Molecular phylogenetics reveal multiple tertiary vicariance origins of the African rain forest trees

BMC Biology

Volumn 6, Issue , 2008, Pages

  Couvreur, Thomas L P ^a,c   Chatrou, Lars W ^a   Sosef, Marc S M ^a   Richardson, James E ^b  

^a UNIVERSITEIT LEIDEN BRANCH   (Netherlands)

^b ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^c NEW YORK BOTANICAL GARDEN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICA; ANNONACEAE; ARTICLE; CELL LINEAGE; CLADISTICS; COMMUNITY SUCCESSION; FOREST DYNAMICS; GEOLOGICAL TIME; MOLECULAR CLOCK; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGEOGRAPHY; PLEISTOCENE; SPECIES DIFFERENTIATION; SPECIES ENDEMICITY; TROPICAL RAIN FOREST; VICARIANCE; BAYES THEOREM; CALIBRATION; CHEMISTRY; CLIMATE; ECOSYSTEM; GENETICS; PHYLOGENY; TREE;

ANNONACEAE;

CHLOROPLAST DNA;

AFRICA; BAYES THEOREM; CALIBRATION; CLIMATE; DNA, CHLOROPLAST; ECOSYSTEM; EVOLUTION, MOLECULAR; GENETIC SPECIATION; PHYLOGENY; TREES;

EID: 61349089221     PISSN: None     EISSN: 17417007     Source Type: Journal    
DOI: 10.1186/1741-7007-6-54     Document Type: Article

References (77)

1. Hubbell SP A unified theory of biogeography and relative species abundance and its application to tropical rain forests and coral reefs Coral Reefs 1997, 16:S9-S21 10.1007/s003380050237
2. Molino JF Sabatier D Tree diversity in tropical rain forests: A validation of the intermediate disturbance hypothesis Science 2001, 294:1702-1704 10.1126/science.1060284 11721052
3. Wills C Harms KE Condit R King D Thompson J He F Muller-Landau HC Ashton P Losos E Comita L Hubbell S LaFrankie J Bunyavejchewin S Dattaraja HS Davies S Esufali S Foster R Gunatilleke N Gunatilleke S Hall P Itoh A John R Kiratiprayoon S Loo de Lao S Massa M Nath C Supardi Noor MN Rahman Kassim A Sukumar R Suresh HS Sun I Tan S Yamakura T Zimmerman J Nonrandom processes maintain diversity in tropical forests Science 2006, 311:527-531 10.1126/science.1117715 16439661
4. Moritz C Patton JL Schneider CJ Smith TB Diversification of rainforest faunas: An integrated molecular approach Annu Rev Ecol Syst 2000, 31:533-563 10.1146/annurev.ecolsys.31.1.533
5. Pennington RT Richardson JE Lavin M Insights into the historical construction of species-rich biomes from dated plant phylogenies, neutral ecological theory and phylogenetic community structure New Phytol 2006, 172:605-616 10.1111/j.1469-8137.2006.01902.x 17096788
6. Mace GM Gittleman JL Purvis A Preserving the Tree of Life Science 2003, 300:1707-1709 10.1126/science.1085510 12805539
7. Myers N Mittermeier RA Mittermeier CG da Fonseca GAB Kent J Biodiversity hotspots for conservation priorities Nature 2000, 403:853-858 10.1038/ 35002501 10706275
8. White F The Guineo-Congolian region and its relationships to other phytochoria Bull Jard Bot Nat Belg 1979, 49:11-55 10.2307/3667815
9. Burgess ND Clarke GP Rodgers WA Coastal forests of eastern Africa: status, endemism patterns and their potential causes Biol J Linn Soc Lond 1998, 64:337 10.1111/j.1095-8312.1998.tb00337.x
10. Burgess ND Butynski TM Cordeiro NJ Doggart NH Fjeldså J Howell KM Kilahama FB Loader SP Lovett JC Mbilinyi B Menegon M Moyer DC Nashanda E Perkin A Rovero F Stanley WT Stuart SN The biological importance of the Eastern Arc Mountains of Tanzania and Kenya Biol Conserv 2007, 134:209-231 10.1016/j.biocon.2006.08.015
11. Burgess ND Clarke GP Coastal Forests of Eastern Africa Gland: IUCN 2000
12. Wasser SK Lovett JC Biogeography and Ecology of the Rainforests of Eastern Africa Cambridge: Cambridge University Press 1993
13. Morley RJ Origin and Evolution of Tropical Rain Forests New York: John Wiley & Sons 2000
14. Coetzee JA African flora since the terminal Jurassic Biological relationships between Africa and South America New Haven: Yale University Press Goldblatt P 1993:37-61
15. Axelrod DI Raven PH Late Cretaceous and Tertiary vegetation history of Africa Biogeography and Ecology of Southern Africa The Hague: W Junk bv Publishers Werger MJA 1978:77-130
16. Jacobs BF Kingston JD Jacobs LL The origin of grass-dominated ecosystems Ann Missouri Bot Gard 1999, 86:590-643 10.2307/2666186
17. Davis CC Bell CD Fritsch PW Mathews S Phylogeny of Acridocarpus-Brachylophon (Malpighiaceae): Implications for tertiary tropical floras and Afroasian biogeography Evolution 2002, 56:2395-2405 12583580
18. Couvreur TLP Richardson JE Sosef MSM Erkens RHJ Chatrou LW Evolution of syncarpy and other morphological characters in African Annonaceae: A posterior mapping approach Mol Phylogenet Evol 2008, 47:302-318 10.1016/ j.ympev.2008.01.018 18343689
19. Punyasena SW Eshel G McElwain JC The influence of climate on the spatial patterning of Neotropical plant families J Biogeogr 2008, 35:117-130
20. Couvreur TLP Gereau RE Wieringa JJ Richardson JE Description of four new species of Monodora and Isolona (Annonaceae) from Tanzania and an overview of Tanzanian Annonaceae diversity Adansonia (Paris) 2006, 28:243-266
21. Rogers ME Abernethy K Bermejo M Cipolletta C Doran D McFarland K Nishihara T Remis M Tutin CEG Western gorilla diet: A synthesis from six sites Am J Primatol 2004, 64:173-192 10.1002/ajp.20071 15470742
22. Gentry A Diversity and floristic composition of lowland tropical forest in Africa and South America Biological Relationships between Africa and South America New Haven: Yale University Press Goldblatt P 1993:500-547
23. Couvreur TLP Monograph of the syncarpous African genera Isolona and Monodora (Annonaceae) Syst Bot Monogr
24. Richardson JE Chatrou LW Mols JB Erkens RHJ Pirie MD Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae Philos Trans R Soc Lond B Biol Sci 2004, 359:1495-1508 1693429 15519968 10.1098/rstb.2004.1537
25. Qiu YL Lee J Bernasconi-Quadroni F Soltis DE Soltis PS Zanis M Zimmer EA Chen Z Savolainen V Chase MW Phylogeny of basal angiosperms: Analyses of five genes from three genomes Int J Plant Sci 2000, 161:S3-S27 10.1086/ 317584
26. Sauquet H Doyle JA Scharaschkin T Borsch T Hilu KW Chatrou LW Le Thomas A Phylogenetic analysis of Magnoliales and Myristicaceae based on multiple data sets: Implications for character evolution Bot J Linn Soc 2003, 142:125-186 10.1046/j.1095-8339.2003.00171.x
27. Doyle JJ Doyle JL A rapid DNA isolation procedure from small quantities of fresh leaf tissue Phyt Bull 1987, 19:11-15
28. Bakker FT Hellbriigge D Culham A Gibby M Phylogenetic relationships within Pelargonium sect. Peristera (Geraniaceae) inferred from nrDNA and cpDNA sequence comparisons Plant Syst Evol 1998, 211:273-287 10.1007/ BF00985364
29. Taberlet P Gielly L Pautou G Bouvet J Universal primers for amplification of 3 noncoding regions of chloroplast DNA Plant Mol Biol 1991, 17:1105-1109 10.1007/BF00037152 1932684
30. Hamilton MB Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation Mol Ecol 1999, 8:521-523 10199016
31. Shaw J Lickey EB Beck JT Farmer SB Liu W Miller J Siripun KC Winder CT Schilling EE Small RL The tortoise and the hare II: Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis Am J Bot 2005, 92:142-166 10.3732/ajb.92.1.142
32. Erkens RHJ Chatrou LW Maas JW Pirie MD Phylogenetic relationships, saturation and marker-use in the Long Branch Clade of Annonaceae PhD thesis, From morphological nightmare to molecular conundrum. Phylogenetic, evolutionary and taxonomic studies on Guatteria (Annonaceae) Utrecht University, Utrecht Erkens RHJ 2007:25-41
33. Olmstead RG Sweere JA Combining data in phylogenetic systematics: An empirical approach using three molecular data sets in the Solanaceae Syst Biol 1994, 43:467-481 10.2307/2413546
34. Staden Package WWW site http://staden.sourceforge.net
35. Swofford DL PAUP* Phylogenetic Analysis Using Parsimony (* and other methods), v. 4.0 beta 10 Sunderland: Sinauer Associates 2002 12504223
36. Simmons MP Ochoterena H Gaps as characters in sequence-based phylogenetic analyses Syst Biol 2000, 49:369-381 10.1080/ 10635159950173889 12118412
37. Levinson G Gutman G Slipped-strand mispairing: A major mechanism for DNA sequence evolution Mol Biol Evol 1987, 4:203-221 3328815
38. Drummond AJ Ho SYW Phillips MJ Rambaut A Relaxed phylogenetics and dating with confidence PLoS Biol 2006, 4:699-710 10.1371/ journal.pbio.0040088
39. Drummond AJ Rambaut A BEAST: Bayesian evolutionary analysis by sampling trees BMC Evol Biol 2007, 7:214 2247476 17996036 10.1186/1471-2148-7-214
40. Ho SYW Phillips MJ Drummond AJ Cooper A Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation Mol Biol Evol 2005, 22:1355-1363 10.1093/molbev/msi125 15758207
41. Sanderson M A nonparametric approach to estimating divergence times in the absence of rate constancy Mol Biol Evol 1997, 14:1218-1231
42. Thorne JL Kishino H Painter IS Estimating the rate of evolution of the rate of molecular evolution Mol Biol Evol 1998, 15:1647-1657 9866200
43. Sanderson MJ Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach Mol Biol Evol 2002, 19:101-109 11752195
44. BEAST partitioning http://tlpcouvreur.googlepages.com/beastpartitioning
45. Akaike H Information theory as an extension of the maximum likelihood principle Second International Symposium on Information Theory Budapest: Akademiai Kiado Petrov BN, Csaki F 1973:267-281
46. Nylander JAA MrModeltest v2 Program distributed by the author Uppsala: Evolutionary Biology Centre, Uppsala University 2004
47. Rambaut A Drummond AJ Tracer. Version 1.4 2003 http://evolve.zoo.ox.ac.uk/
48. Loader SP Pisani D Cotton JA Gower DJ Day JJ Wilkinson M Relative time scales reveal multiple origins of parallel disjunct distributions of African caecilian amphibians Biol Lett 2007, 3:505-508 2396187 17609171 10.1098/rsbl.2007.0266
49. Dilcher DL Crane PR Archaeanthus - an early angiosperm from the Cenomanian of the western interior of North-America Ann Missouri Bot Gard 1984, 71:351-383 10.2307/2399030
50. Doyle JA Sauquet H Scharaschkin T Le Thomas A Phylogeny, molecular and fossil dating, and biogeographic history of Annonaceae and Myristicaceae (Magnoliales) Int J Plant Sci 2004, 165:S55-S67 10.1086/421068
51. Friis EM Pedersen KR Crane PR Cretaceous anglosperin flowers: Innovation and evolution in plant reproduction Palaeogeogr Palaeoclimatol Palaeoecol 2006, 232:251-293 10.1016/j.palaeo.2005.07.006
52. Crepet WL Nixon KC Gandolfo MA Fossil evidence and phylogeny: The age of major angiosperm clades based on mesofossil and macrofossil evidence from cretaceous deposits Am J Bot 2004, 91:1666-1682 10.3732/ ajb.91.10.1666
53. Pirie MD Chatrou LW Mols JB Erkens RHJ Oosterhof J 'Andean-centred' genera in the short-branch clade of Annonaceae: Testing biogeographical hypotheses using phylogeny reconstruction and molecular dating J Biogeogr 2006, 33:31-46 10.1111/j.1365-2699.2005.01388.x
54. Chesters KIM Some plant remains from the Upper Cretaceous and Tertiary of West Africa: Maastrichtian seeds of Annonaceae Ann Mag Nat Hist Ser 1955, 12:498-504
55. Kvacek J Eklund H A report on newly recovered reproductive structures from the Cenomanian of Bohemia (Central Europe) Int J Plant Sci 2003, 164:1021-1039 10.1086/378824
56. Mohr BAR Bernardes-de-Oliveira MEC Endressinia brasiliana, a magnolialean angiosperm from the Lower Cretaceous Crato Formation (Brazil) Int J Plant Sci 2004, 165:1121-1133 10.1086/423879
57. Mohr BAR Eklund H Araripia florifera, a magnoliid angiosperm from the Lower Cretaceous Crato Formation (Brazil) Rev Palaeobot Palynol 2003, 126:279-292 10.1016/S0034-6667(03)00092-7
58. Crepet WL The fossil record of angiosperms: Requiem or renaissance? Ann Missouri Bot Gard 2008, 95:3-33 10.3417/2007065
59. Pirie MD The age of clades in Annonaceae: Progress in molecular dating The Natural History of the Annonaceae Regnum Vegetabile Chatrou LW, Erkens RHJ, Richardson JE
60. Wikström N Savolainen V Chase MW Evolution of the angiosperms: calibrating the family tree Proc Biol Sci 2001, 268(1482):2211-2220 1088868 11674868 10.1098/rspb.2001.1782
61. Zhou SL Renner SS Wen J Molecular phylogeny and intra- and intercontinental biogeography of Calycanthaceae Mol Phylogenet Evol 2006, 39:1-15 10.1016/j.ympev.2006.01.015 16495090
62. Berry PE Hahn WJ Sytsma KJ Hall JC Mast A Phylogenetic relationships and biogeography of Fuchsia (Onagraceae) based on noncoding nuclear and chloroplast DNA data Am J Bot 2004, 91:601-614 10.3732/ajb.91.4.601
63. Renner SS Relaxed molecular clocks for dating historical plant dispersal events Trends Plant Sci 2005, 10:550-558 10.1016/j.tplants.2005.09.010 16226053
64. Shaul S Graur D Playing chicken (Gallus gallus): Methodological inconsistencies of molecular divergence date estimates due to secondary calibration points Gene 2002, 300:59-61 10.1016/S0378-1119(02)00851-X 12468086
65. Ho SYW Calibrating molecular estimates of substitution rates and divergence times in birds J Avian Biol 2007, 38:409-414
66. Peng ZG Ho SYW Zhang YG He SP Uplift of the Tibetan plateau: Evidence from divergence times of glyptosternoid catfishes Mol Phylogenet Evol 2006, 39:568-572 10.1016/j.ympev.2005.10.016 16364665
67. Sanderson MJ r8s: Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock Bioinformatics 2003, 19:301-302 10.1093/bioinformatics/19.2.301 12538260
68. Zachos J Pagani M Sloan L Thomas E Billups K Trends, rhythms, and aberrations in global climate 65 Ma to present Science 2001, 292:686-693 10.1126/science.1059412 11326091
69. Jacobs BF Palaeobotanical studies from tropical Africa: Relevance to the evolution of forest, woodland and savannah biomes Philos Trans R Soc Lond B Biol Sci 2004, 359:1573-1583 1693443 15519973 10.1098/ rstb.2004.1533
70. Sepulchre P Ramstein G Fluteau F Schuster M Tiercelin JJ Brunet M Tectonic uplift and Eastern Africa aridification Science 2006, 313:1419-1423 10.1126/science.1129158 16960002
71. Cerling TE Harris JM MacFadden BJ Leakey MG Quade J Eisenmann V Ehleringer JR Global vegetation change through the Miocene/Pliocene boundary Nature 1997, 389:153-158 10.1038/38229
72. Haffer J Speciation in Amazonian forest birds Science 1969, 165:131-137 10.1126/science.165.3889.131 17834730
73. Evans BJ Kelley DB Tinsley RC Melnick DJ Cannatella DC A mitochondrial DNA phylogeny of African clawed frogs: Phylogeography and implications for polyploid evolution Mol Phylogenet Evol 2004, 33:197-213 10.1016/ j.ympev.2004.04.018 15324848
74. Mumbi CT Marchant R Hooghiemstra H Wooller MJ Late Quaternary vegetation reconstruction from the Eastern Arc Mountains, Tanzania Quaternary Research 2008, 69:326-341 10.1016/j.yqres.2007.10.012
75. Marchant R Mumbi C Behera S Yamagata T The Indian Ocean dipole - the unsung driver of climatic variability in East Africa Afr J Ecol 2007, 45:4-16 10.1111/j.1365-2028.2006.00707.x
76. Yamagata T Balmford A Manning JC Proches S Bank van der M Reeves G Hedderson TAJ Savolainen V Preserving the evolutionary potential of floras in biodiversity hotspots Nature 2007, 445:757-760 10.1038/ nature05587 17301791
77. Sechrest W Brooks TM da Fonseca GAB Konstant WR Mittermeier RA Purvis A Rylands AB Gittleman JL Hotspots and the conservation of evolutionary history Proc Natl Acad Sci USA 2002, 99:2067-2071 122320 11854502 10.1073/pnas.251680798