Increasing attention has been given marine benthic macrofauna due to its importance in marine ecosystems and for its value as bioindicator of environmental changes. One of the most abundant groups among benthic macrofauna are echinoderms which often hold keystone positions in the ecosystems and have proven to be good bioindicators. The aim of this study was to inventory echinoderms and analyze whether species diversity has change over time in Gullmarsfjorden, a fjord with limited water exchange and hence highly sensitive to environmental fluctuations. Also, what may have caused any changes and what potential effects can it have on ecosystems in the fjord, and which species may be valuable as bioindicators. The results show that species diversity of echinoderms has decreased significantly since the early 1900s and the main reduction have occured among species living on/in soft or sandy bottoms. Many of the lost echinoderms species are essential bioturbators and thus important to marine ecosystems. However, Echinocyamus pennatifidum, a sea urchin which is a valuable bioturbator may have established in the fjord during the last century judging from this study. Species like Asterias rubens and Psammechinus miliaris, which are common in the fjord, have also proved to be valuable bioindicators for abiotic changes such as increased CO2-levels and pollution of heavy metals and PCB.

Thesis (Ph.D.) -- James Cook University, 2006. / Typescript (photocopy) Bibliography: leaves 92-104.

Dissertation (Ph.D.)--Auburn University, 2006. / Abstract. Vita. Includes bibliographic references.

Thesis (M.S.)--Oregon State University, 2001. / Typescript (photocopy). Includes bibliographical references (leaves 67-78). Also available on the World Wide Web.

Plankton play a key role in regulating nutrient and carbon cycles in freshwater ecosystems. The uptake and processing of nutrients in planktonic biomass are highly sensitive to changes in the environment, such as alterations in the availability of limiting nutrients, increasing temperature due to climate change, and changes to the composition of interacting species. The focus of this thesis is to use a variety of experimental and theoretical methods to assess and predict the impact of multiple perturbations on community structure, dynamics and ecosystem function, with a particular focus on interactions between phytoplankton and their consumers (zooplankton). Increases in both temperature and phytoplankton species diversity independently decreased CO2 concentrations when the number of non-resource species (those inedible to the zooplankton) were high. Using structural equation modeling I show that the effect is indirect, resulting largely from the positive impacts on total biomass of phytoplankton. Phytoplankton are limited by a range of resources, and differences in the functional traits used to utilize light and nutrients can explain the distributions of species under different temperature regimes. I found that under light and nitrogen limitation, resource requirements are generally lowest at intermediate temperatures, and that changes in temperature may therefore alter the competitive hierarchy amongst species. Using the model freshwater phytoplankton Chlamydomonas reinhardtii, I also find that previous selection environments govern future competitive abilities in phytoplankton. Adaptation to a high salt and low nutrient stress increases competitive ability under light limited conditions, indicating a strong dependency of selection environment for overall competitiveness. This thesis provides a mechanistic insight into the role of diverse plankton communities for community dynamics and ecosystem functioning.

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.

Statisticians often focus on sampling or experimental design and data analysis while paying less attention to how the response is measured. However, the ideas of statistics may be applied to measurement problems with fruitful results. By examining the errors of measured responses, we may gain insight into the limitations of current measures and develop a better understanding of how to interpret and qualify the results. The first chapter considers the problem of measuring taxonomic richness as an index of habitat quality and stream health. In particular, we investigate numerical taxa richness (NTR), or the number of observed taxa in a fixed-count, as a means to assess differences in taxonomic composition and reduce cost. Because the number of observed taxa increases with the number of individuals counted, rare taxa are often excluded from NTR with smaller counts. NTR measures based on different counts effectively assess different levels of rarity, and hence target different parameters. Determining the target parameter that NTR is "really" estimating is an important step toward facilitating fair comparisons based on different sized samples. Our first study approximates the parameter unbiasedly estimated by NTR and explores alternatives for estimation based on smaller and larger counts. The second investigation considers response error resulting from panel evaluations. Because people function as the measurement instrument, responses are particularly susceptible to variation not directly related to the experimental unit. As a result, observed differences may not accurately reflect real differences in the products being measured. Chapter Two offers several linear models to describe measurement error resulting from unanchored responses across successive evaluations over time, which we call u-errors. We examine changes to Type I and Type II error probabilities for standard F-tests in balanced factorial models where u-errors are confounded with an effect under investigation. We offer a relatively simple method for determining whether or not distributions of mean square ratios for testing fixed effects change in the presence of u-error. In addition, the validity of the test is shown to depend both on the level of confounding and whether not u-errors vary about a nonzero mean. / Graduation date: 2002

Graduation date: 1994