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Conservation genetics theory predicts that isolated populations on the periphery of a species range will display reduced levels of genetic diversity compared to those more centrally located. Low levels of diversity can potentially compromise individual fitness and population viability among peripheral populations and so from a conservation perspective, understanding genetic structure among populations with low levels of diversity is a priority. Here I examine the levels and spatial distribution of both neutral and adaptive DNA polymorphisms across populations of the palmate newt (Lissotriton helveticus); including both island and mainland populations at the northern extent of their distribution and putative source populations from which postglacial expansion occurred. Five different classes of molecular marker were assayed: (1) mitochondrial DNA sequence variation, (2) micro satellite length variation, (3) MHC allelic diversity, (4) AFLP profiling and (5) candidate nuclear locus (sodium-calcium exchanger) allelic diversity, with an overall prediction that neutral markers will exhibit reducing diversity with increasing latitude and then from mainland to island; and that neutral diversity will be a poor predictor for adaptive diversity given the additional effects of selection on these genes. These predictions were not wholly confirmed. Mitochondrial data demonstrated that refugial populations harboured more genetic diversity than postglacial populations. Conversely, micro satellite diversity did not decline gradually with increasing latitude and insular populations were not necessarily depauperate compared to those on the mainland. Adaptive diversity was not reduced among peripheral or island populations but a signature of directional selection was detected. Lastly, genome-wide AFLP diversity was not reduced among island populations whilst no clear inference was possible from the sodium-calcium exchanger gene. There was a lack of concurrence between neutral and adaptive markers and the results are discussed in relation to the effects of micro-evolutionary processes acting in populations of varying size and isolation. The significance of these findings is discussed in relation to the long term conservation of palmate newt populations.

The way malaria parasites are transmitted in space will have an influence on their genetic relationships. It can be expected that parasites collected within close geographic distances of each other would be more closely related than those across large geographic distances. Further to this, because malaria transmission is focal and heterogeneous in space, then the genetic relatedness between malaria parasites in these foci of malaria transmission would be greater within tightly clustered regions. Thus, using the level of genetic relatedness of these parasites would reveal how they are transmitted not only within these foci but at different geographic settings. This knowledge would offer insight on how malaria control methods can be effectively disseminated. In field settings malaria infections are polyclonal and each of the clones represented within these infections occur at different proportions. With the aid of genetic markers such as single nucleotide polymorphisms (SNPs) or microsatellites, parasite clonal genotypes can be identified. In this study, the genetic markers of choice are SNPs. Using a method that can quantify these SNPs representing the different clones occurring at different proportions in an isolate, then each of the clonal genotypes can be determined. Microsatellites were also used as additional markers in the study. In this thesis, 1.Genetic markers (SNPs) across the P. falciparum genome were identified (Chapter 3); 2. PyrosequencingTM was validated as a technique that would enable the identification of each genetically distinct clone represented in an infection by assigning proportions to the SNPs representing each genetically distinct clone and enabling the identification of parasite clonal genotypes in every isolate analysed. This was validated using laboratory prepared clone mixtures of P. falciparum. In addition; the progeny from a cross derived from genetically characterised 3D7 and HB3 isolates was analysed in preparation for the analysis of the field isolates (Chapter 4). , 4. In Chapter 5, field isolates were tested and clonal genotypes identified using both SNPs and microsatellites. A detailed population genetic analysis was also performed and finally in Chapter 6, evidence for correlation between the genetic relationships of these parasites and geographic distance was investigated. The results from field isolates summarised in this thesis were from analysis of 54 isolates; 7 samples collected from Cameroon, 13 from Kenya and 34 from Mali. The data consists of 13 SNPs analysed by PyrosequencingTM and 8 microsatellites. 84 clonal genotypes were identified by both genetic markers from the analysed isolates. Analysis of both SNPs and microsatellites revealed that microsatellites were more informative than the SNPs based on the observed allelic richness and heterozygosity (genetic diversity) across all loci analysed. The overall FST value was 0.061 using SNPs and 0.043 by microsatellites analysis. These values were low but consistent with what is typically observed in African P falciparum populations. Finally, analyses of the combined data set revealed that no statistically significant levels of spatial autocorrelation existed within the studied parasite populations. However, there was evidence of within host mixed parasite infections exhibiting a high level of genetic relatedness compared to between host infecting clones.

Studying how new insect species originate can help us better understand the evolutionary processes that lead to the rich insect biodiversity found in the tropics. New insect species arise via the evolution of reproductive isolation, a result of the accumulation of reproductive isolating barriers. Reproductive isolating barriers can arise in the context of geographical isolation and/or can be influenced by differences in ecology. Complex evolutionary mechanisms may underlie the origins of the more than 40 species of neotropical fruit flies in the genus Blepharoneura (Diptera: Tephritidae). The immature stages of these flies are specialist feeders on plants in the Cucurbitaceae (cucurbit) family in Central and South America. Previous research focusing on six geographically widespread Blepharoneura species used 18 microsatellite loci to identify patterns of geographical and ecological divergence. While conclusions from microsatellite data are valid, these markers provide only a limited signal of genetic structure. Fine-scale, genome-wide data can reveal patterns of genetic differentiation that may help us discover and date historical and recent lineage divergence. Here I use double-digest restriction-associated DNA (ddRAD) sequencing to explore the hypothesis that geographic and ecologic barriers are restricting gene flow in one species of Blepharoneura, B. sp10. First, I use two methods to detect population structure within B. sp10 individuals. I find evidence for three distinct genetic groups characterized by geography and one genetic group defined by a difference in host plant use. Then I investigate these relationships using Mantel tests and pairwise spatial-genetic plots, which reveal distinct biogeographical genetic patterns. Finally, I infer the evolutionary history of B. sp10 using approximate Bayesian computation and find that the timing of divergence between flies collected from the Amazon Basin and those collected from the Guiana Shield coincides with the late Pleistocene, between 24,412 and 83,000 years ago. Connecting these results to historical climate data from the Late Pleistocene may help explain evolutionary processes that contributed to the patterns of genetic diversity that we see in Blepharoneura. This research provides a framework for investigating the biogeographic and evolutionary history of the more than 50 species in the Blephaorneura genus, a step towards understanding the complexity of insect diversity in the tropics.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (p. 80-86).

Thesis--M. Phil., University of Hong Kong, 1987.