| Summary: | <p>Abstract</p> <p>Background</p> <p>South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of <it>Rattus tanezumi</it>, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive <it>Rattus </it>species present.</p> <p>Results</p> <p>To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 <it>Rattus </it>specimens. Cytochrome <it>b </it>gene sequencing revealed the presence of two <it>R. tanezumi</it>, seven <it>Rattus rattus </it>and five <it>Rattus norvegicus </it>haplotypes in south Africa. Phylogenetic results were consistent with a single, recent <it>R. tanezumi </it>introduction and indicated that <it>R. norvegicus </it>and <it>R. rattus </it>probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. <it>Rattus norvegicus </it>and <it>R. rattus </it>each occurred sympatrically with <it>Rattus tanezumi </it>at one and five sites, respectively. Karyotyping of selected <it>R. rattus </it>and <it>R. tanezumi </it>individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by <it>R. tanezumi </it>in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species.</p> <p>Conclusions</p> <p>This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.</p>
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