Genetic differentiation and immunogenetics of two sympatric storm petrel species on the Azores

This thesis investigates genetic differentiation, mate choice and immunogenetics in two recently diverged species of storm petrels breeding on the Azores – the geographically widespread H. castro and the Azores endemic H. monteiroi. Previous work found the two species largely distinct for mitochondrial and nuclear loci, but the degree of reproductive isolation or breeding time switching between the two seasonally separated taxa remains unclear. In chapter 2, a method for rapid and cost-effective screening for mitochondrial clade membership was developed, tested, and applied to both species. The method did not reveal any mismatches between presumed sample identity and mitochondrial clade, but future application may do so, allowing further investigation of the biology and genomics underlying mismatches. In chapter 3, a method for PCR amplification of Major Histocompatibility Complex (MHC) DAB loci was developed, demonstrating the retention of an ancient duplication of the MHC Class IIB region in both species. In chapter 4, this method was used for high-throughput sequencing of family trios from both species. A bioinformatic allele filtering pipeline was developed, revealing 65 DAB1 and 27 DAB2 alleles across both species (individuals for DAB1/DAB2: H. castro n=111/110; H. monteiroi n= 99/91). DAB1 was more variable than DAB2 within each species, and the ‘vulnerable’ Azores endemic H. monteiroi was found to exhibit similar immunogenetic variability as H. castro, suggesting that variability has been retained despite recent declines in H. monteiroi. Extensive signals of incomplete lineage sorting were found for DAB alleles of both species, likely reflecting balancing selection and their recent speciation. Nevertheless, DAB allele sharing between the two was limited, and multi-locus analyses found them to be clearly differentiated for MHC genotypes. This thesis contributes valuable molecular insights into the ecology and evolutionary history of H. castro and H. monteiroi, including a comprehensive characterisation of their immunogenetic variability and differentiation

High rates of infection by blood parasites during the nestling phase in UK Columbids with notes on ecological associations

Studies of blood parasite infection in nestling birds rarely find a high prevalence of infection. This is likely due to a combination of short nestling periods (limiting the age at which nestlings can be sampled) and long parasite prepatent periods before gametocytes can be detected in peripheral blood. Here we examine rates of blood parasite infection in nestlings from three Columbid species in the UK. We use this system to address two key hypotheses in the epidemiology of avian haemoparasites: first, that nestlings in open nests have a higher prevalence of infection; and second, that nestlings sampled at 14 days old have a higher apparent infection rate than those sampled at 7 days old. Open-nesting individuals had a 54% infection rate compared with 25% for box-nesters, probably due to an increased exposure of open-nesting species to dipteran vectors. Nestlings sampled at 14 days had a 68% infection rate compared with 32% in nestlings sampled at 7 days, suggesting that rates of infection in the nest are high. Further work should examine nestlings post-fledging to identify rates of successful parasite infection (as opposed to abortive development within a dead-end host) as well as impacts on host post-fledging survival and behaviour

Non-cultured faecal and gastrointestinal seed samples fail to detect Trichomonad infection in clinically and sub-clinically infected columbid birds

Trichomonosis, caused by the protozoan Trichomonas gallinae, is an emerging infectious disease in finches, and is more commonly found in columbids and raptors. Infections can be sub-clinical or cause morbidity and mortality, but the parasite is currently only detectable by incubation of an oral swab. Here, we test whether T. gallinae parasites can be detected by PCR from faecal or non-cultured samples from the oral cavity and gastrointestinal tract of infected Turtle Doves (Streptopelia turtur). PCR did not detect T. gallinae parasites in any faecal samples screened, and in only 1 of 11 oral / gastrointestinal samples (from the mouth of a nestling suspected to have died from trichomonosis). We conclude that both oral swabs and parasite culture are still necessary to detect the sub-clinical presence of T. gallinae infection in birds

Search for Higgs and ZZ Boson Decays to J/ψγJ/\psi\gamma and Υ(nS)γ\Upsilon(nS)\gamma with the ATLAS Detector

A search for the decays of the Higgs and $Z$ bosons to $J/\psi\gamma$ and $\Upsilon(nS)\gamma$ ($n=1,2,3$) is performed with $pp$ collision data samples corresponding to integrated luminosities of up to $20.3\mathrm{fb}^{-1}$ collected at $\sqrt{s}=8\mathrm{TeV}$ with the ATLAS detector at the CERN Large Hadron Collider. No significant excess of events is observed above expected backgrounds and 95% CL upper limits are placed on the branching fractions. In the $J/\psi\gamma$ final state the limits are $1.5\times10^{-3}$ and $2.6\times10^{-6}$ for the Higgs and $Z$ bosons, respectively, while in the $\Upsilon(1S,2S,3S)\,\gamma$ final states the limits are $(1.3,1.9,1.3)\times10^{-3}$ and $(3.4,6.5,5.4)\times10^{-6}$, respectively