Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Within southern Africa, the widely distributed four-striped mouse Rhabdomys is parasitized by, amongst others, the host-specific ectoparasitic sucking louse, Polyplax arvicanthis. The present study investigated this parasite-host association from a phylogenetic and phylogeographic perspective utilizing mitochondrial and nuclear DNA markers. The findings support the existence of four species within Rhabdomys (three distinct lineages within the previously recognized arid-adapted R. pumilio and the mesic-adapted R. dilectus). These species have distinct geographic distributions across vegetational biomes with two documented areas of sympatry at biome boundaries. Ecological niche modelling supports a strong correlation between regional biomes and the distribution of distinct evolutionary lineages of Rhabdomys. A Bayesian relaxed molecular clock suggests that cladogenesis within the genus coincides with paleoclimatic changes (and the establishment of the biomes) at the Miocene-Pliocene boundary. Strong evidence was also found that the sucking louse P. arvicanthis consists of two genetically divergent lineages, which probably represent distinct species. The two lineages have sympatric distributions throughout most of the sampled range across the various host species and also occasionally occur sympatrically on the same host individual. Further, the absence of clear morphological differences among these parasitic lineages suggests cryptic speciation. Limited phylogeographic congruence was observed among the two P. arvicanthis lineages and the various Rhabdomys species and co-phylogenetic analyses indicated limited co-divergence with several episodes of host-switching, despite the documented host-specificity and several other traits predicted to favour congruence and co-divergence. Also, despite the comparatively smaller effective population sizes and elevated mutational rates found for P. arvicanthis, spatial genetic structure was not more pronounced in the parasite lineages compared to the hosts. These findings may be partly attributed to high vagility and social behaviour of Rhabdomys, which probably promoted parasite dispersal among hosts through frequent inter-host contact. Further, the complex biogeographic history of Rhabdomys, which involved cyclic range contractions and expansions, may have facilitated parasite divergence during periods of host allopatry, and host-switching during periods of host sympatry. Intermittent contact among Rhabdomys lineages could also have prevented adaptation of P. arvicanthis to specific host lineages, thus explaining the lack of host-specificity observed in areas of host sympatry. It is thus evident that the association between Polyplax arvicanthis and Rhabdomys has been shaped by the synergistic effects of parasite traits, biogeography, and host-related factors over evolutionary time. / AFRIKAANSE OPSOMMING: Binne suidelike-Afrika word die wyd-verspreide gestreepte veldmuis, Rhabdomys, onder andere deur die gasheer-spesifieke ektoparasitiese luis, Polyplax arvicanthis, geparasitiseer. Die huidige studie het hierdie parasiet-gasheer interaksie vanuit ‘n filogenetiese en filogeografiese oogpunt ondersoek deur van beide mitokondriale en nukluêre merkers gebruik te maak. Die bevindinge dui op die bestaan van vier spesies binne Rhabdomys, waaronder drie nuwe genetiese groepe binne die voorheen erkende R. pumilio asook R. dilectus. Hierdie spesies het nie-oorvleulende geografiese verspreidings binne spesefieke plantegroei biome met twee geidentifiseerde areas van simpatriese voorkoms by bioom grense. Ekologiese nis modellering ondersteun ‘n sterk korrelasie tussen biome en die verspreiding van die evolusionêre groepe binne Rhabdomys. ‘n Bayesiaanse verslapte molekulêre klok dui daarop dat kladoginese binne die genus gedurende paleoklimatiese veranderinge, wat tot die totstandkoming van die huidige biome gelei het, by die Mioseen-Plioseen grens plaasgevind het. Sterk bewyse is ook gevind dat die parasitiese luis P. arvicanthis uit twee geneties verskillende groepe, wat heel moontlik afsonderlike spesies verteenwoordig, bestaan. Hierdie genetiese groepe het simpatriese verspreidings oor meeste van die gebestudeerde geografiese area op die verskeie gasheer spesies en mag ook soms simpatries op dieselfde gasheer individu voorkom. Verder dui die afwesigheid van duidelike morfologiese verskille tusssen die parasiet genetiese groepe op moontlike kriptiese spesiasie. Beperkte filogeografiese ooreenstemming is tussen die P. arvicanthis genetiese groepe en die Rhabdomys spesies waargeneem en die vergelykende-filogenetiese analises het aangedui dat daar beperkte gesementlike-divergensie plaasgevind het met verskeie episodes van gasheer-wisseling, ten spyte van die gasheer-spesifieke aard van die parasiete asook verskeie ander kenmerke wat veronderstel is om filogeografiese ooreenstemming en gesementlike-divergensie te bevorder. Ten spyte van die vergelykbaar kleiner effektiewe bevolking groottes en verhoogde mutasie tempo wat vir P. arvicanthis gevind is, is die geografiese genetiese struktuur nie meer gedifferensieёrd in die parasiet groepe as in die gasheer nie. Hierdie bevindinge mag deels verklaar word deur die hoё beweeglikheid asook die sosiale gedrag van Rhabdomys, wat waarskynlik parasiet beweging tussen gashere bevorder deur gereelde tussen-gasheer kontak. Die komplekse biogeografiese geskiedenis van Rhabdomys, wat sikliese inkrimping en uitsetting van die geografiese verspreiding behels het, het heel moontlik parasiet divergensie tydens tydperke van gasheer allopatrie asook gasheer-wisseling tydens tydperke van gasheer simpatrie, gefasiliteer. Tussentydse kontak tussen Rhabdomys genetiese groepe kon aanpassing van P. arvicanthis tot sekere gasheer genetiese groepe verhoed het en verklaar dus die afwesigheid van waargenome gasheer-spesifisiteit in areas van gasheer simpatrie. Dit is dus duidelik dat die assosiasie tussen P. arvicanthis en Rhabdomys deur die sinergistiese uitwerking van parasiet kenmerke, biogeografie, asook gasheer-verwante faktore oor evolusionêre tyd gevorm is. / National Research Foundation (NRF)

Thesis (MScConsEcol)--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: Anthropogenic habitat transformation and subsequent fragmentation of natural vegetation is regarded as one of the largest threats to biodiversity in the world. The Cape Floristic Region (CFR) in the Western Cape Province of South Africa is classified as a biodiversity hotspot due to its high plant species diversity and endemism. Increasing growth in agricultural activities in this region has contributed to fragmentation of pristine natural vegetation. A diverse assemblage of small mammal species are found in this region, but very little is known with regard to their ectoparasite diversity. More importantly, no information is available on the effect of fragmentation on parasite burdens or species assemblages. The aims of the study were first to record relative density, average body size and body condition of an endemic rodent, Rhabdomys pumilio, trapped in two habitat types (pristine natural areas and remnant fragments). Secondly, compare diversity and species composition of ectoparasite species on this rodent in the two habitat types. In addition, body size measurements of the two most abundant flea species were recorded and compared for the two habitat types. Lastly, temporal variation in mean abundance of fleas, mites, ticks and the louse were recorded within a habitat fragment surrounded by vineyards. Three hundred and ten individuals of the Four-striped mouse, R. pumilio, were trapped and euthanized at 8 localities (4 remnant habitat fragments and 4 pristine natural areas) in the CFR. All ectoparasites were removed and identified. A total of 8361 ectoparasites that consisted of 6 flea, 1 louse, 8 mites and 11 tick species were recorded. Mites and fleas were found to be more abundant on mice during cool wet months, whereas ticks and the louse were more abundant during the hot dry months of the year. Rodent host body size was larger and they were in better body condition in remnant fragments compared to pristine natural localities. A positive body size relationship was found between the flea, Listropsylla agrippinae, and the host, with larger fleas recorded on rodents that occur in fragments. Mean abundance and prevalence of overall ectoparasites combined and separately for ticks, mites, louse and fleas were higher in fragments compared to natural localities. The study shows that R. pumilio is host to a large diversity of ectoparasite species in the CFR. Moreover, habitat fragments within agricultural landscapes can facilitate higher parasite burdens and prevalence in rodent populations. This can lead to an increase in disease risk given that several of the parasite species are important vectors of pathogens that can cause disease in domestic, wild animals and humans. / AFRIKAANSE OPSOMMING: Menslike habitat transformasie en die daaropvolgende fragmentasie van natuurlike plantegroei word beskou as een van die grootste bedreigings vir biodiversiteit in die wêreld. Die Kaap Floristiese Streek (KFS) in die Wes-Kaap Provinsie van Suid-Afrika word geklassifiseer as 'n biodiversiteit ‘hotspot’ as gevolg van sy hoë plant spesies diversiteit en endemisme. Toenemende groei in landbou-aktiwiteite in hierdie streek het ook bygedra tot die fragmentasie van ongerepte natuurlike plantegroei. 'n Diverse versameling van die klein soogdier spesies word in hierdie streek aangetref, maar baie min is bekend met betrekking tot hul ektoparasiet diversiteit. Meer belangrik, geen inligting is beskikbaar oor die effek van fragmentasie op parasietladings of spesie samestelling nie. Die doel van die studie was eerstens om relatiewe digtheid, gemiddelde liggaams grootte en kondisie van Rhabdomys pumilio aan te teken vir twee habitat tipes (ongerepte natuurlike area en oorblyfsel fragment). Tweedens was die diversiteit en spesiesamestelling van ektoparasiete op R. pumilio vergelyk vir die twee habitat tipes. Daarna was die liggaams grootte metings van die twee mees volopste vlooi spesies aangeteken en vergelyk vir die twee habitat tipes. Laastens was die seisonale variasie van die gemiddelde hoeveelheid vlooie, myte, bosluise en die luis aangeteken binne 'n habitat fragment omring deur wingerde. Drie honderd en tien individue van die vier-gestreepte muis, R. pumilio, was gevang op 8 plekke (4 oorblyfsel habitat fragmente en 4 ongerepte natuurlike areas) in die KFS en daarna was die diere uitgesit. Alle ektoparasiete was verwyder en geïdentifiseer. 'n Totaal van 8361 ektoparasiete wat bestaan het uit 6 vlooie, 1 luis, 8 myte en 11 bosluis spesies was aangeteken. Myte en vlooie gevind was meer volop op muise tydens die koel nat maande, terwyl bosluise en die luis meer volop was gedurende die warm droë maande van die jaar. Knaagdier gasheer liggaam was groter en in 'n beter kondisie in die habitat fragmente in vergelyking met ongerepte natuurlike areas. 'n Positiewe liggaam grootte verwantskap was tussen die vlooi, Listropsylla agrippinae, en die gasheer gevind, met groter vlooie aangeteken op knaagdiere wat voorkom in fragmente. Gemiddelde hoeveelheid en voorkoms van die totale ektoparasiete gekombineer en afsonderlik vir bosluise, myte, die luis en vlooie was hoër in fragmente in vergelyking met natuurlike areas. Die studie toon dat R. pumilio gasheer is vir 'n groot verskeidenheid van ektoparasiet spesies in die KFS. Daarbenewens kan habitat fragmente binne landbou landskappe hoër parasietladings en voorkoms in knaagdier bevolkings fasiliteer. Dit kan lei tot 'n toename in siekte risiko, gegee dat verskeie van die parasietspesies belangrike vektore is van patogene wat siektes kan veroorsaak in huishoudelike, wilde diere en die mens.