51: 492-508.
72. Shimodaira H and M Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114-1116.
73. Shimodaira H and M Hasegawa. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics (Oxford, England) 17: 1246-1247.
74. Simmons, M. P., K. M. Pickett and M Miya. 2004. How meaningful are Bayesian support values? Molecular Biology and Evolution 21: 188-199.
75. Smith, J. F., J. C. Wolfram, K. D. Brown, C. L. Carroll and D. S. Denton. 1997. Tribal relationships in the Gesneriaceae: Evidence from DNA sequences of the chloroplast gene ndhF. Annals of the Missouri Botanical Garden 84: 50-66.
76. Soltis, D. E., M. A. Gitzendanner and P. S. Soltis. 2007. A 567-taxon data set for angiosperms: The challenges posed by Bayesian analyses of large data sets. International Journal of Plant Sciences 168: 137-157.
77. Soltis, D. E., S. A. Smith N Cellinese, K. J. Wurdack, D. C. Tank, S. F. B rockington, NF Refulio-Rodriguez et al. 2011. Angiosperm phy-logeny: 17-genes, 640 taxa. American Journal of Botany 98: 704-730.
78. Soltis, D. E., P. S. Soltis, M. W. Chase, ME Mort, D. C. Albach, M Zanis, V Savolainen et al. 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Botanical Journal of the Linnean Society 133: 381-461.
79. Soltis, D. E., P. S. Soltis, D. L. Nickrent, L. A. Johnson, W. J. Hahn, S. B. Hoot, J. A. Sweere et al. 1997. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Annals of the Missouri Botanical Garden 84: 1-49.
80. Spangler, R. E., and R. G. Olmstead. 1999. Phylogenetic analysis of the Bignoniaceae based on the cpDNA gene sequences rbc L and ndhF. Annals of the Missouri Botanical Garden 86: 33-46.
81. Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (Oxford, England) 22: 2688-2690.
82. Stebbins, G. L. 1974. Flowering plants: Evolution above the species level. Harvard University Press, New York, New York, USA.
83. Stefanović, S. L., and R. G. Olmstead. 2004. Testing the phylogenetic position of a parasitic plant (Cuscuta, Convolvulaceae, Asteridae): Bayesian inference and the Parametric Bootstrap on data drawn from three genomes. Systematic Biology 53: 384-399.
84. Suzuki Y., G. V. Glazko and M Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proceedings of the National Academy of Sciences, USA 99: 16138-16143.
85. Swofford, D. L. 2002. PAUP *: Phylogenetic analysis using parsimony (*and other methods), version 4. Sinauer, Sunderland, Massachusetts, USA.
86. Takhtajan, A. 1987. Systema magnoliophytorum. Nauka, Leningrad.
87. Takhtajan, A. L. 1997. Diversity and classification of flowering plants. Columbia University Press, New York, New York, USA.
88. Tank, D.C., P. Beardsley, S Kelchner and R.G. Olmstead. 2006. L.A.S. Johnson Review No, 7. Review of the systematics of Scrophulariaceae s.l. and their current disposition. Australian Systematic Botany 19: 289-307.
89. Tank, D. C., and M. J. Donoghue. 2010. Phylogeny and phylogenetic nomenclature of the Campanulidae based on an expanded sample of genes and taxa. Systematic Botany 35: 425-441.
90. Wagstaff, S. J., and R GOlmstead. 1997. Phylogeny of the Labiatae and Verbenaceae inferred from rbcL sequences. Systematic Botany 22: 165-179.
91. Wagstaff, S. J., P. A. Reeves, L Hickerson, R. E. Spangler and R. G. Olmstead. 1998. Phylogeny of Labiatae s.l. inferred from cpDNA sequences. Plant Systematics and Evolution 209: 265-274.
92. Wallander E., and V. A. Albert. 2000. Phylogeny and classification of Oleaceae based on rps16 and trnL-F sequence data. American Journal of Botany 87: 1827-1841.
93. Weigend M and H. H. Hilger. 2010. Codonaceae-a newly required family name in Boraginales. Phytotaxa 10: 26-30.
94. Weigend M, F Luebert, M Gottschling, T.L.P. Couvreur, H.H. Hilger and J. S. Miller. 2013. From capsules to nutlets-phyloge-netic relationships in the Boraginales. Cladistics 10.1111/cla.12061.
95. Wortley, A. H., D. J. Harris and R. W. Scotland. 2007. On the taxonomy and phylogenetic position of Thomandersia. Systematic Botany 32: 415-444.
96. Wortley, A. H., P. J. Rudall, D. J. Harris and R. W. Scotland. 2005. How much data are needed to resolve a difficult phylogeny? Case study in Lamiales. Systematic Biology 54: 697-709.
97. Xia, X., Y.Z. Wang and J. F. Smith. 2009. Familial placement and relations of Rehmannia and Triaenophora (Scrophulariaceae s.l.) inferred from five gene regions. American Journal of Botany 9 6: 519-530.
98. Yang Z and B Rannala. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Molecular Biology and Evolution 14: 717-724.
99. Yatskievych G and C. T. Mason Jr. 1986. A revision of the Lennoaceae. Systematic Botany 11: 531-548.
100. Young, N. D., K. E. Steiner and CW De Pamphilis. 1999. The evolu-tion of parasitism in Scrophulariaceae/Orobanchaceae: plastid gene sequences refute an evolutionary transition series. Annals of the Missouri Botanical Garden 86: 876-893.