Phylodynamic modelling of foot-and-mouth disease virus sequence data

The under-reporting of cases of infectious diseases is a substantial impediment to the control and management of infectious diseases in both epidemic and endemic contexts. Information about infectious disease dynamics can be recovered from sequence data using time-varying coalescent approaches, and phylodynamic models have been developed in order to reconstruct demographic changes of the numbers of infected hosts through time. In this study I have demonstrated the general concordance between empirically observed epidemiological incidence data and viral demography inferred through analysis of foot-and-mouth disease virus VP1 coding sequences belonging to the CATHAY topotype over large temporal and spatial scales. However a more precise and robust relationship between the effective population size (

Patterns in the space use of the Bearded Reedling, Panurus biarmicus, on the Tay Reedbeds, Scotland

This thesis presents research into the space use of a specialist reedbed Passerine, the Bearded Reedling, or Bearded Tit, Panurus biarmicus, with a view to inform the conservation of this species and reedbeds as a whole. How a species uses space, and how space use changes between individuals or over time, can influence: the ability to forage and hunt effectively, breeding success, susceptibility to predation, genetic health, disease spread, robustness against environmental change and ultimately, colonisation or extinction. Thus, understanding the space use of animals can provide critical insight into ecological systems. Birds offer interesting models when studying animal space use, as, by being intrinsically mobile, many bird species can occupy multiple spatial scales. As a consequence of being completely dependent on patchy and ephemeral reedbed habitats, the Bearded Reedling, has a clustered, inhomogeneous distribution throughout its range. This drives the existence of distinct spatial scales upon which space use studies should be characterised. Distribution and movement within a single reedbed can be considered local-scale, while spatial processes between reedbeds can be considered wide-scale. Temporal processes may act upon both of these scales. For example, changing interactions with predators may influence nest positioning at a local-scale, while seasonal changes in resource requirements might drive processes such as migration at a wide-scale. The Bearded Reedling has a wide temperate breeding range, extending over much of Eurasia. On the IUCN’s red list, it is listed as ‘of least concern’, with an estimated European population between 240,000-480,000 breeding pairs. Despite its relatively favourable conservation status, its dependence on reedbed habitats drives a fragmented distribution, with populations being concentrated in small, isolated, stands. Over the last century reedbed wetlands have suffered rapid declines caused by drainage schemes undertaken to improve land for development or agriculture. Additionally, many remaining reed stands are subject to extensive commercial management to produce thatch or biofuel. Conversely, in other areas, management is driven by conservation motives which recognise the present threats to reedbeds, and aim to encourage the diversity of species associated with these habitats. As the Bearded Reedling is fundamentally linked to the quality and structure of a reed stand, understanding the space use of this species will offer information for the direct conservation of this specialist species, and for the effects of reedbed management as a whole. This thesis first presents studies of space use at a local-scale. All local-scale research is conducted at the Tay Reedbeds in eastern Scotland. Mist netting and bird ringing data are used within capture recapture models, which include an explicit spatial component, to gain insight into the abundance of the Bearded Reedling on the Tay. This abundance estimation approach suggests the Tay reedbeds are a stronghold for this species on the British Isles, and that, as a high latitude site, the Tay may have importance for range expansion. A combination of transect surveys and radio-tracking data are then used to establish the local-scale space use of this species during the breeding and autumnal seasons. These data are related to changes in the structure of reed caused by local management in the form of mosaic winter reed cutting. Results suggest that birds exploit young and cut patches of reed as foraging resources when they are available, and that old, unmanaged reed is critical for nesting and winter foraging. Further local-scale studies concern the spatial patterns in the nesting habits of this species. Mosaic reed cutting creates clear edges in a reedbed. Artificial nests placed in the Tay Reedbeds demonstrate increased nest predation rates closer to the edges of cut patches. Additionally, high predation rates become reduced as the cut reed re-grows, suggesting that reed cutting may increase accessibility of the stand to predators. As Bearded Reedling nests are uncommon and difficult to locate, the timing, site selection and structure of a sample of real nests from the Tay is then detailed. These demonstrate an early, and relatively rigid breeding onset in this species, the importance of dense, compacted reeds as nesting sites and a degree of flexibility in nest structure. Conservation efforts will also benefit from studies into wide-scale spatial processes. These may be important when establishing how colonisation events occur and when predicting the effects of climatic change. The Bearded Reedling has been traditionally considered a resident species which only occasionally undertakes wide-scale, between-reedbed, movements. Indeed, the ecology of this species suggests strict year round local residency to reedbeds, with distinct seasonal changes in diet allowing occupation of these habitats year round. The European ringing recoveries of this species, since the 1970s are investigated to better characterise the wider movements of specialist resident. These suggest residency in southern populations, but higher instances of movement than expected in more northerly regions. In these regions wide-scale movement patterns resemble those of partial regular migratory species. An understanding of local and wide-scale spatial processes can offer a strong foundation on which to build conservation strategies. This thesis aims to use studies of space use to provide this foundation for the Bearded Reedling and offer further insight into the ecology of reedbed habitats as a whole. The thesis concludes by proposing an effective strategy for the conservation management of reedbeds that will especially benefit the Bearded Reedling.