Data from: Unravelling the complexities of temporal biotic homogenisation and heterogenization: Avian assemblage dynamics in Britain
Data files
May 30, 2024 version files 5.58 MB
Abstract
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.
README: 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
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
- 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
- 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
- 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
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.