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• The fragmentation of Afro-Mediterranean Cupressus gene pools dates back to the Pliocene • The history of C. dupreziana as relic species started in the Pleistocene. • Cupressus sempervirens var. numidica is endemic of Tunisia and belongs to the central Mediterranean gene pool since the Pleistocene. Only few woody species of North Africa have been the subject of biogeographical studies, despite the importance of this region, in the Mediterranean area, for the presence of hotspots of endemism and biodiversity, and of refugia. Here, we present research on the Afro-Mediterranean Cupressus spp., which have a discontinuous and fragmented distribution, resulting from population dynamics experienced during their life history. We aim to retrace their demographic history, by combining Bayesian clustering and approximate Bayesian computation (ABC) methods. The fragmentation of the cypress gene pool dates back to Pliocene, when the Mediterranean and the North African lineages separated from a common ancestor. The separation of C. atlantica and C. dupreziana dates back to the Pleistocene, when the history of C. dupreziana as relic species started. Finally, C. sempervirens var. numidica is likely endemic of Tunisia, belonging to the cypress gene pool of the central Mediterranean since the Pleistocene. [ABSTRACT FROM AUTHOR]

This study represents the first large-scale analysis using nuclear molecular markers to assess genetic diversity and structure of Cupressus sempervirens L.. Genetic and fossil data were combined to infer the possible role of human activity and evolutionary history in shaping the diversity of cypress populations. We analysed 30 populations with six polymorphic nuclear microsatellite markers. Dramatic reductions in heterozygosity and allelic richness were observed from east to west across the species range. Structure analysis assigned individuals to two main groups separating central Mediterranean and eastern populations. The two main groups could be further divided into five subgroups which showed the following geographical distributions: Turkey with the Greek islands Rhodes and Samos, Greece (Crete), Southern Italy, Northern Italy, Tunisia with Central Italy. This pattern of genetic structure is also supported by SAMOVA and Barrier analyses. Palaeobotanical data indicated that Cupressus was present in Italy in the Pliocene, Pleistocene and Holocene. Furthermore, our molecular survey showed that Italian cypress populations experienced bottlenecks that resulted in reduced genetic diversity and allelic richness and greater genetic differentiation. Recent colonization or introduction may also have influenced levels of diversity detected in the Italian populations, as most individuals found in this range today have multilocus genotypes that are also present in the eastern range of the species. The data reveal a new interpretation of the history of cypress distribution characterized by ancient eastern populations (Turkey and Greek islands) and a mosaic of recently introduced trees and remnants of ancient, depauperate populations in the central Mediterranean range.