Genetic diversity and differentiation among the species of African mahogany (Khaya spp.) based on a large SNP array

Abstract

The genus Khaya includes some of the highest-value timber species in natural forests in Africa, which are under heavy exploitation pressure. Genetic identification of Khaya species is important to confirm the taxonomic classification for biodiversity conservation purposes and as a forensic tool aiding law enforcement in the fight against illegal logging. We collected samples from a total of 2222 trees belonging to five or six (depending on classification) different Khaya species (K. ivorensis, K. anthotheca/K. nyasica, K. grandifoliola, K. senegalensis, K. madagascariensis). Representative sampling was conducted over the natural ranges of all sampled Khaya species, in humid tropical forest and savanna zones. We genotyped individuals based on 101 molecular markers (67 nuclear, 11 chloroplast and 22 mitochondrial SNPs, 1 chloroplast indel). Bayesian clustering produced three main genetic groups assigning all K. ivorensis and all K. senegalensis trees, respectively, in two different clusters and all remaining individuals in a third cluster. Genetic self-assignment tests with all 101 SNPs had success rates of 97–100% for all species except for K. nyasica and K. madagascariensis, which could not be clearly distinguished from each other. A success rate for species identification nearly as high was observed using a subset of 15 highly differentiated SNPs. There was only very little evidence for hybridization among species and the vast majority (> 97%) of individuals were assigned to the same species group as identified based on morphological characters.

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Data availability

Upon acceptance for publication of the manuscript all data (information on individuals, country of origin and SNP data) will be made available on OSF (Open Science Framework, https://osf.io, Accession number osf.io/v86jh). For SNP/indel marker sequence data (including primer sequences) see Pakull et al. (2016).

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Acknowledgments

This work was supported by the German Federal Ministry of Food and Agriculture (BMEL), the International Tropical Timber Organization (ITTO), the Prince Albert II of Monaco Foundation, the CGIAR Research Program on Forests, Trees and Agroforestry (FTA), the Service de Coopération et d’Action culturelle (SCAC) of the Embassy of France in Congo, the Fondation Internationale pour la Science (FIS), the Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD) and DoubleHelix Tracking Technologies. MassARRAY®MultiPLEX™ genotyping was performed at the Genome and Transcriptome Facility of Bordeaux and funded by grants from the Conseil Regional d’Aquitaine (n°20030304002FA and n°20040305003FA), from the European Union (FEDER n°2003227) and from Investissements d’Avenir (Convention attributive d’aide N°ANR-10-EQPX-16-01). We thank Maike Paulini, Vivian Kuhlenkamp, Susanne Bein and Adline Delcamp for their excellent technical assistance.

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Correspondence to Bernd Degen.

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Pakull, B., Ekué, M.R.M., Bouka Dipelet, U.G. et al. Genetic diversity and differentiation among the species of African mahogany (Khaya spp.) based on a large SNP array. Conserv Genet 20, 1035–1044 (2019). https://doi.org/10.1007/s10592-019-01191-3

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Keywords

  • Africa
  • Genetic assignment
  • Species identification
  • Timber
  • Tropical tree