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Delimitation of African tree species of the genus Pterocarpus and development of DNA-based species identification tools

par Albreht, Laura
Président du jury Mardulyn, Patrick
Promoteur Hardy, Olivier J.
Co-Promoteur Bourland, Nils
Publication Non publié, 2026-06-16

Thèse de doctorat

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Résumé :

Reliable species delimitation is fundamental for the sustainable harvest of economically important organisms. African Pterocarpus (Fabaceae) includes several highly valuable timber-producing species that face increasing pressure from intensive logging. However, long-standing taxonomic uncertainty has hindered the development of effective logging and trade regulations. The main objectives of this thesis were therefore to reassess species boundaries in African Pterocarpus and to develop a DNA-based test for species identification suitable for forensic timber identification in law enforcement.We sampled all previously recognised African Pterocarpus species across their distribution ranges using herbarium material and re-evaluated species boundaries following an integrative taxonomy approach. The resulting taxonomic framework subsequently served as the basis for developing a DNA-based species identification test.In Chapter 1, we reconstructed a comprehensive species phylogeny using DNA sequences from more than 300 nuclear genes (Angiosperms353 markers) under maximum likelihood and multispecies coalescent approaches. We additionally assessed the utility of high-copy DNA originating from the chloroplast genome or ribosomal DNA by reconstructing phylogenies from genome-skimming data and using maximum likelihood approach. Nine species were recovered as reciprocally monophyletic, and species delimitation based on high-copy DNA was largely congruent with nuclear data, supporting the use of chloroplast and ribosomal markers for species identification.Chapter 2 focuses on the Pterocarpus rotundifolius s.l., which has undergone extensive taxonomic revision and was recovered as paraphyletic in Chapter 1. By integrating genomic, morphological, and ecological data, we resolved synonymy, reinstated four species, and re-circumscribed P. rotundifolius s.s. This revised taxonomy has direct conservation implications, as three reinstated species are provisionally assessed as Near Threatened, whereas P. rotundifolius s.l. was previously listed as Least Concern.In Chapter 3, we developed 13 chloroplast SNP markers that differentiate 11 of the 16 currently recognised African Pterocarpus species and two subspecies. Corresponding KASP primer sets were designed to enable cost-effective species identification suitable for forensic applications.Overall, this thesis provides an updated taxonomic framework for African Pterocarpus and demonstrates the value of integrative taxonomy for resolving species boundaries in economically important tree groups. The DNA-based identification test developed here has the potential to support CITES enforcement and contribute to more sustainable logging and trade of African Pterocarpus.