MSc., Faculty of Science, University of the Witwatersrand, 2011 / A selection of southern African bird species were modelled in terms of the probability of these species colliding with or being electrocuted on overhead power lines in South Africa, based on morphological and behavioral factors. Species were included in the model on the basis of internationally recognized vulnerability to these interactions at the family level. The collision model performed poorly when tested against the actual reported mortalities for species contained in the Eskom-EWT Strategic Partnership Central Incident Register CIR)(chi-square of goodness of fit) at the individual species, family and within family levels. The electrocution model performed slightly better at the family, and within family level. Both collision and electrocution models performed better for the physically larger species (and families) and for those species with higher modelled probability of collision or electrocution. As the product of random carcass detection and reporting, the CIR data are biased in various ways. Testing the models against the CIR is therefore equally important for highlighting inadequacies in the CIR, as in the model. A number of new species have emerged as being of high collision (including most importantly African Pygmy Goose, Southern Ground Hornbill, Black-bellied Bustard, Yellow-throated Sandgrouse, Caspian Tern, Hooded Vulture, Bateleur, African Marsh Harrier, Black Harrier, Pink-backed Pelican and Yellow-billed Stork) or electrocution (Southern Bald Ibis) probability in theoretical terms, and will require further investigation to determine their actual probability of interaction. By mapping the combined distributions of those species with high probabilities of collision and/or electrocution mortality, a number of priority high risk geographic areas emerge around the country.

The house sparrow, Passer domesticus, is one of the most successful invading bird species in the world. It was introduced to southern Africa around 1900 and has since spread through the region. Its dispersal was characterised by an initial slow phase followed by a rapid increase in the rate of spread. Following 50 years of slow spread, the rate of dispersal accelerated to over 80 km/year. The initial slow rate can be attributed to an Allee effect, defined as "a disproportionate reduction in reproduction below a threshold population density due to reduced probability of finding a mate". The rapid phase involved a combination of long-range jumps (leap-frogging dispersal) and diffusive movement over short distances. Dispersal was significantly faster along railway lines. Introduction of the house sparrow, Passer domesticus, to southern Africa involved unknown numbers of both the domesticus race of Europe and indicus of Asia, resulting in the establishment of a genetically diverse founder population along coastal South Africa. The birds have undergone significant differentiation since introduction about 100 years ago. Significant sexual size dimorphism was detected among southern African house sparrows, especially in flight structures. Males were larger than females in all characters except tarsus and claw length. Overall body size variation was clinaly ordered with a general increase in size with latitude in conformity with Bergmann's rule. Tarsus length also increased southwards, with the longest tarsi in birds of coastal sites in South Africa and the shortest in Zimbabwe. Patterns of variation in morphological characters paralleled climatic trends, especially minimum temperature and humidity. Beak size and shape of Zimbabwean birds appeared to be under the greatest influence of climatic factors. Shorter and more conicaly shaped beaks were selected for in females in Zimbabwe. Natural selection was modifying the morphological characters resulting in adaptive radiation in morphology of southern African populations. Few studies of microevolution (change in morphology over a short period) have been conducted in birds and none in invading bird species in the tropics. A founding population comprising both the Asian and the European races of the house sparrow, P. d. domesticus and P. d. indicus first arrived in Zimbabwe 30 years ago. Because of its recent introduction to Zimbabwe and because of its known potential for rapid adaptation and differentiation elsewhere in its new range, the house sparrow provided the ideal case study in microevolution in tropical Africa. Morphological differentiation in Zimbabwean populations of the house sparrow was analysed to determine temporal variation in local samples and the extent of variation from parent populations of Asia and Europe. Samples collected since arrival in Zimbabwe up to 1980 were compared with those collected from current populations in 1998/1999 to determine local changes over time. The Zimbabwean samples were then contrasted with samples from Asian and European populations to determine the extent of differentiation in the introduced birds of Zimbabwe. Zimbabwean populations had differentiated from their Asian parents in six of the seven morphological characters examined. The greatest differentiation was in beak size and shape for both males and females. Males developed larger beaks and shorter wings than the Asian birds and female beaks became more conical. A large proportion of the potential phenetic diversity of the founding population of both domesticus and indicus genes had been realised in Zimbabwe. / Thesis (M.Sc.)-University of Natal, Durban, 2001.

Thesis (M.Sc. (Zoology)) -- University of Limpopo, 2019 / It cannot be overemphasised that birds, which form a group of animals that are conspicuous in many habitats, occur worldwide, and are ecologically diverse and better known than any other vertebrate groups. Some species present no geographical variation while others exhibit complex geographic variation rendering them polytypic. The Southern Boubou Laniarius ferrugineus (Gmelin, 1788) is a polymorphic and highly vocal resident species endemic to Southern Africa. It overlaps with the Tropical Boubou Laniarius aethiopicus in the extreme north of South Africa. The taxonomic circumscription presents six subspecies of L. ferrugineus which vary in size and plumage colourations. Although L. ferrugineus is of least concern (LC), its wide distribution range calls for its precise taxonomic delineation and our knowledge of its genetic structure hence the need to investigate the status and level of morphological, genetic and vocal differentiation in this species complex. Morphological, genetic and song variation were analysed from museum study skins, DNA sequences spanning one coding mitochondrial gene and three noncoding nuclear introns generated from modern and ancient samples and songs from various sound libraries respectively. While morphometric analyses and Bayesian phylogenetic inference recovered two major lineages in L. ferrugineus: 1) L. f. ferrugineus / L. f. pondoensis / L. f. natalensis (southern clade) and 2) L. f. transvaalensis / L. f. tongensis / L. f. savensis (northern clade), L. f. transvaalensis overlapped between the two lineages in MDS and Box and whisker plots. The 95% parsimony ATP6 network similarly revealed two distinct lineages with the population demographic histories of the two clades showing expansion. The divergence between the two lineages occurred approximately 1.5 million years ago during the Pleistocene epoch. Laniarius ferrugineus pondoensis is the most distinctly dark morph. The moist habitat of L. f. pondoensis could be having an effect on plumage while there is no genetic basis for the difference in plumage colouration. Almost all L. ferrugineus subspecies render a tonal song duet made up of ‘bou’ and ‘whistle’ elements with the significant difference being observed in maximum peak frequency. Laniarius ferrugineus (Gmelin, 1788) should at best be split into two species, one representing members of the southern clade to be named Laniarius ferrugineus (Gmelin, 1788) and another species representing members of the northern clade iv named Laniarius transvaalensis Roberts, 1922 based on the Principle of Priority. The current study expanded our knowledge base as far as ornithology is concerned and shed light on the phylogeographic patterns of the Southern Boubou Laniarius ferrugineus (Gmelin, 1788). The findings significantly contributed to our understanding of the evolutionary processes governing the geographical variation in Laniarius ferrugineus complex and the findings could possibly be extrapolated to other species. It was critical that the taxonomic affinities of L. ferrugineus were investigated due to its extensive distribution range for better management and conservation. Future work should further unravel the less differentiation within the south and north lineages with additional songs being analysed to understand the song pattern across the range. / National Research Foundation (NRF)

The blue crane (Grus paradisea) is endemic to southern Africa and has the smallest geographical range of the 15 crane species occurring world-wide. Although this species is still found throughout most of its historic range, it has experienced a significant and rapid decline in numbers over the last 20 years. One factor causing this decline is the illegal removal of chicks from the wild. Permits are required to keep, trade in and breed cranes in captivity. However, birds must be captive bred in order to obtain a permit. Therefore, chicks taken illegally from the wild are fraudulently incorporated into an existing captive population under the pretence that they offspring of a legal captive pair. This study describes the development of a set of microsatellite markers to assist the identification of illegal trade in the blue crane. These markers can ultimately be used to verify the relationship between the offspring and its claimed parents by performing parentage analyses. Forty microsatellite loci were obtained from genomic libraries previously developed in two other crane species and tested for cross-species utility in the blue crane. In addition, 42 loci were developed for this study from a blue crane species-specific genomic microsatellite library, of which 19 were tested for polymorphism in this species. The microsatellite markers characterised here were also tested for their utility in two other crane species: wattled crane (G. carunculatus) and grey-crowned crane (Balearica regulorum). One locus, Gamu007, was found to be sex-linked and therefore excluded from the set of markers. A total of 28 polymorphic loci were tested for the suitability in parentage analysis in the blue crane. Of these, a set of 16 loci were determined to be as suitable for this purpose. These loci were shown to be inherited in a Mendelian fashion in a single blue crane family. In addition, statistical analysis of the loci were identified as exhibiting linkage equilibrium, this was supported by their distant association on a predicted Grus microsatellite map based on the chicken genome. The selected loci were also identified as having a low frequency of null alleles as well as a total first and second parent exclusion power of 0.9999 and 1.0000, respectively. These loci provide a valuable tool for parentage testing in blue crane, and may also be valuable in population genetic studies to assist conservation strategies. In addition, this set may be used to assist legal cases involving the illegal trade in blue cranes upon completion of additional microsatellite marker validation procedures. Twenty-seven loci were polymorphic in the wattled and grey-crowned crane. These could provide a valuable source of micro satellite loci in these species, and could potentially eliminate the need for the development of a species-specific microsatellite library. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2007.

Cranes are large elegant birds that occur on all continents of the world except for South America and Antarctica. Of the fifteen species of crane worldwide, three predominantly occur in southern Africa; the Wattled crane (Bugeranus carunculatus), the Blue crane (Anthropoides paradisea) and the Crowned crane (Balearica regulorum). Crane numbers throughout the world are diminishing, mostly because of the destruction of their habitat and illegal bird trading. Efforts are underway to prevent species extinction, legally and through the compilation of a studbook that contains descriptions of physical attributes, ownership, location and possible kinships of birds in captivity . This investigation, first of its kind, WdS undertaken to assess whether twelve published and unpublished microsatellite primers developed for the related Whooping crane and Red-Crowned crane could be used to fingerprint the southern African crane species using cost effective polyacrylamide gel electrophoresis. The results obtained were then used to determine the extent of genetic variation within species and distance between species. All primer sets amplified heterologous microsatellite loci in the three crane species, however, the unpublished primers produced poorly defined fingerprints even after extensive optimization. Of the twelve microsatellite loci investigated, the Blue crane and the Wattled crane revealed a high level of polymorphism. The Blue crane displayed 76% polymorphism and the Wattled crane 92%. In contrast, for the Crowned crane, that belongs to a different subfamily, Balearicinae, only 50% of the loci were polymorphic. The alleles displayed sizes similar to that of the species for which the primers were developed. Little variation in size, less than 10 bp, was noted for the different alleles of the polymorphic loci. The number of alleles, on the other hand, at each of the polymorphic loci was found to be low. The frequency of the most prevalent allele at most of the loci was generally reasonably high. These results therefore suggest that these primer sets are not suitable for individual identification and differentiation using polyacrylamide gel electrophoresis. Xll The observed heterozygosity of the three crane species was low; 12% in Blue crane; 7% in Crowned crane; and 13% in Wattled crane. Nei's identity further confirmed the high similarity between individuals; 66-100% for Blue crane; 55-100% for Crowned crane and 41-95% for Wattled crane. This low genetic variation is attributed to possible relatedness between birds supplied by aviculturists whom have a limited number of birds in captivity. A Hardy-Weinberg test for equilibrium revealed that most of the microsatellite loci displayed a deficiency of heterozygotes, while a few loci displayed an excess of heterozygotes. In general, the Hardy Weinberg test of equilibrium supported the notion that the individuals within each of the species might have been related. Differentiation between the three crane species ranged from 3-5%, with Blue and Wattled crane displaying a higher degree of genetic similarity when compared to the Crowned crane, known to be the oldest extant crane species. The limited allelic variation within the microsatellite loci tested, as well as the extensive genetic similarity between individuals suggests that a wide-ranging search for additional microsatellite loci that are more polymorphic and contain a larger number of alleles should be undertaken for the southern African crane species. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.