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Please read the abstract in the section 00front of this document / Dissertation (MSc (Zoology))--University of Pretoria, 2006. / Zoology and Entomology / unrestricted

The Yellow Warbler (Dendroica petechia) is a highly polytypic bird species with a vast breeding range in the Americas. To assess the level of population structuring within the northern part of its range, I surveyed the nucleotide variation present in a 344bp segment of the mitochondrial DNA (mtDNA) control region I (CR-I) from 155 breeding individuals. These birds were caught at seven locations in Canada and Alaska. Fifty-nine haplotypes were observed in this sample, with pairwise distances between haplotypes ranging from 0.29 to 4.35%. The number of nucleotide sites with multiple hits indicates a high rate of evolution in this region. A homologue to the CR-I was also identified and likely originated from a paralogous duplication event, as suggested by the comparison of sequences from the two regions. Significant population structuring in Yellow Warblers across North America was revealed by analyses of nucleotide diversity and molecular variance, which demonstrated the existence of a major subdivision between eastern (Manitoba to Newfoundland) and western (Alaska and British Columbia) warbler populations. This finding provides evidence for very low levels of gene flow between these two groups. Fifteen out of 21 pairs of populations differ significantly in their genetic composition, indicating further structuring at a smaller geographic scale. Within the eastern group of populations, both the high mutation rate of the CR-1 and an isolation-by-distance process seem to be responsible for differences between locations. Phylogenetic analyses indicate that western birds form a monophyletic group whereas eastern birds are paraphyletic with respect to the western ones. However this conclusion remains hypothetical because of a lack of statistical support for the monophyly of western haplotypes. Nevertheless, this situation is consistent with a historical splitting of warbler populations by a vicariant event, possibly of Pleistocene origin, and provides intraspecific support for vicariance as a mechanism leading to isolation and speciation of western warbler taxa, as hypothesized by Mengel (1964). However, other scenarios, such as a founder event in the west from an eastern stock, cannot be excluded, although they are less likely based on mtDNA data. The absence of phylogeographic structure in the East suggests a recent expansion of Yellow Warbler populations from a restricted geographic range. These findings demonstrate that populations of continentally distributed North American passerine species can show high level of population structuring when assayed with an hypervariable molecular marker such as the mtDNA control region I. / Thesis / Master of Science (MSc)

Thesis (M.S.)--University of Minnesota, 2001. / Includes bibliographical references (leaves 47-51) Also available on the World Wide Web as a PDF file.

Seasonal long-distance bird migration between wintering and breeding grounds is oneof the most remarkable phenomena in the history of life on earth. Migration strategies androutes vary greatly. Some birds migrate in social groups whilst others migrate alone at night,some cross few hundreds of km whilst others cover thousands of km. Avian migration has beenstudied extensively nevertheless numerous important questions remain unanswered. This studyaims to contribute to the understanding of the genetic basis of the innate migratory program ofa common songbird.From results of classical crossbreeding and orientation experiments with captiveblackcaps (Sylvia atricapilla) we can be sure that songbird migration directions as well asdurations are traits that are being inherited genetically and most likely have a multi-locusgenetic architecture. The chosen model species for my project is the willow warbler(Phylloscopus trochilus), one of the most common leaf warblers in the Palearctic. The willowwarbler has a continuous breeding distribution from the coast of the Atlantic to the coast ofPacific. They overwinter in sub-Saharan Africa. Three subspecies have been recognized: P. t.trochilus (breeding in central/western Europe and migrating SSW to western Africa), P. t.acredula (breeding in northern and eastern Europe, migrating SSE to east and south Africa)and P. t. yakutensis (breeding east of Ural Mountains, presumably migrating to SouthernAfrica). Morphological differences across the willow warbler subspecies are subtle and it has been previously shown that genome wide FST is close to zero. The low level of neutral back-ground divergence offers a good system for studying the genetics of passerine migration. This report contributes with novel data on phenotypes and genotypes of the subspecies yakutensisstudied at Chaun river delta, at the very eastern range limit of the species. As a proxy for thewintering location of yakutensis I used C and N stable isotope signatures from winter grownfeathers and inferred wintering range to be in Southern Africa. I genotyped 36 yakutensis fromChaun on four nuclear markers, of which three are located on the only divergent regions thatdiffers between the migratory phenotypes in Europe + CLOCK gene (a candidate for timing ofmigration). Analyzes revealed that yakutensis, despite strong differences in migration direction,distance, timing and wintering ground location cannot be separated from acredula genetically.

Differences in patterns of species richness and taxonomic composition across continents are well documented. However, less is known about how these patterns originate from the fundamental processes that contribute to the assembly of continental biotas: speciation, extinction, immigration, and emigration. To truly decipher how these processes operate at a continental scale, it is crucial to understand how Earth-history events and environmental change shaped the biogeographical history of the taxa occurring in a region. The Pleistocene glacial cycles have been hypothesized to be a significant geological event which affected the Earth’s biota over the past three million years. During this period, multiple cycles, in which ice sheets covered a large portion of the Northern Hemisphere, have been hypothesized to facilitate allopatry and ecological differentiation. The central goal of this dissertation is to understand the assembly of continental biotas by integrating the role of Earth’s geological and environmental history and recent (late Quaternary) changes in distributions. Here, I studied the North American wood-warblers, which are passerine birds belonging to the family Parulidae. In the first chapter of this dissertation, I examined the extent to which recent diversification is underestimated by ignoring recently diverged taxa. To do so, I evaluated the effect of taxonomic delimitation on the inferred temporal patterns of diversification of wood-warblers in the genus Setophaga. My results show that species-level taxonomic delimitation in ecological and evolutionary studies is crucially important but is often ignored. Evaluating the effect of taxonomic delimitation in the genus Setophaga is particularly relevant because it has been widely cited as an ideal example of niche saturation, and previous studies suggested that lineages in this particular radiation exhibited an asymptotic accumulation of diversity through time. In this chapter, however, I demonstrate that this pattern was likely a consequence of the ways in which taxonomic diversity was sampled. In the second chapter, I examined how biotic and abiotic factors limit the distribution of species of the genus Oreothlypis at a continental scale. For most of the taxa examined, climatic- and biotic-based areas of suitability were equivalent, and therefore the relative importance of these factors could not be disentangled. However, in some cases, biotic variables limited the distribution in areas climatically suitable, and vice versa. The results of this chapter highlight the importance of considering potential effects of biotic interactions in the study of climate-driven range shifts. This paper is also an important methodological contribution to the general field of ecological niche modeling (ENM) by integrating climatic and palynological data to empirically estimate both abiotically and biotically suitable areas which that has only been done theoretically so far. In the third chapter, I integrated phylogenetic data, biotic and climatic ENMs, and reconstructions of environments during the LGM to test how cycles of fragmentation, differentiation, and expansion during the Pleistocene shaped the biogeographical patterns of the genus Oreothlypis in North America. Based on a time-calibrated phylogeny I identified two groups of taxa that diversified during the last million years and therefore were potentially affected by glacial cycles. My analyses suggest that there were rapid switches in the environmental conditions in which species of the genus occur and that glacial cycles resulted in dramatic range shifts from glacial maxima to interglacials. Distribution patterns during the LGM suggest that divergence in areas isolated by glaciers presumably contributed to the geographical structuring of Oreothlypis, as well as to their taxonomic and ecological diversity in the present. In summary, this work illustrates how wood-warblers are an ideal model system for examining the large-scale history of the North America biota and environment, particularly over the Pleistocene. They are highly diverse, have endemics in virtually all of North America's areas of endemism and ecosystems, and many of these patterns are repeated within and across clades. Furthermore, distributional patterns in warblers show high congruence with those of other organisms; thus inferences made about the history of this group likely have implications for understanding the biotic history of North America in general. In addition, many warblers have narrow ecological preferences in that they occupy forest environments with specific tree compositions. As a consequence, ecological models of their distributions, integrated with the North American pollen record of forest change, provide a new perspective on ecosystem change during glacial cycles, and its impact on the origin and maintenance of biodiversity in the continent.

Over the last 50 to 150 years there has been widespread conversion of grassland to shrubland throughout the western United States. A major management concern on the Edwards Plateau is the encroachment of Ashe Juniper (Juniperus ashei). To facilitate brush management programs, I investigated relationships of two endangered species, the black-capped vireo (Vireo atricapillus) and the golden-cheeked warbler (Dendroica chrysoparia), with their habitats at the landscape level. GIS (Geographic Information Systems) and remotely sensed data, such as Landsat imagery, DEMs (Digital Elevation Maps), and DOQQs (Digital Ortho Quarter Quads) were used to evaluate vegetative and geomorphic features within both 100m- and 400m-radius areas surrounding occupied and (assumed) unoccupied sites. Stepwise-logistic regression was used to develop probability models for each species within a catchment and was then applied to the entire Leon River Watershed and evaluated for accuracy. Golden-cheeked warblers were identified in areas with mean juniper cover greater than 70%, mean departure from North (aspect), and maximum slope. For black-capped vireos, mean shrub cover, mean departure from North, and mean slope were important in habitat selection. Variables at the 400m spatial scale best identified areas of probable occurrence for both species, indicating that features of landscape surrounding a territory may play an important role in habitat selection.

Over the last 50 to 150 years there has been widespread conversion of grassland to shrubland throughout the western United States. A major management concern on the Edwards Plateau is the encroachment of Ashe Juniper (Juniperus ashei). To facilitate brush management programs, I investigated relationships of two endangered species, the black-capped vireo (Vireo atricapillus) and the golden-cheeked warbler (Dendroica chrysoparia), with their habitats at the landscape level. GIS (Geographic Information Systems) and remotely sensed data, such as Landsat imagery, DEMs (Digital Elevation Maps), and DOQQs (Digital Ortho Quarter Quads) were used to evaluate vegetative and geomorphic features within both 100m- and 400m-radius areas surrounding occupied and (assumed) unoccupied sites. Stepwise-logistic regression was used to develop probability models for each species within a catchment and was then applied to the entire Leon River Watershed and evaluated for accuracy. Golden-cheeked warblers were identified in areas with mean juniper cover greater than 70%, mean departure from North (aspect), and maximum slope. For black-capped vireos, mean shrub cover, mean departure from North, and mean slope were important in habitat selection. Variables at the 400m spatial scale best identified areas of probable occurrence for both species, indicating that features of landscape surrounding a territory may play an important role in habitat selection.

Presented in this thesis is the mitochondrial DNA (mtDNA) cytochrome b gene analysis of the phylogenetic relationships within the Apalis thoracica complex (600bp) as well as among selected African Bradypterus species (603bp). Within A. thoracica 28 individuals from 20 subspecies were analysed. There was only molecular support for 13 historically isolated clades as opposed to the 21 subspecies recognized based on morphology. Among these molecularly defmed clades were clades lynesi, juscigularis and flavigularis, all three of which are of conservation concern and were previously treated as species by some based on their distinct morphology. Molecular clock dating estimated the clades to be of Pliocene age, whereas genetic differentiation within clades was of Plio-Pleistocene to Pleistocene age. This result is consistent with that of other African montane birds. Under the phylogenetic species concept all 11 clades could be recognised as species although a multifaceted approach to species recognition which will include vocalisation data is suggested. Contrary to expectation, the isolated East African clades did not exhibit more variation than the continuously distributed clades within southern Africa. In fact, significant phylogeographic breaks were identified within South Africa that need further investigation. For the African Bradypterus, 13 individuals from six of the 10 African species were analysed. These species were not monophyletic. Based on sequence divergence B. victorini was as different from the other members of the genus as it was from the out groups. In addition its song is very distinct and both males and females sing. Therefore, based on the molecular results presented in this thesis as well as vocalisation data and, it is proposed that B. victorini is not a Bradypterus. This result is particularly significant in light of the growing evidence that the Cape region acted as a repository for ancient animal taxa and holds implications for the conservation status of the region. The molecular data supported the classification of the taxa based on habitat and song but in addition clarified the placement of B. victorini and B. sylvaticus. The basal position of the latter among the remaining members of the genus indicates that Bradypterus is primarily a forest taxon that radiated into other habitats. It must however be kept in mind that the current dataset is based on six of the 10 African Bradypterus and none of the Asian species. The possibility of hybridisation between B. sylvaticus and B. barratti was raised and needs to be tested through additional sampling. / Dissertation (MSc (Genetics))--University of Pretoria, 2006. / Genetics / unrestricted

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