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The reduction of natural populations is a major conservation problem and the main cause of increased extinction risk. I investigated conservation issues that limit the growth of the pink pigeon population, including infection with Trichomonas gallinae, biased sex ratios and the reduction in both reproductive fitness and life history traits. In particular, I examined the association between these issues in the pink pigeon and genome-wide genetic variation using 45,841 single nucleotide polymorphisms (SNPs) generated using restriction site associated DNA sequencing (RAD-seq). The average observed and expected heterozygosity (Ho and He respectively) were low, at 0.27 and 0.28 respectively. Rapid genetic loss has increased inbreeding depression in the population. The effective population size was found to be particularly small in one subpopulation, Ile aux Aigrettes. Examining genome-wide heterozygosity for both immune and non-immune genes between males and females showed that males have a higher level of gene variation than females, which may explain the male-biased sex ratio in fledglings that this study found to be significant. A significant negative association was found between genome-wide heterozygosity and infection with Trichomonas gallinae. The longevity and body weight of adult birds and fledgling success showed a significant positive relationship with the level of genome-wide heterozygosity. Reproductive success, in terms of the number of nests, eggs laid and hatched young that died before fledging, did not show any significant relationship with the level of genome-wide heterozygosity. However, using genome-wide association studies (GWAS), this study identified a genomic region close to the progesterone receptor gene (PRG) that potential affects egg-laying in the pink pigeon. The findings of this thesis suggest an association between the problems limiting the growth of the pink pigeon population and a reduction in genome-wide variation, suggesting that the pink pigeon may be entering a vortex that may drive the species to extinction and thus emphasising the urgent need for conservation management to avoid its extinction.

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This thesis describes studies on the epidemiology of the avian influenza virus (AIV) and other respiratory viruses such as Newcastle disease (NDV), infectious bronchitis (IBV) and avian metapneumovirus (aMPV) in backyard poultry in Oman. Also, I utilized backyard birds as sentinels to detect the presence of West Nile virus (WNV) in Oman backyard poultry. Additionally, I tried to investigate the risk factors contributing to the spatial distribution of AIV and NDV diseases in backyard poultry farms. Management biosecurity and health programmes in commercial broiler poultry farms were also examined. Chapter 3 reviews the epidemiology of the viral respiratory diseases affecting poultry in the Middle East (ME) in relation to diseases reported in Oman. The review was undertaken to identify knowledge gaps. The review focused more on the highly pathogenic avian influenza H5N1 outbreak in the ME since most of the published poultry articles were on this virus. There was a clear gap in the knowledge on the epidemiology of respiratory viral pathogens except for H5N1. Chapter 4 describe a sero-surveillance study on backyard poultry flocks in Oman. A snapshot two-stage cluster sampling was done during the summer of 2012 on 2350 backyard poultry birds from 238 farms from all of the Oman’s regions and governorates. The dominant poultry species in the visited farms was the chickens; however, ducks, turkeys, geese and guinea fowls were present and sampled. The overall seroprevalence of the avian influenza and Newcastle disease viruses were 37.5% and 42.1%, respectively, and the flock’s positive level was 84% and 90.2%, respectively. The mean within-flock seroprevalences were 37.6% and 43.4%. All the PCR results were negative for NDV and AIV. In conclusion, both disease viruses are endemic in the backyard poultry in Oman. Chapter 5 studies the risk factors associated with the intensity of the infection of both avian influenza and Newcastle disease in Omani backyard farms (serological results from chapter 4). A number of previous studies have investigated and identified a number of risk factors for both diseases, especially the highly pathogenic avian influenza. I obtained the risk factors that are present in Oman from those previously identified and modelled their association with the intensity of the AIV and NDV infection in Omani backyard flocks using general linear models (GLM). There was a regional effect on the level of exposure to both viruses; however there was no North-South pattern. Also, there was a highly significant association between the presence of AIV and NDV infection which may be attributed to the level of biosecurity applied in the farms. Furthermore; there was a negative association between the farm altitude and the AIV intensity of infection. The flock size was marginally negatively associated with the NDV infection rate. Chapter 6 describes a study on the prevalence of IBV and aMPV using molecular methods including RT-PCR, sequencing and phylogenetic analysis from the same sampled backyard flocks. Five flocks from the northern regions were positive for aMPV subtype B and 39 flocks were positive for 5 different genotypes of the IBV virus. The 793B like was the most prominent genotype. However, genotypes M41, IS885, IS94 and D274 were also identified. The presence of the IBV viral genome in the FTA card collected from ducks and turkeys raises the question of their role in IBV epidemiology. The study concluded that both viruses are endemic in Oman backyard poultry. Chapter 7 describes a study of the serological prevalence of the West Nile virus using backyard birds as sentinels. The sera from backyard birds were used for the detection of antibodies against WNV. The total flock prevalence was 45% and the total bird prevalence was 21%. All the tested bird species showed positive ELISA results. Later a snapshot mosquito sampling was done in 16 of the previously identified WNV positive farms. The mosquito species recorded on WN positive farms were Culex quinquefasciatus, a known vector of WNV, and Anopheles stephensii, a malaria vector. The study concluded that WNV is endemic in backyard poultry in Oman. Management, biosecurity and health practices are the core of poultry farming success and the main defence against the introduction of diseases to the farm, as well as dissemination between farms. Chapter 8 describes the management and health practices applied in commercial poultry production farms in Oman. A questionnaire designed to investigate the management, biosecurity and health practices in broiler production poultry farms was filled in by Ministry of Agriculture and Fisheries animal production engineers for 69 broiler poultry farms. These 69 broiler farms produce around 95% of the poultry meat produced in Oman. The Southern region Dhofar governorate, has the highest reported number of birds, nearly 20 million, which makes up almost (82%) of the responding broiler production farms. The majority of the farms use closed houses with evaporating/cooling fans and cooling beds (46/69, 66.7%). All farms vaccinate against Newcastle disease. infectious bursal disease (IBD), avian influenza virus H9N2, avian infectious bronchitis and aMPV were also been reported in vaccination programs with different percentages. The bigger farms apply better biosecurity measures and their managers have better knowledge. Medium and small farms vary greatly in their application of biosecurity measures.

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The oxygen requirements of the chick embryo have been found to increase by at least 100% during hatching. This rise is probably a result of ventilating the newly functioning lungs and maintaining the body temperature at its pre-hatching level. Sustained homeothermic responses become evident only at the moment of escape the shell membranes. There are two essential phenomena in the termination of the embryonic existence. The first is the initiation of pulmonary respiration which appears to result from a high partial pressure of carbon dioxide in the blood stimulating the respiratory centres. Active hatching is the second essential phenomenon and is probably stimulated by an increase in the rate of thyroid hormone secretion. The body temperature of the chick rises after hatching, and is probably a result of the progressive replacement of the yolk with actively metabolizing tissues. There is also a rise in the metabolic rate at this time. Both the absolute oxygen requirements and the metabolic pattern of the growing fowl may be affected by the diet. There is a difference in the response to the diet according to the sex. A period of almost constant oxygen uptake was consistently noted and appeared to be virtually independent of the diet although high levels of dietary protein tended to reduce this depression in the metabolism. At 4 weeks of age a large fall in the metabolic rate was found, especially in RIR x IS chickens. The significance of the fall is not known, but a fundamental change in the physiology of the fowl is indicated.

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