Parasites and hosts interact across both micro- and macroevolutionary scales where congruence among their phylogeographic and phylogenetic structures may be observed. Within southern Africa, the four-striped mouse genus, Rhabdomys, is parasitized by the ectoparasitic sucking louse, Polyplax arvicanthis. Molecular data recently suggested the presence of two cryptic species within P. arvicanthis that are sympatrically distributed across the distributions of four putative Rhabdomys species. We tested the hypotheses of phylogeographic congruence and cophylogeny among the two parasite lineages and the four host taxa, utilizing mitochondrial and nuclear sequence data. Despite the documented host-specificity of P. arvicanthis, limited phylogeographic correspondence and nonsignificant cophylogeny was observed. Instead, the parasite-host evolutionary history is characterized by limited codivergence and several duplication, sorting and host-switching events. Despite the elevated mutational rates found for P. arvicanthis, the spatial genetic structure was not more pronounced in the parasite lineages compared with the hosts. These findings may be partly attributed to larger effective population sizes of the parasite lineages, the vagility and social behaviour of Rhabdomys, and the lack of host-specificity observed in areas of host sympatry. Further, the patterns of genetic divergence within parasite and host lineages may also be largely attributed to historical biogeographic changes (expansion-contraction cycles). It is thus evident that the association between P. arvicanthis and Rhabdomys has been shaped by the synergistic effects of parasite traits, host-related factors and biogeography over evolutionary time.

Within the Macroscelidea 15 species of elephant-shrews are recognized, of which nine occur in the southern African subregion. The Cape rock elephant-shrew (Elephantulus edwardii) is the only strictly endemic South African elephant-shrew species. Recent distribution data suggest that E. edwardii is continuously distributed from Namaqualand in the Western Cape Province to Port Elizabeth in the Eastern Cape Province. Molecular sequences from the mitochondrial cytochrome b gene and variable control region indicate significant substructure within the Cape rock elephant-shrew across its distribution. Our data unequivocally showed the presence of a northern Namaqua and central Fynbos clade with four evolutionary lineages identified within the latter. The geographical delimitation of the northern and central clades corresponds closely with patterns reported for other rock-dwelling vertebrate species, indicating a shared biogeographical history for these taxa in South Africa. A coalescent method revealed the effects of ancestral polymorphism in shaping the Namaqua and Fynbos populations since their divergence ~1.7 million years ago. Furthermore, our analyses uncovered a distinct Karoo lineage(s) that does not correspond to any of the previously described and/or currently recognized species, and we therefore argue for the possible recognition of a new sister taxon to E. edwardii. The taxonomic affinities of this clade were examined by sequencing corresponding regions from the type specimens of species described in the past, but which presently are synonimized within E. edwardii. Our results reveal the morphological misidentification of one of these types, accentuating the problems of field identification.

The speed of range expansion in many invasive species is often accelerating because individuals with stronger dispersal abilities are more likely to be found at the range front. This ‘spatial sorting’ of strong dispersers will drive the acceleration of range expansion. In this study, we test whether the process of spatial sorting is at work in an invasive bird population (Common myna, Acridotheris tristis) in South Africa. Specifically, we sampled individuals across its invasive range and compared morphometric measurements relevant and non-relevant to the dispersal ability. Besides testing for signals of spatial sorting, we further examined the effect of environmental factors on morphological variations. Our results showed that dispersal-relevant traits are significantly correlated with distance from the range core, with strong sexual dimorphism, indicative of sex-biased dispersal. Morphological variations were significant in wing and head traits of females, suggesting females as the primary dispersing sex. In contrast, traits not related to dispersal such as those associated with foraging showed no signs of spatial sorting but were significantly affected by environmental variables such as the vegetation and the intensity of urbanisation. When taken together, our results support the role of spatial sorting in facilitating the expansion of Common myna in South Africa despite its low propensity to disperse in the native range.

Anthropogenic hybridization is an increasing conservation threat worldwide. In South Africa, recent hybridization is threatening numerous ungulate taxa. For example, the genetic integrity of the near‐threatened bontebok (Damaliscus pygargus pygargus) is threatened by hybridization with the more common blesbok (D. p. phillipsi). Identifying nonadmixed parental and admixed individuals is challenging based on the morphological traits alone; however, molecular analyses may allow for accurate detection. Once hybrids are identified, population simulation software may assist in determining the optimal conservation management strategy, although quantitative evaluation of hybrid management is rarely performed. In this study, our objectives were to describe species‐wide and localized rates of hybridization in nearly 3,000 individuals based on 12 microsatellite loci, quantify the accuracy of hybrid assignment software (STRUCTURE and NEWHYBRIDS), and determine an optimal threshold of bontebok ancestry for management purposes. According to multiple methods, we identified 2,051 bontebok, 657 hybrids, and 29 blesbok. More than two‐thirds of locations contained at least some hybrid individuals, with populations varying in the degree of introgression. HYBRIDLAB was used to simulate four generations of coexistence between bontebok and blesbok, and to optimize a threshold of ancestry, where most hybrids will be detected and removed, and the fewest nonadmixed bontebok individuals misclassified as hybrids. Overall, a threshold Q‐value (admixture coefficient) of 0.90 would remove 94% of hybrid animals, while a threshold of 0.95 would remove 98% of hybrid animals but also 8% of nonadmixed bontebok. To this end, a threshold of 0.90 was identified as optimal and has since been implemented in formal policy by a provincial nature conservation agency. Due to widespread hybridization, effective conservation plans should be established and enforced to conserve native populations that are genetically unique.

Morphological characters have historically been used as the basis for mammalian taxonomic designations and, in a geographic context, subspecies descriptions. Geographic genetic structuring of a species, however, often reflects a contrasting classification for sampled populations. To investigate morphological and genetic congruence, geometric morphometrics and phylogeographic mitochondrial DNA sequence analyses of a South African plainsdwelling species, Myotomys unisulcatus, the Karoo bush rat, was performed across its range. A Bayesian population structure analysis identified two closely-related distinct genetic assemblages: the first contains populations from both the eastern, southern, and western parts of the species range (coastal lowland group), and the second comprises individuals from the Little Karoo (central interior group). Areas of sharp elevation (the Great Escarpment), coupled to vegetational differences, appeared to be the main factor limiting gene flow between these two groups. Geometric morphometric analyses on the ventral and dorsal views of the crania of M. unisulcatus failed to support the genetic groupings. Instead environmental factors in the respective biomes appeared to play a more important role in shaping the crania of both genders. The contrasting patterns obtained between morphology and genetics in M. unisulcatus is probably indicative of phenotypic plasticity throughout the range of the species, and it is hypothesized that regional environmental factors play a prominent role in explaining geographic morphological variation within the species.