Considering South Africa’s richness in aquatic species, very little knowledge exists regarding copepods that are symbiotic on hosts ranging from invertebrates to marine mammals. In order to have any indication of the existing biodiversity of this group of organisms in South African waters, a thorough investigation of all possible hosts needs to be conducted, which in turn will most likely increase the number of recorded symbiotic copepods considerably. The current descriptive study was done in an effort to contribute to a larger study of metazoan parasites of elasmobranch hosts along the KwaZulu-Natal coast of South Africa. A total of 40 (31 Mobula kuhlii; two Mobula eregoodootenkee and seven Manta alfredi) mobulids were examined for infection by symbiotic copepods at the KwaZulu-Natal Sharks Board (KZNSB). More than 90% of all examined hosts were infected with different types of symbiotic siphonostomatoids. Collected copepod specimens were fixed and preserved in 70% ethanol and studied with both the stereo- and light microscopes using the wooden slide technique. Some selected specimens were further studied using Scanning Electron Microscopy (SEM) to elaborate on ill-defined features. A total of 13 different species of the order Siphonostomatoida distributed over five families were identified. The five families include Eudactylinidae (Eudactylina oliveri, Eudactylina diabolophila and Nemesis sp.); Caligidae (Caligus crysophrysi, Pupulina sp. 1, Pupulina sp. 2; Pupulina sp. 3, Unidentified sp. 1, Unidentified sp. 2 and Unidentified sp. 3); Kroyeriidae (Kroeyerina mobulae); Dichelesthiidae (Anthosoma crassum) and Cecropidae (Entepherus laminipes). Two of the 13 species (E. laminipes and A. crassum) are monotypic and were therefore easily identified. Eudactylina oliveri exhibited a prevalence of 75% and 100%; mean intensity of 42 and 130 parasites per host and a mean abundance of 32 and 130 individuals per host while Pupulina sp. 1 exhibited a prevalence of 61.29% and 100%; mean intensity of 41 and 5 individuals per host and a mean abundance of 2 and 5 individuals per host on M. kuhlii and M. eregoodootenkee respectively. Component populations of E. oliveri and Pupulina sp. 1 exhibited an aggregated distribution pattern on their examined hosts. The phylogenetic relationship between nine caligid species (three known Pupulina species, three collected Pupulina species and three Unidentified sp. species as ingroup) with Caligus glandifer as out-group was determined and analysed using a morphological dataset (40 characters) from previous and current descriptions. The ii exhaustive search with PAUP* retained a single most parsimonious tree with a tree length (TL) = 85; consistency index (CI) = 0.7; retention index (RI) = 0.7; homoplasy index (HI) = 0.3 and a rescaled consistency index (RCI) = 0.5. Bootstrap support for the estimated clades was mostly low with values less than 95%. The phylogenetic hypothesis of the 10 caligid species presented in the current study was derived from the phylogenetic analysis of the information for adult females and is therefore not intended to be a definitive theory but should be treated as a testable hypothesis that can be further analysed using more data. The current study provides the first record of C. chrysophrysi, Pupulina sp. 1, Pupulina sp. 2, K. mobulae and E. laminipes on M. kuhlii; E. oliveri, Pupulina sp. 1, Pupulina sp. 2 and Pupulina sp. 3 on M. eregoodootenkee; and E. diabolophila, Nemesis sp., C. chrysophrysi, E laminipes, A. crassum and the three Unidentified species on M. alfredi frequenting the east coast of South Africa and thus contributes to the knowledge of our marine biodiversity. Mobulid hosts were not carefully studied for copepod infection previously and the copepods that were reported from the mobulids were probably found by chance. Therefore future investigation into the symbiotic siphonostomatoids of more mobulid hosts and other host species may result in more reports of symbiotic Copepoda from South African waters. / Thesis (MSc. (Zoology)) -- University of Limpopo, 2013

Thesis (MSc. (Zoology)) -- University of Limpopo, 2014 / One of the 11 families of the siphonostomatoids found parasitic on elasmobranchs is the Kroyeriidae which has three accepted genera namely Kroyeria, Kroeyerina and Prokroyeria. Parasites from this family are found living on the gills (Kroyeria spp. and Prokroyeria sp.) or in the nasal fossae (Kroeyerina spp.) of Chondrichthyes. There are currently 21 nominal species in the genus Kroyeria. Kroyeria specimens were collected from the gill filaments of their elasmobranch hosts which were caught: (1) in the nets of the KwaZulu-Natal Sharks Board (KZNSB) installed along the east coast of South Africa, (2) by commercial fishermen off the west coast at Gansbaai as well as (3) during the demersal trawls of Department of Agriculture, Forestry and Fishery (DAFF) off the south and west coasts. Collected specimens were fixed and preserved in 70% ethanol. Morphological features were drawn where necessary to illustrate differences from previously described features. Host-parasite relationships of the different species were determined by calculating prevalence, mean abundance and mean intensity on their hosts as well as estimating the pattern of dispersion by calculating the coefficient of dispersion. DNA was extracted from selected identified samples. A partial fragment of the COI gene was amplified via PCR using the forward and reverse universal primers LCO 1490 and HCO 2198, or those with additional M13 tails, LCO 1490_t1 and HCO 2198_t1. Additionally, the complete 18S rDNA gene of some species was amplified using the forward and reverse primers as follows: 18Sf and 1282r for the first fragment, 554f and 614r for the second fragment and 1150f and 18sr for the third fragment. Phylogenetic relationships among different Kroyeria species were estimated by employing neighbor joining (NJ), parsimony (MP) and maximum likelihood (ML) in PAUP*. The use of real-time PCR and melt curve analysis to distinguish among different Kroyeria species based on their different melt temperatures of a part of the COI gene was also attempted. Eleven Kroyeria species were found on the gill filaments of elasmobranchs belonging to the families Carcharhinidae, Sphyrnidae and Triakidae off the coasts of South Africa. These include K. carchariaeglauci from C. leucas; K. decepta from C. obscurus; K. deetsi from C. brevipinna; K. dispar from G. cuvier; K. elongata from R. acutus; K. lineata from M. palumbes; K. longicauda from C. limbatus; K. papillipes viii from G. cuvier; K. procerobscena from both C. leucas and C. amboinensis; K. sphyrnae from both Sphyna lewini and S. zygaena and a new Kroyeria sp. from G. galeus. This is the first record of K. lineata from the south coast of South Africa and is also as a new host record for Mustelus palumbes. Three Kroyeria species have previously been reported from G. galeus, namely K. brasiliense, K. lineata and K. rhophemophaga. The new Kroyeria sp. is most similar to K. rhophemophaga which in turn shares morphological features with K. triakos. However, the Kroyeria sp. can be distinguished from both K. rhophemophaga and K. triakos in the armature of the legs. Most Kroyeria species are relatively host specific, infecting a single host or related group of host species. During this study two species, K. dispar and K. papillipes were collected from G. cuvier, while K. procerobscena and K. sphyrnae were each collected from two host species. Kroyeria sp. and K. dispar displayed very high prevalence values, 95.7% and 94.1% respectively, in contrast to the other Kroyeria species which have lower values (6.3–68.6%). Additionally, when compared to other siphonostomatoid species such as Nemesis lamna, Kroyeria species have relatively low prevalence values. Kroyeria species generally have low parasite loads (between 4 and 33 copepods per infected host), except for K. dispar which has a high mean intensity of 74 copepods per infected host. The mean abundance of Kroyeria species is also generally low (between 0 and 23 per examined host), with K. dispar (69 individuals per examined host) being an exception. Furthermore Kroyeria species generally display an aggregative pattern of distribution which is common in most copepod species indicating that individuals have social interactions. A preliminary estimation of the phylogenetic relationships among seven Kroyeria species revealed topologies with unresolved polytomies. The 18S rDNA gene did not make any significant changes on the topology, except that it produced very minimal resolution in one of the groupings. Therefore, COI is found to be a gene of choice that can be used in estimating molecular phylogenetics and population genetics of siphonostomatoids as it provides useful sequence divergence within individuals of the same species as well as among congeneric species due to its fast evolving rate. However, in this study, single species did not form monophyletic groupings. ix The 18S rDNA gene is found to be very conservative, providing no sequence divergence within individuals of the same species and very little divergence among conspecifics due to its low mutation rate and is therefore more useful at genus and family levels. With polytomies in the estimated phylogenetic relationships, haplotype networks were used to compare the distribution of different haplotypes among the different species. Haplotype sharing did occur between species e.g. for COI, H1 is shared by K. lineata, Kroyeria sp. and K. sphyrnae. This haplotype sharing by different species is unexpected and could be due to specimen misidentification before DNA extraction. Specimen misidentification is common for Kroyeria species because some of them are not easy to identify. The haplotype network results confirmed the relationships shown by the phylogenetic trees, dividing Kroyeria species into three different groupings. Real-time PCR and melt curve analysis have the potential to distinguish among Kroyeria species. However, the quality of the extracted DNA is an important factor in producing successful amplifications and determining the Tm. Therefore it is necessary to ensure that the extracted DNA has the ideal concentration of 50 ng/μl and is free of Taq polymerase inhibitors such as phenol, RNA and guanine residuals from the extraction process.

ABSTRACT This thesis examines phylogenetic patterns in three New Zealand amphipod taxa in relation to current geographic distributions and historical climatic (e.g. glaciation, marine inundation) and geological (e.g. mountain building) events using DNA sequencing and distributional data. It also examines how recognition behaviour can be used to delineate potential species boundaries and to assess the role of sexual selection. The endemic genus Phreatogammarus has been found in only a limited number of sites and is not very abundant. An analysis of the genetic variation of two species within the genus using allozyme electrophoresis revealed high levels of genetic differentiation among populations but low levels within populations. This suggested that limited dispersal occurred among habitats with one population possibly representing a cryptic species. The endemic freshwater genus Paraleptamphopus is thought to contain a large number of undescribed species with a number of these existing in small waterbodies such as seepages. Examination of the phylogeographic patterns using both mtDNA (CO1) and nuclear DNA (28S) showed that a number of distinct genetic lineages exist, with CO1 revealing 21 haplotypes with genetic distance of over 20%. Using a molecular clock rate of 2.4%, most haplotypes diverged approximately 8-12 million years ago during the Miocene era, possibly as a result of greater land availability increasing habitat diversity or by allopatric speciation. Morphological and genetic differences were not congruent, with morphologically similar taxa appearing among highly genetically distinct lineages, and some morphologically distinct forms appearing within single lineages. The distribution and habitat variables of 419 sites were analysed to determine what was affecting the presence or absence of Paraleptamphopus. The presence of native vegetation in catchments had a positive affect on Paraleptamphopus distribution suggesting that large anthropogenic changes in catchment vegetation could have a negative effect on their abundance. I found smaller waterbodies to be more important than larger ones highlighting the need to study such sites as rare taxa may be ignored. A better understanding is needed on the role of small waterbodies in promoting overall species diversity in catchments. Examination of Paracalliope fluviatilis phylogenetic patterns using the mtDNA gene CO1 showed that a number of separate clades existed suggesting long term isolation and limited dispersal among catchments. Due to the large genetic divergences among some populations there was the possibility that cryptic species might exist. Species recognition experiments were conducted on seven populations to help determine whether cryptic species were present. For the three most genetically divergent crosses there was bias against inter-population pairings, suggesting that there were between two or three separate species. Using a combined field and laboratory approach, size assortative mating was examined in Paracalliope fluviatilis. The field study showed positive size assortative mating and that larger females carried more eggs, suggesting they were more fecund. A series of laboratory experiments examining four existing theories explaining the phenomenon found that none adequately explained positive size assortative mating in P. fluviatilis. I therefore presented two new explanations to explain size assortative mating: a combination of female resistance and size-related variation in a male's capacity to amplex larger females or a form of indirect intra-sexual competition.

The morphological phenotypic characters involving sexual selection but with highly individual variability are likely to challenge the prezygotic isolating mechanism driven by differentiation of mechanical structures. This kind of characters may also puzzle species identification and taxonomy. Therefore clarifying the correlation between the phenotypic variability and biological/non-biological factors becomes necessary in order to understand the role of this phenomenon under natural selection and sexual selection. The Syntomini represents one of the few lepidopterous groups that exhibit highly individual variability in both wing pattern and reproductive structures. The evolutionary and taxonomic significance of this phenomenon, however, has never been studied using modern methods although it has been documented for long. In order to test several hypotheses relevant to phenotypic variability, the present study focuses the phylogenetic relationship of Amata wilemani Rothschild, 1914, a subalpine moth species with extremely high variability in wing coloration and genitalia. The phylogenetic relationship between the three color morphs of A. wilemani and 38 Syntomini species plus 2 Lithosiinae outgroups was reconstructed using fragments of COI, EF1a and 28S. All color morphs of A. wilemani were recovered to form a monophyletic group under all data partitioning strategies with Amata formosensis (Wileman, 1928) or its closely related species in China as the potential sister group. The result of gene network analysis suggests low divergence between haplotypes of A. wilemani. Because no correlation between color morphs, phenology, geographical distribution, altitudinal gradient, and genitalic morphlogy was detected, it is concluded that A. wilemani should be regarded as a single species with high phenotypic variability, and this may suggest existence of intraspecific competition. The present study also found that Amata karapinensis (Strand, 1915), which was synonymized with A. wilemani by previous authors, should be revived. The incongruence between the phylogenetic relationships based on morphological and molecular characters shows a need of a comprehensive phylogenetic study of this highly diverse group.

Restoration of streams that were formerly channelized for timber-floating has become increasingly common. Generally, this restoration returns boulders from riparian zones to streams, leading to wider, more heterogeneous channels with slower flows. The primary goal is to enhance fish populations, but riparian vegetation is also expected to be favoured. However, increases in floristic diversity have not been observed and reasons for this slow response are still unknown. One possible explanation might be the lack of colonist pools. I therefore investigated how surrounding plant compositions influence riparian recovery. The vascular plant flora was identified in riparian sites and in adjacent upstream riparian and upland sites. Four reach types were included: unchannelized, channelized, restored and demonstration restored. Species richness and floristic similarities among types of sites and reaches were compared. Correlations with upland and upstream channel slopes were made and the importance of variation in seed floating ability was tested. The results show that unchannelized reaches were floristically similar to their adjacent upstream riparian and upland sites, whereas channelized reaches showed more different floras. Restoration created a somewhat more homogeneous flora among the three site types and demonstration restored reaches were most similar to upstream sites. Soil moisture conditions (i.e. wetland vs. forest) in the uplands had stronger impacts on species similarities than upland or upstream channel slopes. I conclude that adjacent sites are important for floristic recovery of riparian reaches and that demonstration restoration is most advantageous for riparian recovery. I recommend protection of upland sites from forestry to facilitate recovery. / Local- and landscape-scale effects on biodiversity after stream restoration

No description available.

The herbivory experienced by non-native invasive plants may depend on their local environments, such as herbivore abundance. In this study, I performed a common garden experiment with plants sampled from 11 populations of Arctium minus, from southern Ontario to near its northern range limit. I also compared performance and herbivory of burdock in open and understory habitats. Finally, I conducted freezing tolerance experiments with the lepidopteran seed predator Metzneria lapella, and palatability tests with plants from different populations. Results suggested that the previously described latitudinal trends in herbivore damage among populations are due to environmental differences rather than genotypic differences among populations. At a local scale, plants of open habitat were less damaged and had better performance than understory plants. Burdock has not escaped damage by herbivores in its invaded range; instead variation among sites in herbivore populations and impacts may significantly affect the invasiveness of this species.

The herbivory experienced by non-native invasive plants may depend on their local environments, such as herbivore abundance. In this study, I performed a common garden experiment with plants sampled from 11 populations of Arctium minus, from southern Ontario to near its northern range limit. I also compared performance and herbivory of burdock in open and understory habitats. Finally, I conducted freezing tolerance experiments with the lepidopteran seed predator Metzneria lapella, and palatability tests with plants from different populations. Results suggested that the previously described latitudinal trends in herbivore damage among populations are due to environmental differences rather than genotypic differences among populations. At a local scale, plants of open habitat were less damaged and had better performance than understory plants. Burdock has not escaped damage by herbivores in its invaded range; instead variation among sites in herbivore populations and impacts may significantly affect the invasiveness of this species.

Molecular based species identification is a useful tool in forensic investigations as well as routine work. The ability to cheaply and quickly determine the species of origin of a sample has become increasingly necessary as incidents of wildlife poaching, illegal meat trade and the trade of wildlife products has increased. The current methods of species identification tend to be expensive, time consuming and unreliable. The use of species-specific primers designed to bind to specific areas in the mitochondrial DNA, has been published. This application has been developed for a small number of domestic animals, however the application of these primers to African wildlife species has yet to be done. This method is relatively simple and is based on specific fragment size amplification using polymerase chain reaction and genotyping. A total of thirty seven different species were analyzed with this method and 30 of these species were found to have species-specific fragment sizes. A number of different sample types and conditions were tested including uncommon diagnostic samples such as rhinoceros horn, teeth and claws. In addition, the sensitivity of the method was investigated and determined to be very high, detecting species at a DNA concentration of just 0.1 pg/μl. This method was found to be a highly sensitive, efficient and a fast way to determine species in a number of different sample types and would therefore be of great value in the wildlife trade as these samples can often be of a lower quality or only available in small amounts. The use of this method in forensic science must be done with care due to the problem of cross species amplification. In addition not all of the African Wildlife mammals were available to test, limiting the detection power and specificity of the test. Copyright / Dissertation (MSc)--University of Pretoria, 2012. / Production Animal Studies / unrestricted

Biological invasions represent both an urgent conservation problem and an opportunity to advance ecological theory. Development of pertinent research questions and proactive management strategies require knowledge of which introduced species are present and of spatiotemporal trends in the distribution of natives and invaders. In Chapter 2 we developed a quantitative framework to identify spreaders and decliners and estimate invasion chronologies based on a historical fish presence data set for upper and middle New River (UMNR) tributaries. Our framework accounts for spatiotemporal variability in sampling effort by aggregating presences by watershed and expressing range size as a function of the number of watersheds sampled per time period. The majority (55%) of fish species present in the study area were introduced, 51% of which were spreaders. Most spreaders (84%) appeared to be spreading exponentially. The rate of new introductions detected in the study area has slowed since the mid-20th century. Two natives, the mound-spawning bluehead chub Nocomis leptocephalus and its strong nest associate (reproductive mutualist), mountain redbelly dace Chrosomus oreas, were among the most rapid spreaders. Four natives showed evidence of decline. Our framework leverages historical presence data to reconstruct temporal trends in species distributions. It sets the stage for further study of factors driving stream fish invasions and declines in the Appalachian region, and is transferable to diverse taxonomic groups and geographic regions. Species traits and human activities mediating stream-fish invasions remain poorly understood. In Chapter 3 we modeled the contribution of species traits to invasion success of UMNR tributary fishes during the colonization and spread stages. Biological traits accurately explained colonization and spread success, whereas ecological traits resulted in less accurate models. Colonization success was positively related to time since introduction, benthic feeding, an equilibrium life history, and nest spawning. Successful spread was positively related to winter air temperature in the native range and an equilibrium life history. Variables estimating human use and propagule pressure were non-informative. Traits that influenced invasion success were consistent with the hypothesis that human land-use practices have increased the invasibility of highland watersheds by creating novel conditions suited to lowland and equilibrium invaders. / Master of Science