BackgroundSouth 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.ResultsTo 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 species.ConclusionsThis 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.

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The taxonomic status and species limits of the South African-endemic rodent species Otomys saundersiae were revised using G-banding karyotypic analysis, assessment of pelage colour and craniodental traits, multivariate analysis of eight cranial distance measurements, and geometric morphometric analysis of 11 landmarks of the dorsal image of the skull. In the Western Cape, the recognized subspecies Otomys saundersiae karoensis differed in karyotype from sympatrically-occurring populations of O. irroratus (cytotype "C") in having six (as opposed to four) pairs of biarmed chromosome pairs and in the absence of pair number 14. Discriminant analysis of linear craniometric variables in positively identified (karyotyped) samples of Otomys irroratus and Otomys s. karoensis separated the two species without any overlap, as did pelage colour and certain qualitative cranial characters such as nasal angle; such clear-cut differences however were not apparent between unkaryotyped samples of O. s. saundersiae and O. irroratus from the Eastern Cape. Centroid size (from geometric morphometric analysis of cranial landmarks) was significantly correlated with both non-affine and affine components of skull shape, indicating strong allometric effects. Both cranial shape and size differed significantly between Western Cape O. s. karoensis and O. irroratus; size, but not shape, varied significantly between Eastern Cape O. s. saundersiae and O. irroratus. Within both currently recognized species, significant geographical differences in cranial shape were detected between eastern and western Cape populations occupying distinct ecological biomes. Problems with defining species limits in this complex case were discussed with reference to available data and alternative species concepts.

Non-geographic morphometric variation, particularly at the level of sexual dimorphism and ontogenetic (agerelated) variation, has been documented in rodents, and useful for establishing whether to analyse sexes separately or together, and for selecting adult specimens for subsequent data recording and analysis. However, such studies have largely been based on traditional morphometric analyses of linear measurements that mainly focus on overall size, rather than shape-related morphometric variation. Unit-free, landmark/outline-based geometric morphometric analyses are considered to offer a more appropriate tool for assessing shape-related morphometric variation. In this study, we used geometric cranial morphometric analysis to assess the nature and extent of sexual dimorphism and age variation within the Tete veld rat, Aethomys ineptus (Thomas and Wroughton, 1908) from southern Africa and the African Nile rat, Arvicanthis niloticus (Desmarest, 1822) from Sudan. The results obtained were in turn compared with previously published results based on independent geometric and traditional cranial morphometric data from the same sampled populations examined in the present study. While our geometric morphometric results detected statistically significant sexual dimorphism in cranial shape within Ar. niloticus only, previously published results based on traditional morphometric data failed to detect significant sexual dimorphism within this species. However, similar to previously published traditional morphometric data, our geometric morphometric results detected statistically significant age-related variation in cranial shape and size within both Ae. ineptus and Ar. niloticus, with individuals of age classes 5 and 6 being considered to represent adult specimens. Our results highlight the importance of carefully evaluating both size-and shape-related non-geographic morphometric variation prior to the analysis of geographic variation and the delineation of species. Erroneous conclusions of non-geographic variation may have implications in the interpretation of geographic and evolutionary processes that may be responsible for morphological differences at both the inter-and intra-specific levels.

The present study clarified the taxonomy, phylogeny and historical demography of semicommensal Nile rats (Arvicanthis) from the Nile Valley in Sudan. Nile rats are important crop pests and zoonotic disease reservoirs and are closely associated with agricultural settlements in the Nile Valley. Phylogenetic analysis of the complete cytochrome b gene (1140 bp) of 23 individuals from six localities in Sudan (from two previously recognized species, Arvicanthis niloticus and Arvicanthis testicularis), supported the existence of only a single species, A. niloticus, from the Nile Valley. Historical demography of the Sudanese Nile Valley population inferred from mismatch coefficients indicated that an exponential population expansion event occurred approximately 144 000-288 000 years ago, corresponding in time with early human expansion and colonization from Africa to the Middle East, Europe, and the world. The inferred high level of gene flow and large size of Sudanese Nile populations of A. niloticus is consistent with historically recent (300 years ago) exponential human population growth and intense agricultural activity inferred from archaeological and historical evidence. Two African Arvicanthis clades were well supported by the broader phylogenetic analysis: (1) A. niloticus, Arvicanthis abyssinicus and Arvicanthis neumanni and (2) Arvicanthis rufinus and Arvicanthis ansorgei from western Africa. Within the first clade, divergence between lineages of A. niloticus s.s. from west and north-east Africa (8.9%) suggests specific recognition, but sampling of geographically intermediate localities is required. Based on hypothesized palaeodrainage and palaeoclimatic patterns, we propose a simple model for speciation of Arvicanthis in Africa.

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Liver homogenates from 12 populations of the vlei rat Otomys irroratus (Brants 1827) were subjected to Sodium Dodecyl Sulfate Polyacrylamide electrophoresis on 7-17% gradient gels followed by Western blotting. Detection of antigenic proteins was carried out with an antiserum against liver proteins of one of these populations. Blots thus obtained were digitized into computer images and the gray level values of all electromorphs were recorded. A matrix of these values was then constructed and subjected to statistical analyses (discriminant function and cluster analysis by the Unweighed Pair Group Method with Averages). Boot-strapping parsimony analysis was performed on a multistate character matrix derived from the gray level data. Although immunoblotting seemed to be sufficiently sensitive to detect extensive individual variation, there was only partial agreement between the dendrograms thus generated and the trees previously obtained from chromosome studies (CoNTRAFATTO et a!. 1992b). Evolutionary implications of the findings are discussed and it is concluded that lack of congruence is most likely due to the detection, by this method, of old synapomorphies which pre-date the establishment of chromosomally defined groups of this species. This is taken as confirmation of a hypothesis which suggests that speciation can occur by chromosomal rearrangements before gene mutations, usually associated with speciation, become established.

Results of chromosome G- and C-banding studies on 12 specimens of the ice rat, Otomys sloggetti robertsi, from three localities and allozyme analyses of seven individuals from two localities are reported. The subspecies karyotype contains 42, mostly acrocentric, chromosomes. No chromosomal variation was detected among animals from these localities. Allozyme analysis tentatively suggested a limited gene flow between the two populations examined.