Divergence time estimation in Cichorieae (Asteraceae) using a fossil-calibrated relaxed molecular clock

Organisms Diversity and Evolution

Volumn 13, Issue 1, 2013, Pages 1-13

  Tremetsberger, Karin ^a,b   Gemeinholzer, Birgit ^c,d   Zetzsche, Holger ^c   Blackmore, Stephen ^e   Kilian, Norbert ^c   Talavera, Salvador ^b  

^a UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^b UNIVERSITY OF SEVILLE   (Spain)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

^d JUSTUS LIEBIG UNIVERSITY   (Germany)

^e ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

Author keywords

Bering land bridge; Lactuceae; Miocene; Oligocene; Pollen evolution; Uncorrelated relaxed molecular clock

Indexed keywords

BIOGEOGRAPHY; CALIBRATION; DISPERSAL; DIVERGENCE; ESTIMATION METHOD; FOSSIL RECORD; GENETIC ANALYSIS; HERB; LAND BRIDGE; MOLECULAR ANALYSIS; NEOGENE; NORTHERN HEMISPHERE; OLIGOCENE; PHYLOGENETICS;

MEDITERRANEAN REGION;

ASTERACEAE; CICHORIEAE; CICHORIUM INTYBUS; ZANCLEA;

EID: 84873406900     PISSN: 14396092     EISSN: 16181077     Source Type: Journal    
DOI: 10.1007/s13127-012-0094-2     Document Type: Article

References (78)

1. Álvarez, I.; Wendel, J. F. (2003). Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29, 417-434.
2. Babcock, E. B. (1947). The genus Crepis: part one. The taxonomy, phylogeny, distribution, and evolution of Crepis. Berkeley: University of California Press.
3. Baldwin, B. G.; Sanderson, M. J.; Porter, J. M.; Wojciechowski, M. F.; Campbell, C. S.; Donoghue, M. J. (1995). The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden, 82, 247-277.
4. Blackmore, S. (1981). Palynology and intergeneric relationships in subtribe Hyoseridinae (Compositae: Lactuceae). Botanical Journal of the Linnean Society, 82, 1-13.
5. Blackmore, S. (1982a). The apertures of Lactuceae (Compositae) pollen. Pollen et Spores, 24, 453-462.
6. Blackmore, S. (1982b). A functional interpretation of Lactuceae (Compositae) pollen. Plant Systematics and Evolution, 141, 153-168.
7. Blackmore, S. (1982c). Palynology of subtribe Scorzonerinae (Compositae: Lactuceae) and its taxonomic significance. Grana, 21, 149-160.
8. Blackmore, S. (1984). The Northwest European Pollen Flora, 32: Compositae - Lactuceae. Review of Palaeobotany and Palynology, 42, 45-85.
9. Blackmore, S. (1986). The identification and taxonomic significance of lophate pollen in the Compositae. Canadian Journal of Botany, 64, 3101-3112.
10. Blackmore, S.; Van Campo, E.; Crane, P. R. (1986). Lophate Compositae pollen from the Miocene and Pliocene of the Mediterranean region. Pollen et Spores, 28, 391-401.
11. Blattner, F. R. (1999). Direct amplification of the entire ITS region from poorly preserved plant material using recombinant PCR. BioTechniques, 27, 1180-1186.
12. Bremer, K. (1994). Asteraceae: cladistics and classification. Portland: Timber.
13. Bremer, K.; Friis, E. M.; Bremer, B. (2004). Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification. Systematic Biology, 53, 496-505.
14. Demarcq, G.; Méon-Vilain, H.; Miquet, R.; Kujawski, H. (1976). Un bassin paralique Néogène: celui de Skanes-Monastir (Tunisie orientale). Notes du Service Géologique de Tunisie, 42, 97-147.
15. Donoghue, M. J.; Bell, C. D.; Li, J. (2001). Phylogenetic patterns in northern Hemisphere plant geography. International Journal of Plant Sciences, 162(6 Suppl.), S41-S52.
16. Drummond, A. J.; Ho, S. Y. W.; Phillips, M. J.; Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
17. Drummond, A. J.; Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
18. Drummond, A. J.; Rambaut, A.; Suchard, M. A. (2002-2010). BEAST, Version 1.6.1, available from http://beast.bio.ed.ac.uk/.
19. Drummond, A. J.; Rambaut, A.; Xie, W. (2002-2010). BEAUti, Version 1.6.1, available from http://beast.bio.ed.ac.uk/.
20. Eldenäs, P.; Anderberg, A. A.; Källersjö, M. (1998). Molecular phylogenetics of the tribe Inuleae s. str. (Asteraceae), based on ITS sequences of nuclear ribosomal DNA. Plant Systematics and Evolution, 210, 159-173.
21. Enke, N.; Gemeinholzer, B. (2008). Babcock revisited: new insights into generic delimitation and character evolution in Crepis L. (Compositae: Cichorieae) from ITS and matK sequence data. Taxon, 57, 756-768.
22. Fehrer, J.; Gemeinholzer, B.; Chrtek, J.; Jr.; Bräutigam, S. (2007). Incongruent plastid and nuclear DNA phylogenies reveal ancient intergenic hybridization in Pilosella hawkweeds (Hieracium, Cichorieae, Asteraceae). Molecular Phylogenetics and Evolution, 42, 347-361.
23. Funk, V. A.; Bayer, R. J.; Keeley, S.; Chan, R.; Watson, L.; Gemeinholzer, B.; et al. (2005). Everywhere but Antarctica: using a supertree to understand the diversity and distribution of the Compositae. Biologiske Skrifter, 55, 343-374.
24. Funk, V. A.; Chan, R.; Keeley, S. C. (2004). Insights into the evolution of the tribe Arctoteae (Compositae: subfamily Cichorioideae s.s.) using trnL-F, ndhF, and ITS. Taxon, 53, 637-655.
25. Garnatje, T.; Susanna, A.; Garcia-Jacas, N.; Vilatersana, R.; Vallès, J. (2005). A first approach to the molecular phylogeny of the genus Echinops (Asteraceae): Sectional delimitation and relationships with the genus Acantholepis. Folia Geobotanica, 40, 407-419.
26. Gemeinholzer, B.; Bachmann, K. (2005). Examining morphological and molecular diagnostic character states in Cichorium intybus L. (Asteraceae) and Cichorium spinosum L. Plant Systematics and Evolution, 253, 105-123.
27. Gemeinholzer, B.; Dröge, G.; Zetzsche, H.; Haszprunar, G.; Klenk, H.-P.; Güntsch, A.; et al. (2011). The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking, 9, 51-55.
28. Goertzen, L. R.; Cannone, J. J.; Gutell, R. R.; Jansen, R. K. (2003). ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. Molecular Phylogenetics and Evolution, 29, 216-234.
29. Graur, D.; Martin, W. (2004). Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. Trends in Genetics, 20, 80-86.
30. Gustaffson, M. H. G.; Pepper, A. S.-R.; Albert, V. A.; Källersjö, M. (2001). Molecular phylogeny of the Barnadesioideae (Asteraceae). Nordic Journal of Botany, 21, 149-160.
31. Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
32. Heads, M. (2011). Old taxa on young islands: a critique of the use of island age to date island-endemic clades and calibrate phylogenies. Systematic Biology, 60, 204-218.
33. Hochuli, P. A. (1978). Palynologische Untersuchungen im Oligozän und Untermiozän der Zentralen und Westlichen Paratethys. Beiträge zur Paläontologie von Österreich, 4, 1-132.
34. Hugall, A. F.; Foster, R.; Lee, M. S. Y. (2007). Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Systematic Biology, 56, 543-563.
35. Ivanov, D. A. (1997). Miocene palynomorphs from the Southern part of the Forecarpathian basin (Northwest Bulgaria). Flora Tertiaria Mediterranea, 6, 1-81.
36. Ivanov, D. A.; Slavomirova, E. (2000). New palynological data on the Late Miocene flora and vegetation in Gotse-Delchev Basin (Southwestern Bulgaria). Review of the Bulgarian Geological Society, 61, 39-46.
37. Karis, P. O.; Eldenäs, P.; Källersjö, M. (2001). New evidence for the systematic position of Gundelia L. with notes on delimitation of Arctoteae (Asteraceae). Taxon, 50, 105-114.
38. Kay, K. M.; Whittall, J. B.; Hodges, S. A. (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.
39. Kilian, N.; Gemeinholzer, B.; Lack, H. W. (2009). Tribe Cichorieae Lam. & DC. (1806). In V. A. Funk, A. Susanna, T. Stuessy, & R. J. Bayer (Eds.), Systematics, evolution, and biogeography of Compositae (pp. 343-383). Vienna: International Association for Plant Taxonomy.
40. Kim, S.-C.; Crawford, D. J.; Francisco-Ortega, J.; Santos-Guerra, A. (1996). A common origin for woody Sonchus and five related genera in the Macaronesian islands: molecular evidence for extensive radiation. Proceedings of the National Academy of Sciences USA, 93, 7743-7748.
41. Kimball, R. T.; Crawford, D. J. (2004). Phylogeny of Coreopsideae (Asteraceae) using ITS sequences suggests lability in reproductive characters. Molecular Phylogenetics and Evolution, 33, 127-139.
42. Lavin, M.; Herendeen, P. S.; Wojciechowski, M. F. (2005). Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. Systematic Biology, 54, 575-594.
43. Lee, J.; Baldwin, B. G.; Gottlieb, L. D. (2002). Phylogeny of Stephanomeria and related genera (Compositae-Lactuceae) based on analysis of 18 S-26S nuclear rDNA ITS and ETS sequences. American Journal of Botany, 89, 160-168.
44. Lee, J.; Baldwin, B. G.; Gottlieb, L. D. (2003). Phylogenetic relationships among the primarily North American genera of Cichorieae (Compositae) based on analysis of 18 S-26S nuclear rDNA ITS and ETS sequences. Systematic Botany, 28, 616-626.
45. Mai, D. H. (1995). Tertiäre Vegetationsgeschichte Europas. Jena: Fischer.
46. Marincovich, L.; Gladenkov, A. Y. (1999). Evidence for an early opening of the Bering Strait. Nature, 397, 149-151.
47. Marjanović, D.; Laurin, M. (2007). Fossils, molecules, divergence times, and the origin of lissamphibians. Systematic Biology, 56, 369-388.
48. Mavrodiev, E. V.; Edwards, C. E.; Albach, D. C.; Gitzendanner, M. A.; Soltis, P. S.; Soltis, D. E. (2004). Phylogenetic relationships in subtribe Scorzonerinae (Asteraceae: Cichorioideae: Cichorieae) based on ITS sequence data. Taxon, 53, 699-712.
49. Muller, J. (1981). Fossil pollen records of extant angiosperms. Botanical Review, 47, 1-146.
50. Nagy, E. (1969). Palynological elaborations on the Miocene layers of the Mecsek Mountains. Annales Instituti Geologici Publici Hungarici, 52, 287-648.
51. Panero, J. L.; Funk, V. A. (2002). Toward a phylogenetic subfamilial classification for the Compositae (Asteraceae). Proceedings of the Biological Society of Washington, 115, 909-922.
52. Pérez-Losada, M.; Høeg, J. T.; Crandall, K. A. (2004). Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches. Systematic Biology, 53, 244-264.
53. Posada, D.; Crandell, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
54. Potts, R.; Behrensmeyer, A. K. (1992). Late Cenozoic terrestrial ecosystems. In A. K. Behrensmeyer, J. D. Damuth, W. A. DiMichele, R. Potts, H.-D. Sues, & S. L. Wing (Eds.), Terrestrial ecosystems through time (pp. 419-541). Chicago: The University of Chicago Press.
55. Poux, C.; Chevret, P.; Huchon, D.; De Jong, W. W.; Douzery, E. J. P. (2006). Arrival and diversification of caviomorph rodents and platyrrhine primates in South America. Systematic Biology, 55, 228-244.
56. Rambaut, A.; Drummond, A. J. (2003-2009). Tracer, Version 1.5.0, available from http://beast.bio.ed.ac.uk/.
57. Rambaut, A.; Drummond, A. J. (2002-2010). TreeAnnotator, Version 1.6.1, available from http://beast.bio.ed.ac.uk/.
58. Renner, S.; Zhang, L.-B. (2004). Biogeography of the Pistia clade (Araceae): based on chloroplast and mitochondrial DNA sequences and Bayesian divergence time inference. Systematic Biology, 53, 422-432.
59. Renner, S. S. (2005). Relaxed molecular clocks for dating historical plant dispersal events. Trends in Plant Science, 10, 550-558.
60. Rieseberg, L. H.; Soltis, D. E. (1991). Phylogenetic consequences of cytoplasmic gene flow in plants. Evolutionary Trends in Plants, 5, 65-84.
61. Rivas-Carballo, M. R.; Alonso-Gavilán, G.; Valle, M. F.; Civis, J. (1994). Miocene palynology of the central sector of the Duero basin (Spain) in relation to palaeogeography and palaeoenvironment. Review of Palaeobotany and Palynology, 82, 251-264.
62. Robinson, H. (1994). Notes on the tribes Eremothamneae, Gundelieae, and Moquinieae, with comparisons of their pollen. Taxon, 43, 33-44.
63. Samuel, R.; Gutermann, W.; Stuessy, T. F.; Ruas, C. F.; Lack, H.-W.; Tremetsberger, K.; et al. (2006). Molecular phylogenetics reveals Leontodon (Asteraceae, Lactuceae) to be diphyletic. American Journal of Botany, 93, 1193-1205.
64. Samuel, R.; Stuessy, T. F.; Tremetsberger, K.; Baeza, C. M.; Siljak-Yakovlev, S. (2003). Phylogenetic relationships among species of Hypochaeris (Asteraceae, Cichorieae) based on ITS, plastid trnL intron, trnL-F spacer, and matK sequences. American Journal of Botany, 90, 496-507.
65. Skvarla, J. J.; Larson, D. A. (1965). An electron microscopic study of pollen morphology in the Compositae with special reference to the Ambrosiinae. Grana Palynologica, 6, 210-269.
66. Susanna, A.; Garcia-Jacas, N.; Hidalgo, O.; Vilatersana, R.; Garnatje, T. (2006). The Cardueae (Compositae) revisited: insights from ITS, trnL-trnF and matK nuclear and chloroplast DNA analysis. Annals of the Missouri Botanical Garden, 93, 150-171.
67. Swofford, D. L. (2003). PAUP: Phylogenetic Analyses Using Parsimony (and Other Methods), Version 4.0b10. Sunderland: Sinauer.
68. Thompson, J. D.; Gibson, T. J.; Plewniak, F.; Jeanmougin, F.; Higgins, D. G. (1997). The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876-4882.
69. Tiffney, B. H.; Manchester, S. R. (2001). The use of geological and paleontological evidence in evaluating plant phylogeographic hypotheses in the northern Hemisphere Tertiary. International Journal of Plant Sciences, 162(6 Suppl.), S3-S17.
70. Tomb, A. S. (1975). Pollen morphology in tribe Lactuceae (Compositae). Grana, 15, 79-89.
71. Tremetsberger, K.; Weiss-Schneeweiss, H.; Stuessy, T.; Samuel, R.; Kadlec, G.; Ortiz, M. Á.; Talavera, S. (2005). Nuclear ribosomal DNA and karyotypes indicate a NW African origin of South American Hypochaeris (Asteraceae, Cichorieae). Molecular Phylogenetics and Evolution, 35, 102-116.
72. Wen, J. (1999). Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Annual Review of Ecology and Systematics, 30, 421-455.
73. White, T. J.; Bruns, T.; Lee, S.; Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR protocols: a guide to methods and applications (pp. 315-322). San Diego: Academic.
74. Whitton, J.; Wallace, R. S.; Jansen, R. K. (1994). Phylogenetic relationships and patterns of character change in the tribe Lactuceae (Asteraceae) based on chloroplast DNA restriction site variation. Canadian Journal of Botany, 73, 1058-1073.
75. Wodehouse, R. P. (1935). Pollen grains: their structure, identification and significance in science and medicine. New York: McGraw-Hill.
76. Won, H.; Renner, S. S. (2006). Dating dispersal and radiation in the gymnosperm Gnetum (Gnetales) - clock calibration when outgroup relationships are uncertain. Systematic Biology, 55, 610-622.
77. Xiang, Q.-Y.; Soltis, D. E.; Soltis, P. S.; Manchester, S. R.; Crawford, D. J. (2000). Timing the eastern Asian-eastern North American floristic disjunction: molecular clock corroborates paleontological estimates. Molecular Phylogenetics and Evolution, 15, 462-472.
78. Zhao, Z.; Skvarla, J. J.; Jansen, R. K. (2006). Mutisieae (Asteraceae) pollen ultrastructure atlas. Lundellia, 9, 51-76.