Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae)

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Gustafsson, A Lovisa S ^a,b   Verola, Christiano F ^c   Antonelli, Alexandre ^d  

^a UNIVERSITY OF GOTHENBURG   (Sweden)

^b UNIVERSITY OF OSLO   (Norway)

^c FEDERAL UNIVERSITY OF MATO GROSSO   (Brazil)

^d GOTHENBURG BOTANICAL GARDEN   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BAYESIAN ANALYSIS; CLADISTICS; COMMON ANCESTRY; CRETACEOUS; DATING METHOD; DIVERGENCE; EOCENE; FOSSIL RECORD; GLOBAL WARMING; HERB; MOLECULAR ANALYSIS; NEW RECORD; PALEOBOTANY; PHYLOGENY; RARE SPECIES; SPECIES DIVERSITY; TAXONOMY; TEMPORAL EVOLUTION;

EPIDENDROIDEAE; ORCHIDACEAE; ORCHIDOIDEAE;

PLANT DNA; RIBOSOMAL SPACER DNA;

ARTICLE; BAYES THEOREM; CLASSIFICATION; DNA SEQUENCE; FOSSIL; GENETICS; MOLECULAR EVOLUTION; ORCHIDACEAE; PHYLOGENY; SEQUENCE ALIGNMENT; SOUTH AMERICA; STATISTICAL MODEL;

BAYES THEOREM; DNA, PLANT; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; FOSSILS; LIKELIHOOD FUNCTIONS; ORCHIDACEAE; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOUTH AMERICA;

EID: 77953346846     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-177     Document Type: Article

References (54)

1. The Orchids, natural history and classification. RL Dressler, Cambridge: Harward University Press 1990
2. Evolution of the Angiosperms: Calibrating the family tree. N Wikström V Savolainen MW Chase, Proceedings of the Royal Society of London. Biological Sciences 2001 268 2211 2220 10.1098/rspb.2001.1782 (Pubitemid 33032897)
3. Early Cretaceous lineages of monocot flowering plants. K Bremer, Proceedings of the National Academy of Sciences of the United States of America 2000 97 9 4707 4711 10.1073/pnas.080421597 10759567
4. Dating the origin of the Orchidaceae from a fossil orchid with its pollinator. SR Ramirez B Gravendeel RB Singer CR Marshall NE Pierce, Nature 2007 448 1042 1045 10.1038/nature06039 17728756
5. The age of major monocot groups inferred from 800+ rbcL sequences. T Janssen K Bremer, Botanical Journal of the Linnean Society 2004 146 385 398 10.1111/j.1095-8339.2004.00345.x (Pubitemid 40033205)
6. Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points. CL Anderson K Bremer EM Friis, American Journal of Botany 2005 92 10 1737 1748 10.3732/ajb.92.10.1737
7. The age of the Angiosperms: A molecular timescale without a clock. CD Bell DE Soltis PS Soltis, Evolution 2005 59 6 1245 1258 16050101
8. Explosive radiations and the reliability of molecular clocks: Island endemic radiations as a test case. L Bromham M Woolfit, Systematic Biology 2004 53 5 758 766 10.1080/10635150490522278 15545253
9. The impact of fossils and taxon sampling on ancient molecular dating analyses. LA Hug AJ Roger, Molecular biology and evolution 2007 24 8 1889 1897 10.1093/molbev/msm115 17556757
10. Taxon sampling effects in molecular clock dating: An example from the African Restionaceae. HP Linder CR Hardy F Rutschmann, Molecular Phylogenetics and Evolution 2005 35 3 569 582 10.1016/j.ympev.2004.12.006 15878126
11. 'Andean-centred' genera in the short-branch clade of Annonaceae: Testing biogeographical hypotheses using phylogeny reconstruction and molecular dating. MD Pirie LW Chatrou JB Mols RHJ Erkens J Oosterhof, Journal of Biogeography 2006 33 1 31 46 10.1111/j.1365-2699.2005.01388.x
12. Relaxed molecular clocks for dating historical plant dispersal events. SS Renner, Trends in Plant Science 2005 10 11 550 558 10.1016/j.tplants.2005.09. 010 16226053
13. Estimating diversification rates from phylogenetic information. RE Ricklefs, Trends in Ecology and Evolution 2007 22 11 601 610 10.1016/j.tree.2007.06.013 17963995
14. Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times. F Rutschmann, Diversity and Distributions 2006 12 1 35 48 10.1111/j.1366-9516.2006.00210.x
15. Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds. KL Sanders MSY Lee, Biology letters 2007 3 3 275 279 10.1098/rsbl.2007.0063 17363358
16. The origin of a mega-diverse genus: dating Begonia (Begoniaceae) using alternative datasets, calibrations and relaxed clock methods. WP Goodall-Copestake DJ Harris PM Hollingsworth, Botanical Journal of the Linnean Society 2009 159 3 363 380 10.1111/j.1095-8339.2009.00948.x
17. A nonparametric approach to estimating divergence times in the absence of rate constancy. MJ Sanderson, Molecular biology and evolution 1997 14 12 1218 1231
18. Estimating absolute rates of molecular evolution and divergence times: a Penalized Likelihood approach. MJ Sanderson, Molecular Biology and Evolution 2002 19 101 109 11752195
19. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. MJ Sanderson, Bioinformatics 2003 19 2 301 302 10.1093/bioinformatics/19.2.301 12538260
20. Relaxed phylogenetics and dating with confidence. AJ Drummond SYW Ho MJ Phillips A Rambaut, PLoS Biology 2006 4 5 88. 10.1371/journal.pbio.0040088 16683862
21. BEAST: Bayesian evolutionary analysis by sampling trees. AJ Drummond A Rambaut, BMC Evolutionary Biology 2007 7 214 10.1186/1471-2148-7-214 17996036
22. Dates from the molecular clock: how wrong can we be? MJF Pulquério RA Nichols, Trends in Ecology & Evolution 2007 22 4 180 184
23. Dating lineages: Molecular and paleontological approaches to the temporal framework of clades. SA Magallán, International Journal of Plant Sciences 2004 165 S4 7 S21 10.1086/383336
24. Molecular evidence on plant divergence times. MJ Sanderson JL Thorne N Wikström K Bremer, American Journal of Botany 2004 91 10 1656 1665 10.3732/ajb.91.10.1656
25. Phylogenetic position and biogeography of Hillebrandia sandwicensis (Begoniaceae): A rare Hawaiian relict. WL Clement MC Tebbitt LL Forrest JE Blair L Brouillet T Eriksson SM Swensen, American Journal of Botany 2004 91 6 905 917 10.3732/ajb.91.6.905
26. Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) - A multigene phylogenetic approach with relative dating. B Frajman F Eggens B Oxelman, Systematic Biology 2009 58 3 328 345 10.1093/sysbio/syp030 20525587
27. Earliest orchid macrofossils: Early Miocene Dendrobium and Earina (Orchidaceae: Epidendroideae) from New Zealand. JG Conran JM Bannister DE Lee, American Journal of Botany 2009 96 2 466 474 10.3732/ajb.0800269
28. Phylogeny and classification of the orchid family. RL Dressler, Portland Oregon: Dioscorides Press 1993
29. A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences. KM Cameron MW Chase WM Whitten PJ Kores DC Jarrell VA Albert T Yukawa HG Hills DH Goldman, American Journal of Botany 1999 86 2 208 224 10.2307/2656938
30. A phylogenetic analysis of laeliinae (orchidaceae) based on sequence data from internal transcribed spacers (ITS) of nuclear ribosomal DNA. C Van den Berg WE Higgins RL Dressler WM Whitten M Soto Arenas A Culham MW Chase, Lindleyana 2000 15 96 114
31. Hoffmannseggella viridiflora (Orchidaceae, Laeliinae), a new species from Brazilian campus rupestris. CF Verola J Semir, Novon 2007 17 125 129 10.3417/1055-3177(2007)17[125:HVOLAN]2.0.CO;2 (Pubitemid 46846290)
32. Mudança de nomenclatura dentro do gnero Laelia Lindl. GR Chiron VP Castro Neto, Richardiana 2002 2 4 28
33. Duas novas especies de orquideas do Brasil. MA Campacci, Boletim CAOB 2005 57 24 31
34. Une nouvelle espèce d'Hoffmannseggella (Orchidaceae) du Brésil. VP Castro Neto GR Chiron, Richardiana 2003 3 64 68
35. Contribution la connaissance des orchidées du Brésil. VI - Une nouvelle espèce de Hoffmannseggella du Minas Gerais (Brésil). GR Chiron VP Castro Neto, Richardiana 2005 4 7 15
36. Deux nouveaux taxons de Hoffmannseggella du Minas Gerais (Brésil). KG Lacerda VP Castro Neto, Richardiana 2005 5 15 25
37. Studies in Brazilian Laeliinae. Part 2: A New species in Hoffmannseggella. F Miranda, Orchids 2005 74 458 461
38. Studies in Brazilian Laeliinae. Part 1: New species and natural hybrids in Hoffmannseggella. F Miranda KG Lacerda, Orchids 2003 72 848 857
39. Hoffmannseggella pendula, une nouvelle espèce d'Orchidaceae du Brésil. RC Mota PL Viana KG Lacerdo, Richardiana 2003 4 1 8
40. Trends, rhythms, and aberrations in Global Climate 65 Ma to present. J Zachos M Pagani L Sloan E Thomas K Billups, Science 2001 292 686 693 10.1126/science.1059412 11326091
41. An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics. JC Zachos GR Dickens RE Zeebe, Nature 2008 451 7176 279 283 10.1038/nature06588 18202643
42. Alternative models of vertebrate speciation in Amazonia: An overview. J Haffer, Biodiversity and Conservation 1997 6 3 451 476 10.1023/A:1018320925954
43. Biosystematic studies in Brazilian endemic genus Hoffmannseggella H.G.Jones (Orchidaceae: Laeliinae): a multiple approach applied to conservation. CF Verola J Semir A Antonelli I Koch, Lankesteriana 2007 7 1-2 419 422
44. Climate cooling promoted the expansion and radiation of a threatened group of South American orchids (Epidendroideae: Laeliinae). CF Verola ALS Gustafsson, Biological Journal of the Linnean Society 2010 100 3 596 606
45. Tracer v1.4. A Rambaut AJ Drummond, 2007 http://beast.bio.ed.ac.uk/Tracer
46. An examination of phylogenetic models of substitution rate variation among lineages. SYW Ho, Biology letters 2009 5 3 421 424 10.1098/rsbl.2008.0729 19324651
47. MAFFT version 5: improvement in accuracy of multiple sequence alignment. K Katoh K-I Kuma H Toh T Miyata, Nucleic Acid Research 2005 33 2 511 518 10.1093/nar/gki198 (Pubitemid 40360980)
48. A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. CN Steward LE Via, BioTechniques 1993 14 5 748 749 8512694
49. Inferring the history of the polyploidy Silene aegaea (Caryophyllaceae) using plastid and homoeologous nuclear DNA sequences. M Popp B Oxelman, Molecular Phylogenetics and Evolution 2001 20 3 474 481 10.1006/mpev.2001.0977 11527472
50. Origin and evolution of a circumpolar polyploidy species complex in Silene (Caryophyllaceae) inferred from low copy nuclear RNA polymerase introns, rRNA, and chloroplast DNA. M Popp F Eggens P Erixon B Oxelman, Systematic Botany 2005 30 2 302 313 10.1600/0363644054223648 (Pubitemid 40850168)
51. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. TJ White T Bruns S Lee JW Taylor, PCR protocols: a guide to methods and applications New York, N.Y: Academic Press, Inc, Innis MA, Gelfand DH, Sninsky JJ, White TJ, Innis MA, Gelfand DH, Sninsky JJ, White TJ, 1990 315 322
52. Araceae from the Early Cretaceous of Portugal: Evidence on the emergence of monocotyledons. EM Friis KR Pedersen PR Crane, Proc Natl Acad Sci USA 2004 101 47 16565 16570 10.1073/pnas.0407174101 15546982
53. MrModeltest v2. Program distributed by the author. JAA Nylander, Evolutionary Biology Centre, Uppsala University 2004
54. A rough guide to BEAST 1.4. AJ Drummond SYH Ho HN Rawlence A Rambaut, 2007 http://beast.bio.ed.ac.uk/Main-Page