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This thesis explores inter-organisational relationships and behaviours when complex healthcare pathways are planned, designed, procured and implemented in the English National Health Service (NHS) in a process known as commissioning. Commissioning and healthcare provision in the NHS is organised separately and operates as a quasi-market system. Clinical Commissioning Groups (CCGs) commission the majority of local healthcare for their populations and purchase services accordingly from many different types of healthcare provider organisations. Poor integration between different provider organisations has been suggested a contributing factor to the unsustainable demands the NHS is currently facing. New models of provision have been recommended in policy as a commissioning strategy to improve integration and these require collaboration and effective inter-organisational working between organisations. Healthcare is a highly complex institutional field and the institutional logics perspective offers a theoretical framework to explore how institutions embedded within a field guide behaviour. Bureaucratic, market, corporate and professional logics are known to exist in healthcare and can be used to break down institutional complexity into abstract constructs to understand the demands organisations face but enquiry has tended to focus on sole organisations rather than inter-organisational behaviour. However the institutional logics perspective offers the opportunity to explore the influence of institutional demands on inter-organisational relationships in complex institutional fields. This study sought to explain how logics influence inter-organisational behaviours as organisations work together to develop integrated care pathways. Using stroke service commissioning as a contextual example, the study explored three comparative case studies of the commissioning processes used to reorganise and develop stroke services into integrated care pathways across acute and community providers. Using methods associated with the ethnographic tradition, fifty-four semi-structured interviews with commissioners, providers, patient representatives and advisory bodies were completed, ten commissioning meetings were observed and strategic documentation for each organisation were collected. Thematic analysis was used to identify key themes which were then viewed through the institutional logics framework lens to explore how logics were present and influencing the commissioning processes as they progressed. The empirical findings suggest that an organisation’s interpretation of the institutional environment influences how an organisation and their individuals behave. In turn those behaviours influence how the organisations they are attempting to work with respond. Establishing a shared goal between the organisations was crucial but an organisations response to institutional demands may make this difficult to achieve. Collaboration was considered key to successful integration but this was only successful when commissioners were able to negotiate complex logics to facilitate shared goals and means of achieving them. This was most successful when organisations co-opted an alternative logic to compliment the organisations they were attempting to work with for different phases of the commissioning process. When complimentary logics were op-opted, organisations were better equipped to work collaboratively but if contradictory logics were in play, there was increased risk of inter-organisational relationships breaking down. Some commissioners used this strategy effectively to develop inter-organisational relationships while hiding the logic which informed their underlying goal which allowed them to maintain control of the commissioning process. This suggested that an organisations interpretation of the institutional environment and skills at using logics to manipulate the means of achieving goals was important. In conclusion, when logics are used by organisations to compliment the beliefs and behaviours of other organisations when they attempt to work together, they are able to establish effective inter-organisational relationships that allow collaborative work towards shared goals. This may be an important characteristic of commissioning organisations as they attempt to commission new models of integrated care.

Chromosomal (karyotypic) analysis in animals is performed for three primary reasons: to diagnose genetic disease; to map genes to their place in the genome and to retrace evolutionary events by cross species comparison. Technology for analysis has progressed from chromosome banding (cytogenetics), to fluorescence in-situ hybridisation (FISH - molecular cytogenetics) through to microarrays and ultimately whole genome sequence analysis (cytogenomics or chromonomics). Indeed, the past 10-15 years has seen a revolution in whole genome sequencing, first with the human genome project, followed by those of key model and agricultural species and, more recently, ~60 de novo avian genome assemblies. Whole genome analysis provides detailed insight into the biology of chromosome rearrangements that occur both in individuals (for diagnostic purposes) and at an evolutionary level. It permits the study of gene mapping, trait linkage, phylogenomics, and gross genomic organisation and change. An essential pre-requisite however is an unbroken length of contiguous DNA sequence along the length of each chromosome. Most recent de novo genome assemblies fall short of this level of resolution producing lengths of contiguous sequence that are sub-chromosomal in size (scaffolds). Chromosome rearrangements can affect reproductive capability at an individual level (causing reduced fertility) and at a population level leading to reproductive isolation and subsequent speciation. The purpose of this thesis was to implement a step change in the combination of FISH technology with genome sequence data to provide greater insight into the nature of chromosomal rearrangement at an individual and evolutionary level. It therefore had four specific aims: The first was to isolate sub-telomeric sequences from the pig, cattle and chicken genome assemblies to develop a tool for the rapid screening of chromosome rearrangements. Now routinely used for porcine translocation screening (and in the future bovine screening), development work revealed serious integrity errors in the pig genome. The second aim was to isolate evolutionary conserved sequences from avian chromosomes to create a means of screening for macro-and microchromosomal rearrangements in birds. Results confirmed the hypothesis that microchromosomal rearrangements were rare in birds, except for previously known whole chromosomal fusions. The third was to use the above tools to complete scaffold based genome assemblies in two key avian species - the peregrine falcon and the pigeon. Finally, bioinformatic tools were used to infer the overall genome structure of hypothetical saurian and avian ancestors. Retracing of the evolutionary changes that occurred up until the emergence of birds allowed an assessment of chromosome evolution along the saurischia-maniraptora- avialae lineage. Analysis of evolutionary breakpoint regions (EBRs) allowed testing of the hypothesis that the ontology of genes within EBRs corresponded to measurable phenotypic change in the lineage under investigation. An enrichment of genes associated with body height corresponded to rapid size change in the dinosaur linage that led to modern birds. Taken together, these results paint a picture of a genome that, from about 260 million years ago formed a 'signature' highly successful avian-dinosaur karyotype that remained largely unchanged interchromosomally to the present day. These results represent significant insight into amniote genomic organization with the added benefit of developing tools that are widely applicable and transferrable for commercial animal breeding, for constructing de novo genome assemblies and for reconstructing, by inference, the overall genomic structure and evolution of extinct animals.