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Modelling Biodiversity Trends from Occurrence Records

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Modelling Biodiversity Trends from Occurrence Records Modelling Biodiversity Trends from Occurrence Records Charlotte Louise Outhwaite A thesis submitted for the degree of: Doctor of Philosophy University College London September 2018 Primary supervisor: Dr Nick J. B. Isaac Secondary supervisors: Dr Ben Collen Prof. Richard E. Chandler Prof. Richard D. Gregory | 2 I, Charlotte Louise Outhwaite, confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. Charlotte Outhwaite, 21st September 2018 | 3 Abstract Large-scale studies of biodiversity change are limited in their taxonomic coverage: a lot is known about the trends of groups such as birds, butterflies and mammals, but little is known about invertebrates and plants. This is due to the lack of abundance data for these groups. However, alternative data such as occurrence records are available for a vast range of species and advances in methodologies are enabling their robust analysis. Here, I analyse UK occurrence records using Bayesian occupancy modelling techniques to determine the status, patterns and drivers of change in less well-studied taxa. First, variations of an occupancy modelling framework were tested to determine whether methods could be improved. This resulted in a “random walk” model that could analyse sparse occurrence records while producing results with increased precision and reduced bias when compared to other variants. This enabled the application of the model to data for over 12,000 species from 32 taxa including vascular plants and numerous invertebrate groups. The resulting estimates of annual occupancy present new information on large-scale change from fine-grained data. Exploration of these estimates showed that trends are not consistent with those of well-studied taxa. Occupancy estimates were then used to assess change in three forms of biodiversity trend: local alpha diversity, regional alpha diversity and regional beta diversity. This revealed the multifaceted nature of biodiversity change and the need to monitor across metrics and scales. Finally, a Bayesian, multispecies, dynamic occupancy model was used to determine the effect of water quality on the population dynamics of freshwater invertebrates. This work highlights the potential of occurrence records to investigate biodiversity change and brings to light new information on many species that have not previously been studied at a national scale. | 4 Impact Statement This work provides new information on the status and trends of UK biodiversity for over 6,500 species from taxonomic groups that have not been analysed at a national scale to- date. Outputs generated as a part of this study have already been used outside of academia to communicate change in UK biodiversity. Firstly, the preliminary analyses and methodological advances derived from this work have been used within recent iterations of the UK biodiversity indicators. These indicators are produced annually by the Joint Nature Conservation Committee and are used to track progress towards the biodiversity targets set by the Convention on Biological Diversity. Preliminary results from this work were also included in the 2016 State of Nature report. This report is produced every three years by the State of Nature Partnership and communicates change in UK biodiversity to a wide range of audiences including governmental and non- governmental organisations, policy makers and the public. Within academia, this work highlights the huge potential that the analysis of occurrence records can bring to large-scale biodiversity research, as well as providing a greater understanding of biodiversity change occurring within less well-studied taxa. This will encourage researchers to take advantage of this form of data which could lead to a reduction of the taxonomic bias that is inherent in biodiversity research. This study also takes the first step into the determination of relationships between different forms of biodiversity trend, starting a dialogue that will aid in the understanding of differences observed between metrics and across scales. This has become a strongly debated topic in the field. The advancement of the occupancy modelling framework for the analysis of sparse occurrence records will provide a useful tool for any practitioner interested in estimating trends from this form of data. This may be researchers within academia, but could also be non-governmental organisations, local record centres or even the general public. The modelling framework and other associated tools are available in two R packages which make the application of such methods accessible. The species level estimates of occupancy and trends in occupancy are available via the Environmental Information Data Centre, an open access repository, allowing the re-use of key outputs of this study. This will allow researchers to continue to generate new findings in relation to the taxa studied here, or allow the inclusion of the results in further | 5 publications and reports. These data are set to be included in the next State of Nature report due for publication in 2019. | 6 Additional Contribution During my PhD, I have contributed to a variety of outputs beyond the thesis chapters. These projects have involved collaboratively working with colleagues within The Centre for Ecology & Hydrology (my main institution, CEH) as well as groups outside of my own organisation. I have worked closely with a number of people at the RSPB, my CASE partner, to contribute to the State of Nature Report 2016. This involved the estimation of species occupancy over time for 1,600 species, the preliminary work for this thesis, and the development of a method to determine the major habitat associations of species using occurrence records. This work has resulted in my contribution to the following publications: Burns, F., Eaton, M.A., Hayhow, D.B., Outhwaite, C.L., Al Fulaij, N., August, T.A., Boughey, K.L., Brereton, T., Brown, A., Bullock, D.J., Gent, T., Haysom, K.A., Isaac, N.J.B., Johns, D.G., Macadam, C.R., Mathews, F., Noble, D.G., Powney, G.D., Sims, D.W., Smart, S.M., Stroh, P., Walker, K.J., Webb, J.R., Webb, T.J., Gregory, R.D., 2018. An assessment of the state of nature in the United Kingdom: A review of findings, methods and impact. Ecol. Indic. 94, 226–236. Hayhow, D.B., Burns, F., Eaton, M.A., Al Fulaij, N., August, T.A., Babey, L., Bacon, L., Bingham, C., Boswell, J., Boughey, K.L., Brereton, T., Brookman, E., Brooks, D.R., Bullock, D.J., Burke, O., Collis, M., Corbet, L., Cornish, N., De Massimi, S., Densham, J., Dunn, E., Elliott, S., Gent, T., Godber, J., Hamilton, S., Havery, S., Hawkins, S., Henney, J., Holmes, K., Hutchinson, N., Isaac, N.J.B., Johns, D., MacAdam, C.R., Mathews, F., Nicolet, P., Noble, D.G., Outhwaite, C.L., Powney, G.D., Richardson, P., Roy, D.B., Sims, D., Smart, S., Stevenson, K., Stroud, R.A., Walker, K.J., Webb, J.R., Webb, T.J., Wynde, R., Gregory, R.D., 2016. State of Nature 2016. I have also been able to work closely with my colleagues, Tom August and Gary Powney, and my supervisor Nick Isaac on the development and production of recent UK Biodiversity Indicators; specifically the priority species indicator and the indicator for pollinating insects. I have been able to contribute to various technical documents related to these indicators and a published paper: Eaton, M.A., Burns, F., Isaac, N.J.B., Gregory, R.D., August, T.A., Barlow, K.E., Brereton, T., Brooks, D.R., Al Fulaij, N., Haysom, K.A., Noble, D.G., Outhwaite, C., Powney, G.D., Procter, D., Williams, J., 2015. The priority species indicator: measuring the trends in threatened species in the UK. Biodiversity. 1–12. Outhwaite, C., Powney, G. August, A., Isaac, N. Indicator C4b. Status of UK priority species: distribution. Technical background report, 2018. DEFRA | 7 Isaac, N., Powney, G., August, T., Outhwaite, C., Freeman, S. UK Biodiversity Indicators 2018. Technical background document: Deriving indicators from occupancy models. DEFRA Powney, G.D., Harrower, C.A., Outhwaite, C., Isaac, N.J.B. UK Biodiversity Indicators 2018. D1c - Biodiversity and Ecosystem Services – status of pollinating insects – technical background document. DEFRA Outhwaite, C., Powney, G. August, A., Isaac, N. UK Biodiversity Indicators 2017. Indicator C4b. Status of UK priority species: distribution. Technical background report. DEFRA Isaac, N., Powney, G., August, T., Outhwaite, C., Freeman, S. UK Biodiversity Indicators 2017. Technical background document: Deriving indicators from occupancy models. DEFRA Isaac, N., Powney, G., August, T., Outhwaite, C., Freeman, S. UK Biodiversity Indicators 2015. Technical background document: Deriving indicators from occupancy models. DEFRA Outhwaite, C., Powney, G. August, A., Isaac, N. UK Biodiversity Indicators 2015. Indicator C4b. Status of UK priority species: distribution. Technical background report. DEFRA Collaborative work with my colleagues at CEH has also resulted in the development of an R package, sparta, for the analysis of unstructured data. Models developed within Chapter 2 of this thesis are available for use within this package alongside other methods. August, T., Powney, G., Outhwaite, C., Harrower, C., Hill, M., Isaac, N., 2018. sparta: Trend Analysis for Unstructured Data. R package version 0.1.40. https://github.com/BiologicalRecordsCentre/sparta Finally, I also contributed to the following publications: Thomas, J.A., Bell, J.R., Johns, T., Stefanescu, C., Kuussaari, M., Pöyry, J., Plattner, M., van Swaay, C., van Strien, A. Settele, J., Musche, M., Forister, M., Shapiro, A.M., Salcido, D., Dyer, L.A., Brereton, T., Spalding, A., Outhwaite, C.L., Powney, G. D., Isaac, N.J.B. and Roy, D. B. (in revision) Long-term changes in insect abundance: an assessment of potentially devastating global declines. Science Pescott, O.L., Walker, K.J., Pocock, M.J.O., Jitlal, M., Outhwaite, C.L., Cheffings, C.M., Harris, F., Roy, D.B., 2015. Ecological monitoring with citizen science: the design and implementation of schemes for recording plants in Britain and Ireland.
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