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

Volumn 13, Issue 1, 2013, Pages

  Duminil, Jerome ^a,b   Brown, Richard P ^c   Ewédjè, Eben Ezer Bk ^a,d   Mardulyn, Patrick ^a   Doucet, Jean Louis ^e   Hardy, Olivier J ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b BIOVERSITY INTERNATIONAL   (Italy)

^c LIVERPOOL JOHN MOORES UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF ABOMEY CALAVI   (Benin)

^e Unite de Gestion des Ressources forestieres et des Milieux naturels   (Belgium)

Author keywords

Cluster analysis; Fragmentation; Last glacial maximum; Phylogeography; Range expansion; Refugium; Species delimitation; Tropical rainforest

Indexed keywords

BAYESIAN ANALYSIS; CHLOROPLAST; CLIMATE VARIATION; CLUSTER ANALYSIS; DICOTYLEDON; DRY FOREST; ENVIRONMENTAL GRADIENT; EVERGREEN FOREST; GENE FLOW; GENETIC DIFFERENTIATION; GENETIC MARKER; GENETIC STRUCTURE; HABITAT FRAGMENTATION; INTROGRESSION; LAST GLACIAL MAXIMUM; MITOCHONDRIAL DNA; PALEOCLIMATE; PHYLOGEOGRAPHY; PLEISTOCENE; RAINFOREST; RANGE EXPANSION; REFUGIUM; SPECIATION (BIOLOGY); TAXONOMY; TROPICAL REGION;

CAMEROON; CENTRAL AFRICA;

ERYTHROPHLEUM; ERYTHROPHLEUM IVORENSE; ERYTHROPHLEUM SUAVEOLENS; FABACEAE;

PLANT DNA;

AFRICA; ARTICLE; BAYES THEOREM; BIODIVERSITY; CENTRAL AFRICA; CLASSIFICATION; CLIMATE; ECOSYSTEM; EVOLUTION; FABACEAE; GENE POOL; GENETIC DRIFT; GENETICS; PHYSIOLOGY; TREE;

AFRICA, CENTRAL; AFRICA, WESTERN; BAYES THEOREM; BIODIVERSITY; BIOLOGICAL EVOLUTION; CLIMATE; DNA, PLANT; ECOSYSTEM; FABACEAE; GENE POOL; GENETIC DRIFT; TREES;

EID: 84883661493     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-13-195     Document Type: Article

References (41)

1. White F, The vegetation of Africa: A Descriptive Memoir to Accompany the UNESCO/AETFAT/UNSO Vegetation Map of Africa, Natural Resources Research no. 20 Paris: UNESCO 1983
2. The Guineo-Congolian region and its relationships to other phytochoria. White F, Bulletin du jardin botanique nationale de Belgique 1979 49 11 55 10.2307/3667815
3. Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities. Gomez C, Dussert S, Hamon P, Hamon S, De Kochko A, Poncet V, BMC Evol Biol 2009 9 167 10.1186/1471-2148-9-167 19607674
4. Insights into the biogeographical history of the lower Guinea forest domain: evidence for the role of refugia in the intraspecific differentiation of Aucoumea klaineana. Born C, Alvarez N, McKey D, Ossari S, Wickings EJ, Hossaert-McKey M, Chevallier MH, Mol Ecol 2010 20 131 142 21091559
5. Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Dainou K, Bizoux JP, Doucet JL, Mahy G, Hardy OJ, Heuertz M, Mol Ecol 2010 19 4462 4477 10.1111/j.1365-294X.2010.04831.x 20854478
6. Chloroplast DNA polymorphism and phylogeography of a Central African tree species widespread in mature rainforests: Greenwayodendron suaveolens (Annonaceae). Dauby G, Duminil J, Heuertz M, Hardy OJ, Trop Plant Biol 2010 3 4 13 10.1007/s12042-010-9041-6
7. Population history and gene dispersal inferred from spatial genetic structure of a Central African timber tree, Distemonanthus benthamianus (Caesalpinioideae). Debout GDG, Doucet JL, Hardy OJ, Heredity 2010 104
8. CpDNA-based species identification and phylogeography: application to African tropical tree species. Duminil J, Heuertz M, Doucet JL, Bourland N, Cruaud C, Gavory F, Doumenge C, Navascues M, Hardy OJ, Mol Ecol 2010 19 5469 5483 10.1111/j.1365-294X.2010.04917.x 21091558
9. Genomic signals of diversification along ecological gradients in a tropical lizard. Freedman AH, Thomassen HA, Buermann W, Smith TB, Mol Ecol 2010 19 3773 3788 10.1111/j.1365-294X.2010.04684.x 20618893
10. A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae). Holstein N, Renner SS, BMC Evol Biol 2011 11 28 10.1186/1471-2148-11-28 21269492
11. Climate and palaeoceanographic changes in west Central Africa during the last deglaciation: palynological investigation. Marret F, Scourse J, Jansen JHF, Schneider R, Cr Acad Sci II A 1999 329 721 726
12. Mid-Pleistocene environmental change in tropical Africa began as early as 1.05 Ma. Dupont LM, Bonner B, Schneider R, Wefer G, Geology 2001 29 195 198 10.1130/0091-7613(2001)029<0195:MPECIT>2.0.CO;2
13. Abrupt onset and termination of the African humid period: rapid climate responses to gradual insolation forcing. Demenocal P, Ortiz J, Guilderson T, Adkins J, Sarnthein M, Baker L, Yarusinsky M, Quaternary Sci Rev 2000 19 347 361 10.1016/S0277-3791(99)00081-5
14. The dahomey Gap: an abrupt climatically induced rain forest fragmentation in West Africa during the late holocene. Salzmann U, Hoelzmann P, Holocene 2005 15 190 199 10.1191/0959683605hl799rp
15. Vegetation response to the "african Humid Period" termination in Central Cameroon (7° N)- new pollen insight from Lake Mbalang. Vincens A, Buchet G, Servant M, Clim Past 2010 6 281 294 10.5194/cp-6-281-2010
16. Flore Analytique Du Bénin Leiden, Netherlands: Backhuys Publishers, Akoègninou A, Burg WJ Van Der, Maesen LJG Van Der, 2006 1034
17. La flore forestière de la Côte d'Ivoire, Tome 1. Aubréville A, Nogent-sur-Marne, Centre technique forestier tropical (Ctft) 1959 1 370
18. Aubréville A, Légumineuses-Caesalpinioidées, in Aubréville A. & Leroy J.-F., Flore du Cameroun 9 Paris: Muséum national d'Histoire naturelle 1970 1-339 24073400
19. Hawthorne WD, Jongkind C, Guide to the Woody Plants of Western Africa Kew, U.K.: Royal Botanic Gardens 2006
20. Isolation of SSR markers for two African tropical tree species Erythrophleum suaveolens and E. ivorense (Caesalpinioideae). Duminil J, Koffi KG, Debout GDG, Sebastiani F, Vendramin GG, Heuertz M, Gonzalez-Martinez SC, Hardy OJ, Am J Bot Prim Notes Pro 2011 98 106 E108
21. FSTAT (Version 1.2): a computer program to calculate F-statistics. Goudet J, J Hered 1995 86 485 486
22. Maximum likelihood from incomplete data via the EM algorithm. Dempster AP, Laird NM, Rubin DB, J R Stat Soc 1977 39 1 38
23. Microsatellite null alleles and estimation of population differentiation. Chapuis M-P, Estoup A, Mol Biol Evol 2007 24 621 631 17150975
24. Inference of population structure using multilocus genotype data. Pritchard JK, Stephens M, Donnelly P, Genetics 2000 155 945 959 10835412
25. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Falush D, Stephens M, Pritchard JK, Genetics 2003 164 1567 1587 12930761
26. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Jakobsson M, Rosenberg NA, Bioinformatics 2007 23 1801 1806 10.1093/bioinformatics/btm233 17485429
27. Detecting the number of clusters of individuals using the software structure: a simulation study. Evanno G, Regnaut S, Goudet J, Mol Ecol 2005 14 2611 2620 10.1111/j.1365-294X.2005.02553.x 15969739
28. SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Hardy OJ, Vekemans X, Mol Ecol Notes 2002 2 618 620 10.1046/j.1471-8286.2002.00305.x
29. Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Hardy OJ, Charbonnel N, Freville H, Heuertz M, Genetics 2003 163 1467 1482 12702690
30. Universal primers for amplification of three non-coding regions of chloroplast DNA. Taberlet P, Gielly L, Pautou G, Bouvet J, Plant Mol Biol 1991 17 1105 1109 10.1007/BF00037152 1932684
31. Median-joining networks for inferring intraspecific phylogenies. Bandelt H-J, Forster P, Röhl A, Mol Biol Evol 1999 16 37 487 10.1093/ oxfordjournals.molbev.a026036 10331250
32. Phylogenetic patterns and diversification in the caesalpinioid legumes. Bruneau A, Mercure M, Lewis GP, Herendeen PS, Can J Bot 2008 86 697 718 10.1139/B08-058
33. BEAST: Bayesian evolutionary analysis by sampling trees. Drummond AJ, Rambaut A, Bmc Evol Biol 2007 7 214 10.1186/1471-2148-7-214 17996036
34. jModelTest: Phylogenetic Model Averaging. Posada J, Molecular Biology & Evolution 2008 25 7 1253 1256 10.1093/molbev/msn083 24073432
35. Testing for genetic evidence of population expansion and contraction: an empirical analysis of microsatellite DNA variation using a hierarchical Bayesian model. Storz JF, Beaumont MA, Evolution 2002 56 154 166 11913661
36. The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes. Chikhi L, Sousa VC, Luisi P, Goossens B, Beaumont MA, Genetics 2010 186 983 995 10.1534/genetics.110.118661 20739713
37. Inferring population decline and expansion from microsatellite data: a simulation-based evaluation of the MSVAR method. Girod C, Vitalis R, Leblois R, Freville H, Genetics 2011 188 165 U287 10.1534/genetics.110.121764 21385729
38. R: a language for data analysis and graphics. Ihaka A, Gentleman R, J Comput Graph Stat 1996 5 299 314
39. Mechanisms and tempo of evolution in the African Guineo-Congolian rainforest. Plana V, Philos T Roy Soc B 2004 359 1585 1594 10.1098/rstb.2004. 1535
40. Ndiade Bourobou D, Dynamique Spatiale et Temporelle de la Diversité Génétique d'une espèce rare en Afrique Centrale: Baillonella toxisperma Pierre (le Moabi) France: PhD, Montpellier University 2011
41. The biogeographic evidence supporting the Pleistocene forest refuge hypothesis. Mayr E, O'Hara RJ, Evolution 1986 40 55 67 10.2307/2408603