Using high-throughput sequencing to track habitat use by thrushes exploiting heterogeneous farmland landscapes

Agricultural intensification can affect farmland birds by altering prey availability and reducing the distribution, visibility and/or accessibility of key invertebrate resources. A novel environmental genomics approach was used to track habitat use by thrushes exploiting different habitat elements for food within two contrasting farmland landscapes; a complex landscape in South Wales and a relatively simple landscape in East Anglia. The spatial variation, relative abundance and diversity of ground dwelling invertebrates was determined across different landscape elements, which revealed the links between habitat complexity and prey availability (Chapter 2). A comprehensive examination of suitable COI primer pairs was conducted (Chapter 3), in order to determine the full dietary breadth of farmland thrushes, using a metabarcoding high-throughput sequencing approach (Chapter 4). Application of this approach revealed variation in diet and nestling growth related to spatial factors (between-farm and within-farm location) and temporal factors (between-year and seasonal), as well as substantial overlap in diet between Blackbirds and Song Thrushes (Chapter 4). Comparisons of the relative abundance of different prey taxa in farmland habitats (described in Chapter 2), with the occurrence of prey in the diet of Blackbirds and Song Thrushes, indicated strong preferences for or against particular prey taxa available in the landscape (Chapter 5). The selection by thrushes of prey taxa that are habitat specialists allowed the use of different parts of the farm landscape by foraging thrushes to be deduced. These results together show that a fine-scale mosaic of agricultural elements provides birds with redundancy in terms of the abundance and diversity of suitable prey items to exploit. This novel study provides a model for using high-throughput sequencing to measure trophic relationships, via habitat-linked food webs, to understand the mechanisms which underlie foraging decisions and habitat use in thrushes and the consequences for breeding productivity, nestling growth and condition.