Comparative phylogeography in rainforest trees from lower Guinea, Africa

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Heuertz, Myriam ^a,b,f   Duminil, Jérôme ^a,c   Dauby, Gilles ^a   Savolainen, Vincent ^d,e   Hardy, Olivier J ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b INIA   (Spain)

^c BIOVERSITY INTERNATIONAL   (Italy)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

^e JODRELL LABORATORY   (United Kingdom)

^f UNIVERSITY OF FRIBOURG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

ALLELE; ARTICLE; CLIMATE; COMPARATIVE STUDY; CONTROLLED STUDY; DNA SEQUENCE; ENVIRONMENT; EQUATORIAL GUINEA; GENETIC LINE; GENETIC VARIABILITY; GREENWAYODENDRON SUAVEOLENS; MILICIA EXCELSA; NONHUMAN; PHYLOGEOGRAPHY; PLANT EVOLUTION; PLASTID; SAMPLE SIZE; SAMPLING; SEASON; SEASONAL VARIATION; SIMULATION; SPECIES ENDEMICITY; SYMPHONIA GLOBULIFERA; TAXON; TREE; TRICHOSCYPHA ACUMINATA; TROPICAL RAIN FOREST;

AFRICA; ANALYSIS OF VARIANCE; BIODIVERSITY; CLIMATE; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PHYLOGEOGRAPHY; RAIN; TREES;

EID: 84897428445     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0084307     Document Type: Article

References (82)

1. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GA, Kent J (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853-858. (Pubitemid 30130979)
2. Küper W, Sommer JH, Lovett JC, Mutke J, Peter H, et al. (2010) Africa's hotspots of biodiversity redefined. Annals of the Missouri Botanical Garden 91:525-535.
3. Barthlott WB, Mutke JM, Rafiqpoor D, Kier G, Kreft H (2005) Global centers of vascular plant diversity. Nova Acta Leopoldina 342: 61-83.
4. Mayaux P, Holmgren P, Achard F, Eva H, Stibig H-J, et al. (2005) Tropical forest cover change in the 1990s and options for future monitoring. Philos Trans R Soc Lond B Biol Sci 360: 373-384. (Pubitemid 41529631)
5. Duveiller G, Defourny P, Desclée B, Mayaux P (2008) Deforestation in Central Africa: Estimates at regional, national and landscape levels by advanced processing of systematically-distributed Landsat extracts. Remote Sens Environ 112: 1969-1981.
6. Plana V (2004) Mechanisms and tempo of evolution in the African Guineo-Congolian rainforest. Philos Trans R Soc Lond B Biol Sci 359: 1585-1594.
7. Knowles LL (2003) The burgeoning field of statistical phylogeography. J Evolution Biol 17: 1-10.
8. Richards CL, Carstens BC, Knowles LL (2007) Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses. J Biogeogr 34: 1833-1845. (Pubitemid 47610616)
9. Hickerson MJ, Stahl EA, Lessios HA (2006) Test for simultaneous divergence using approximate Bayesian computation. Evolution 60: 2435-2453. (Pubitemid 46220855)
10. Petit R, Aguinagalde I, de Beaulieu J-L, Bittkau C, Brewer S, et al. (2003) Glacial refugia: hotspots but not melting pots of genetic diversity. Science 300: 1563-1565. (Pubitemid 36682886)
11. Andrew Jones F, Cerón-Souza I, Hardesty BD, Dick CW (2013) Genetic evidence of Quaternary demographic changes in four rain forest tree species sampled across the Isthmus of Panama. J Biogeogr 40: 720-731.
12. Turchetto-Zolet A, Pinheiro F, Salgueiro F, Palma-Silva C (2013) Phylogeographical patterns shed light on evolutionary process in South America. Mol Ecol 22: 1193-1213.
13. Alvarez N, Thiel-Egenter C, Tribsch A, Holderegger R, Manel S, et al. (2009) History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants. Ecol Lett 12: 632-640.
14. Huntley B, Birks HJB (1983) An atlas of past and present pollen maps of Europe: 0-13000 years ago. Cambridge Univ Press Cambridge UK.
15. White F (1979) The Guineo-Congolian Region and its relationships to other phytochoria. Bulletin du Jardin Botanique national de Belgique 49: 11-55.
16. Barthlott W, Lauer W, Placke A (1996) Global distribution of species diversity in vascular plants: Towards a World map of phytodiversity. Erdkunde 50: 317-327.
17. Vande Weghe JP (2004) Forests of Central Africa. Lannoo Publishers, Tielt, Belgium.
18. Maley J (1996) Le cadre paléoenvironnemental des refuges forestiers africains: quelques données et hypothéses. In: Maesen LJG van der, Burgt XM van der, Rooy JM van M de, editors. The biodiversity of African plants. Proceedings XIVth AETFAT Congress, Wageningen, The Netherlands.Kluwer Academic Publishers, Dordrecht. 519-535.
19. Olson DM, Dinerstein E, Wikramanayake ED, Burgess ND, Powell GVN, et al. (2001) Terrestrial ecoregions of the World: A new map of life on Earth. BioScience 51: 933.
20. Letouzey R (1985) Notice de la carte phytogéographique du Cameroun au 1/500 000. IRA, Yaoundé, Cameroun & Institut de la Carte Internationale de la Végétation, Toulouse, France.
21. Gartlan S (1989) La conservation des écosystèmes forestiers du Cameroun. IUCN Gland, Switzerland and Cambridge, UK.
22. Linder H (2001) Plant diversity and endemism in sub-Saharan tropical Africa. J Biogeogr: 169-182.
23. Gonmadje CF, Doumenge C, McKey D, Tchouto GPM, Sunderland TCH, et al. (2011) Tree diversity and conservation value of Ngovayang's lowland forests, Cameroon. Biodivers Conserv 20: 2627-2648.
24. Maley J, Brenac P (1998) Vegetation dynamics, palaeoenvironments and climatic changes in the forests of western Cameroon during the last 28,000 years B.P. Rev of Palaeobot Palyno 99: 157-187. (Pubitemid 28224461)
25. Sosef MS (1996) Begonias and African rain forest refuges: general aspects and recent progress. In: Maesen LJG van der, Burgt XM van der, Rooy JM van M de, editors. The biodiversity of African plants. Proceedings XIVth AETFAT Congress, Wageningen, The Netherlands. Kluwer Academic Publishers, Dordrecht. 602-611.
26. Hamilton AC, Taylor D (1991) History of climate and forests in tropical Africa during the last 8 million years. Climatic Change 19: 65-78. (Pubitemid 23371930)
27. Lézine A-M (2007) Pollen records, postglacial. Africa. In: Elias SA, editor. Encyclopaedia of Quaternary Sciences Elsevier. Vol.4. Elsevier. 2682-2698.
28. Bonnefille R (2007) Rainforest responses to past climatic changes in tropical Africa. In: Bush MB, Flenley JR, Gosling WD, editors. Tropical rainforest responses to climate change. Chichester: Praxis Publishing. 117-170.
29. Dupont L (2011) Orbital scale vegetation change in Africa. Quat Sci Rev 30: 3589-3602.
30. Sosef MS, Issembé Y, Bourobou Bourobou H, Koopman W (2004) Monts Doudou, Gabon. A floral and faunal inventory with reference to elevational distribution. Memoirs of the California Academy of Sciences 28: 308.
31. Tchouto MGP, de Wilde JJFE, de Boer WF, van der Maesen LJG, Cleef AM (2009) Bio-indicator species and Central African rain forest refuges in the Campo-Ma'an area, Cameroon. Systematics and Biodiversity 7: 21-31.
32. Stevart T, Droissart V (2004) Diversity of Orchids in the Gamba Complex, Gabon. Bulletin of the Biological Society of Washington: 275-284.
33. Anhuf D, Ledru M-P, Behling H, Da Cruz FW, Cordeiro RC, et al. (2006) Paleo-environmental change in Amazonian and African rainforest during the LGM. Palaeogeogr Palaeocl 239: 510-527. (Pubitemid 44608192)
34. Duminil J, Heuertz M, Doucet J-L, Bourland N, Cruaud C, et al. (2010) CpDNA-based species identification and phylogeography: application to African tropical tree species. Mol Ecol 19: 5469-5483.
35. Ibrahim KM, Nichols RA, Hewitt GM (1996) Spatial patterns of genetic variation generated by different forms of dispersal during range expansion. Heredity 77: 282-291.
36. Hardy O, Born C, Budde K, Daïnou K, Dauby G, et al. (2013) Comparative phylogeography of African rain forest trees: a review of genetic signatures of vegetation history in the Guineo-Congolian region. Comptes rendus Geoscience 345: 284-296.
37. Gonmadje CF, Doumenge C, Sunderland TCH, Balinga MPB, Sonké B (2012) Analyse phytogéographique des forêts d'Afrique Centrale: le cas du massif de Ngovayang (Cameroun). Plant Ecology and Evolution 145: 152-164.
38. Dauby G, Duminil J, Heuertz M, Hardy OJ (2010) Chloroplast DNA polymorphism and phylogeography of a Central African tree species widespread in mature rainforests: Greenwayodendron suaveolens (Annonaceae). Tropical Plant Biol 3: 4-13.
39. Koffi KG, Heuertz M, Doumenge C, Onana JM, Gavory F, et al. (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.
40. Daïnou K, Bizoux J-P, Doucet J-L, Mahy G, Hardy OJ, et al. (2010) Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Mol Ecol 19: 4462-4477.
41. Muloko-Ntoutoume N, Petit RJ, White L, Abernethy K (2000) Chloroplast DNA variation in a rainforest tree (Aucoumea klaineana, Burseraceae) in Gabon. Mol Ecol 9: 359-363. (Pubitemid 30152756)
42. Born C, Alvarez N, McKey D, Ossari S, Wickings EJ, et al. (2011) Insights into the biogeographical history of the Lower Guinea Forest Domain: evidence for the role of refugia in the intraspecific differentiation of Aucoumea klaineana. Mol Ecol 20: 131-142.
43. Lowe A, Harris D, Dormott E, Dawson I (2010) Testing putative African tropical forest refugia using chloroplast and nuclear DNA phylogeography. Tropical Plant Biol 3: 50-58.
44. Debout GDG, Doucet J-L, Hardy OJ (2011) Population history and gene dispersal inferred from spatial genetic structure of a Central African timber tree, Distemonanthus benthamianus (Caesalpinioideae). Heredity 106: 88-99.
45. Koffi KG, Hardy OJ, Doumenge C, Cruaud C, Heuertz M (2011) Diversity gradients and phylogeographic patterns in Santiria trimera (Burseraceae), a widespread African tree typical of mature rainforests. Am J Bot 98: 254-264.
46. Kenfack D (2011) A synoptic revision of Carapa (Meliaceae). Harvard Papers in Botany 16: 171-231.
47. Duminil J, Kenfack D, Viscosi V, Grumiau L, Hardy OJ (2012) Testing species delimitation in sympatric species complexes: the case of an African tropical tree, Carapa spp. (Meliaceae). Mol Phylogenet Evol 62: 275-285.
48. Breteler FJ (2001) A new species of Strombosiopsis (Olacaceae) from Gabon. Adansonia 23: 303-306.
49. Senterre B (2005) Recherches méthodologiques pour la typologie de la végétation et la phytogéographie des forêts denses d'Afrique tropicale.
50. Clark CJ, Poulsen JR (2001) The role of arboreal seed dispersal groups on the seed rain of a lowland tropical forest. Wildlife Conservation 33: 606-620. (Pubitemid 34134843)
51. Davies A, Oates J, Dasilva G (1999) Patterns of frugivory in three West African Colobine Monkeys. Int J Primatol 20: 327-357. (Pubitemid 29345321)
52. Gautier-Hion A, Duplantier J-M, Quris R, Feer F, Sourd C, et al. (1985) Fruit characters as a basis of fruit choice and seed dispersal in a tropical forest vertebrate community. Oecologia: 324-337.
53. Hardesty BD, Parker VT (2002) Community seed rain patterns and a comparison to adult community structure in a West African tropical forest. Plant Ecology: 49-64. (Pubitemid 36251402)
54. Mitani M (1999) Does fruiting phenology vary with fruit syndrome? An investigation on animal-dispersed tree species in an evergreen forest in southwestern Cameroon. Ecol Res 14: 371-383.
55. Budde K, González-Martinez S, Hardy O, Heuertz M (2013) The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa. Heredity 111: 66- 76.
56. Breteler FJ (2004) The genus Trichoscypha (Anacardiaceae) in Lower Guinea and Congolia: A synoptic revision. Adansonia 26: 97-127.
57. Doyle J, Doyle J (1987) A rapid DNA isolation method for small quantities of fresh tissues. Phytochemical Bulletin 19: 11-15.
58. Kress WJ, Wurdack KJ, Zimmer E a, Weigt L, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci U S A 102: 8369-8374. (Pubitemid 40803501)
59. Demesure B, Sodzi N, Petit RJ (1995) A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol Ecol 4: 129-131.
60. Lee C, Wen J (2004) Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of plants. Mol Phylogenet Evol 31: 894-903. (Pubitemid 38610962)
61. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
62. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics (Oxford, England) 25: 1451-1452.
63. Nei M (1987) Molecular Evolutionary Genetics. MacIntyre RJ, editor. Columbia University Press.
64. Watterson GA (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7: 256-276.
65. Clement M, Posada D, Crandall K a (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9: 1657-1659.
66. Pons O, Petit R (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237-1245. (Pubitemid 26378263)
67. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2: 618-620. (Pubitemid 35436766)
68. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resources 10: 564-567.
69. Kalinowski ST (2005) Hp-Rare 1.0: a computer program for performing rarefaction on measures of allelic richness. Mol Ecol Notes 5: 187-189.
70. Petit R, el Mousadik A, Pons O (1998) Identifying populations for conservation on the basis of genetic markers. Conservation Biology 12: 844-855. (Pubitemid 28395189)
71. Ihaka R, Gentleman R (1996) R: A Language for Data Analysis and Graphics. Journal of Computational and Graphical Statistics 5: 299-314.
72. Hardy OJ (2003) Estimation of pairwise relatedness between individuals and characterization of isolation-by-distance processes using dominant genetic markers. Mol Ecol 12: 1577-1588.
73. Excoffier L, Foll M (2011) fastsimcoal: a continuous-time soalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27: 1332-1334.
74. Manni F, Guerard E, Heyer E (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: How barriers can be detected by using Monmonier's algorithm. Human Biology 76: 173-190. (Pubitemid 39014211)
75. Jaramillo-Correa J, Grivet D, Terrab A, Kurt Y, De-Lucas A, et al. (2010) The Strait of Gibraltar as a major biogeographic barrier in Mediterranean conifers: a comparative phylogeographic survey. Mol Ecol 19: 5452-5468.
76. Fazekas AJ, Kesanakurti PR, Burgess KS, Percy DM, Graham SW, et al. (2009) Are plant species inherently harder to discriminate than animal species using DNA barcoding markers? Mol Ecol Resources 9: 130-139.
77. Petit RJ, Hampe A (2006) Some evolutionary consequences of being a tree. Ann Rev Ecol Evol Syst 37: 187-214. (Pubitemid 44907617)
78. Qiu Y-X, Fu C-X, Comes HP (2011) Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world's most diverse temperate flora. Mol Phylogenet Evol 59: 225-244.
79. Vekemans X, Hardy O (2004) New insights from fine-scale spatial genetic structure analyses in plant populations. Mol Ecol: 921-935. (Pubitemid 38390597)
80. Aguinagalde I, Hampe A, Mohanty A, Jordano P (2005) Effects of life-history traits and species distribution on genetic structure at maternally inherited markers in European trees and shrubs. J Biogeogr: 329-339. (Pubitemid 40210665)
81. Duminil J, Fineschi S, Hampe A, Jordano P, Salvini D, et al. (2007) Can population genetic structure be predicted from life-history traits? Am Nat 169: 662-672. (Pubitemid 46656062)
82. Fine PVA, Zapata F, Daly DC, Mesones I, Misiewicz TM, et al. (2013) The importance of environmental heterogeneity and spatial distance in generating phylogeographic structure in edaphic specialist and generalist tree species of Protium (Burseraceae) across the Amazon Basin. J Biogeogr 40: 646-661.