17 August 2011 | By Prof Amanda Bastos and Prof Chris Chimimba

South Africa’s long and extensive trade activity has ensured ample opportunities for the introduction of non-native species. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, alien vertebrates are generally overlooked despite their potential negative impacts on biodiversity, human health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present.

Rattus sampling in Hammanskraal
Ms Rolanda Julius (C·I·B M.Sc. student) sampling Rattus from a warehouse in the vicinity of an informal settlement in the Hammanskaal Area, north of Pretoria

To this end, in a recent paper in BMC Genetics, C·I·B Research Associate, Professor Amanda Bastos, core team member, Professor Chris Chimimba, C·I·B M.Sc. student, Elmarie Mostert and their collaborators undertook an intensified sampling survey from 28 South African localities and at one site in Swaziland and identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in South Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus 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. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi 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 R. tanezumi 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.

Rattus in an informal settlement in the Hammanskraal
One of the sampling sites for Rattus in an informal settlement in the Hammanskraal area, north of Pretoria.

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.

Read the paper Bastos et al., Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa. BMC Genetics 2011, 12:26

Contact the author For further details, email adbastos@zoology.up.ac.za or ctchimimba@zoology.up.ac.za

Sampling for Rattus in Diepsloot
Typical sampling site for Rattus in Diepsloot, northern-western Johannesburg associated with informal garbage disposal