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The canine transmissible venereal tumour (CTVT) is a contagious cancer that is naturally transmitted between dogs by the allogeneic transfer of living cancer cells during coitus. CTVT first arose several thousand years ago and has been reported in dog populations worldwide. The goals of this Thesis were (1) to gain further understanding of CTVT distribution patterns and prevalence around the world, (2) to use genetics to trace the historical spread of CTVT and (3) to map the genetic as well as phenotypic diversity of CTVT tumours around the world. To understand the distribution patterns of CTVT, I obtained information from 645 veterinarians and animal health workers in 109 countries, and generated a snapshot of the locations in which this disease is found. Additionally, as preparation for further genetic analysis, I collected samples from over one thousand CTVT cases from more than 50 countries, optimised methods for high-throughput DNA extraction and quantification and optimised a qPCR-based assay for CTVT diagnosis and host contamination detection. With the goal of tracing the historical spread of CTVT and learning about the genetic diversity of this disease, I sequenced complete mitochondrial genomes of 449 CTVT tumours and their matched hosts. The analysis of the CTVT mitochondrial diversity revealed that CTVT has captured mitochondrial DNA (mtDNA) through horizontal transfer events at least five times during the history of the lineage, delineating five tumour clades. CTVT appears to have spread rapidly around the world within the last 2,000 years, perhaps transported by dogs travelling along historic maritime trade routes. This work indicated that negative selection has operated to prevent accumulation of deleterious mutations in captured mtDNA, and that recombination has caused occasional mtDNA re-assortment. A histology-based screen of CTVT clades did not show any significant phenotypic differences between groups. In order to determine how the five mtDNA clades relate to each other, I analysed data from 539 CTVT exomes. This revealed that a single canine mtDNA haplogroup has recurrently and recently undergone multiple horizontal transfer events. Analysis of this haplotype highlighted a number of candidate genetic variants which may be conferring a selective advantage to this haplotype in CTVT, possibly by influencing mtDNA transcription or replication. Overall, genetic and phenotypic analysis of CTVT tumours from across the globe has broadened our understanding of CTVT diversity, and provided important insights into the biology of a unique transmissible cancer.

Beaked whales are comparatively unknown social mammals due to their deep-ocean distribution and elusive habits. The deep-ocean is the largest biome on Earth and the final frontier for human expansion. Since their first discovery, beaked whales have remained largely hidden from science. In this era of rapid technological advancement, genetic and genomic methods are key tools for population biologists and are particularly useful in describing rarely seen species. Using DNA-barcoding and nuclear markers, the publications in this thesis provide data on the distribution and external appearance of two species of beaked whale: the spade-toothed (Mesoplodon traversii) and Derinayagala’s whale (Mesoplodon hotaula). These whales were previously known from only a handful of tissue and bone specimens. Long-term efforts have facilitated the collection of samples of Gray’s beaked whale (Mesoplodon grayi) and we have used shot-gun sequencing to characterise the mitochondrial genome and isolate species-specific nuclear microsatellite loci. Using genetic species and sex identification, together with museum specimens and multivariate analyses, we provide clear evidence of sexual dimorphism in cranial dimensions and geographic variation in external morphology. No genetic differentiation was evident in Gray’s beaked whales across a large study area (~ 6,000 km). With a large female effective population size (Ne) and genetic homogeneity, we hypothesise that gene flow is facilitated by large-scale oceanographic features, such as the sub-tropical convergence. Genetic kinship analyses within Gray’s beaked whale groups suggest that the whales that strand together are not related. Both sexes disperse from their parents and these groups are not formed through the retention of kin. These results are consistent with a ‘fission-fusion’ social system that has been observed in some oceanic dolphin species. Taken together, these data provide the first insights into the population dynamics, dispersal and social organisation in Gray’s beaked whales. These publications highlight the value of using genetics alongside other techniques to describe inter- and intraspecific diversity. For beaked whales, the dead can tell us much about the living.

Immune activation is generally acknowledged to be costly. These costs are frequently assumed to result from trade-offs arising due to the reallocation of resources from other life-history traits to be invested in immunity. Here, I investigated the energetic basis of the costs associated with immune activation in Drosophila melanogaster. I found that immune activation significantly reduced fly fecundity (45%) and also caused a decline in metabolic rate (6%) but had no effect on body weight. To understand the factors behind reduced fecundity and metabolic rate I measured feeding and found that food intake was reduced by almost 31% in immune-challenged D. melanogaster. These findings suggest that fecundity costs of immune activation result not from the commonly accepted resource reallocation hypothesis but probably because resource acquisition is impaired during immune responses. The individuals of any animal population generally vary greatly in their ability to resist infectious disease. This variation arises due to both environmental heterogeneity and genetic diversity. Genetic variation in disease susceptibility has generally been considered to lie in the nuclear genome. Here, for the first time, I explored the influence of mitochondrial genetic (mtDNA) variation on disease susceptibility. I crossed 22 mitochondrial haplotypes onto a single nuclear genome and also studied epistasis interactions between mitochondrial and nuclear genomes (mitonuclear epistasis) by crossing five haplotypes onto five different genetic backgrounds. I found that fly susceptibility to Serratia marcescens was influenced significantly by mtDNA allelic variation. Furthermore, the effect of mitonuclear epistasis on fly susceptibility to S. marcescens was twice as great as the individual effects of either mitochondrial or nuclear genome. However, susceptibility to Beauveria bassiana was not affected by mtDNA allelic variation. These findings suggest the mitochondrial genome may play an important role in host-parasite coevolution. The Mother’s Curse hypothesis suggests that sex-specific selection due to maternal mitochondrial inheritance means that mitochondria are poorly adapted to function in males, resulting in impaired male fitness. Mother’s Curse effects have previously only been studied for two phenotypic traits (sperm-infertility and ageing) and their generality for broader life-history has not been explored. I investigated the impact of mtDNA allelic variation on 10 phenotypic traits and tested whether the patterns of phenotypic variation in males and females conformed to the expectations of the Mother’s Curse hypothesis. I found that seven of the 10 traits were significantly influenced by mtDNA allelic variation. However, there was no evidence that the effects of this variation differed between males and females. I therefore concluded that Mother’s Curse is unlikely to be a general phenomenon, nor to provide a general explanation for sexual dimorphism in life-history traits. Overall, this thesis explored the impacts of immunity costs, mitochondrial genetic variation, mitonuclear epistasis and sex-specific mitochondrial selection on D. melanogaster life-history.

Contemporary and historical changes in marine environmental conditions influence biodiversity drastically. In marine invertebrates with highly dispersive planktonic larvae, diversification is facilitated or constrained by tectonic plate movements altering geography, prevailing current patterns, and climate. The decapod crustacean infraorder Achelata, which contains the spiny (fam. Palinuridae) and slipper (fam. Scyllaridae) lobsters, is characterized by a long-lived phyllosoma larvae stage. Panulirus is the most economically significant and speciose genus of spiny lobsters, with 20 recognized extant species and 5 subspecies distributed throughout shallow tropical and subtropical oceans worldwide. Diversification within these lineages has been proposed to be primarily driven by geological changes causing dispersal and vicariance events that affect population distribution and influence the settlement and dispersal potential of long-lived larvae by oceanic currents. To reveal phylogenetic relationships within the Achelata, maximum likelihood (ML) and Bayesian inference (BI) morphological and molecular phylogenies were constructed. Next, a historical biogeographic scenario for the Achelata was modeled on the time-calibrated molecular ML phylogeny. The Achelata and the Palinuridae emerged in the Tethys during the Triassic epoch. After the ancestor of Panulirus diverged during the late Jurassic (~161 Mya), Panulirus Lineages 1 and 2 originated in the Western and Indo-Pacific during the early (~133 Mya) and late (~85 Mya) Cretaceous. The genus Panulirus experienced the most diversification during the Eocene (~52 Mya), then continued to diversify until the Pliocene (~3 Mya), with the greatest concentration of Panulirus ancestral species existing in the Indo-West Pacific. Ultimately, Panulirus diversification occurred due to global dispersal and vicariance events from the late Jurassic to the Pliocene. As Panulirus species and populations diverged in response to geographic change over time, they colonized habitats with variable environmental conditions and different selective pressures. Regional environmental conditions are known to drive the evolution of morphological, behavioral, and physiological traits in marine crustaceans. Therefore, the Achelata were also expected to respond to selective pressures on a molecular scale. As such, environmental conditions are expected to prompt the adaptive evolution of mitochondrial protein-coding genes (PCGs), which are vital for energy production via the oxidative phosphorylation pathway. I examined the effect of temperature and low oxygen on the adaptive evolution of mitochondrial PCGs. In the Achelata, mitochondrial PCGs exhibited a strong negative selection background. Signatures of positive selective pressure were detected in mitochondrial PCGs in equatorial Panulirus spp. inhabiting tropical equatorial regions with relatively consistent high temperatures and in deepwater Scyllaridae inhabiting low-oxygen depths. These results suggest that, following the initial diversification of Panulirus spp. temperature and oxygen levels have influenced the evolution of the 13 mitochondrial PCGs in equatorial Panulirus spp. and deepwater Scyllaridae. In general, this study has demonstrated how environmental conditions drive diversification as well as the adaptive evolution of mitochondrial PCGs in the Achelata.

Taxonomic changes are made based on checkered beetle (Coleoptera: Cleridae) types of the Natural History Museum, London (BMNH).Lectotypes are designated (and holotypes and paralectotypes recognized) for 44 species of Hydnocerinae, including the type species for Isolemidia, Parmius, Paupris, Allelidea, Blaesiopthalmus and Lemidia, four species of Enoclerus (Clerinae), and 14 species of Cymatodera (Tillinae). Annotations include comments on additional type material, new type locality, previous (type series) locality, and questionable or missing types. Phyllobaenus pallipes(Gorham) and P. rufithorax (Gorham) are synonymized with P. flavifemoratus(Gorham), P. chapini (Wolcott) is synonymized under P. lateralis (Gorham), and P. villosus (Schenkling) is synonymized under P. longus (LeConte), new synonymies. The first molecular phylogeny of the clerid lineage (Coleoptera: Cleridae, Thanerocleridae) is presented and compared with the two most recent phylogenetic hypotheses of the group. Phylogenetic relationships of checkered beetles wareere inferred from approximately 5,000 nucleotides amplified from four loci (28S, 16S, 12S, COI). A worldwide sample of ~70 genera is included and phylogenies are reconstructed using Bayesian Inference and Maximum Likelihood. The results are not entirely congruent with either of the current classification systems. Three major lineages are recognized. Tillinae are supported as the sister group to all other subfamilies, whereas Thaneroclerinae, Korynetinae sensu latu and a new subfamily formally described here, Epiclininae, new subfamily, form a sister group to Clerinae + Hydnocerinae. To assess the phylogeny and evolution of Hemiptera, a comprehensive mitogenomic analysis integrating mitogenome-based molecular phylogenetics, fossil-calibrated divergence dating (using BEAST), and ancestral state reconstructions are presented. The 81 sampled mitogenomes represent the most extensive mitogenomic analyses of Hemiptera to date. The putatively primitive “Homoptera” was previously rendered paraphyletic by Heteroptera, whereas the presented results support each group as monophyletic. The results from both diet and habitat ancestral state reconstructions support that 1) Heteroptera (and Homoptera) evolved from a phytophagous ancestor, contrary to the popular hypothesis that the ancestor was predaceous; and 2) family-level radiation of Heteroptera is coincident with the apically-produced labium and the novel hemelytron. It is here proposed these morphological innovations facilitated multiple independent shifts from phytophagy to predation and multiple independent colonizations of aquatic habitats.

In spite of significant progress in our knowledge of mechanisms that control blood pressure, our understanding of the pathogenesis of hypertension, its genetics, and population efforts to control blood pressure, hypertension remains the leading risk factor for mortality worldwide. It’s estimated that 1 out of every 3 adults has hypertension. Hypertension is a major risk factor for cardiovascular disease and stroke, and is considered a primary or contributing cause of death to more than 2.4 million US deaths each year. Although spontaneous hypertension has been the subject of substantial research, many critical questions remain unanswered. To investigate mechanisms underlying spontaneous hypertension, a unique rodent breeding approach was used to isolate nuclear and mitochondrial genes contributing to the disease. By diluting the nuclear genome of the Spontaneously Hypertensive Rat on a normotensive Brown Norway background while maintaining the SHR mitochondrial genome, I investigated both intrinsic and extrinsic mechanisms of the kidney and its relationship to hypertension. Chapter 2 documents the dominance of the hypertensive phenotype in our rodent colony, despite the dilution of the nuclear genome of the SHR. Chapter 3 presents data indicating that the renin-angiotensin system, particularly the location and abundance of the AT1 receptor may play an important role in the manifestation of spontaneous hypertension. Chapter 4 presents that rats in our rodent colony exhibited normal pressure-natriuresis and kidney function; however, hypertensive rats had a reduced ability to sense orally ingested sodium chloride, thus necessitating chronic elevations of arterial pressure in order to maintain sodium balance. This chronic pressure-natriuresis relationship shifts the renal function curve to the right, thus sustaining elevated blood pressure. Chapter 5 presents data that genes important for oxidative phosphorylation may play a critical role in the development of hypertension. Both nuclear and mitochondrial oxidative phosphorylation genes were downregulated in hypertensive rats compared with normotensive rats. Data presented in every chapter highlights the importance of the kidney in the pathogenesis of hypertension. Humoral, genetic and genomic mechanisms of the kidney appear to play a dominant role in the development and maintenance of the disease.

Pupillid land snails (Family Pupillidae) are small (

Mitochondria act as the cell’s powerhouse for aerobic energy production. Mitochondria carry their own genetic material (mtDNA), which is maternally inherited and has a high mutation rate. Hence the mtDNA is an ideal genetic tool to trace human evolution and migrations, and a candidate for somatic mutation studies in cancer. These aspects of mitochondrial genetics form the two main foci of this thesis. Southern Africa is known to encompass the world’s greatest genomic diversity, and genetic, anthropological, and archaeological studies support the region as a candidate for the origin of modern humans. In summary, this study used mitochondrial genomes to identify great maternal diversity in the Southern Bantu. Haplogroup distributions in each population suggest a migration route from the Bantu homeland in Western Africa, across Central Africa to the Eastern Great Lakes region, and down the Eastern side of Southern Africa, absorbing indigenous Khoesan lineages to their present day home resulting in the Southern Bantu of today. This study also identified new mtDNA haplogroups, many of which are among the earliest diverging lineages. This study contributes to the global mitochondrial haplogroup diversity knowledge bank. The role of mitochondrial genetic mutations was studied in the context of altered metabolism in cancer, where biosynthesis and maintenance of redox capacity is favoured over energy production via oxidative phosphorylation in tumour cells. 24 somatic mutations were identified in the mitochondrial genomes of 12 patient-derived pancreatic cancer tumour cell lines, most of which were nonsynonymous and located in coding regions for electron transport chain (ETC) subunits or important control regions, in addition to another 18 mutations in nuclear genes predicted to have important mitochondrial or metabolic function. Additionally, significant variation was observed in metabolic phenotype between normal pancreatic cells and tumour cells, including decreased oxygen consumption in tumours, altered metabolomic profiles with an upregulation in biosynthetic pathways such as fatty acid synthesis in tumour cells, and reduced expression of various mitochondrial electron transport chain subunits in tumours. These findings may inform development of new therapeutic strategies targeting these pathways.

The relationship among oxidative stress, mitochondrial DNA integrity, and longevity continues to be without a general consensus. Here, we hypothesize that short- and long-lived birds, including the budgerigar (Melopsittacus undulatus), guineafowl (Numida meleagris), quail (Corturnix japonica), and turkey (Meleagris gallopavo) differ in oxidative stress measured by blood markers and that this difference correlates with mitochondrial genomic integrity both within and among species. In preliminary studies and to establish a reference and standard for the search for single nucleotide polymorphisms (SNPs), we used a combination of experimental and in silico tools for genome analysis to screen selected regions of the chicken (Gallus gallus) mitochondrial genome (mtGenome) for SNPs. A total of 113 SNPs was identified which formed 17 haplotypes. The length of the turkey mtGenome sequence developed was 16,967 bp in length, while that of the budgie was 18,193 bp. Annotation of both sequences revealed a total of 13 genes and 24 RNA (22 tRNA and 2 rRNA). Within the budgie mtGenome sequence, a duplicated control region was observed, and there was an additional nucleotide in the NADH dehydrogenase subunit 3 sequence of both the turkey and budgie. The total number of SNPs within the D-loop and 16S rRNA in each of the four species ranged from zero in the quail to 22 in the budgie. The new mtGenome sequences revealed that the turkey was most closely related to the chicken and quail, and the budgie was closest to kakabo (Strigops habroptilus). Oxidative stress, estimated by biomarkers thiobarbiturate acid reacting substance (TBARS), plasma uric acid (PUA), and glutathione (GSH) and at 10, 30, 55, and 80 wks-of-age within each species, was not consistent. The level of GSH was highest in guineafowl, but lowest in budgie. While PUA, an antioxidant, exhibited a significantly (P

The transformation of genomic data into functionally relevant information about the composition of biological systems hinges critically on the field of computational genome biology, at the core of which lies comparative genomics. The aim of comparative genomics is to extract meaningful functional information from the differences and similarities observed across genomes of different organisms. We develop and test a novel framework for applying complex models of nucleotide evolution to solve phylogenetic and comparative genomic problems, and demonstrate that these techniques are crucial for accurate comparative evolutionary inferences. Additionally, we conduct an exploratory study using vertebrate mitochondrial genomes as a model to identify the reciprocal influences that genome structure, nucleotide evolution, and multi-level molecular function may have on one another. Collectively this work represents a significant and novel contribution to accurately modeling and characterizing patterns of nucleotide evolution, a contribution that enables the enhanced detection of patterns of genealogical relationships, selection, and function in comparative genomic datasets. Our work with entire mitochondrial genomes highlights a coordinated evolutionary shift that simultaneously altered genome architecture, replication, nucleotide evolution and molecular function (of proteins, RNAs, and the genome itself). Current research in computational biology, including the advances included in this dissertation, continue to close the gap that impedes the transformation of genomic data into powerful tools for the analysis and understanding of biological systems function.

Studying patterns of nucleotide substitution rates at multiple loci can help provide clues to the evolution and function of genes. The computational drawback of the maximum likelihood version of relative ratio tests becomes a concern when a large number of pairwise comparisons are performed among multiple genes. We propose a new version of relative ratio test, including four procedures, based on the use of pairwise sequence distances. The first is based on ANOVA two-way model and allows covariances between branch lengths. The second method applies generalized estimation equations (GEEs) to Poisson regression in a log-linear model. The third one is a nonparametric approach based on bootstrap percentile confidence intervals. The fourth method is based on weighted least squares estimation with covariances. Simulation studies have been conducted to compare Type I errors and powers between the likelihood version of test and the first three proposed methods. The formula have been derived for the last method as well as the numerical steps. The ANOVA-based method is the least computationally expensive and it has desirable Type I errors in most cases as well as good powers. The bootstrap-based method is the slowest among the four methods, but with smallest Type I errors and powers similar to the ANOVA-based method. The Likelihood-based method is the second slowest and has more desirable Type I errors than those of the ANOVA-based method, but has less powers than the ANOVA-based method. The GEE-based method is suitable only for very long genes, but has good statistical properties. The ANOVA-based method is applied to mtDNA sequences from a broad range of animal mitochondrial genomes. The results indicate that it is uncommon that branch lengths are conserved well among animal mitochondrial genes.