This study identified 12 <i>HLA-DQB1</i> alleles and investigated reproduction and health of 44 non-consanguineous (NC) and 36 consanguineous (C) families in Bangladesh. Hair or buccal cell (mouthwash) samples, socio-demographic, reproduction and health information were collected from families. Allele identification was achieved for 336 individuals. Socio-demographic differences between NC and C families included dissimilar paternal occupations, uncertainty of offspring birth dataset/ages and marriage dates, and occurrences of first maternal menses. Parental consanguinity did not affect general health and reproduction in this community. Patrilineal consanguinity may also be a tradition in this community. Therefore, generational consanguinity may have previously purged deleterious HLA alleles from the gene pool. Bangladeshis did not preferentially choose mates with dissimilar <i>HLA-DQB1</i> alleles. Neither parental HLA-DQB1 sharing nor particular alleles were associated with pregnancy loss, stillbirths or offspring mortality. However, an excess of homozygous offspring was detected compared to Mendelian segregation ratios by mating type. This excess may be a consequence of purging deleterious alleles from the gene pool, limited effects of HLA-DQB1 on fitness, assaying small groups and/or low population pathogen loads. Deviations from Hardy Weinberg Equilibrium were detected in NC and C groups and could be due to selection, genetic drift, non-random mating, illegitimate offspring production and/or a consequence of small sample size. A reduction of allelic diversity was observed in C families. Although <i>HLA-DQB1</i> alleles were not associated with most diseases, <i>HLA-DQB1*030302, *060101, *0602 </i>and <i>*0603 </i>were associated with malaria resistance. Genome homozygosity may affect human health and reproduction over time, since decreases in genetic diversity over generations of close-kin marriage may reduce a population’s potential to adapt to future changes in their environment.

By studying the patterns of nucleotide variation in conserved non-coding (CNC) sequences in comparison to coding and non-coding regions of the genome, I demonstrated that not only coding sequence but also CNC sequences have been under active selective constraint in humans. I identified a subset of CNC sequences with a significantly accelerated nucleotide substitution rate in the human lineage (relative to chimpanzee) by comparing whole genome alignments of human, chimpanzee and macaque. SNPs within these ‘accelerated CNCs’ (or ANCs) have a significant excess of high frequency derived alleles and high FST values relative to control CNC sequences, indicating that accelerated sequence evolution and positive selection is recent in human populations. ANC sequences are also enriched within the most recent segmental duplications, suggesting recent changes in selective constraint following duplication. A substantial number of SNPs within ANC sequences (34%) are associated with changes in gene expression phenotypes. This analysis suggests ANC sequences have played, and still play, a role in human evolution – potentially through changes in gene regulation. I designed and validated a paralog-specific gene expression array to array the expression of recent human paralogs in diverse human tissues. I then analysed this novel dataset to investigate the influence of the mode of duplication on the patterns of differential expression, and attempted to reconcile the observed patterns with those of the predicted models of paralog fates.

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Is bacterial evolution phylogenetic or reticulate? Darwin showed that life's history W;J.S mappable with trees. For almost everytfillg that we can see about us, this is largely correct, but beyond the limit of our sight thrives the unseen majority: The tiny, singlecelled prokaryotes do not reserve their genes only for the next generation. Through lateral gene transfer they swap genes with contemporaries, regardless of species. Discovered in the war years, the true place of lateral gene transfer within evolution has not yet been settled. As work on it.has multiplied, so its apparent extent has grown. Here a reappraisal of lateral gene transfer is carried out. The methods of its detection are examined and refined. The ~sults show that lateral transfer is not nearly so prevalent as some say. Less frequent, but still important, lateral gene transfer is shown to be a key mover in the evolution of the entire eukaryote domain. Its effect on individual genes, how it can increase rates of evolution and even trigger 'positive selection regimes, is exposed. The interconnectivity of species is then explored. Species that are the source of many genes receive many. Species that receive lots of genes through lateral transfer hold fewer unique genes. In addition, it is as if all species are connected through a massive network of lateral transfers. But any new information must be placed in its proper context: lateral gene transfer is only one of evolution's tools. Convergent evolution is exposed as a problem, both when trying to detect lateral transfer and perhaps also when constructing phylogenies. For all our problems with bacterial phylogenies, with building and interpreting them, the lesson of lateral gene transfer is that we can have faith in the idea of bacterial species and, after almost a hundred and fifty years, in Darwin too.

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This thesis addresses two questions of fundamental importance to evolutionary ecology - how genetic variation in traits that affect interactions between and within species are maintained within populations, and how such variation .affects patterns of intra- and interspecific interactions in the field. In chapter one, I,review the evidence concerning these issues. I also introduce the pea aphid Acyrthosiphon pisum Harris (Homoptera: Aphididae) - natural enemy model system used in the following experimental chapters. In chapter two, I describe a field experiment that illustrates how pea aphid clonal variation can affect natural enemy recruitment and community structure. The major predator in this system is the hoverfly Episyrphus balteatus De Geer (Diptera: Syrphidae). I measured the costs of parasitoid attack in E. balteatus (chapter three), finding that parasitized E. balteatus consumed fewer aphids, took longer to pupate and experienced higher pupal mortality, and flies that survived attack had reduced life spans. Chapter four describes a series of experiments that test whether a trade-off between competitive ability and dispersal ability could maintain clonal variatiqn in these traits among clones of the pea aphid. Significant clonal variation was detected for interspecific competitive ability, lifetime fecundity and dispersal ability. Lifetime fecundity was found to correlate positively. with the production of winged offspring. Chapter five describes an experiment in which we tested whether the variation in interspecific competitive ability detected in the laboratory (chapter four) could alter the outcome of interspecific competition in the field. In the laboratory the pea aphid populations were always larger than populations of a single clone of the vetch aphid M~,.oura viciae Buckton (Homoptera: Aphididae), but in the field the outcome of interspecific competition depended on pea aphid genotype. Chapter six describes a field experiment that measured the effects of competition and predation on the population dynamics of two clones of the pea aphid. Both clones did equally well in monoclonal colonies, while in mixed colonies one clone was competitively superior. The strength of predation depended on aphid density. One clone did better when sharing a patcli, but not a plant, with the second clone compared with when sharing a patch with a second colony of the same clone (apparent mutualism). In chapte'r seven, I review the principal results of these experiments and discuss how these new insights fit into the wider evolutionary and applied ecological literature.

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