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The Greater Himalaya has been identified as a key conservation region that supports high levels of biodiversity but has exceptionally high proportions of threatened species. One taxonomic group that is thought to be of particular concern is the bird order Galliformes. The Greater Himalaya is home to 24 species of resident Galliformes with a variety of ecological characteristics, geographical distribution patterns and abundance levels. Our current knowledge of South Asian Galliformes and Himalayan species in particular, contains many gaps. For example, it is suspected that many Himalayan Galliformes have undergone marked population declines but as to what extent they have declined and even the current status of some species is not fully known. There is a similar paucity of knowledge regarding both the distributions of the rarest of Himalayan Galliformes species and how well the current protected area network represents such distributions. Here I provide new insights into the distribution of the rarest Himalayan Galliform, the Critically Endangered Himalayan Quail (Orphrysia superciliosa) by using two proxy species with similar habitat preferences to create an environmental niche model. I show that by calculating an estimate of extinction likelihood, we have good reason to believe that the Himalayan quail to be extant and that recent searches in Nepal would be better targeted in North East India. Moving from single species to multiple species, I then examine long-term population changes across all Himalayan Galliformes by using changes in geographic range size as a proxy. I show that population changes for this suite of species both within and outside the Himalaya can help us to set conservation priorities and baselines. In addition, it can help us to identify species that have undergone large population changes that are not reflected in contemporary IUCN Red List statues. Species with small geographic ranges are currently top priorities for conservation efforts because they are thought to be at a greater risk of extinction. However, because it is also easier to track long term population changes over smaller spatial scales, concern exists that we may have underestimated the declines and therefore the extinction risk of more i widespread species. I show that across the entire Galliformes taxon, geographic range size does not predict the rate of geographic range decline. Finally, I move from population declines across all Galliformes to distributions of Himalayan Galliformes and assess how well the current protected area network represents such species. Using a combination of species distribution modelling and spatial prioritisation software, I show that the current protected area network in the greater Himalayas could be improved to offer better coverage for Himalayan Galliformes. I conclude by discussing the generality of my results and how they can be applied to other taxa and localities. Finally I make a series of recommendations for future Galliformes research and conservation within the Himalaya.

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Avian embryos have played an important role in the study of vertebrate development but further understanding of their development may also benefit the commercial poultry industry. Manipulation and use of primordial germ cells (PGCs) as a vehicle for constructed genotypes will be increasingly important for future improvement of commercial poultry including the turkey. However, the manipulation and use of PGCs will depend on a basic understanding of PGC migration. PGCs are known to migrate considerable distances before colonising the gonad. Previous work in the chick and quail have suggested that avian PGCs arise from the ventral surface of the area pellucida before the blastoderm undergoes gastrulation, translocate to the germinal crescent during primitive streak stages and penetrate the extraembryonic blood vessels (stage 10) after they have formed. PGCs are subsequently carried by the blood stream into the embryo proper during stages 12-14 and then leave the blood vessels and migrate to the developing gonads. However, the factors controlling PGC migration are poorly understood. The developmental stages of older turkey embryos are not well documented. Therefore, this study started by classifying them. It was found that turkey embryos at stage 4 and younger were slightly different from chick embryos, but from stages 5 onwards, turkey embryos could be staged using criteria described for the chick (Hamburger and Hamilton, 1951). Avian PGCs can be recognized by their distinctive morphology being large cells with large and eccentrically placed nuclei, and a cytoplasm containing refractile granules. These characteristics were confirmed for turkey PGCs. In order to manipulate PGCs, cells need to be identified using appropriate markers. A panel of markers previously used for chick, quail, mouse, rat and rabbit were tested with turkey PGCs at different stages. It was found that turkey PGCs could be detected by the histochemical stains, periodic acid-Schiff (PAS) and alkaline phosphatase (AP) or using antibodies to stage-specific embryonic antigen-1 (SSEA-1), fucosylated polylactosamine carbohydrate groups (EMA-1) and ovomucin-like protein (OLP). At primitive streak stages, turkey PGCs were located in the area pellucida. During stages 11 - 15, they were found in the blood reaching maximal numbers at stage 14. After stage 15, most PGCs were located outside the circulatory system. From stage 18, PGCs began to settle in gonadal ridges and after stage 28, PGCs were found only in the gonads. Turkey PGCs were isolated from the blood with a micropipette, during visual selection under the microscope, and their Identity confirmed using the above markers. These PGCs could be cultured on a gonadal stromal cell layer or on coverslips coated with rat-tail collagen. Isolated PGCs adhered to coated coverslips were prepared and examined with scanning electron microscope (SEM). Such cells had typical features of PGCs seen in situ and some had the morphology of motile cells. PGC movement in vitro, in response to a variety of potential chemoattractants, was then studied. Conventional chemotaxis assays could not be used to study such small numbers of cells. Therefore, the assay was carried out using a Dunn chemotaxis chamber which allows direct observation of cells and detailed analysis of their movement from a timed series of images. A positive chemotactic response was observed with cells exposed to a gradient of medium conditioned by stromal cells or 10 ng/ml transforming growth factor beta-1 (TGFbeta1). Cells exposed to 100 ng/ml stem cell factor (SCF) or control medium showed no such response. These observations indicate that TGF?l can play a role in directed migration of PGCs in vitro, but further experiments are required to determine whether this factor is similarly involved in vivo.

No description available.

No description available.

No description available.

Population numbers change in space and time. The construction of models to investigate the spatial and temporal dynamics of populations may offer a means to identify the processes driving this change. In this thesis, we make use of models to examine the population ecology of three species of upland birds: red grouse, meadow pipit and capercaillie. Populations of red grouse in the British Isles exhibit cyclic fluctuations in abundance. Time series data from 287 grouse moors across the United Kingdom were analysed to investigate co-variation in these fluctuations. Results indicate high levels of synchrony between populations on neighbouring moors, with synchrony declining with increasing intermoor distance. At distances greater than 100km, populations exhibit only weak synchrony. Synchrony is shown to be a product of strong coupling events, which occur on average every one in six years. In the absence of such events, synchrony is shown to dissipate within three years. Further, we present evidence which suggests this coupling is driven (at least in part) by dispersal between populations. The density dependent structures are also found to be sufficiently homogeneous to allow correlations in climate to synchronise dynamics, but examination of three climate variables failed to detect a relationship. We also studied the population dynamics of meadow pipits in upland grassland ecosystems. Data, collected as part of an ongoing grazing field experiment, were analysed to construct a Bayesian model of population growth, and predict the effect of grazing intensity on meadow pipit populations. Results suggest grazing has a significant impact on population growth. Grazing may act to improve meadow pipit foraging efficiency and thus productivity. Finally, a spatially explicit population viability model was constructed to predict changes in the future abundance and distribution of capercaillie. Published estimates of key demographic variables were drawn from the literature to parameterise the model. The spatial structure of the population was inferred from spatial data, documenting the extent and configuration of remnant pine woodlands in Scotland. The model predicts a low probability of extinction for capercaillie in the future, and offers insights into key processes affecting the distribution and abundance of this species. The development of these models has advanced our understanding of the environmental processes driving changes in the spatial and temporal dynamics of these species. The results of these studies may be useful in anticipating the future consequences of various drivers of change on the ecology of upland species.

Classified as critically endangered since 1994, the Trinidad Piping guan (Pipile pipile) is an endemic species estimated to number less than 200 individuals. Known to locals of Trinidad as the ‘Pawi’ this bird has been the subject of substantial hunting pressures and much of the species habitat has been destroyed through deforestation. Although officially protected since 1958, occasional recreational hunting of this elusive species still occurs. Due to difficulties locating and capturing the species, no genetic research has previously been performed using samples obtained from Trinidad. All previous research studies have been conducted using biological materials obtained from captive birds outside Trinidad and island data has never been obtained or compared. The genetic diversity of the remaining population was therefore examined through the investigation of mitochondrial haplotypes, pairwise comparison and SNP analysis. With the intention of assisting the protection of this endangered species by the location of remaining areas of habitation, methods of genetic identification were established for the Trinidad Piping guan utilising non-invasive feather samples. Species specific primers were created in the regions of the ND2 and cyt b genes of the mitochondrial genome to identify Pipile pipile. Species detection was further verified with the use of PCR-RFLP of the same gene regions digested with BsaXI, EcoRV and BsrDI. This combined approach allowed the separation of closely related taxa based on single inter-species SNPs. Confirmation of species identification was subsequently performed through the use of forensically informative nucleotide sequencing. The established methodologies were used in the current study to correct the classification of a UK breeding population of Piping guans thought to be Pipile pipile and to identify Trinidad field samples. These detection methods have implications for ecological studies through the location of populations from trace evidence collected in the field. In addition this method could be used to assist Trinidadian police forces in the identification of bushmeats or simply act as a deterrent to hunters. The sequence data obtained in the present study were also used to re-assess the phylogeny of Piping guans. As genetic sequence from a true island bird was previously unstudied, differences between phylogenies created using non-island and island bird data sets were examined. Combined analysis was performed on 1884bp of the ND2 and cyt b genes and placement of Trinidad Piping guan was found to differ from that which has been previously published.

This study involves two village chicken populations sampled from Horro and Jarso regions of Western and Eastern Ethiopia respectively. This study maps the phenomic and genomic landscape of the two chicken populations using morphological markers and a high density (600K) SNP array. Although the two chicken populations tend to display nondescript morphological characteristics, they show a subtle variation except for rare morph variants that have been in most instances scored on Jarso chickens. Morphological analysis uncovers a vast array of intrapopulation variation. Genetic diversity and population structure analyses assign the two chicken populations to two distinct genepools representing their population of origin. A high intrapopulation genetic diversity is uncovered, which shows a broad genetic base (high genetic diversity) of the two chicken populations. We hypothesized that a clearly evident genetic divergence observed between the two chicken populations may be attributed to difference in demographic history, origin (routes of introduction to Africa), breeding history of the two chicken populations and demographic structure of subsistence farmers. Absence of gene flow owing to their distant geographic location and ecological variation may have also contributed to this divergence. A population structure analysis performed on a random subset of the two Ethiopian chicken populations along with village chickens sampled from other African countries, Asia and Latin America, commercial populations and the junglefowl species reveals a unique genetic structure of Ethiopian chickens, which implicates the need for further study on the genetic landscape of the latter. To infer the extent of inbreeding we performed a run of homozygosity analysis (ROH). Our analysis indicates that ROH is more intense in Jarso than Horro chickens and in macrochromosomes than microchromosomes. The extensive ROH mapped in some chickens implicates the need to restructure the existing traditional breeding practice of subsistence farmers. Our analysis confirms the commonness of ROH in genic regions. For the first time, we detect twenty three putative uniparental disomy in twenty two Ethiopian village chickens. Signature of selection analysis detects divergently selected genomic regions in the two chicken populations indicating a considerable divergent selection imposed on the two populations. Genes involving in melanogenesis pathway are among those subjected to a divergent selection. However, some overlapping regions were also mapped in the two chicken populations implicating the ubiquitous impact of natural selection on genes regulating vital biological processes. A genome-wide association study performed on pigmentation (earlobe, plumage and shank) traits and variants of crest, comb and a lightly feathered shank maps a number of putative loci that may underlie variations in these traits. Our GWAS analysis on pigmentation traits produced a long list of loci than that have been known to involve in the genetic control of pigmentation in the chicken, with most of these have been mapped in the mouse. We also refined further the causative variants underlying a lightly feathered shank mutation. Our GWAS analysis map a number of putative novel loci that may underlie the genetic control of the traits analysed and this has laid a foundation for subsequent work that would involve targeted sequencing and a candidate gene approach. This study is the first of its kind in Africa that uses a large number of samples and a high density SNP array to unlock phenomic and genomic landscape of the true type village chickens.