Genetic diversity of the Rattus complex (Rodentia: Muridae) in KwaZulu-Natal.

Master of Science in Zoology. University of KwaZulu-Natal, Westville 2010.The rodent genus Rattus is considered to be the single largest genus of mammals in the world. One species of Rattus is usually more dominant than another within a specific geographical area; however within the province of KwaZulu-Natal South Africa current observations indicate that Norway rats (R. norvegicus), black rats (R. rattus) and the indistinct Asian house rat (R. tanezumi) exist sympatrically. DNA sequencing of the cytochrome b and D-loop regions of the mitochondrion were used in conjunction with karyotyping of bone marrow and tissue culture cells to analyse the genetic diversity of selected Rattus populations from KwaZulu-Natal. Comparison of sequence data obtained during the study to reference sequences obtained from the NCBI GenBank revealed three well-supported monophyletic groups in maximum parsimony and Bayesian analyses. These three monophyletic groups indicated the existence of three species of the Rattus complex within KwaZulu-Natal, namely Rattus rattus, Rattus norvegicus and Rattus tanezumi. Analysis of cytochrome b sequence data revealed the presence of 6, 3 and 2 haplotypes in 20 R. norvegicus, 8 R. rattus and 5 R. tanezumi specimens, respectively. The R. norvegicus haplotypes were separated from R. rattus and R. tanezumi haplotypes by 60 mutational steps, while R. rattus haplotypes were separated from R. tanezumi haplotypes by 24 mutational steps. Analysis of D-loop sequence data revealed the presence of 6, 2 and 1 haplotypes in 14 R. norvegicus, 4 R. rattus and 3 R. tanezumi specimens, respectively. R. norvegicus haplotypes were separated from R. rattus and R. tanezumi haplotypes by 15 mutational steps, while R. rattus haplotypes were separated from R. tanezumi haplotypes by 11 mutational steps. Karyotype analysis of specimens revealed that: (1) R. rattus specimens sampled presented with a karyotype of either 2n = 38 or 2n = 40; (2) R. tanezumi specimens sampled presented with a karyotype of 2n = 42 and (3) R. norvegicus specimens sampled presented with a karyotype of 2n = 42 which was very distinct from that of R. tanezumi

Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa

Background: 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 R. rattus and five R. 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 R. 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. 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