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Invasive plants pose substantial threats to protected areas globally. Although management can limit impacts, spread and reinvasion from neighbouring areas into protected areas are a major and an on-going problem for land managers. However, identifying the main sources of propagules and the dimensions of invasion pathways is challenging. This study used population genetic markers [inter simple sequence repeats (ISSRs) and amplified fragment length polymorphisms (AFLPs)] to infer the source(s) of re-colonization and dispersal patterns for a typical invader of riparian and terrestrial habitats (Lantana camara) along the Sabie-Sand catchment, one of the most important river systems flowing into and across South Africa’s flagship protected area, the Kruger National Park (KNP). Results indicate that populations located along the lower reaches of the Sabie and Sand tributaries harboured substantially higher genetic diversity than those in the upper Sabie catchment. Bayesian assignments indicated that the upper Sabie tributary contributed far fewer propagules than the Sand tributary to the lower Sabie River. Current invasion patterns are due to a combination of a major flood event in 2000 and differences in the degree to which the upstream reaches were managed after the flooding. The major flood of 2000 effectively cleared lantana from the riparian areas. However, whereas on-going management efforts against riparian species in the KNP have been effective, rendering the upper Sabie relatively clear of lantana, only a small part of the Sand tributary falls under jurisdiction of the KNP and has received consistent management attention. The reinvasion of the lower Sabie in the KNP was therefore almost entirely by propagules from the Sand tributary. The study highlights the important role that molecular tools can play in determining dispersal dynamics and directing invasive species management. For invasive plant species that invade both riparian habitats and landscapes away from rivers in protected areas, such as lantana, management must focus on all major sources of propagules to limit reinvasion.