Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (leaves 276-317). Also available in print.

Graduation date: 1998

Thesis (Ph.D.) - University of Queensland, 2005. / 2 papers by the author and others, folded in pocket inside back cover. Includes bibliography.

Oceanographic features such as currents, fronts and upwelling cells have been recognised as possible factors driving population differentiation within species. The Benguela Current is one of the oldest upwelling systems in the world, located off the west coast of Southern Africa, and represents a biogeographical boundary between the Atlantic and Indo-Pacific Oceans. Previous studies have reported the influence of this system in isolating several marine taxa between the two oceans. However, few have been conducted within the Benguela Current boundaries, in order to understand its role in shaping population genetic structure of fish species at a regional level. The present study documents the influence of the Benguela Current oceanographic features on the genetic differentiation, population connectivity and evolutionary history of five coastal fish species (Diplodus capensis, Argyrosomus inodorus, Argyrosomus coronus, Atractoscion aequidens and Lichia amia), and one oceanic pelagic fish species (Thunnus albacares). Results for both mitochondrial and nuclear marker variation in all coastal species revealed a similar geographical pattern of population genetic structuring despite distinct differences in life history features. The oceanic species exhibited shallow population differentiation between Atlantic and Indian Oceans. For coastal species, different depths of differentiation were observed, ranging from speciation events (A. aequidens, A. coronus and A. japonicus) to shallow structuring (A. inodorus and T. albacares). Furthermore, in these cases, population structures were coincident with the Benguela Current oceanographic features, suggesting that the system may represent a vicariant barrier to dispersal of coastal fish species. Congruence between mitochondrial and nuclear markers suggests that population isolation was not a single historical event, but has persisted over large timescales and is still active. The existence of cryptic speciation events, and the high levels of genetic diversity and differentiation documented make the Benguela Current a natural laboratory to study evolutionary mechanisms shaping biodiversity and genetic population structure of marine fish species.

The effect of human activity on the natural world is increasingly shaping the evolution of species. The capacity of evolution to occur in individuals of a species, via natural selection acting on the genotypes of local populations through successive generations, is known as local adaptation. In southwest England, historical mining activity has resulted in a patchwork of highly metal-contaminated rivers across the region. Where the ecological diversity in many of these rivers has been decimated, metal-tolerant brown trout (Salmo trutta L.) populations seem to thrive. What are the mechanisms underlying this apparent metal-tolerance? And can it be attributed to processes of local adaptation? This thesis takes a multi-faceted approach in assessing this, by exploring the patterns and processes involved in metal-tolerance in brown trout populations in southwest England. A series of investigations were undertaken, including the use of neutral genetic markers (microsatellites), reduced representation genome sequencing (RAD-seq), common-garden exposure experiments, and genome-wide analysis of hepatic gene expression (RNA-seq). The microsatellite analysis illustrated that metal-tolerant trout have a different genetic architecture compared to fish in clean rivers and, using Bayesian analysis, these demographic differences were correlated with key periods of mining history. We then developed an approach to facilitate robust screening of genome-wide polymorphic loci through a method of parameter optimisation for RAD-seq. This approach formed the basis for identifying loci for investigating the genomic processes of local adaptation in metal-tolerant trout. We present genome-wide (RAD-seq) data highly indicative that neighbouring trout populations, differently impacted by unique ‘cocktails’ of metal pollutants have evolved both parallel and convergent mechanisms of metal tolerance. Through a common garden experiment, exposing metal-tolerant and metal-naïve fish to a mixture of metals, we were able to hone in on the physiological mechanisms underlying metal-tolerance. Finally, through RNA-seq, we observed that metal-tolerant fish showed little to no changes in hepatic gene expression when exposed to metals, pointing to innate mechanisms of metal handling. Together, the marriage of these various investigations showcases the remarkable ability of local adaptation in conferring metal-tolerance to brown trout populations in southwest England, and, importantly, the resilience of species’ in the face of human-altered environments.

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 97-117).

The Earth’s atmosphere supports microorganisms and they include potential pathogens and microbial allergens. Whilst indoor environments have been well studied, relatively little is known of bio-aerosols in outdoor locations and their potential influence on human health, particularly with regard to urban development. Hong Kong provides an ideal model system for testing hypotheses related to the impact of urbanization on bio-aerosols, with a well-defined gradient of urbanization and large population. This thesis describes work to establish the biodiversity and spatio-temporal dynamics of outdoor bio-aerosols in Hong Kong. A comprehensive study of multi-domain microbial diversity and allergen levels in urban aerosols over a contiguous annual timescale and along a gradient of urbanization was carried out. A comprehensive suite of climatic and pollutant variables were also recorded during the sampling interval. Terminal restriction fragment length polymorphism (T-RFLP) was employed to investigate variations in bacterial and eukaryal assemblages, followed by phylogenetic assessment using high-throughput sequencing. The results revealed a strong seasonality in both bacterial and eukaryal assemblages, with Archaea forming a negligible part of the urban bio-aerosols. The most abundant bacteria were proteobacteria but community shifts were seen due to increases in algae in summer, and betaproteobacteria and cyanobacteria in winter. This was most parsimoniously explained by considering the backward trajectory analysis of air mass. A greater abundance of marine-associated phylotypes such as Bacillariophyta and Chlorophyta were identified when the dominant air mass arriving in Hong Kong in the summer originated from oceanic sources. In contrast, betaproteobacteria, which indicated soil sources were prevalent when the origin of air mass was from terrestrial sources. A trend in fungal phylotypes was also apparent, with summer samples dominated by basidiomycetous Agaricales, and winter samples by the ascomycete genus Cladosporium. This was likely due to favourable climatic conditions during wetter summer months enhancing release of fungal basidiospores. A range of airborne human pathogens was also detectable at low levels including pathogenic bacteria such as Acinetobacter baumannii, Clostridium perfringens, Escherichia coli O157:H7, and Ricinus communis, and the pathogenic fungus Aspergillus terreus. Microbial allergens including bacterial endotoxins and fungal glucans were also quantified with immunological assays. These generally followed variations in biomass, and during some months were recorded at levels that may impact human health upon chronic exposure. Carbon dioxide levels were the only climatic or pollutant variable that correlated with allergen levels. Conversely changes in microbial assemblages were strongly correlated to several climatic variables including temperature, rainfall, air pressure and relative humidity, but not with the degree of urbanization or airborne pollutants. This study highlights the importance of including microbial assessments in future bio-surveillance of urban aerosols. / published_or_final_version / Biological Sciences / Doctoral / Doctor of Philosophy

Successful preservation of Earth’s biodiversity requires an understanding of the processes that generate new species. The generation of species without gene exchange is considered predominant; however, a growing body of evidence indicates that populations can diverge while exchanging genes, and that this may be common. Previous research hypothesized that blue-footed (Sula nebouxii) and Peruvian (S. variegata) boobies diverged from their common ancestor while exchanging genes. Here, I combine ecological and genetic perspectives to thoroughly evaluate this hypothesis. Using a panel of eight molecular markers, I estimate population differentiation for each species. I find evidence of weak population differentiation for both species, an uncommon pattern in seabirds, and argue that specialization to an unpredictable food resource has shaped contemporary population differentiation. Next, I use molecular markers and morphology to evaluate the hybrid status of five morphologically aberrant individuals. I report that all are likely F1 (first generation) hybrids, and are the product of crosses between female Peruvian boobies and male blue-footed boobies. Sex biases in pairing may occur because of an underlying preference for elaborate courtship displays. I then expand the dataset to 19 loci and use cline theory and Bayesian assignment tests to characterize the hybrid zone, to examine introgression, and to evaluate the hybrid status of the aberrant individuals. The hybrid zone is most likely maintained by strong endogenous and exogenous selection against hybrids and dispersal of parentals into the hybrid zone (a tension zone), and introgression is low for nuclear loci and absent for mitochondrial loci. Finally, I test the hypothesis that this species pair diverged from their common ancestor with gene flow using recently developed analyses and multiple loci. Divergence without gene flow is rejected and unidirectional introgression of sex-linked loci during divergence is reported. The results of this study support the hypotheses that: 1) populations can diverge while exchanging genes; 2) the Z chromosome may play a role in avian speciation; and 3) organisms specialized to variable foraging environments should exhibit low population differentiation. This study adds to our understanding of both population differentiation and speciation in seabirds, and the generation of new species more generally. / Thesis (Ph.D, Biology) -- Queen's University, 2011-04-06 13:55:32.151

Population structure, genetic diversity and social system were investigated in four species of dolphins, thought to present contrasting habitat preferences and social organisation: spinner dolphins, rough-toothed dolphins, long-finned and short-finned pilot whales. To overcome methodological limitations, I combined molecular markers (mitochondrial DNA, -or mtDNA-, and microsatellite loci) and observational data (photo-identification and mass strandings) where possible. Genetic samples were obtained from skin biopsies of free-ranging (n = 243) and stranded (n = 375) dolphins. As with many species of delphinids, spinner dolphins (Stenella longirostris) form communities in which social and reproductive boundaries are poorly understood. In French Polynesia, capture-recapture analyses based on photographs of distinctly marked individuals (DMIs) and microsatellite genotypes (12 loci) indicated a community of about 150 dolphins around Moorea that is relatively closed on a generational time scale. Distinct communities, likely to follow a similar demographic pattern, were observed around neighbouring islands (Tahiti, Raiatea, Huahine and Bora Bora), as indicated by photo-identification data and restricted gene flow (FST = 0.143, n = 154). Surprisingly high levels of insular mtDNA genetic diversity (average pi = 1.44%, suggesting Nef ~ 100,000) contrasted with demographic characteristics of these communities. There was no evidence for a recent bottleneck effect, suggesting that this pattern is the result of metapopulation structure, based on numerous insular communities connected through male and female gene flow. Investigation of the worldwide mtDNA diversity and phylogeography of long-finned and short-finned pilot whale species revealed a complex evolutionary history (Globicephala melas, n = 434; and G. macrorhynchus, n = 134, including published and unpublished sequences). Strong genetic differentiation between long-finned pilot whales from the North Atlantic (G. m. melas) and Southern Hemisphere (G. m. edwardii) indicated severely restricted gene flow, although shared haplotypes suggested some recent contact between the two subspecies. Low genetic distances among haplotypes and a star-like phylogeny suggested a recent worldwide expansion for this species. Higher levels of diversity (although low compared to other cetaceans) were found in short-finned pilot whales, in particular among samples from around Japan. Phylogeographic studies suggested that Japanese samples originate from three distinct populations, one of which could be the ancestral population of the species. Overall, my results confirmed that worldwide mtDNA diversity is low in the two species, probably due to a recent worldwide population expansion and, potentially, to a matrilineal social structure. The molecular ecology of the mass strandings of long-finned pilot whales around New Zealand was investigated to test the hypothesis that individuals stranding together are part of an extended matrilineal group. Analyses of mtDNA sequences indicate that more than one haplotype was found in five of the seven mass strandings investigated (n = 275), demonstrating that groups are sometimes composed of unrelated maternal lineages. This was further supported by analyses of relatedness within and between strandings based on microsatellites (14 loci). These analyses discount kinship as the only factor causing large mass strandings in long-finned pilot whales. Parentage analyses confirmed some aspects of previous studies in the North Atlantic, suggesting a social system with at least some level of male and female philopatry to the maternal group, and infrequent paternities within the group. In a detailed study of a large mass stranding (Stewart Island 2003, n = 122), there was no correlation between position of the whales on the beach and genetic relatedness (based on 20 microsatellite loci), discounting the assumption that kinship bonds are maintained during these traumatic events. This was further supported by the striking separation of stranded mothers and dependant calves. This disruption of kinship bonds could help explain the behavioural distress of stranded individuals and the tendency of many whales to re-strand even after being re-floated. Finally, a study of rough-toothed dolphins (Steno bredanensis) in the Society Archipelago, French Polynesia, provided new insights in the ecology of this poorly-known species. Although traditionally viewed as a pelagic dolphin, analyses supported a pattern of local communities, in some ways similar to spinner dolphins, with fine-scale population genetic structure (FST = 0.60, p < 0.001 based on mtDNA, n = 65) and local fidelity. These communities also showed a low level of mtDNA haplotype diversity (four unique haplotypes at Moorea compared to 18 for spinner dolphins), suggesting the potential influence of a matrilineal social structure similar to long-finned pilot whales.

Population structure, genetic diversity and social system were investigated in four species of dolphins, thought to present contrasting habitat preferences and social organisation: spinner dolphins, rough-toothed dolphins, long-finned and short-finned pilot whales. To overcome methodological limitations, I combined molecular markers (mitochondrial DNA, -or mtDNA-, and microsatellite loci) and observational data (photo-identification and mass strandings) where possible. Genetic samples were obtained from skin biopsies of free-ranging (n = 243) and stranded (n = 375) dolphins. As with many species of delphinids, spinner dolphins (Stenella longirostris) form communities in which social and reproductive boundaries are poorly understood. In French Polynesia, capture-recapture analyses based on photographs of distinctly marked individuals (DMIs) and microsatellite genotypes (12 loci) indicated a community of about 150 dolphins around Moorea that is relatively closed on a generational time scale. Distinct communities, likely to follow a similar demographic pattern, were observed around neighbouring islands (Tahiti, Raiatea, Huahine and Bora Bora), as indicated by photo-identification data and restricted gene flow (FST = 0.143, n = 154). Surprisingly high levels of insular mtDNA genetic diversity (average pi = 1.44%, suggesting Nef ~ 100,000) contrasted with demographic characteristics of these communities. There was no evidence for a recent bottleneck effect, suggesting that this pattern is the result of metapopulation structure, based on numerous insular communities connected through male and female gene flow. Investigation of the worldwide mtDNA diversity and phylogeography of long-finned and short-finned pilot whale species revealed a complex evolutionary history (Globicephala melas, n = 434; and G. macrorhynchus, n = 134, including published and unpublished sequences). Strong genetic differentiation between long-finned pilot whales from the North Atlantic (G. m. melas) and Southern Hemisphere (G. m. edwardii) indicated severely restricted gene flow, although shared haplotypes suggested some recent contact between the two subspecies. Low genetic distances among haplotypes and a star-like phylogeny suggested a recent worldwide expansion for this species. Higher levels of diversity (although low compared to other cetaceans) were found in short-finned pilot whales, in particular among samples from around Japan. Phylogeographic studies suggested that Japanese samples originate from three distinct populations, one of which could be the ancestral population of the species. Overall, my results confirmed that worldwide mtDNA diversity is low in the two species, probably due to a recent worldwide population expansion and, potentially, to a matrilineal social structure. The molecular ecology of the mass strandings of long-finned pilot whales around New Zealand was investigated to test the hypothesis that individuals stranding together are part of an extended matrilineal group. Analyses of mtDNA sequences indicate that more than one haplotype was found in five of the seven mass strandings investigated (n = 275), demonstrating that groups are sometimes composed of unrelated maternal lineages. This was further supported by analyses of relatedness within and between strandings based on microsatellites (14 loci). These analyses discount kinship as the only factor causing large mass strandings in long-finned pilot whales. Parentage analyses confirmed some aspects of previous studies in the North Atlantic, suggesting a social system with at least some level of male and female philopatry to the maternal group, and infrequent paternities within the group. In a detailed study of a large mass stranding (Stewart Island 2003, n = 122), there was no correlation between position of the whales on the beach and genetic relatedness (based on 20 microsatellite loci), discounting the assumption that kinship bonds are maintained during these traumatic events. This was further supported by the striking separation of stranded mothers and dependant calves. This disruption of kinship bonds could help explain the behavioural distress of stranded individuals and the tendency of many whales to re-strand even after being re-floated. Finally, a study of rough-toothed dolphins (Steno bredanensis) in the Society Archipelago, French Polynesia, provided new insights in the ecology of this poorly-known species. Although traditionally viewed as a pelagic dolphin, analyses supported a pattern of local communities, in some ways similar to spinner dolphins, with fine-scale population genetic structure (FST = 0.60, p < 0.001 based on mtDNA, n = 65) and local fidelity. These communities also showed a low level of mtDNA haplotype diversity (four unique haplotypes at Moorea compared to 18 for spinner dolphins), suggesting the potential influence of a matrilineal social structure similar to long-finned pilot whales.