Species delimitation and phylogenomics of economically important African Pterocarpus trees, with an implication for the development of DNA-based species identification tools.

Reliable species delimitation is fundamental for establishing clear and equitable guidelines on the sustainable harvest of economically important organisms. Pterocarpus (Fabaceae) is a pantropical tree genus including several highly valuable timber-producing species, that face significant threats from intensive logging. However, a lack of taxonomic clarity has hindered the advance of logging regulations and has led to the inclusion of all African Pterocarpus populations under CITES regulations (CoP19). In our study, we addressed this issue by reassessing species delimitation of all twelve accepted African Pterocarpus species, including neotropical samples of the two trans-Atlantic species. Based on DNA sequences obtained by the Angiosperms353 probe set, we reconstructed a comprehensive phylogeny applying maximum likelihood and multispecies coalescent approaches. Additionally, we explored the potential of high-copy DNA for identifying African Pterocarpus species. This involved reconstructing chloroplast and ribosomal DNA phylogenies, using genome skimming and maximum likelihood approaches. Our results confirmed the monophyly of eleven Pterocarpus species and a paraphyletic P. rotundifolius, which presented geographically coherent subclades, suggesting the possibility of cryptic diversity within the complex. A similar situation arose in P. lucens, exhibiting two sister clades with disjunct distributions. Species delimitation based on high-copy DNA was congruent with the Angiosperms353 data for most species, indicating the reliability of chloroplast and ribosomal DNA markers for Pterocarpus species identification. Our findings give valuable insights into African Pterocarpus species delimitation, highlighting the need for further investigation of potential cryptic diversity within a clade including P. rotundifolius, P. brenanii and P. lucens. Finally, our study lays the groundwork for developing DNA-based tools aimed at improving logging regulations for African Pterocarpus species.