Thesis (M.S.)--Florida State University, 2004. / Advisor: Dr. Scott Steppan, Florida State University, College of Arts and Sciences, Dept. of Biological Science. Title and description from dissertation home page (viewed Jan. 18, 2005). Includes bibliographical references.

Thesis (Ph.D.)(Entomology)--University of Pretoria, 2005. / Title from opening screen (viewed March 20, 2006). Includes summary. Includes bibliographical references.

Thesis (Ph. D.)--University of Canterbury, 2005. / Typescript (photocopy). "April 2005." Includes bibliographical references (leaves 116-130). Also available via the World Wide Web.

Thesis (Ph. D.)--James Cook University, 2003. / Title from PDF title page (viewed on May 14, 2007). Includes bibliographical references (p. 126-139).

The use of phylogeography in plant systems has been on the increase in recent years with the use of chloroplast DNA to detect sufficient intraspecific variation to reach significant conclusions about plant species histories, both temporally and spatially. In this study, the geographic structure and possible origin of the morphologically variable Themeda triandra is explored. The trnF - trnC and psbD - trnS gene regions of the cpDNA were used to find 12 haplotypes found in 11 populations of T. triandra that encompass the species large distributional range. A haplotype tree was constructed that showed the relationship of the 11 haplotypes (haplotype_H12 was excluded as it fell outside of the 95% confidence limit), with haplotype H6 inferred to be the ancestral haplotype. A nested clade analysis was performed with the results used to infer the geographic structure of T. triandra within South Africa. Significant results showed that there was restricted gene flow with nested clades involving the three Free State populations, indicating that there are barriers to gene flow with other haplotypes. The ancestral haplotype showed long distance colonisation, with a probable root of this colonisation being the Kruger National Park. This is the proposed point of introduction of T. triandra into South Africa, with results from this study supporting this proposal. A substantial amount of gene flow (25.49%; AMOV A) between populations is observed, with this probably being due to the widespread distribution of haplotypes H6 and H10. It is thought that T. triandra followed two migration routes within South Africa: one along the coast, with the other inland above the escarpment where populations became genetically isolated from populations below the escarpment. Further studies may look for a correlation between morphological variants of T. triandra and the cpDNA haplotypes found within the species.

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 thesis is focused on the issue of the Squalius genus phylogeography in Albania in the Balkan region. Phylogenetic analyses of sequence variation at mitochondrial genes (cytochrome b) were used to examine these issues for the freshwater fish genus Squalius from various river systems in the Adriatic Sea region. There were identified 3 genetic lineages of vague taxonomic position where the genetic variation amount to 1.6-2.1 %. The first lineage is distributed in north of Albania and in the whole Periadriatic region, the second lineage is especially spread to northern part of Albania and the third lineage covers especially the zone of the European ancient lake systems on the Balkan Peninsula (Lake Ohrid and Prespa), from where expands to the southern part of Albania. There sympatrically coincide the both lineage in the hydrological river-lake system of Drin and Skadar. The phylogenetic and taxonomic position of the Squalius genus in the region seems to be interesting topic for subsequent and more detailed study. Keywords: Squalius, Albania, cytochrome b, phylogeography

Herein we tested the repeatability of RAD-seq phylogeographic construction by creating a second, independent phylogeography of the pitcher-plant mosquito, Wyeomyia smithii. We sampled 25 populations drawn from different localities nearby previous collection sites and used these new data to construct a second, independent phylogeography to test the reproducibility of phylogenetic patterns. Our previous phylogeography was based on 3,741 phylogenetically informative markers from 21 populations and rooted with mitochondrial COI. The present phylogeography was based on 16,858 informative markers and rooted with RAD-seq. We found correspondence between clades at the extremes of W. smithii's distribution; however, there were several discrepancies between the trees, including the refugium that gave rise to all post-glacial populations. We observed that combining all 46 populations resolved these discrepancies and, equally importantly, that extensive taxon sampling in areas of historical importance is more valuable than increasing the number of informative sites in establishing an accurate, robust phylogeography. This thesis includes unpublished co-authored material.

A central concept in evolutionary biology is to understand how new species arise and are maintained. Studying the temporal and spatial distribution of genealogical lineages provides insight into evolutionary processes which govern diversification while the study of disease vectors has additional implications for human health. Within Africa, medically important Aedes mosquitoes provide an interesting case in which to study evolutionary processes because they are behaviourally and morphologically diverse. These mosquitoes are also inherently dependent of forests and so provide an ideal study organism in which to test the refuge hypothesis of historical climate change, which has been suggested as a pivotal force in species evolution. Before their evolutionary history can be determined, reliable identification of target species is required. In Chapter 3, we have developed a PCR mediated method to distinguish between isomorphic species of the Simpsoni Complex and use this method to provide inferences on ecology and species distributions; findings reveal an east-west difference in the distribution of the yellow fever vector Ae. bromeliae and non-vector Ae. lilii across the African continent, while these species meet in Uganda where they use the same larval habitats. In Chapters 4 and 5 we use a standard phylogeographic approach coupled with Approximate Bayesian Computation to uncover the evolutionary history of Aedes mosquitoes. Analysis reveals common phylogeographic signals within Aedes species which show populations have been subject to historical lineage diversification, admixture and recent demographic structure, in accordance with the refuge hypothesis of climate induced vicariance and secondary contact. Findings suggest that recent climate change throughout the late Pleistocene and early Holocene was important in generating African biodiversity. We find additional differences in the population structure of species between East and West Africa which could reflect more general biodiversity patterns within Africa. As the region connecting East and West African populations, Central Africa could be an important area regarding the diversification of species, including diseases and their vectors. We have identified a putative role for ecological speciation; for example in Chapter 4 we have provided additional evidence that worldwide populations of Ae. aegypti stem from a particularly successful source, indicating these mosquitoes possessed a trait integral for range expansion. In Chapters 4 and 5 we find that historical admixture within Africa characterises populations of Aedes mosquitoes and so may have played a key role in their evolutionary success. Since admixture can combine novel combinations of genetic material and raise adaptive potential, admixture may have been selectively advantageous for Aedes mosquitoes. Similarly, climate related secondary contact is likely to have been an important force for the evolution of other forest dependent species within Africa.

Achalinus niger is an endemic species of Taiwan. It distributes from 1000 to 3000 m in altitude. The effect of geological isolation, especially mountains and valleys may influence the population genetic structure of the species. The ND2 gene was used as genetic marker to analyze the genetic structure of populations and phylogeography of A. niger. The mean genetic distance is 3.87¢H and the mean nucleotide diversity 3.5¢H. The Meifeng population was distinct in genetic structure from other populations. The data suggest that A. niger had more than one incursion events. In phylogenetic analyses, there were three major lineages in A. niger, and these lineages were correlated to geographic distribution. Lineage¢¹ was sampled from northern Taiwan, lineage¢º from southern Taiwan, while lineage ¢» from Meifeng only. The result of AMOVA indicated that there were high genetic variations among groups. The genetic isolation and geographic distribution of these groups probably resulted from the geographic barriers.