The main goal of this thesis was to develop new methods and knowledge that will explain and predict species differences in sensitivity to dioxin-like compounds (DLCs) in birds. The important achievements and results obtained from the four experimental chapters of this thesis are summarized as follow: (1) an efficient luciferase reporter gene (LRG) assay was developed for use with 96-well cell culture plates; (2) the results obtained from LRG assay were shown to be highly correlated to available in ovo toxicity data; (3) amino acids at positions 324 and 380 within the aryl hydrocarbon receptor 1 ligand binding domain (AHR1 LBD) were shown to be responsible for reduced Japanese quail (Coturnix japonica) AHR1 activity to induce a dioxin-responsive reporter gene in comparison to chicken (Gallus gallus domesticus), and ring-necked pheasant (Phasianus colchicus) AHR1 in response to different DLCs; (4) AHR1 LBD sequences of 86 avian species were studied and differences at amino acid sites 256, 257, 297, 324, 337 and 380 were identified. It was discovered that only positions 324 and 380 play a role in AHR1 activity to induce a dioxin-responsive gene; (5) in COS-7 cells expressing chicken AHR1, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 2,3,4,7,8-pentachlorodibenzofuran (PeCDF) are equipotent inducers of the reporter gene and bind with similar affinity to chicken AHR1, however, in the cells expressing pheasant, Japanese quail and common tern (Sterna hirundo) AHR1, PeCDF is a stronger inducer than TCDD. PeCDF also binds with higher affinity to pheasant and quail AHR1 than TCDD. The results of this thesis show that embryo lethal effect of DLCs in avian species can be predicted by use of two new non-lethal methods: (1) the LRG assay and (2) determination of the identity of the amino acids at positions 324 and 380. The findings and methods described in this thesis will be of use for environmental risk assessments of DLCs.

Analytical models of avian flight have previously been used to predict mechanical and metabolic power consumption during cruise. These models are limited, in that they neglect details of wing kinematics, and model power by assuming a fixed or rotary wing (actuator disk) weight support mechanism. Theoretical methods that incorporate wing kinematics potentially offer more accurate predictions of power consumption by calculating instantaneous aerodynamic loads on the wing. However, the success of these models inherently depends on the availability and accuracy of experimental kinematic data. The predictive simulation approach offers an alternative strategy, whereby kinematics are neither neglected nor measured experimentally, but calculated as part of the solution procedure. This thesis describes the development of a predictive tool for simulating avian wingbeat kinematics and wakes. The tool is designed in a modular format, in order to be extensible for future research in the biomechanics community. The primary simulation module is an inverse dynamic avian wing model that predicts aerodynamic forces and mechanical power consumption for given wing kinematics. The model is constructed from previous experimental studies of avian wing biomechanics. Wing motion is defined through joint kinematic time histories, and aerodynamic forces are predicted using blade element momentum theory. Mechanical power consumption at the shoulder joint is derived from both aerodynamic and inertial torque components associated with the shoulder joint rotation rate. An optimisation module is developed to determine wing kinematics that generate aerodynamic loads for propulsion and weight support in given flight conditions, while minimising mechanical power consumption. For minimum power cruise, optimisation reveals numerous local minima solutions that exhibit large variations in wing kinematics. Validation of the model against wind tunnel data shows that optimised solutions capture qualitative trends in wing kinematics with varying cruise speed. Sensitivity analyses show that the model outputs are most affected by the defined maximum lift coefficient and wing length, whereby perturbations in these parameters lead to significant changes in the predicted amount of upstroke wing retraction. Optimised solutions for allometrically scaled bird models show only small differences in predicted advance ratio, which is consistent with field study observations. Accelerating and climbing flight solutions also show similar qualitative trends in wing kinematics to experimental measurements, including a reduction in stroke plane inclination for increasing acceleration or climb angle. The model predicts that both climb angle and climb speed should be greater for birds with more available instantaneous mechanical power. Simulations of the wake using a discrete vortex model capture fundamental features of the wake geometry that have been observed experimentally. Reconstruction of the velocity field shows that this method overpredicts induced velocity in retracting-wing wakes, and should therefore only be applied to extended-wing phases of an avian wingbeat.

<p>Laser deterrents have been used as a method of deterring birds from problem areas such as fisheries, agricultural fields and airports. This method is considered a nonlethal means of control although lasers are known to cause visual lesions and loss of visual acuity in humans and other animals. Birds have a complex visual system which is necessary for behaviors critical to their survival, such as hunting and foraging, and predator vigilance. The purpose of this study is to determine the safety of laser deterrents for avian eyes using two species of birds: house sparrows (<i>Passer domesticus</i>) and European Starlings (<i>Sturnus vulgaris</i>). We found evidence that laser exposure can cause corneal edema, cataracts, retinal atrophy, displacement of the photoreceptor nuclei, and degeneration of the scleral cartilage. The laser exposure time was an important factor in the likelihood of developing corneal edema and retinal atrophy in starlings. Our findings suggest that lasers may not be completely safe for use as bird deterrents, but further research should be done to find possible solutions to improve laser safety from the avian viewpoint. </p>

Please read the abstract in the thesis. / Thesis (PhD)--University of Pretoria, 2013. / gm2014 / Paraclinical Sciences / Unrestricted

Thesis (M. Sc. (Zoology)) -- University of Limpopo, 2021 / The larks (Passeriformes, Passeri, Alaudidae) are small to medium-sized (10-23 cm) birds that are primarily terrestrial and cryptically plumaged hence they are difficult to encounter and recognise. The current taxonomic circumscription places these birds in a group that is comprised of 21 genera and 98 species, with all the genera occurring in Africa, 13 in Eurasia, and a single genus occurs in Australia and the Americas. Up until Alström et al. (2013), morphologically, the lark family was distinguished by having two unique and primitive features: i) the tarsus morphology (latiplantar and scutellate) consisting of the flat posterior surface covered with prominent scales, instead of being narrow and smooth as in other families, and ii) the syrinx (voice-generating organ). Despite that the structure of the syrinx of larks has been studied, literature reveals confusion pertaining to either the presence or absence of the pessulus, its level of development and size. To date, the work in Alström et al. (2013) remains the most comprehensive multi-locus phylogeny of the larks in which three strongly supported major clades (clade A – hereafter the Alaudid, clade B – the Mirafrid, clade C – the Ammomanid) emerged though with some uncertainty in some parts of the tree. In this study, the aim was to investigate the utility of syringeal and vocal characters in classifying the species of larks, finding out how syringeal and vocal characters evolved and identifying characters that define clades. The gross morphology and histology of the syringes and song strophes of larks and their putative outgroups were studied. Gross morphologically and histologically, the larks were found to possess a typical syrinx classified as a ‘syrinx tracheo-bronchialis’ and pessulus was observed in larks and the outgroups studied. There were differences observed in the syringeal gross morphological structure across all the three major clades (A, B and C). This is with regard to the presence or absence of the divided or double bronchial rings variably observed in clade A, B and C. In clade B and C, the ossification is variably restricted to the centre of bronchial rings forming a serial pattern while in clade A, bronchial rings are variably almost fully ossified without forming any serial pattern. The prominent oblique muscle-like structure runs ventrally and it was only observed in clade C in Chersomanes albofasciata. On the other hand, the syringeal histology revealed differences in the shape of the pessulus (blunt, pointy or sharp), the pessulus position relative to bronchial rings 1, 2 and 3 (B1, B2 and B3 respectively), length of the internal tympaniform membranes and connective tissue along the internal tympaniform membrane. The position of the pessulus was variably found to align with B2, to be below B2 and to be positioned beyond B2. One-way Anova clearly showed that among the three clades (A, B and C) identified in Alström et al. (2013), a statistically highly significant difference (P < 0.01) was found between the song strophes of species in clade C and A. The species in clade A generally give song strophes defined by high maximum frequency, high peak frequency and broad bandwidth frequency. The species in clade B have a similar trend with those in clade A, possibly explaining the overlap between these clades and the statistically significantly difference between clade A and C. These findings may be in support of the phylogenetic findings in Alström et al. (2013) and this study wherein clade A and B shared a sister relationship while clade C was placed basally. Clade C, on the other hand, comprises song strophes that are defined by low maximum frequency, lower peak frequency and narrow bandwidth frequency and this clade differed significantly from clade A. Despite that not all of the species could be correctly classified to their respective clades based on the Discriminant Function Analysis’ partition plot, the largest number of correct classifications were for clade A (70%). In addition, the distinction among the clades was also observed in either the presence or the absence of wing clappings in the song strophes, either being detached from or attached to the song strophes. Clade B is the only one which was marked by the presence of wing clappings particularly, genus Mirafra, although they are reported in Chersophilus duponti which belongs to clade A but not included in this study. With regard to the vocal phylogeny, the topology was highly unresolved, and no relationships could be inferred. The tracing of the evolution of characters of eight vocal and five syringeal characters revealed that among the 13 characters for which the ancestral state reconstructions were performed, 12 are polymorphic that is, they underwent multiple state changes ranging from four to 18. Most character states were found to plesiomorphous and mainly leading to clades of which their ancestral nodes were defined largely by autapormorphic and symplesiomorphic states. These do not assist in explaining how the various characters evolved. In conclusion, the findings have shed some light concerning the general syringeal morphology and histological structures of larks, revealed that lark songs are not suitable for reconstructing the phylogeny, shed light on the evolution of the selected vocal and syringeal characters as well as identifying characters that define the three major clades of larks (the Alaudid, Mirafrid and the Ammomanid).

Although Newcastle disease is reported to be endemic in Nigeria, little information exists on the molecular epidemiology and the lineage distribution of the Newcastle disease viruses (NDVs) in the country, especially in the live bird markets. Recent studies reported the identification of three distinct sub-lineages namely; 5f, 5g and 5h in West Africa, particularly sub-lineages 5f and 5g were identified in Nigeria. In this study a total of 41 NDV isolates were analysed. Thirty six NDVs were recovered from a variety of poultry species from live bird markets in the six geo-political zones of Nigeria during active surveillance from 2007 to 2008. Five NDVs recovered from outbreaks in backyard and commercial poultry farms within the same period were also genetically characterized. A commonly used region of the virus genome that spans nucleotide 61 to nucleotide 374 of the Fusion protein, including the cleavage site was targeted. Based on sequence analysis, 39 of the isolates were classified as virulent. Of these, 20 were classified as sub-lineage 5g and 17 were classified as sub-lineage 5f. One isolate differ markedly from all other strains included in the phylogeny. Interestingly, 13 strains from the 5f group formed a distinct cluster that was not identified by other groups in similar studies. Phylogenetic analysis, amino acid sequence determination of the F0 cleavage site sequence analysis, pair wise distance analysis of the partial fusion protein gene sequences and Geographic Information System (GIS) mapping was done. Results showed close genetic similarities and provided evidence for the first time of the epidemiological link between the viruses circulating in the LBMs and those identified in outbreaks in backyard and commercial farms in Nigeria between 2007 and 2008. The emergence and identification of new sub-lineages gives an insight in to the high rate of genetic drift occurring in NDV strains in Nigeria, and raises concerns about the efficacy of current NDV control measures in the country. Thus there is need for continuous surveillance and characterization of NDV from Nigeria to monitor the emergence of new lineages and sub-lineages in the Nigerian poultry industry. Copyright / Dissertation (MSc)--University of Pretoria, 2011. / Production Animal Studies / unrestricted

abstract: Although many studies have identified environmental factors as primary drivers of bird richness and abundance, there is still uncertainty about the extent to which climate, topography and vegetation influence richness and abundance patterns seen in local extents of the northern Sonoran Desert. I investigated how bird richness and abundance differed between years and seasons and which environmental variables most influenced the patterns of richness and abundance in the Greater Phoenix Metropolitan Area. I compiled a geodatabase of climate, bioclimatic (interactions between precipitation and temperature), vegetation, soil, and topographical variables that are known to influence both richness and abundance and used 15 years of bird point count survey data from urban and non-urban sites established by Central Arizona–Phoenix Long-Term Ecological Research project to test that relationship. I built generalized linear models (GLM) to elucidate the influence of each environmental variable on richness and abundance values taken from 47 sites. I used principal component analysis (PCA) to reduce 43 environmental variables to 9 synthetic factors influenced by measures of vegetation, climate, topography, and energy. I also used the PCA to identify uncorrelated raw variables and modeled bird richness and abundance with these uncorrelated environmental variables (EV) with GLM. I found that bird richness and abundance were significantly different between seasons, but that richness and winter abundance were not significantly different across years. Bird richness was most influenced by soil characteristics and vegetation while abundance was most influenced by vegetation and climate. Models using EV as independent variables consistently outperformed those models using synthetically produced components from PCA. The results suggest that richness and abundance are both driven by climate and aspects of vegetation that may also be influenced by climate such as total annual precipitation and average temperature of the warmest quarter. Annual oscillations of bird richness and abundance throughout the urban Phoenix area seem to be strongly associated with climate and vegetation. / Dissertation/Thesis / Masters Thesis Applied Biological Sciences 2019

Commercial forestry has expanded across the Rio de la Plata Grasslands (RPG) of South America in recent decades. I conducted a resource-use based study on bird communities during the 2013-2014 austral breeding season in northern Uruguay. I assessed relationships between habitat types and bird abundance as a function of vegetation structure. To compare avian responses to treatments, I included native environments, pine and eucalyptus plantations of different ages and thinning regimes. I detected differences in species richness and composition and species-specific responses in abundance along structural gradients sampled. Although poorer in species than native habitat types, tree plantations were extensively used by birds. Birds associated with plantations were primarily habitat generalists and forest dependent species, with low incidence of grassland specialists. Results of my study provide baseline information for stand-level management and future landscape design of timber plantations to benefit conservation of bird communities in afforested landscapes in the RPG.

No description available.

Urbanization is a growing threat to biodiversity across the globe. As more and more habitats are being destroyed and species extinction rates are rising, we have started looking at how we might decrease this loss of biodiversity. One answer is changing our urban environments to more biodiversity friendly ones. Since conditions within a city and a natural landscape might differ, it is important to understand how landscape variables affect biodiversity in urban areas. The purpose of this study was to investigate how landscape variables (Coniferous/mixed forest, Open uncultivated land, Fields, Deciduous forest, Water, High and Low urban development, and Industrial area) affect bird diversity, richness, and community assembly in a small city in central Sweden. Surveys were conducted on 33 sites. Results from a multiple regression comparing the environmental variables to richness or diversity showed that Water was positively correlated to both diversity and richness. A redundancy analysis (RDA) showed that bird species assemblage was significantly affected by Coniferous/mixed forest, Water, and Fields when the whole bird community was considered. However, when only passerines were included in the RDA, Urban development and Coniferous/mixed forest had the strongest impact. When conservation efforts are made in urban areas, these variables need to be considered since they are correlated with different species and they might not be the same ones that are associated with richness or diversity of birds.