DOI: 10.5061/dryad.hx3ffbgm6
title: Data from: Unravelling the complexities of temporal biotic homogenisation and heterogenization: Avian assemblage dynamics in Britain

description: Biotic homogenization is a process whereby species assemblages become more
 similar through time.  The standard way of identifying the
 process of biotic homogenization is to look for decreases in spatial
 beta-diversity. However, using a single assemblage-level metric to assess
 homogenization can mask important changes in the occupancy patterns of
 individual species. Here, we analysed changes in the spatial
 beta-diversity patterns (i.e., biotic heterogenization or homogenization)
 of British bird assemblages within 30km x 30km regions between two periods
 (1988-1991 and 2008-2011). We partitioned the change in spatial
 beta-diversity into extirpation and colonisation resultant change (i.e.,
 change in spatial beta-diversity within each region resulting from both
 extirpation and colonisation). We used measures of abiotic change in
 combination with Bayesian modelling to disentangle the drivers of biotic
 heterogenization and homogenization. We detected both heterogenization and
 homogenization across the two time periods and three measures of diversity
 (taxonomic, phylogenetic, and functional). In addition, both extirpation
 and colonisation contributed to the observed changes, with
 heterogenization mainly driven by extirpation and homogenization by
 colonisation. These assemblage-level changes were primarily due to
 shifting occupancy patterns of generalist species. Compared to habitat
 generalists, habitat specialists had significantly (i) higher average
 contributions to colonisation resultant change (indicating
 heterogenization within a region due to colonisation) and (ii) lower
 average contributions to extirpation resultant change (indicating
 homogenization from extirpation). Generalists showed the opposite pattern.
 Increased extirpation resultant homogenization within regions was
 associated with increased urban land cover and decreased habitat
 diversity, precipitation, and temperature. Changes in extirpation
 resultant heterogenization and colonisation resultant heterogenization
 were associated with differences in elevation between regions and changes
 in temperature and land cover. Many of the ‘winners’ (i.e.,
 species that increased in occupancy) were species that had benefitted from
 conservation action (e.g., buzzard (Buteo buteo)). The ‘losers’ (i.e.,
 those that decreased in occupancy) consisted primarily of previously
 common species, such as cuckoo (Cuculus canorus). Our results
 show that focusing purely on changes in spatial beta-diversity over time
 may obscure important information about how changes in the occupancy
 patterns of individual species contribute to homogenization and
 heterogenization.
description: # Data and code from: Unravelling the complexities of temporal biotic
 homogenisation and heterogenization: avian assemblage dynamics in Britain
 [https://doi.org/10.5061/dryad.hx3ffbgm6](https://doi.org/10.5061/dryad.hx3ffbgm6) ## Description of the data and file structure Data is contained within the "Datafiles" folder. This data consists of: * Bird_list.csv: List of birds present in the study area during the study periods * Centroids_10.csv: Centroids (latitude and longitude) of the centers of each hectad (10 km x 10 km grid). * ClimChaprec_30.csv: Change in precipitation between the two study periods * ClimChatavg_30.csv: Change in average temperature between the two study periods * consensus_jetz_3000: Jetz consensus trees (see Jetz et al. 2012 for more information) * data_30km.csv: the full dataset (if only the data is needed without running the script to obtain metrics and combine into one datafile) * elev_30km: Elevation data for Britain in 30 km x 30vkm grids * Func: Functional traits for bird species in the study (see Tobias et al. 2022 for more information) * graph_2291_1.5: Spatial graph for use within the modelling * grid_10: Shapefile of the 10 km x 10 km hectads * LandChange.csv: Land cover change between 1990 and 2015 (see Rowland et al. 2020 for more information) * pa_1990_10.csv: Presence absence data for each hectad in BA1990 (see Gillings et al. 2019 for more information) * pa_2010_10.csv: Presence absence data for each hectad in BA2010 (see Gillings et al. 2019 for more information) * Shan1990_30.csv: Shannon's diversity for landcover in each 30 km x 30 km grid in 1990. * Shan2015_30.csv: Shannon's diversity for landcover in each 30 km x 30 km grid in 2015. * ShanCha_30.csv: Change in Shannon's diversity between the two time periods. * Specialisation.csv: Habitat specialisation values and quartiles for British birds (see Sullivan et al. 2016 for more information). * status_sp.csv: A database of information for each bird species found within the study area. ## Sharing/Access information Data was derived from the following sources: * Gillings, S., Balmer, D. E., Caffrey, B. J., Downie, I. S., Gibbons, D. W., Lack, P. C., Reid, J. B., Sharrock, J. T. R., Swann, R. L., & Fuller, R. J. (2019). Breeding and wintering bird distributions in Britain and Ireland from citizen science bird atlases. *Global Ecology and Biogeography*, *28*(7), 866–874. [https://doi.org/10.1111/geb.12906](https://doi.org/10.1111/geb.12906) * Hollis, D., McCarthy, M., Kendon, M., Legg, T., & Simpson, I. (2019). HadUK‐Grid—A new UK dataset of gridded climate observations. Geoscience Data Journal, 6(2), 151-159. * Jetz, W., Thomas, G. H., Joy, J. B., Hartmann, K., & Mooers, A. O. (2012). The global diversity of birds in space and time. *Nature*, *491*(7424), Article 7424. [https://doi.org/10.1038/nature11631](https://doi.org/10.1038/nature11631) * Rowland, C., Marston, C., Morton, D., & O'Neil, A. (2020). Land Cover Change 1990-2015 (25m raster, GB). * Sullivan, M. J. P., Newson, S. E., & Pearce-Higgins, J. W. (2016). Changing densities of generalist species underlie apparent homogenization of UK bird communities. *Ibis*, *158*(3), 645–655. [https://doi.org/10.1111/ibi.12370](https://doi.org/10.1111/ibi.12370) * Tobias, J. A., Sheard, C., Pigot, A. L., Devenish, A. J. M., Yang, J., Sayol, F., Neate-Clegg, M. H. C., Alioravainen, N., Weeks, T. L., Barber, R. A., Walkden, P. A., MacGregor, H. E. A., Jones, S. E. I., Vincent, C., Phillips, A. G., Marples, N. M., Montaño-Centellas, F. A., Leandro-Silva, V., Claramunt, S., … Schleuning, M. (2022). AVONET: Morphological, ecological and geographical data for all birds. *Ecology Letters*, *25*(3), 581–597. [https://doi.org/10.1111/ele.13898](https://doi.org/10.1111/ele.13898) ## Code/Software *All scripts and functions (sub-folder) are included within the folder* for analysing the data to produce the outputs found in the manuscript: *Unravelling the complexities of temporal biotic homogenisation and heterogenization: avian assemblage dynamics in Britain.* All code is for use within the R coding environment (v4.2.1; R Core Team 2022). The *main.script* script loads all necessary data and packages from the script *source.script*. The script then runs through all of the necessary steps to reproduce the results found in the manuscript.