Population ecology and conservation of red-billed choughs in Scotland. Final report on Knowledge Transfer Project

This report summarises the results of a Knowledge Transfer Research Project that was undertaken by Dr Jane Reid (University of Aberdeen), Professor Pat Monaghan, (University of Glasgow), Dr Eric and Mrs Sue Bignal (Scottish Chough Study Group) and Dr Davy McCracken (Scottish Agricultural College). Dr Maria Bogdanova was employed as the postdoctoral research assistant on the project. The work was carried out in partnership with Scottish Natural Heritage (SNH) and the Royal Society for the Protection of Birds (RSPB). Funding was provided by a Knowledge Transfer Grant from the Natural Environment Research Council (NERC, PIs P. Monaghan & J. Reid), with matching partnership funding and in-kind support from SNH and RSPB. The overall aims of the project were to develop the scientific understanding of the population ecology of choughs on Islay, and to use this understanding to inform the development of appropriate conservation strategies and policies. The project built on existing long-term research on Islay’s choughs. It involved further analysis of long-term data, plus two years of intensive fieldwork designed to answer specific questions. The work aimed primarily to understand the ecology of choughs in their sub-adult years (ie, from fledging to breeding age). Survival from fledging to breeding is a key factor in causing population change. However, relatively little was previously known about the behaviour and ecology of choughs during this time. This report provides an overview of the results of the scientific study and focuses on presenting the scientific evidence on which resulting recommendations for chough conservation management on Islay are based. The report is written with the intention of presenting the results of the data analyses, and the rationale underlying those analyses, in a way that is accessible to non-specialists. Further details of analyses and technicalities are provided in published, peer-reviewed papers and/or are available on request. The report provides information that will be of use to policy makers and conservation practitioners, and also highlights topics where further research is required before informed management decisions can be taken

Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity

We thank everyone who helped with fieldwork on Islay, in particular Sue Bignal and Pat Monaghan, as well as all land-owners and farmers who allowed access to nest sites. We thank Bernt-Erik Sӕther, Steinar Engen and Henrik Jensen for their generous help and discussions. AET was funded by the Natural Environment Research Council and Scottish Natural Heritage. JMR was supported by the European Research Council.Peer reviewedPostprin

Within-year and among-year variation in impacts of targeted conservation management on juvenile survival in a threatened population

Acknowledgements We thank all Islay landowners and farmers who allowed access to nest sites and supported supplementary feeding, especially Donald Jones and Robert and Tom Epps, and everyone who contributed to fieldwork and data collection. We thank NatureScot for funding supplementary feeding, led by Rae McKenzie, Jess Shaw and Des Thompson, and Royal Society for the Protection of Birds for logistic support. This work was supported by a Natural Environment Research Council iCASE studentship (NE/P009719/1) with NatureScot, and the Scottish Government’s 2011-2016 and 2016-2021 Strategic Research Programmes. Open access via Wiley agreement.Peer reviewedPublisher PD

Integrating advances in population and evolutionary ecology with conservation strategy through long-term studies of red-billed choughs

Acknowledgements The long-term study could not have been achieved without long-term support from numerous people, including Islay farmers and land-owners who facilitated access to nest sites and observation locations; all current and previous members of the Scottish Chough Forum; and NatureScot and RSPB (summarised in Appendix S2). We particularly thank Rae McKenzie of NatureScot, without whose enthusiasm and willingness to engage with apparently abstract ideas we would likely never have got beyond phase 1. Aspects of the work were funded by Natural Environment Research Council, NatureScot, University of Aberdeen, University of Glasgow, RSPB, Scottish Government’s Strategic Research Programme, Scotland’s Rural College, Killam Trusts and the Royal Society (details in Appendix S2). We thank David Jardine for his valuable contributions, and Rae McKenzie, Jess Shaw and Morven Laurie (NatureScot), and Jen Smart, Gillian Gilbert, Jack Fleming and Paul Walton (RSPB) for commenting on a manuscript draft.Peer reviewedPublisher PD

Bats in the anthropogenic matrix: Challenges and opportunities for the conservation of chiroptera and their ecosystem services in agricultural landscapes

Intensification in land-use and farming practices has had largely negative effects on bats, leading to population declines and concomitant losses of ecosystem services. Current trends in land-use change suggest that agricultural areas will further expand, while production systems may either experience further intensification (particularly in developing nations) or become more environmentally friendly (especially in Europe). In this chapter, we review the existing literature on how agricultural management affects the bat assemblages and the behavior of individual bat species, as well as the literature on provision of ecosystem services by bats (pest insect suppression and pollination) in agricultural systems. Bats show highly variable responses to habitat conversion, with no significant change in species richness or measures of activity or abundance. In contrast, intensification within agricultural systems (i.e., increased agrochemical inputs, reduction of natural structuring elements such as hedges, woods, and marshes) had more consistently negative effects on abundance and species richness. Agroforestry systems appear to mitigate negative consequences of habitat conversion and intensification, often having higher abundances and activity levels than natural areas. Across biomes, bats play key roles in limiting populations of arthropods by consuming various agricultural pests. In tropical areas, bats are key pollinators of several commercial fruit species. However, these substantial benefits may go unrecognized by farmers, who sometimes associate bats with ecosystem disservices such as crop raiding. Given the importance of bats for global food production, future agricultural management should focus on “wildlife-friendly” farming practices that allow more bats to exploit and persist in the anthropogenic matrix so as to enhance provision of ecosystem services. Pressing research topics include (1) a better understanding of how local-level versus landscape-level management practices interact to structure bat assemblages, (2) the effects of new pesticide classes and GM crops on bat populations, and (3) how increased documentation and valuation of the ecosystem services provided by bats could improve attitudes of producers toward their conservation

Theories of Programming: Top−Down and Bottom−Up and Meeting in the Middle

1. Determining the precise timing and location of major demographic bottlenecks, such as periods of low survival, is key to identifying ecological causes of variation in population growth rate. Such understanding is key to designing efficient and effective mitigation. 2. In a protected population of red-billed chough Pyrrhocorax pyrrhocorax on Islay, Scotland, variation in population growth rate largely reflects among-year variation in first-year survival. First-year survival was unprecedentedly low during 2007–2010, threatening population viability. 3. We used colour-ring resightings to estimate monthly survival probabilities (Φm) throughout the first year from fledging for eight chough cohorts (totalling 519 individuals) representing the full observed range of variation in first-year survival. We thereby identify the time and location of recent low survival. 4. On average across all cohorts, Φm varied among months, being low during the first month after ringing (May–June, accounting for c. 24% of all first-year mortality) and high during the last 4 months of the first year (January–May, accounting for c. 6% of all first-year mortality). Most mortality (c. 70%) occurred after fledglings dispersed from natal territories. 5. The 2007–2009 cohorts experienced low Φm during July–December. This represents an additional low survival period compared to previous cohorts rather than decreased Φm across all months or further decreases through periods when Φm was low across all cohorts. 6. Synthesis and applications. These data have general relevance in showing that dramatically low annual survival, which needs to spark rapid management action, can reflect different and unanticipated periods of low survival rather than exaggeration of typical variation. With specific regard to conserving Islay’s chough population, our data show that sub-adult survival has recently been low during July–December, probably reflecting conditions on key grassland foraging areas. Managers aiming to increase population viability should increase invertebrate diversity, abundance and availability at these times and locations, thereby increasing foraging options available to choughs

Data for survival analysis

This file contains the encounter histories required for estimation of mean age-specific survival probabilities using capture-mark-recapture models in program MARK (White & Burnhman 1999)

Data for LD genetic estimation of Ne

This file contains the raw microsatellite genotype data required for the estimation of effective population (Ne) of the Islay red-billed chough population, using linkage disequilibrium (LD) in the program NeEstimator v2.01 (Waples & Do 2008)

Data for demographic estimation of Ne

This file contains data required for the estimation of effective population size (Ne) from population- and individual-level demographic data from a population of red-billed chough on Islay, Scotland, UK. Each row provides data on sex-age-year specific breeding success and survival to the following year

Data for ONeSAMP genetic estimation of Ne

This file contains the raw microsatellite genotype data required for the estimation of effective population (Ne) of the Islay red-billed chough population, using approximate Bayesian computation (ABC) in the program ONeSAMP (Tallmon et al. 2008)