Diversity gradients and phylogeographic patterns in santiria trimera (Burseraceae), a widespread African tree typical of mature rainforests

American Journal of Botany

Volumn 98, Issue 2, 2011, Pages 254-264

  Koffi, K Guillaume ^a   Hardy, Olivier J ^a   Doumenge, Charles ^b   Cruaud, Corinne ^c   Heuertz, Myriam ^a,d,e  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b CIRAD   (France)

^c CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^d Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria   (Spain)

^e CSIC   (Spain)

Author keywords

African rainforests; Burseraceae; cpDNA sequences; Morphotypes; Nuclear copies of plastid DNA (nupts); Phylogeography; Pleistocene refuges; Santiria trimera

Indexed keywords

CHLOROPLAST DNA;

ALLOPATRY; BIRD; CHLOROPLAST; CHROMATOGRAPHY; DICOTYLEDON; DIOECY; DIVERGENCE; GEOGRAPHICAL DISTRIBUTION; MOLECULAR ANALYSIS; PHYLOGENY; PHYLOGEOGRAPHY; PHYTOGEOGRAPHY; PLEISTOCENE; POLYMERASE CHAIN REACTION; RAINFOREST; SPECIES DIVERSITY; TAXONOMY; VOLCANIC ISLAND;

AFRICA; ARTICLE; BURSERACEAE; CHROMATOGRAPHY; CLIMATE; DNA SEQUENCE; ECOSYSTEM; GENETIC POLYMORPHISM; GENETICS; GEOGRAPHY; HAPLOTYPE; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PHYLOGEOGRAPHY; POLYMERASE CHAIN REACTION; RIVER; TREE;

AFRICA; BASE SEQUENCE; BURSERACEAE; CHROMATOGRAPHY; CLIMATE; CLONING, MOLECULAR; DNA, CHLOROPLAST; ECOSYSTEM; GEOGRAPHY; HAPLOTYPES; PHYLOGEOGRAPHY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; RIVERS; SEQUENCE ANALYSIS, DNA; TREES;

WEST AFRICA;

AVES; BURSERACEAE; PRIMATES; PUFFINUS AURICULARIS; SANTIRIA;

EID: 79951471504     PISSN: 00029122     EISSN: None     Source Type: Journal    
DOI: 10.3732/ajb.1000220     Document Type: Article

References (67)

1. Adam, J.-G. 1971. Flore descriptive des Monts Nimba (2ème partie). Paris Editions du Muséum, Paris, France.
2. Anthony, F., L. E. C. Diniz, M.-C. Combes, and P. Lashermes. 2010. Adaptive radiation in Coffea subgenus Coffea L. (Rubiaceae) in Africa and Madagascar. Plant Systematics and Evolution 285: 51-64.
3. Anthony, N. M., M. Johnson-Bawe, K. Jeffery, S. L. Clifford, K. A. Abernethy, C. E. Tutin, S. A. Lahm, et al. 2007. The role of Pleistocene refugia and rivers in shaping gorilla genetic diversity in central Africa. Proceedings of the National Academy of Sciences, USA 104: 20432-20436.
4. Aubréville, A. 1962. Flore du Gabon: Irvingiacées, Simaroubacées, Burseracées. Muséum National d' Histoire Naturelle Laboratoire de Phanérogamie, Paris, France.
5. Avise, J. C. 2004. Molecular markers, natural history and evolution, 2nd ed. Sinauer, Sunderland, Massachusetts, USA.
6. Ayliffe, M. A., N. S. Scott, and J. N. Timmis. 1998. Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants. Molecular Biology and Evolution 15: 738-745.
7. Bailey, M. F., and L. F. Delph. 2007. A field guide to models of sex-ratio evolution in gynodioecious species. Oikos 116: 1609-1617.
8. Birky, C. W. Jr. 2001. The inheritance of genes in mitochondria and chloroplasts: Laws, mechanisms, and models. Annual Review of Genetics 35: 125-148.
9. Born, C. 2007. Diversitégénétique et dynamique des forêts d' Afrique centrale - Uneétude multi-échelle de la structure de la diversitégénétique d' un arbre pionnier, Aucoumea klaineana. Ph.D. dissertation, Université Montpellier II Sciences et Tecniques du Languedoc, Montpellier, France.
10. Clark, C. J., J. R. Poulsen, and V. T. Parker. 2001. The role of arboreal seed dispersal groups on the seed rain of a lowland tropical forest. Biotropica 33: 606-620.
11. Clarkson, J. J., M. W. Chase, and M. M. Harley. 2002. Phylogenetic relationships in Burseraceae based on plastid rps16 intron sequences. Kew Bulletin 57: 183-193.
12. Clifford, S. L., N. M. Anthony, M. Bawe-Johnson, K. A. Abernethy, C. E. G. Tutin, L. J. T. White, M. Bermejo, et al. 2004. Mitochondrial DNA phylogeography of western lowland gorillas (Gorilla gorilla gorilla). Molecular Ecology 13: 1551-1565.
13. Daïnou, K., J.-P. Bizoux, J.-L. Doucet, G. Mahy, O. J. Hardy, and M. Heuertz. 2010. Forest refugia revisited: SSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Molecular Ecology 19: 4462-4477.
14. Dauby, G., J. Duminil, M. Heuertz, and O. J. Hardy. 2010. Chloroplast DNA polymorphism and phylogeography of a Central African tree species widespread in mature rainforests: Greenwayodendron suaveolens (Annonaceae). Tropical Plant Biology 3: 3-14.
15. Debout, G. D. G., J.-L. Doucet, and O. J. Hardy. 2011. Population history and gene dispersal inferred from spatial genetic structure of a Central African timber tree, Distemonanthus benthamianus (Caesalpinioideae). Heredity 106: 88-99.
16. Doyle, J. J., and J. L. Doyle. 1987. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochemical Bulletin 19: 11-15.
17. Duminil, J., M. Heuertz, J.-L. Doucet, N. Bourland, C. Cruaud, F. Gavory, C. Doumenge, et al. 2010. CpDNA-based species identification and phylogeography: Application to African tropical tree species. Molecular Ecology 19: 5469-5483.
18. Dumolin-Lapègue, S., B. Demesure, S. Fineschi, V. L. Corre, and R. J. Petit. 1997. Phylogeographic structure of white oaks throughout the European continent. Genetics 146: 1475-1487.
19. Dupont, L. M., S. Jahns, F. Marret, and S. Ning. 2000. Vegetation change in equatorial West Africa: Time-slices for the last 150 ka. Palaeogeography, Palaeoclimatology, Palaeoecology 155: 95-122.
20. Edgar, R. C. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1795.
21. Excoffier, L., L. G. Laval, and S. Schneider. 2005. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
22. Fitter, J. T., and R. J. Rose. 1993. Investigation of chloroplast DNA heteroplasmy in Medicago sativa L. using cultured tissue. Theoretical and Applied Genetics 86: 65-70.
23. Frey, J. E., B. Frey, and D. Forcioli. 2005. Quantitative assessment of heteroplasmy levels in Senecio vulgaris chloroplast DNA. Genetica 123: 255-261.
24. Gautier-Hion, A., J.-M. Duplantier, R. Quris, F. Feer, C. Sourd, J.-P. Decoux, G. Dubost, et al. 1985. Fruit characters as a basis of fruit choice and seed dispersal in a tropical forest vertebrate community. Oecologia 65: 324-337.
25. Haffer, J. 1969. Speciation in Amazonian forest birds. Science 165: 131-137.
26. Hansen, A. K., L. K. Escobar, L. E. Gilbert, and R. K. Jansen. 2007. Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): Implications for phylogenetic studies. American Journal of Botany 94: 42-46.
27. Hardy, O. J., and X. Vekemans. 2002. SPAGeDi: A versatile computer program to analyse spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2: 618-620.
28. Hecketsweiler, P. 1992. Phénologie et saisonnalitéen forêt Gabonaise. L' exemple de quelques espèces ligneuses. Ph.D. dissertation, UniversitéMontpellier II, Montpellier, France.
29. Heuertz, M., S. Carnevale, S. Fineschi, F. Sebastiani, J. F. Hausman, L. Paule, and G. G. Vendramin. 2006. Chloroplast DNA phylogeography of European ashes, Fraxinus sp. (Oleaceae): Roles of hybridization and life history traits. Molecular Ecology 15: 2131-2140.
30. Hladik, A., and N. Hallé. 1973. Catalogue des phanérogames du nord-est du Gabon (5 ° liste). Adansonia 13: 527-544.
31. Koffi, K. G. 2010. Etude de la variabilité génétique et de la phylogéographie de Santiria trimera (Burseraceae) - Implications pour une conservation durable des forêts humides d' Afrique. Ph.D. dissertation, UniversitéLibre de Bruxelles, Brussels, Belgium.
32. Koffi, K. G., M. Heuertz, C. Doumenge, J. M. Onana, F. Gavory, and O. J. Hardy. 2010. A combined analysis of morphological traits, chloroplast and nuclear DNA sequences within Santiria trimera (Burseraceae) suggests several species following the Biological Species Concept. Plant Ecology and Evolution 143: 160-169.
33. Kress, W. J., K. J. Wurdack, E. A. Zimmer, L. A. Weigt, and D. H. Janzen. 2005. Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences, USA 102: 8369-8374.
34. Lahr, D. J. G., and L. A. Katz. 2009. Reducing the impact of PCRmediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. BioTechniques 47: 857-866.
35. Leal, M. E. 2004. The African rain forest during the Last Glacial Maximum, an archipelago of forests in a sea of grass. Ph.D. dissertation, Wageningen University, Wageningen, Netherlands.
36. Librado, P., and J. Rozas. 2009. DnaSp v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
37. Lira, C. F., S. R. S. Cardoso, P. C. G. Ferreira, M. A. Cardoso, and H. Provan. 2003. Long-term population isolation in the endangered tropical tree species Caesalpinia echinata Lam. revealed by chloroplast microsatellites. Molecular Ecology 12: 3219-3225.
38. M'voubou, M. 2005. Les paléoenvironnements sédimentaires fini-holcènes de trois lacs du Gabon (Kamalété, Nguène et Maridor). Etudes sédimentologique et biogéochimique. Ph.D. dissertation, Universitéde Perpignan, Perpignan, France.
39. Maley, J. 1996. The African rain forest- Main characteristics of changes in vegetation and climate from the Upper Cretaceous to the Quaternary. Proceedings of the Royal Society of Edinburgh: Essays on the ecology of the Guineo-Congo rain forest, Huddersfield, UK, 104B: 31-73.
40. Maley, J. 2001. La destruction catastrophique des forêts d'Afrique centrale survenue il y a environ 2500 ans exerce encore une influence majeure sur la répartition actuelle des formations végétales. Systematics and Geography of Plants 71: 777-796.
41. Maniatis, T., E. F. Fritsch, and J. Sambrook. 1989. Molecular cloning: A laboratory manual, 2nd ed., vol. 2. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
42. Matsuo, M., Y. Ito, R. Yamauchi, and J. Obokata. 2005. The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast-nuclear DNA flux. Plant Cell 17: 665-675.
43. McNeal, J. R., J. V. Kuehl, J. L. Boore, and C. W. de Pamphilis. 2007. Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biology.
44. Mogensen, H. L. 1996. The hows and whys of cytoplasmic inheritance in seed plants. American Journal of Botany 83: 383-404.
45. Muloko-Ntoutoume, N., R. J. Petit, L. White, and K. Abernethy. 2000. Chloroplast DNA variation in a rainforest tree (Aucoumea klaineana, Burseraceae) in Gabon. Molecular Ecology 9: 359-363.
46. Myers, N., C. G. Mittermeier, G. A. B. da Fonseca, and J. Kent. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
47. Ndjelé, M. 1988. Principales distributions obtenues par l'analyse factorielle deséléments phytogéographiques présumés endémiques dans la flore du Zaïre. Monograph of Systematic Botany of the Missouri Botanical Garden 25: 631-638.
48. Nei, M., T. Maruyama, and R. Chakraborty. 1975. The bottleneck effect and genetic variability in populations. Evolution 29: 1-10.
49. Onana, J.-M. 2009. Le genre Santiria (Burseraceae) en Afrique: Redéfinition de Santiria trimera. Systematics and Geography of Plants 79: 215-224.
50. Palmé, A. E., V. Semerikov, and M. Lascoux. 2003a. Absence of geographical structure of chloroplast DNA variation in sallow, Salix caprea L. Heredity 91: 465-474.
51. Palmé, A. E., Q. Su, A. Rautenberg, F. Manni, and M. Lascoux. 2003b. Postglacial recolonization and cpDNA variation of silver birch, Betula pendula. Molecular Ecology 12: 201-212.
52. Petit, R. J., I. Aguianagalde, J.-L. de. Beaulieu, C. Bittkau, S. Brewer, R. Cheddadi, R. Ennos, et al. 2003. Glacial refugia: Hotspots but not melting pots of genetic diversity. Science 300: 1563-1565.
53. Plana, V., A. Gascoigne, L. L. Forrest, D. Harris, and R. T. Pennington. 2004. Pleistocene and pre-Pleistocene Begonia speciation in Africa. Molecular Phylogenetics and Evolution 31: 449-461.
54. Pons, O., and R. J. Petit. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237-1245.
55. Prance, G. T. 1982. Forest refuges: Evidence from woody angiosperms. In G. T. Prance [ed.], Biological diversification in the tropics, 137-158. Columbia University Press, New York, New York, USA.
56. Provan, J., W. Powell, and P. M. Hollingsworth. 2001. Chloroplast microsatellites: New tools for studies in plant ecology and evolution. Trends in Ecology & Evolution 16: 142-147.
57. Reitsma, J. M. 1988. Végétation forestière du Gabon / Forest vegetation of Gabon. Technical series Tropenbos, Stichting Tropenbos, Netherlands.
58. Robbrecht, E. 1996. Geography of African Rubiaceae with reference to glacial rain forest refuges. In L. J. G. van der Maesen, X. M. van der Burgt, J. M. van Medenbach de Rooy [eds.], The biodiversity of African plants, 564-581. Kluwer, Dordrecht, Netherlands.
59. Sosef, M. S. M. 1994. Studies in Begoniaceae 5. Refuge begonias. Taxonomy, phylogeny and historical biogeography of Begonia sect. Loasibegonia and sect. Scutobegonia in relation to glacial rain forest refuges in Africa. Wageningen Agricultural University Papers 94-1: 1-306.
60. Stévart, T. 2003. Etude taxonomique,écologie et phytogéographique des Orchidaceae en Afrique centrale atlantique. Ph.D. dissertation, UniversitéLibre de Bruxelles, Brussels, Belgium.
61. Stocks, S. G., L. Seales, F. Paniagua, E. Maehr, and E. M. Bruna. 2008. The geographical and institutional distribution of ecological research in the tropics. Biotropica 40: 397-404.
62. Suchel, J.-B. 1990. Les modalités du passage du régime climatique boréal au régime climatique austral dans le sud-ouest camerounais. Cahier du Centre de recherches de climatologie de Dijon 13: 63-76.
63. Tchouto, M. G. P., J. J. F. E. de Wilde, W. F. de Boer, L. J. G. van der Maesen, and A. M. Cleef. 2009. Bio-indicator species and Central African rain forest refuges in the Campo-Ma' an area, Cameroon. Systematics and Biodiversity 7: 21-31.
64. Telfer, P. T., S. Souquière, S. L. Clifford, K. A. Abernethy, M. W. Bruford, T. R. Disotell, K. N. Sterner, et al. 2003. Molecular evidence for deep phylogenetic divergence in Mandrillus sphinx. Molecular Ecology 12: 2019-2024.
65. van Rompaey, R. S. A. R. 1993. Forest gradients in West Africa: A spatial gradient analysis. Ph.D. dissertation, Wageningen Agricultural University, Wageningen, Netherlands.
66. White, F. 1979. The Guineo-Congolian region and its relationships to other phytochoria. Bulletin du Jardin Botanique National de Belgique / Bulletin van de National Plantentuin van België 49: 11-55.
67. Wolfe, A. D., and C. P. Randle. 2004. Recombination, heteroplasmy, haplotype polymorphism, and paralogy in plastid genes: Implications for plant molecular systematics. Systematic Botany 29: 1011-1020.