Late Pleistocene molecular dating of past population fragmentation and demographic changes in African rain forest tree species supports the forest refuge hypothesis

Journal of Biogeography

Volumn 42, Issue 8, 2015, Pages 1443-1454

  Duminil, Jérôme ^a,b   Mona, Stefano ^c   Mardulyn, Patrick ^a   Doumenge, Charles ^d   Walmacq, Frédéric ^a   Doucet, Jean Louis ^e   Hardy, Olivier J ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b BIOVERSITY INTERNATIONAL   (Italy)

^c SORBONNE UNIVERSITÉ   (France)

^d TA C 105 D Campus International de Baillarguet   (France)

^e UNIVERSITY OF LIÈGE   (Belgium)

Author keywords

Africa; Coalescence methods; Guineo Congolian forests; Last Glacial Maximum; Nuclear gene; Past climate change; Phylogeography; Refugia theory; Tropical species; Vanishing refuge model

Indexed keywords

CLIMATE VARIATION; DATING METHOD; DECIDUOUS TREE; DEMOGRAPHIC TREND; GENETIC MARKER; HABITAT FRAGMENTATION; HOLOCENE; MOLECULAR ANALYSIS; PARAPATRY; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION BOTTLENECK; RAINFOREST; REFUGE; TROPICAL FOREST;

DAHOMEY GAP; GUINEA;

CAESALPINIOIDEAE; ERYTHROPHLEUM; ERYTHROPHLEUM IVORENSE; ERYTHROPHLEUM SUAVEOLENS; FABACEAE;

EID: 84936986070     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/jbi.12510     Document Type: Article

References (53)

1. Akoègninou, A., van der Burg, W.J. & van der Maesen, L.J.G. (eds) (2006) Flore analytique du Bénin. Backhuys, Leiden.
2. Aubréville, A. (1950) Flore forestière soudano-guinéenne. A.O.F. - Cameroun - A.O.F. Société d'éditions géographiques, maritimes et coloniales, Paris.
3. Avise, J.C., Arnold, J., Ball, R.M., Bermingham, E., Lamb, T., Neigel, J.E., Reeb, C.A. & Saunders, N.C. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics, 18, 489-522.
4. Bonnefille, R. (2007) Rainforest responses to past climatic changes in tropical Africa. Tropical rainforest responses to climate change (ed. by M.B. Bush and J.R. Flenley ), pp. 117-170. Springer, Berlin.
5. Bruneau, A., Mercure, M., Lewis, G.P. & Herendeen, P.S. (2008) Phylogenetic patterns and diversification in the caesalpinioid legumes. Canadian Journal of Botany, 86, 697-718.
6. Budde, K., González-Martínez, S.C., Hardy, O.J. & 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.
7. Daïnou, K., Mahy, G., Duminil, J., Dick, C.W., Doucet, J.-L., Donkpégan, A.S.L., Pluijgers, M., Sinsin, B., Lejeune, P. & Hardy, O.J. (2014) Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae). Heredity, 113, 74-85.
8. Damasceno, R., Strangas, M.L., Carnaval, A.C., Rodrigues, M.T. & Moritz, C. (2014) Revisiting the vanishing refuge model of diversification. Frontiers in Genetics, 5, 353.
9. Dauby, G., Duminil, J., Heuertz, M., Koffi, K.G., Stévart, T. & Hardy, O.J. (2014) Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover. Molecular Ecology, 23, 2299-2312.
10. Debout, G.D.G., Doucet, J.-L. & Hardy, O.J. (2010) Population history and gene dispersal inferred from spatial genetic structure of a Central African timber tree, Distemonanthus benthamianus (Caesalpinioideae). Heredity, 106, 88-99.
11. Dellicour, S. & Mardulyn, P. (2013) spads 1.0: a toolbox to perform spatial analyses on DNA sequence datasets. Molecular Ecology Resources, 14, 647-651.
12. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
13. Duminil, J., Heuertz, M., Doucet, J.-L., Bourland, N., Cruaud, C., Gavory, F., Doumenge, C., Navascués, M. & Hardy, O.J. (2010) CpDNA-based species identification and phylogeography: application to African tropical tree species. Molecular Ecology, 19, 5469-5483.
14. Duminil, J., Brown, R.P., Ewédjè, E.-E.B.K., Mardulyn, P., Doucet, J.-L. & Hardy, O.J. (2013) Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae). BMC Evolutionary Biology, 13, 195.
15. Dupont, L.M., Donner, B., Schneider, R. & Wefer, G. (2001) Mid-Pleistocene environmental change in tropical Africa began as early as 1.05 Ma. Geology, 29, 195-198.
16. El Mousadik, A. & Petit, R.J. (1996) Chloroplast DNA phylogeography of the argan tree of Morocco. Molecular Ecology, 5, 547-555.
17. Evanno, G., Regnaut, S. & Goudet, J. (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology, 14, 2611-2620.
18. Falush, D., Stephens, M. & Pritchard, J.K. (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164, 1567-1587.
19. Gonmadje, C.F., Doumenge, C., Sunderland, T.C.H., Balinga, M.P.B. & Sonké, B. (2012) Analyse phytogéographique des forêts d'Afrique Centrale: le cas du massif de Ngovayang (Cameroun). Plant Ecology and Evolution, 145, 152-164.
20. Hardy, O.J., Born, C., Budde, K., Daïnou, K., Dauby, G., Duminil, J., Ewédjè, E.-E.B.K., Gomez, C., Heuertz, M., Koffi, G.K., Lowe, A.J., Micheneau, C., Ndiade-Bourobou, D., Piñeiro, R. & Poncet, V. (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.
21. Hare, M.P. (2001) Prospects for nuclear gene phylogeography. Trends in Ecology and Evolution, 16, 700-706.
22. Heled, J. & Drummond, A.J. (2010) Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution, 27, 570-580.
23. Hély, C., Braconnot, P., Watrin, J. & Zheng, W. (2009) Climate and vegetation: simulating the African humid period. Comptes Rendus Geoscience, 341, 671-688.
24. Heuertz, M., Duminil, J., Dauby, G., Savolainen, V. & Hardy, O.J. (2014) Comparative phylogeography in rainforest trees from Lower Guinea, Africa. PLoS ONE, 9, e84307.
25. Hewitt, G.M. (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247-276.
26. Hudson, R.R. (1990) Gene genealogies and the coalescent process. Oxford surveys in evolutionary biology (ed. by D.G. Futuyma and J. Antonovics ), pp. 1-44. Oxford University Press, Oxford.
27. Kouadio, L. (2009) Mesures sylvicoles en vue d'améliorer la gestion des populations d'essences forestières commerciales de l'Est du Cameroun. PhD Dissertation, Faculté Universitaire des Sciences Agronomiques de Gembloux, Gembloux, Belgium.
28. Leal, M.E. (2001) Microrefugia, small scale ice forest remnants. Plant systematics and phytogeography for the understanding of African biodiversity (ed. by E. Robbrecht, J. Degreef and I. Friis ), pp. 1073-1077. National Botanic Garden, Meise.
29. Ley, A.C. & Hardy, O.J. (2014) Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests - the case of sympatric and parapatric Marantaceae species. Molecular Phylogenetics and Evolution, 77, 264-274.
30. Li, M., Wunder, J., Bissoli, G., Scarponi, E., Gazzani, S., Barbaro, E., Saedler, H. & Varotto, C. (2008) Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species. Cladistics, 24, 727-745.
31. Librado, P. & Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
32. Lönnberg, E. (1929) The development and distribution of the African fauna in connection with and depending upon climatic changes. Arkiv för Zoology, 21, 1-33.
33. Maley, J. (1996) Le cadre paléoenvironnemental des refuges forestiers africains: quelques données et hypothèses [The palaeoenvironmental structure of African forest reserves: some data and hypotheses]. The biodiversity of African plants: Proceedings of the XIVth AETFAR Congress 22-27 August 1994, Wageningen, The Netherlands (ed. by der Maesen L.J.G., der Burgt X.M. and van Medenbach de Rooy J.M.), pp. 519-535. Kluwer, Dordrecht (in French).
34. Mardulyn, P., Mikhailov, Y.E. & Pasteels, J.M. (2009) Testing phylogeographic hypotheses in a Euro-Siberian cold-adapted leaf beetle with coalescent simulations. Evolution, 63, 2717-2729.
35. Martin, D. & Rybicki, E. (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics, 16, 562-563.
36. Mayr, E. & O'Hara, R.J. (1986) The biogeographic evidence supporting the Pleistocene forest refuge hypothesis. Evolution, 40, 55-67.
37. Moritz, C., Patton, J.L., Schneider, C.J. & Smith, T.B. (2000) Diversification of rainforest faunas: an integrated molecular approach. Annual Review of Ecology and Systematics, 31, 533-563.
38. Nei, M. & Li, W.H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences USA, 76, 5269-5273.
39. Nylander, J.A.A. (2004) MrModeltest 2.3. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala.
40. Pamilo, P. & Nei, M. (1988) Relationships between gene trees and species trees. Molecular Biology and Evolution, 5, 568-583.
41. Plana, V. (2004) Mechanisms and tempo of evolution in the African Guineo-Congolian rainforest. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 1585-1594.
42. Plummer, M., Best, N., Cowles, M.K. & Vines, K. (2008) coda: output analysis and diagnostics for Markov chain Monte Carlo simulations. R package version 0.13-3. Available at: http://cran.r-project.org/package=coda.
43. Pons, O. & Petit, R.J. (1996) Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics, 144, 1237-1245.
44. Pritchard, J.K., Stephens, M. & Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
45. Quinzin, M.C. & Mardulyn, P. (2014) Multi-locus DNA sequence variation in a complex of four leaf beetle species with parapatric distributions: mitochondrial and nuclear introgressions reveal recent hybridization. Molecular Phylogenetics and Evolution, 78, 14-24.
46. Rambaut, A., Suchard, M.A., Xie, D. & Drummond, A.J. (2014) Tracer v1.6. University of Edinburgh, Edinburgh, UK. Available from http://beast.bio.ed.ac.uk/Tracer.
47. Robbrecht, E. (1996) Geography of African Rubiaceae with reference to glacial rain forest refuges. The biodiversity of African plants: Proceedings of the XIVth AETFAR Congress 22-27 August 1994, Wageningen, The Netherlands (ed. by L.J.G. Van Der Maesen, X.M. Van Der Burgt and J.M. Van Medenbach De Rooy ), pp. 564-581. Kluwer, Dordrecht.
48. Rychlik, W. & Rhoads, R.E. (1989) A computer program for choosing optimal oligonucleotides for filter hybridization, sequencing and in vitro amplification of DNA. Nucleic Acids Research, 17, 8543-8551.
49. Salzmann, U. & Hoelzmann, P. (2005) The Dahomey Gap: an abrupt climatically induced rain forest fragmentation in West Africa during the late Holocene. The Holocene, 15, 190-199.
50. Sosef, M.S.M. (1994) Studies in Begoniaceae V. 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. Wageningen Agricultural University, Wageningen.
51. Sosef, M.S.M. (1996) Begonias and African rain forest refuges: general aspects and recent progress. The biodiversity of African plants: Proceedings of the XIVth AETFAR Congress 22-27 August 1994, Wageningen, The Netherlands (ed. by L.J.G. van der Maesen, X.M. van der Burgt And J.M. van Medenbach de Rooy ), pp. 602-611. Kluwer, Dordrecht.
52. Stephens, M. & Donnelly, P. (2003) A comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 73, 1162-1169.
53. White, F. (1983) The vegetation of Africa: a descriptive memoir to accompany the UNESCO/AETFAT/UNSO vegetation map of Africa. Natural Resources Research no. 20. UNESCO, Paris, France.