Tree Genetics & Genomes

, 14:66 | Cite as

The African timber tree Entandrophragma congoense (Pierre ex De Wild.) A.Chev. is morphologically and genetically distinct from Entandrophragma angolense (Welw.) C.DC

  • Franck K. MontheEmail author
  • Jérôme Duminil
  • Emmanuel Kasongo Yakusu
  • Hans Beeckman
  • Nils Bourland
  • Jean-Louis Doucet
  • Marc S. M. Sosef
  • Olivier J. Hardy
Original Article
Part of the following topical collections:
  1. Taxonomy


Interpreting morphological variability in terms of species delimitation can be challenging. However, correcting species delineation can have strong implications for the sustainable management of exploited species. Up to now, species delimitation between two putative timber species from African forests, Entandrophragma congoense and E. angolense, remained unclear. To investigate their differences, we applied an integrated approach which combines morphological traits and genetic markers. We defined 13 morphological characters from 81 herbarium specimens and developed 15 new polymorphic microsatellite markers to genotype 305 samples (herbarium samples and specimens collected in the field across the species distribution ranges). Principal component analysis (PCA) of morphological data and the Bayesian clustering analyses of genetic data were used to assess differentiation between putative species. These analyses support two well-differentiated groups (FST = 0.30) occurring locally in sympatry. Moreover, these two groups present distinct morphological characters at the level of the trunk, leaflets, and seeds. Our genetic markers identified few individuals (4%) that seem to be hybrids, though there is no evidence of genetic introgression from geographic patterns of genetic variation. Hence, our results provide clear support to recognize E. congoense as a species distinct from E. angolense, with a much lower genetic diversity than the latter, and that should be managed accordingly. This work highlights the power of microsatellite markers in resolving species boundaries.


Species delimitation Microsatellite markers The Bayesian assignment Africa rainforest Tiama Entandrophragma Meliaceae 



We are grateful to Meise Botanic Garden (Belgium), the Herbarium and African Botanical Library (BRLU) of Université Libre de Bruxelles (ULB), and Naturalis Biodiversity Center (Leiden, the Netherlands), for making the herbarium specimens available. We thank the forest company PALLISCO, especially Bienvenue Ango for its support to field sampling. We are also grateful to the DynAfFor and P3FAC projects, funded by the Fonds Français pour l’Environnement Mondial, which facilitated access to the field, and to two anonymous referees for their comments.

Data archiving statement

The microsatellite markers are submitted to GenBank (Table 3).

Funding information

We thank the Fonds pour la Formation à la Recherche dans l’Industrie et l’Agriculture (FRIA-FNRS, Belgium) through a PhD grant to the first author, the Fonds de la Recherche Scientifique (FRS-FNRS) through grant X.3040.17, and the Belgian Science Policy (Belspo) for funding the project AFRIFORD.

Supplementary material

11295_2018_1277_MOESM1_ESM.docx (853 kb)
ESM 1 (DOCX 852 kb)


  1. African Plant Database - version 3.4.0 (2018). Conservatoire et Jardin botaniques de la Ville de Genève and South African National Biodiversity Institute, Pretoria. Retrieved June 2018, from <>
  2. Anderson EC, Thompson EA (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160:1217–1229 PubMedPubMedCentralGoogle Scholar
  3. Chessel D, Dufour AB, Thioulouse J et al (2004) The ade4 package-I-One-table methods. R news 4:5–10Google Scholar
  4. Chevalier A (1909) Les végétaux utiles de l’Afrique tropicale française: études scientifiques et agronomiques. Dépot des publicationsGoogle Scholar
  5. Chybicki IJ, Burczyk J (2009) Simultaneous estimation of null alleles and inbreeding coefficients. J Hered 100:106–113. CrossRefPubMedGoogle Scholar
  6. Culley TM, Weller SG, Sakai AK, Putnam KA (2008) Characterization of microsatellite loci in the Hawaiian endemic shrub Schiedea adamantis (Caryophyllaceae) and amplification in related species and genera. Mol Ecol Resour 8:1081–1084CrossRefPubMedGoogle Scholar
  7. Dainou K, Blanc-Jolivet C, Degen B, Kimani P, Ndiade-Bourobou D, Donkpegan AS, Tosso F, Kaymak E, Bourland N, Doucet JL, Hardy OJ (2016) Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia. BMC Evol Biol 16:259. CrossRefPubMedPubMedCentralGoogle Scholar
  8. Daïnou K, Flot J-F, Degen B, Blanc-Jolivet C, Doucet J-L, Lassois L, Hardy OJ (2017) DNA taxonomy in the timber genus Milicia: evidence of unidirectional introgression in the West African contact zone. Tree Genet Genomes 13:90. CrossRefGoogle Scholar
  9. Dayrat B (2005) Towards integrative taxonomy. Biol J Linn Soc 85:407–415CrossRefGoogle Scholar
  10. de Candolle C (1894) Meliaceae novae. 2. Asiaticae et Africanae. Bull Herb Boissier 2:577–584Google Scholar
  11. De Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:879–886CrossRefPubMedGoogle Scholar
  12. de Wilde JJFE (2015) Meliaceae. In: Sosef MSM, Florence J, Ngok BL, Bourobou BHP (eds) Flore du Gabon, vol 47. Margraf Publishers, Wekersheim, pp 5–74Google Scholar
  13. Doyle JJ, Doyle JL (1987) CTAB DNA extraction in plants. Phytochem Bull 19:11–15Google Scholar
  14. Dray S, Dufour AB (2007) The ade4 package: implementing the duality diagram for ecologists. J Stat Softw 22:1–20Google Scholar
  15. Duminil J, Di Michele M (2009) Plant species delimitation: a comparison of morphological and molecular markers. Plant Biosyst 143:528–542CrossRefGoogle Scholar
  16. 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 62:275–285CrossRefPubMedGoogle Scholar
  17. Earl DA, VonHoldt BM, von Reumont B (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361. CrossRefGoogle Scholar
  18. Edwards DL, Knowles LL (2014) Species detection and individual assignment in species delimitation: can integrative data increase efficacy? Proceedings Biol Sci 281:20132765. CrossRefGoogle Scholar
  19. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620. CrossRefPubMedGoogle Scholar
  20. Hardy OJ, Vekemans X (2001) Patterns of allozyme variation in diploid and tetraploid Centaurea jacea at different spatial scales. Evolution 55:943–954CrossRefPubMedGoogle Scholar
  21. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  22. Hardy OJ, Charbonnel N, Fréville H, Heuertz M (2003) Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation. Genetics 163:1467–1482PubMedPubMedCentralGoogle Scholar
  23. Haselhorst M, Buerkle C (2011) Detection of hybrids in natural populations of Picea glauca and Picea englemannii. Univ Wyoming Natl Park Serv Res Cent Annu Rep 33Google Scholar
  24. Ikabanga DUDU, Stévart T, Koffi KGG, Monthé FK, Doubindou ECN, Dauby G, Souza A, M’BATCHI B, Hardy O (2017) Combining morphology and population genetic analysis uncover species delimitation in the widespread African tree genus Santiria (Burseraceae). Phytotaxa 321:166–180. CrossRefGoogle Scholar
  25. Janzen DH, Burns JM, Cong Q, Hallwachs W, Dapkey T, Manjunath R, Hajibabaei M, Hebert PDN, Grishin NV (2017) Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology. Proc Natl Acad Sci U S A 114:8313–8318. CrossRefPubMedPubMedCentralGoogle Scholar
  26. Kasongo-Yakusu E, Monthe FK, Nils B, Hardy OJ, Louppe D, Lokanda FBM, Hubau W, Kahindo J-MM, Van Den Bulcke J, Van Acker J, Beeckman H (2018) Le genre Entandrophragma (Meliaceae): taxonomie et écologie d’arbres africains d’intérêt économique (synthèse bibliographique). Biotechnol Agron société Environ 22:1–15Google Scholar
  27. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. CrossRefPubMedPubMedCentralGoogle Scholar
  28. Klopper RR, Chatelain C, Habashi C, Gautier L, Spichiger R-E (2006) Checklist of the flowering plants of sub-Saharan Africa: an index of accepted names and synonyms. SabonetGoogle Scholar
  29. Le Guyader H (2002) Doit-on abandonner le concept d’espèce? Le Courr l’environnement l’INRA 51–64Google Scholar
  30. Ley A, Hardy O (2010) Species delimitation in the Central African herbs Haumania (Marantaceae) using georeferenced nuclear and chloroplastic DNA sequences. Mol Phylogenet Evol. CrossRefPubMedGoogle Scholar
  31. Ley AC, Hardy OJ (2017) Hybridization and asymmetric introgression after secondary contact in two tropical African climber species, Haumania danckelmaniana and Haumania liebrechtsiana (Marantaceae). Int J Plant Sci 178:421–430. CrossRefGoogle Scholar
  32. Liben L (1970) La répartition géographique d’Entandrophragma congoënse (De Wild.) A. Chev.(Meliaceae). Bull du Jard Bot Natl Belgique/Bulletin van Natl Plantentuin van Belgie 299–300Google Scholar
  33. Liben L, Dechamps R (1966) Entandrophragma congoense (De Wild.) A. Chev. espèce méconnue du Congo. Bull du Jard Bot l’Etat, Bruxelles/Bulletin van den Rijksplantentuin, Brussel 415–424Google Scholar
  34. Mayr E (1992) Species concepts and their application. Units Evol MIT 15–25Google Scholar
  35. Mayr E (1942) Systematics and the origin of species, from the viewpoint of a zoologist. Harvard University PressGoogle Scholar
  36. Meunier Q, Moumbogou C, Doucet J-L (2015) Les arbres utiles du Gabon. Presses Agronomiques de GemblouxGoogle Scholar
  37. Micheneau C, Dauby G, Bourland N, Doucet JL, Hardy OJ (2011) Development and characterization of microsatellite loci in Pericopsis elata (Fabaceae) using a cost-efficient approach. Am J Bot 98:e268–e270. CrossRefPubMedGoogle Scholar
  38. Monthe F, Duminil J, Tosso F, Migliore J, Hardy OJ (2017) Characterization of microsatellite markers in two exploited African trees, Entandrophragma candollei and E. utile (Meliaceae). Appl Plant Sci 5:1600130. CrossRefGoogle Scholar
  39. Peakall R, Smouse PE (2012) GenALEx 6.5: genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537–2539. CrossRefPubMedPubMedCentralGoogle Scholar
  40. Poorter L (1999) Growth responses of 15 rain-forest tree species to a light gradient: the relative importance of morphological and physiological traits. Funct Ecol 13:396–410. CrossRefGoogle Scholar
  41. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedPubMedCentralGoogle Scholar
  42. Schlick-Steiner BC, Steiner FM, Seifert B, Stauffer C, Christian E, Crozier RH (2010) Integrative taxonomy: a multisource approach to exploring biodiversity. Annu Rev Entomol 55:421–438CrossRefPubMedGoogle Scholar
  43. Slik JWF, Arroyo-Rodríguez V, Aiba S-I, Alvarez-Loayza P, Alves LF, Ashton P, Balvanera P, Bastian ML, Bellingham PJ, van den Berg E, Bernacci L, da Conceição BP, Blanc L, Böhning-Gaese K, Boeckx P, Bongers F, Boyle B, Bradford M, Brearley FQ et al (2015) An estimate of the number of tropical tree species. Proc Natl Acad Sci U S A 112:7472–7477. CrossRefPubMedPubMedCentralGoogle Scholar
  44. Sosef MSM, Dauby G, Blach-Overgaard A, van der Burgt X, Catarino L, Damen T, Deblauwe V, Dessein S, Dransfield J, Droissart V, Duarte MC, Engledow H, Fadeur G, Figueira R, Gereau RE, Hardy OJ, Harris DJ, de Heij J, Janssens S, Klomberg Y, Ley AC, Mackinder BA, Meerts P, van de Poel JL, Sonké B, Stévart T, Stoffelen P, Svenning J-C, Sepulchre P, Zaiss R, Wieringa JJ, Couvreur TLP (2017) Exploring the floristic diversity of tropical Africa. BMC Biol 15:15. CrossRefPubMedPubMedCentralGoogle Scholar
  45. Sprague TA (1910) Entandrophragma, Leioptyx and Pseudocedrela. Bull Misc Inf (Royal Gard Kew) 1910:177–182CrossRefGoogle Scholar
  46. Staner P (1941) Les Méliacées du Congo Belge. Bull du Jard Bot l’Etat, Bruxelles/Bulletin van den Rijksplantentuin, Brussel 16:109–251CrossRefGoogle Scholar
  47. Tarasjev A, Barisić Klisarić N, Stojković B, Avramov S (2009) Phenotypic plasticity and between population differentiation in Iris pumila transplants between native open and anthropogenic shade habitats. Genetika 45:1078–1086PubMedGoogle Scholar
  48. The Plant List (2013) Version 1.1. Retrieved June 2018, from
  49. Tosso F, Dainou K, Hardy OJ, Sinsin B, Doucet J-L (2015) Le genre Guibourtia Benn., un taxon à haute valeur commerciale et sociétale (synthèse bibliographique). Biotechnol Agron société Environ 19:71–88Google Scholar
  50. Weber AA-T, Stöhr S, Chenuil A (2017) Species delimitation in the presence of strong incomplete lineage sorting and hybridization. bioRxiv.

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Franck K. Monthe
    • 1
    Email author
  • Jérôme Duminil
    • 1
    • 2
    • 3
  • Emmanuel Kasongo Yakusu
    • 4
    • 5
    • 6
  • Hans Beeckman
    • 4
  • Nils Bourland
    • 4
    • 7
    • 8
  • Jean-Louis Doucet
    • 9
  • Marc S. M. Sosef
    • 10
  • Olivier J. Hardy
    • 1
  1. 1.Faculté des Sciences, Service Evolution Biologique et EcologieUniversité Libre de BruxellesBrusselsBelgium
  2. 2.DIADE, IRDUniv MontpellierMontpellierFrance
  3. 3.Forest Genetic Resources and Restoration Programme, Sub-Regional Office for Central AfricaBioversity InternationalYaoundéCameroon
  4. 4.Wood Biology ServiceRoyal Museum for Central AfricaTervurenBelgium
  5. 5.Laboratory of Wood TechnologyGhent UniversityGhentBelgium
  6. 6.Faculté de Gestion des Ressources Naturelles RenouvelablesUniversité de KisanganiKisanganiDemocratic Republic of the Congo
  7. 7.Center For International Forestry ResearchBogor BaratIndonesia
  8. 8.Resources and Synergies Development Pte LtdSingaporeSingapore
  9. 9.TERRA Teaching and Research Centre, Central African Forests, BIOSE Department, Gembloux Agro-Bio TechUniversité de LiègeGemblouxBelgium
  10. 10.Botanic Garden MeiseMeiseBelgium

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