Conrad A Matthee

Stellenbosch University | SUN · Department of Botany and Zoology

Mastomys natalensis and M. coucha are commensal rodent species endemic to Africa. A recent taxonomic revision within Mastomys leaves the parasite–host list of M. natalensis questionable and that of M. coucha incomplete. The current study aimed to develop a better understanding of the ectoparasite diversity associated with the 2 distinct but closely...

For some marine species, photo‐identification (photo‐ID) data can be used to generate population estimates critical for conservation efforts. For the white shark ( Carcharadon carcharias ), different photo‐ID methods have been proposed: (1) the traditional manual matching method based on non‐organized databases, (2) the notches code method based on...

The factors that influence parasite associated bacterial microbial diversity and the geographic distributions of bacteria are not fully understood. In an effort to gain a deeper understanding of the relationship between the bacterial diversity of Ctenocephalides fleas and host species and the external environment, we conducted a metagenetic analysi...

Genomic information can aid in the establishment of sustainable management plans for commercially exploited marine fishes, aiding in the long-term conservation of these resources. The southern African hakes (Merluccius capensis and M. paradoxus) are commercially valuable demersal fishes with similar distribution ranges but exhibiting contrasting li...

The African continent was subjected to periodic climatic shifts during the Pliocene and Pleistocene. These habitat changes greatly affected the evolutionary processes and tempo of diversification in numerous, widely distributed mammals. The Otomyini (Family Muridae) comprises three African rodent genera, Parotomys, Otomys and Myotomys, characterize...

Quantifying the effect of human-wildlife interactions, and particularly those where negative perceptions exist, can have a benefit towards the conservation of species. The negative perceptions surrounding human-shark interactions can be put forward as a case in point. In this work, we use six relevant statements questions to test human perceptions...

Distinct life stages may experience different selection pressures influencing phenotypic evolution. Morphological evolution is also constrained by early phenotypes, since early development forms the phenotypic basis of later development. This work investigates evolutionary-developmental modification in three life stages and both sexes of 24 Rhipice...

Past climatic change as a driving force of marine diversification is still largely unclear, particularly for Southern Hemisphere species. Here, we present a case using the brown fur seal, Arctocephalus pusillus, assessing the geographical structure and demographic history using mitochondrial and nuclear data. Results show the two previously defined...

Mammals host a wide diversity of parasites. Lice, comprising more than 5,000 species, are one group of ectoparasites whose major lineages have a somewhat patchwork distribution across the major groups of mammals. Here we explored patterns in the diversification of mammalian lice by reconstructing a higher-level phylogeny of these lice, leveraging w...

Shallow-water hake (Merluccius capensis) is a valuable demersal resource distributed throughout the Benguela Current region, from southern Angola to eastern South Africa. Previous molecular work revealed distinct populations confined to the northern and southern Benguela sub-systems, with asymmetrical migratory patterns. Here, we re-evaluated the g...

Aim Pleistocene climate shifts were influential in shaping biodiversity patterns for forest‐dependent species. Within southern Africa, palaeoclimatic shifts possibly homogenised subtropical Afromontane forest biodiversity, yet these forests continue to harbour unique diversity. For the three songbird species with different natural histories, we inv...

Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest‐dependent birds have undergone range declines since 1992, most notably among insectivo...

The riverine rabbit, Bunolagus monticularis, is regarded critically endangered. This endemic South African leporid is believed to have extremely low population numbers, and was traditionally thought to be confined to a small region within the Nama Karoo and Succulent Karoo biomes. Recent discoveries of the species at lower altitudes in the Fynbos b...

Rhipicephalus are a species-diverse genus of ticks, mainly distributed in the Afrotropics with some species in the Palearctic and Oriental regions. Current taxonomic consensus comprise nine informal species groups/lineages based on immature morphology. This work integrates biogeographic, ecological and molecular lines of evidence to better understa...

Background Common names are frequently used inconsistently for marine annelid species used as bait in the peer-reviewed literature, field guides and legislative material. The taxonomy of many such species based on morphology only also ignores cryptic divergences not yet detected. Such inconsistencies hamper effective management of marine annelids,...

Population size is a central parameter for conservation; however, monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data‐poor presenting barriers to the evaluation of conservation management outcomes and the modeling of future solutions. Such is the case f...

To gain a deeper understanding of the mechanisms affecting parasite gene dispersal and subsequent evolution, we investigated mitochondrial and nuclear DNA phylogeographic structures of two ectoparasitic louse species, Polyplax praomydis and Hoplopleura patersoni, and compared this to their host Micaelamys namaquensis. Analyses of mitochondrial and...

The cat flea, Ctenocephalides felis, is an obligate haematophagous ectoparasite of wildlife and domestic cats and dogs worldwide. Since cat fleas can affect the health of humans and their pets, an uncertain taxonomy of this taxon can greatly inhibit pest and disease management. To address the evolution and taxonomy of the cat flea, we set out to de...

Moonshine worms are a popular bait species used for fishing. The taxon was not detected during surveys of the macrobenthos conducted in Knysna in the 1940s and 1990s, and was first reported as a harvested bait species in the mid-2000s, suggesting that it appeared for the first time in the estuary in the last three decades. A previous molecular anal...

Two new species of sucking lice (Phthiraptera: Anoplura), Hoplopleura granti n. sp. (Hoplopleuridae) and Polyplax megacephalus n. sp. (Polyplacidae), are described from Grant's rock mouse, Micaelamys granti (Wroughton), from Northern Cape Province, South Africa. Adults of both sexes are illustrated via line drawings and differential interference co...

Several studies noted similarities between Polydora neocaeca Williams & Radashevsky, 1999, described from the northeast coast of the USA, and shell-boring Polydora haswelli Blake & Kudenov, 1978, described from southeast Australia, and emphasised the need for molecular data to resolve the taxonomy of these species. This study investigates the poten...

Rhipicephalus turanicus ticks are widely distributed across the Palearctic and Afrotropics. These two continental populations display differences in morphological characters that raise the question of a potential species boundary. However, the taxonomic status of these morphologically divergent lineages is uncertain because R. turanicus from Cyprus...

The bloodworm, Arenicola loveni, is commonly used as bait by fishers and may be vulnerable to local extinction owing to its K-selected life history strategies and overexploitation. Accurate population data that can inform management is, however, outdated, whereas demand for bloodworm continues or is even increasing. This study provides genetic data...

Taxonomy based on morphology can be difficult. The challenges arise from different sources such as poor original descriptions, new records based on inadequate knowledge, uncritical application of general assumptions or presence of complexes of cryptic species. One example of problematic taxonomy is the genus Diopatra Audouin & Milne Edwards, 1833 (...

The dispersal and subsequent gene flow within parasite species is the result of a complex interaction between parasite life history, host life history and abiotic environmental factors. To gain more insights into the drivers responsible for parasite dispersal, COI mtDNA genetic data derived from six southern African generalist parasite species, inc...

Parasites are often dependent on their hosts for survival and dispersal and this led to a hypothesis that the evolution of obligate permanent host‐specific parasites specifically will show phylogenetic congruence with their hosts. To investigate the factors influencing parasite evolution, mitochondrial‐ and nuclear DNA sequence data were used to te...

Large-scale and small-scale natural barriers have the ability to mediate the ecological dynamics within a region. In some instances, these barriers greatly influence the presence of predators and prey on spatio-temporal scales. For this study, we aimed to assess how varying densities of sea bamboo (Ecklonia maxima), a kelp species found within Sout...

Background: The specialist-generalist variation hypothesis (SGVH) in parasites suggests that, due to patchiness in habitat (host availability), specialist species will show more subdivided population structure when compared to generalist species. In addition, since specialist species are more prone to local stochastic extinction events with their...

To address factors affecting genetic diversity and dispersal of ectoparasites, we compared mitochondrial DNA (mtDNA) population genetic structures of the generalist soft tick Ornithodoros capensis to the more host-specific nest flea Parapsyllus humboldti. A total of 103 ticks and 92 fleas were sampled at five distinct South African island/mainland...

Measuring contemporary dispersal in highly mobile terrestrial species is challenging, especially when species are characterized by low levels of population differentiation. Directly transmitted viruses can be used as a surrogate for traditional methods of tracking host movement. Feline Immunodeficiency Virus (FIV) is a species‐specific lentivirus,...

The penaeid prawns Fenneropenaeus indicus and Metapenaeus monoceros support shallow-water prawn fisheries in the south-west Indian Ocean. They are sympatric and have similar life histories, including developmental stages that depend on estuarine and marine habitats and a short dispersal duration. Nevertheless, M. monoceros juveniles display a more...

Irion et al. (2017; Mar Ecol Prog Ser 577:251-255) disputed the population estimates of white sharks Carcharodon carcharias along the South African coastline as presented in Andreotti et al. (2016; Mar Ecol Prog Ser 552:241-253), claiming that both the genetic and the capture-markrecapture results are poorly supported by the methods and data provid...

Following a shark attack, local governments often rapidly respond by implementing indiscriminate shark culls. These culls have been demonstrated to have substantial localized and adverse effects on a variety of marine organisms, and therefore there is an increasing need for an eco‐friendly alternative that maximizes both beachgoer and marine organi...

HyalommaKoch, 1844 are ixodid ticks that infest mammals, birds and reptiles, to which 27 recognized species occur across the Afrotropical, Palearctic and Oriental regions. Despite their medical and veterinary importance, the evolutionary history of the group is enigmatic. To investigate various taxonomic hypotheses based on morphology, and also som...

Aim It is predicted that the dispersal and gene flow of ectoparasites with wide host ranges are correlated with the vagilities of their most mobile hosts. To test this, the phylogeographical structure of a widespread generalist tick occurring on large ungulates was determined and compared with previously published host patterns. Location Africa....

When dealing with large marine species, individual photographic identification plays a very important part in capture–mark–recapture studies. The success of this method is determined by the consistent correct identification of individuals, but as the number of images in the database increases, the task becomes increasingly time-consuming, affecting...

Microsatellite analyses suggest that spatial genetic structure among six leopard-sampling sites in southern Africa is the result of isolation by distance.

Environmental gradients have been shown to disrupt gene flow in marine species, yet their influence in structuring populations at depth remains poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis) are demersal species co-occurring in the Benguela Current system, where decades of intense fishing resulted in severely depleted stoc...

The phylogeny of the subfamily Ophioninae (Hymenoptera: Ichneumonidae) is investigated using molecular markers and morphological characters. We analysed the mitochondrial DNA CO1 and the nuclear 28S D2–D3 gene fragments for 74 species of Ophioninae from 25 out of the 32 recognized genera, which collectively represent 98% of described species divers...

The loss of apex marine predators has been reported to have a cascade of detrimental effects on marine ecosystems; however, the general lack of empirical data can severely limit our understanding of the ecological interactions among marine species. In this study we propose an integrated approach using mark-recapture and genetic techniques to assess...

We studied nestedness and its relationships with beta-diversity in flea communities harboured by three closely related rodent species ( Rhabdomys pumilio, Rhabdomys intermedius, Rhabdomys dilectus ) at two spatial scales (within and among host populations) in South Africa and asked (a) whether variation in species composition of flea communities wi...

Boccardia proboscidea is a recently introduced polychaete in South Africa where it is a notorious pest of commercially reared abalone. Populations were originally restricted to abalone farms but a recent exodus into the wild at some localities has raised conservation concerns due to the species’ invasive status in other parts of the world. Here, we...

Background: Ectoparasites exhibit pronounced variation in life history characteristics such as time spent on the host and host range. Since contemporary species distribution (SD) modelling does not account for differences in life history, the accuracy of predictions of current and future species’ ranges could differ significantly between life histo...

In the marine environment, an increasing number of studies have documented introgression and hybridization using genetic markers. Hybridization appears to occur preferentially between sister-species, with the probability of introgression decreasing with an increase in evolutionary divergence. Exceptions to this pattern were reported for the Cape ha...

Annex 3 Supporting references for Table S1.

Showing the genetic identification of samples Identification of M. capensis (white) and M. paradoxus (grey) based on the CR of mtDNA (A) and genotype frequencies as obtained in STRUCTURE for nine microsatellite loci (B).

Annex 1 Papers reviewed on the subject of hybridization between marine species, with information on species, genetic relationships and divergence levels between hybridizing species, genetic marker used and clustering methods employed to describe hybrids.

Microsatellite database Microsatellite database for M. capensis and M. paradoxus

Depicting the distribution of allelic frequencies for M. capensis and M. paradoxus Distribution of allelic frequencies of M. capensis (white) and M. paradoxus (grey) by microsatellite locus.

Annex 2 Merluccius capensis and M. paradoxus individuals identified as hybrids based on nine microsatellite loci (I), eight microsatellite loci (II) and six microsatellite loci (III): C—M. capensis, P—M paradoxus, F2—second generation hybrid, BcP—backcross with M. paradoxus. Individuals labelled as per Fig. 1.

To explore how biogeography, parasite life history and host vagility influences evolutionary codivergences, we followed a comparative phylogeography approach using a host specific non-permanent mite, Laelaps giganteus that occurs on four rodent species within the genus Rhabdomys. A mtDNA COI haplotype network derived for 278 parasite specimens show...

Aim To determine the genetic structure of the white shark population around the South African coastline and, by including data from animals sampled elsewhere in the world, to provide new insights into white shark evolution at the global scale. Methods Mitochondrial and microsatellite analyses were performed on 302 free‐ranging white sharks collect...

The leopard (Panthera pardus) is heavily persecuted in areas where it predates livestock and threatens human well-being. Attempts to resolve human-leopard conflict typically involve translocating problem animals; however, these interventions are rarely informed by genetic studies and can unintentionally compromise the natural spatial genetic struct...

Parasitoid wasps are important from both an ecological and economic standpoint but are, as for many of the world’s regions, poorly known in the Afrotropical region. For the subfamily Banchinae, Bayesian and Maximum Parsimony analyses were conducted using molecular (18S, 28S and COI) and morphological (73 external characters) data for 68 species, sa...

Dinopsyllus ellobius is considered a common and widespread flea in southern Africa and can act as a vector for plague. Due to differences in the interpretation of geographical variation in male sternite VIII, the taxonomy of the species is characterized by uncertainty. In an attempt to provide a better understanding of the systematics of D. ellobiu...

In parasitic taxa, life history traits such as microhabitat preference and host specificity can result in differential evolutionary responses to similar abiotic events. The present study investigates the influence of vicariance and host association on the genetic structure of two generalist flea species, Listropsylla agrippinae, and Chiastopsylla r...

Aim Isolation by distance ( IBD ) analyses are an effective tool for determining genetic connectivity among populations, providing a basis for estimating dispersal and thus contributing to spatial biodiversity planning. Here, we use an IBD approach to determine patterns of connectivity to infer dispersal distances for a phylogenetically diverse ran...

Pleistocene climatic and oceanographic changes have influenced the distribution of marine biodiversity in southern Africa. Most evidence, however, has been derived from rocky shore or demersal taxa; data on sandy shore species are limited, despite severe threats to many sandy beach ecosystems. To test the effects of past climatic changes on sandy s...

The evolutionary clade comprising Nanger, Eudorcas, Gazella, and Antilope, defined by an X;BTA5 translocation, is noteworthy for the many autosomal Robertsonian fusions that have driven the chromosome number variation from 2n = 30 observed in Antilope cervicapra, to the 2n = 58 in present Eudorcas thomsoni and Eudorcas rufifrons. This work reports...

The white shark (Carcharodon carcharias) is an apex predator and is a protected species that suffers from several sources of anthropogenic mortality, such as shark nets. Shark nets are devices used to minimize the interaction between beachgoers and potentially dangerous sharks; however, these nets have negatively impacted local and migratory shark...

The phylogeographic patterns of small mammals in southern Africa are frequently disjunct. This pattern is predominately attributed to vicariant geographical barriers coupled to climate driven diversification. To gain further insights into this hypothesis, we embarked on a comparative mtDNA phylogeographic study of two common rodent species in south...

The evolutionary effects of glacial periods are poorly understood for Southern Hemisphere marine intertidal species, particularly obligatory sessile organisms. We examined this by assessing the phylogeographic patterns of the southern African volcano barnacle, Tetraclita serrata, a dominant species on rocky intertidal shores. Restricted gene flow i...

Marine invasions are recognized as an important threat to global biodiversity and predicting the establishment and spread of an introduced species can aid efforts to mitigate the damage incurred by these species. To determine if the recently introduced polychaete Boccardia proboscidea can establish itself along the South African coast and subsequen...

SUMMARY Laelaps giganteus and Laelaps muricola (Mesostigmata; Laelapidae) are widespread and locally abundant host generalists on small mammals in southern Africa. The large host range and complex life history of these ectoparasites may allude to possible intraspecific cryptic diversity in these taxa. To assess genetic and morphological diversity i...

The white shark Carcharodon carcharias was one of the first elasmobranch species where photo identification was used to identify unique individuals. In this study, we propose guidelines that improve the current photo identification technique for white sharks by presenting a novel categorisation system. Using this method, a high-resolution photograp...

Aim Climate change is expected to drive range shifts among a wide array of organisms. Non‐indigenous species ( NIS ) provide a unique opportunity to observe the establishment of range boundaries in a way that cannot be directly seen for native species. Recent studies have indicated that climate change facilitates biological invasions at local scale...

Penaeid prawns in Ungwana Bay, Kenya, are heavily exploited by artisanal fishers and industrial bottom trawlers. Human activities in mangrove and estuarine areas may affect prawn nursery habitats and influence juvenile recruitment to fished areas, therefore it was important to investigate recruitment patterns in the bay. To test the hypotheses that...

Females of the polychaete Polydora hoplura (Claparède 1869) that produced planktotrophic and adelphophagic larvae were compared genetically to determine whether the different reproductive morphs represented sibling species or poecilogony. Worms were collected from Saldanha Bay, South Africa (33°0′37.71S, 17°56′59.74E), and cultured in a laboratory...