Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa
Bastos, Armanda D.S.; Brettschneider, Helene; Van Hooft, Pim; Chimimba, Christian Timothy; Nair, Deenadayalan; Taylor, P.J. (Peter John); Kirsten, Frikkie; Mostert, Elmarie; Von Maltitz, Emil; Lamb, Jennifer M.; Belmain, Steven R.; Contrafatto, Giancarlo; Downs, Sarah
BACKROUND: 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 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.
RESULTS: To this end, intensified sampling at 28 South African localities and at one site in Swaziland,
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
CONCLUSIONS: 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.