Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae

Journal of Biogeography

Volumn 36, Issue 12, 2009, Pages 2324-2337

  Smith, Stephen A ^a,b  

^a YALE UNIVERSITY   (United States)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

Author keywords

Bayesian; Biogeography; Caprifolieae; Divergence times; Lonicera; Parametric methods; Phylogenetics

Indexed keywords

BAYESIAN ANALYSIS; CENOZOIC; CLADISTICS; DICOTYLEDON; DIVERGENCE; FOSSIL RECORD; PHYLOGENY; PHYLOGEOGRAPHY; RECONSTRUCTION; SPECIES DIVERSITY; TOPOLOGY;

ASIA; EURASIA; EUROPE; NORTH AMERICA;

CAPRIFOLIACEAE; LONICERA; MAGNOLIOPHYTA;

EID: 70350295141     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2009.02160.x     Document Type: Article

References (64)

1. Altekar, G., Dwarkadas, S., Huelsenbeck, J.P. Ronquist, F. (2004) Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics, 20, 407 415.
2. Bell, C.D. (2007) Phylogenetic placement and biogeography of the North American species of Valerianella (Valerianaceae: Dipsacales) based on chloroplast and nuclear DNA. Molecular Phylogenetics and Evolution, 44, 929 941.
3. Bell, C.D. Donoghue, M.J. (2005) Dating the Dipsacales: comparing models, genes, and evolutionary implications. American Journal of Botany, 92, 284 296.
4. Bell, C.D., Edwards, E.J., Kim, S. Donoghue, M.J. (2001) Dipsacales phylogeny based on chloroplast DNA sequences. Harvard Papers in Botany, 6, 481 499.
5. Donoghue, M.J. Moore, B.R. (2003) Toward an integrative historical biogeography. Integrative and Comparative Biology, 43, 261 270.
6. Donoghue, M.J. Smith, S.A. (2004) Patterns in the assembly of temperate forests around the Northern Hemisphere. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 1633 1644.
7. Donoghue, M.J., Bell, C.D. Li, J.H. (2001a) Phylogenetic patterns in Northern Hemisphere plant geography. International Journal of Plant Sciences, 162, S41 S52.
8. Donoghue, M.J., Eriksson, T., Reeves, P.A. Olmstead, R.G. (2001b) Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harvard Papers in Botany, 6, 459 479.
9. Donoghue, M.J., Bell, C.D. Winkworth, R.C. (2003) The evolution of reproductive characters in Dipsacales. International Journal of Plant Sciences, 164, S453 S464.
10. Drummond, C.S. (2008) Diversification of Lupinus (Leguminosae) in the western New World: derived evolution of perennial life history and colonization of montane habitats. Molecular Phylogenetics and Evolution, 48, 408 421.
11. Drummond, A.J. Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
12. Drummond, A.J., Ho, S.Y.W., Phillips, M.J. Rambaut, A. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
13. Eckert, A.J. Hall, B.D. (2006) Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses. Molecular Phylogenetics and Evolution, 40, 166 182.
14. Gould, K.R. Donoghue, M.J. (2000) Phylogeny and biogeography of Triosteum (Caprifoliaceae). Harvard Papers in Botany, 5, 157 166.
15. Graham, A. (1999) Late Cretaceous and Cenozoic history of North American vegetation: north of Mexico. Oxford University Press, New York.
16. Gussarova, G., Popp, M., Vitek, E. Brochmann, C. (2008) Molecular phylogeny and biogeography of the bipolar Euphrasia (Orobanchaceae): recent radiations in an old genus. Molecular Phylogenetics and Evolution, 48, 444 460.
17. Hara, H. (1983) A revision of Caprifoliaceae of Japan with reference to allied plants in other districts and the Adoxaceae. Ginkgoana, No. 5, Contributions to the flora of Asia and the Pacific region. Academia Scientific Books, Tokyo.
18. Hsu, P. Wang, H. (1988) Lonicera. Flora Republicae Popularis Sinicae (ed. by P. Hsu, H. Wang J. Hu pp. 153 257. Science Press, Beijing.
19. Ickert-Bond, S.M. Wen, J. (2006) Phylogeny and biogeography of Altingiaceae: evidence from combined analysis of five non-coding chloroplast regions. Molecular Phylogenetics and Evolution, 39, 512 528.
20. Kass, R.E. Raftery, A.E. (1995) Bayes factor. Journal of the American Statistical Association, 90, 773 795.
21. 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.
22. Mai, D.H. (2001) Die mittelmiozaenen und obermiozaenen Floren aus der Meuroer und Raunoer Folge in der Lausitz. III. Fundstellen und Palaeobiologie. Palaeontographica Abteilung B, 258, 1 8.
23. Manchester, S.R. Donoghue, M.J. (1995) Winged fruit of Linnaeeae (Caprifoliaceae) in the Tertiary of western North America: Diplodipelta gen. nov. International Journal of Plant Sciences, 156, 709 722.
24. Manos, P.S. Stanford, A.M. (2001) The historical biogeography of Fagaceae: tracking the Tertiary history of temperate and subtropical forests of the Northern Hemisphere. International Journal of Plant Sciences, 162, S77 S93.
25. Marshall, C.R. (1997) Confidence intervals on stratigraphic ranges with non-random distributions of fossil horizons. Paleobiology, 23, 165 173.
26. Marshall, C.R. (2008) A simple method for bracketing absolute divergence times on molecular phylogenies using multiple fossil calibration points. The American Naturalist, 171, 726 742.
27. Milne, R.I. (2004) Phylogeny and biogeography of Rhododendron subsection Pontica, a group with a Tertiary relict distribution. Molecular Phylogenetics and Evolution, 33, 389 401.
28. Milne, R.I. Abbott, R.J. (2002) The origin and evolution of Tertiary relict floras. Advances in Botanical Research, 38, 281 314.
29. Morgenstern, B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211 218. (Pubitemid 29196998)
30. Nie, Z.L., Wen, J., Azuma, H., Qiu, Y.L., Sun, H., Meng, Y., Sun, W.B. Zimmer, E.A. (2008) Phylogenetic and biogeographic complexity of Magnoliaceae in the Northern Hemisphere inferred from three nuclear data sets. Molecular Phylogenetics and Evolution, 48, 1027 1040.
31. Nylander, J.A., Olsson, U., Alstrom, P. Sanmartin, I. (2008) Accounting for phylogenetic uncertainty in biogeography: a Bayesian approach to dispersal-vicariance analysis of the thrushes (Aves: Turdus). Systematic Biology, 57, 257 268.
32. Ohta, T. (1992) The nearly neutral theory of molecular evolution. Annual Review of Ecology and Systematics, 23, 263 286.
33. Ozaki, K. (1980) Late Miocene Tatsumitoge flora of Tottori Prefecture, south-west Honshu, Japan. Science Reports of the Yokohama National University, 2, 40 42.
34. Ozaki, K. (1991) Late Miocene and Pliocene floras in central Honshu, Japan. Bulletin of Kanagawa Prefectural Museum Natural Science, Special Issue, Kanagawa Prefectural Museum, Yokohama.
35. Qian, H. Ricklefs, R.E. (2000) Large-scale processes and the Asian bias in species diversity of temperate plants. Nature, 407, 180 182.
36. Rambaut, A. Drummond, A.J. (2007) Tracer v1.4. Available at: http://beast.bio.ed.ac.uk/Tracer (last accessed 16 April 2009).
37. Ree, R.H. Smith, S.A. (2008) Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology, 57, 4 14.
38. Ree, R.H., Moore, B.R., Webb, C.O. Donoghue, M.J. (2005) A likelihood framework for inferring the evolution of geographic range on phylogenetic trees. Evolution, 59, 2299 2311.
39. Rehder, A. (1903) Synopsis of the genus Lonicera. Missouri Botanical Garden Annual Report, 14, 27 232.
40. Renner, S.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.
41. Ronquist, F. (1997) Dispersal-vicariance analysis: a new approach to quantification of historical biogeography. Systematic Biology, 45, 195 203.
42. Ronquist, F. Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572 1574.
43. Sanmartín, I. Ronquist, F. (2004) Southern hemisphere biogeography inferred by event-based models: plant versus animal patterns. Systematic Biology, 53, 216 243.
44. Sanmartín, I., Enghoff, H. Ronquist, F. (2001) Patterns of animal dispersal, vicariance, and diversification in the Holarctic. Biological Journal of the Linnean Society, 73, 345 390.
45. Sanmartín, I., van der Mark, P. Ronquist, F. (2008) Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands. Journal of Biogeography, 35, 428 449.
46. Shaw, J., Lickey, E.B., Beck, J.T., Farmer, S.B., Liu, W., Miller, J., Siripun, K.C., Winder, C.T., Schilling, E.E. Small, R.I. (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany, 92, 142 166.
47. Smith, S.A. Donoghue, M.J. (2008) Mega-phylogenies link rates of molecular evolution to life history in flowering plants. Science, 322, 86 89.
48. Smith, S.A. Dunn, C.W. (2008) Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics, 24, 715 716.
49. Smith, A.B. Peterson, K.J. (2002) Dating the time of origin of major clades: molecular clocks and the fossil record. Annual Review of Earth and Planetary Sciences, 30, 65 88.
50. Theis, N.H., Donoghue, M.J. Li, J.L. (2008) Phylogenetics of the Caprifolieae and Lonicera (Dipsacales) based on nuclear and chloroplast DNA sequences. Systematic Botany, 33, 776 783.
51. Tiffney, B.H. (1985a) Perspectives on the origin of the floristic similarity between eastern Asia and eastern North America. Journal of the Arnold Arboretum, 66, 73 94.
52. Tiffney, B.H. (1985b) The Eocene North Atlantic Land Bridge: its importance in Tertiary and modern phytogeography of the Northern Hemisphere. Journal of the Arnold Arboretum, 66, 243 273.
53. 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, S3 S17.
54. Weinreich, D.M. (2001) The rates of molecular evolution in rodent and primate mitochondrial DNA. Journal of Molecular Evolution, 52, 40 50.
55. Wen, J. (1999) Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Annual Reviews in Ecology and Systematics, 30, 421 455.
56. Wen, J., Shi, S., Jansen, R.K. Zimmer, E.A. (1998) Phylogeny and biogeography of Aralia sect. Aralia (Araliaceae). American Journal of Botany, 85, 866 875.
57. Winkworth, R.C. Donoghue, M.J. (2005) Viburnum phylogeny based on combined molecular data: implications for taxonomy and biogeography. American Journal of Botany, 92, 653 666.
58. Winkworth, R.C., Lundberg, J. Donoghue, M.J. (2008) Toward a resolution of Campanulid phylogeny, with special reference to the placement of Dipsacales. Taxon, 57, 53 65.
59. Xiang, Q. Soltis, D.E. (2001) Dispersal-vicariance analyses of intercontinental disjuncts: historical biogeographical implications for angiosperms in the Northern Hemisphere. International Journal of Plant Sciences, 162, S29 S39.
60. Xiang, Q. Thomas, D.T. (2008) Tracking character evolution and biogeographic history through time in Cornaceae - does choice of method matter? Journal of Systematics and Evolution, 46, 349 374.
61. Xiang, Q., Soltis, D.E., Soltis, P.S., Manchester, S.R. Crawford, D.J. (2000) Timing the eastern Asian - eastern North America floristic disjunction: molecular clock corroborates paleontological estimates. Molecular Phylogenetics and Evolution, 15, 462 472.
62. Xiang, Q., Zhang, W.H., Ricklefs, R.E., Qian, H., Chen, Z.D., Wen, J. Li, J.H. (2004) Regional differences in rates of plant speciation and molecular evolution: a comparison between eastern Asia and eastern North America. Evolution, 58, 2175 2184.
63. Zhang, W.H., Chen, Z.D., Li, J.H., Chen, H.B. Tang, Y.C. (2003) Phylogeny of Dipsacales s.l. based on chloroplast trnL-F and ndhF sequences. Molecular Phylogenetics and Evolution, 26, 176 189.
64. Zhou, S., Renner, S.S. Wen, J. (2006) Molecular phylogeny and intra- and intercontinental biogeography of Calycanthaceae. Molecular Phylogenetics and Evolution, 39, 1 15.