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Native to southern Africa, this species has been extensively harvested for the bark, which is widely used in traditional health practices. Illegal harvesting coupled with habitat degradation has contributed to fragmentation of populations and a severe decline in its distribution. Even though the species is included in the IUCN Red List as <jats:italic>Endangered<\/jats:italic>, genetic data that would help conservation efforts and future re-introductions are absent. We therefore developed new molecular markers to understand patterns of genetic diversity, structure, and gene flow of <jats:italic>W. salutaris<\/jats:italic> in one of its most important areas of occurrence (Mozambique). In this study, we have shown that, despite fragmentation and overexploitation, this species maintains a relatively high level of genetic diversity supporting the existence of random mating. Two genetic groups were found corresponding to the northern and southern locations. Our study suggests that, if local extinctions occurred in Mozambique, the pepper-bark tree persisted in sufficient numbers to retain a large proportion of genetic diversity. Management plans should concentrate on maintaining this high level of genetic variability through both <jats:italic>in<\/jats:italic> and <jats:italic>ex-situ<\/jats:italic> conservation actions.<\/jats:p>","DOI":"10.1038\/s41598-020-76654-6","type":"journal-article","created":{"date-parts":[[2020,11,12]],"date-time":"2020-11-12T11:02:41Z","timestamp":1605178961000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["The genetic legacy of fragmentation and overexploitation in the threatened medicinal African pepper-bark tree, Warburgia salutaris"],"prefix":"10.1038","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7699-0501","authenticated-orcid":false,"given":"Annae M.","family":"Senkoro","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6694-7502","authenticated-orcid":false,"given":"Pedro","family":"Talhinhas","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8503-7563","authenticated-orcid":false,"given":"Fernanda","family":"Sim\u00f5es","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5442-1092","authenticated-orcid":false,"given":"Paula","family":"Batista-Santos","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8489-6136","authenticated-orcid":false,"given":"Charlie M.","family":"Shackleton","sequence":"additional","affiliation":[]},{"given":"Robert A.","family":"Voeks","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9788-4831","authenticated-orcid":false,"given":"Isabel","family":"Marques","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6071-6460","authenticated-orcid":false,"given":"Ana I.","family":"Ribeiro-Barros","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2020,11,12]]},"reference":[{"key":"76654_CR1","volume-title":"Quality Control of Herbal Drugs: An Approach to Evaluation of Botanicals","author":"PW Mukherjee","year":"2002","unstructured":"Mukherjee, P. 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