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Landscape genetics test datasets were simulated using the software SimAdapt (Rebaudo et al., 2013) under four different landscape configurations.
- Uniform: same habitat over the study area, 50x50 cells.
- Chessboard: A favourable and an unfavourable habitat distributed evenly over the study area, 50x50 cells, 2500 cells favourables (50%).
- Random: A favourable and an unfavourable habitat both distributed randomly over the study area, 50x50 cells, 1261 cells favourables (50.44%).
- Fragmented: a favourable habitat highly fragmented by an unfavourable habitat, 55x41 cells, 701 cells favourable (31.09%).
- Gradient: a spatial transition from a favourable to an unfavourable habitat, 58x52 cells, 1507 cells favourable (49.97%).
Shared SimAdapt parameters:
Parameter | Value |
nb_agent | 3 |
biall? | off |
sd_H | 1.414 |
num_microsat | 10 |
mutation_rate | 1E-4 |
proba_dispersion | 1.000 |
r_growth | 0.25 |
nb_move | 2 |
num_locus_per_habitat | 0 |
var_num_generations | 1000 |
output_freq | 1000 |
The costs raster is uniform with 1 in each cell.
Under uniform conditions the carrying capacity was set to 10.
For other landscapes, favourable habitat have a carrying capacity of 20 individuals vs. 2 in not favourable.
For each landscape genetics scenario simulated, 20 independent datasets were produced. For all scenarios and replicates, three spatial sampling strategies and two level of sampling effort were considered.
- Random: sampling of 200 or 500 individuals anywhere across the landscape
- Balanced: sampling of 100 or 250 individuals from each habitat
- Gridded: 22 or 56 individuals from each cell of a 3x3 grid encompassing the landscape
References:
- Rebaudo, F., Le Rouzic, A., Dupas, S., Silvain, J.-F., Harry, M., and Dangles, O.
(2013). SimAdapt: an individual-based genetic model for simulating landscape management impacts on
populations. Methods in Ecology and Evolution, 4(6):595--600. doi:10.1111/2041-210X.12041
- Rebaudo, Francois (2014, October 13). "SimAdapt" (Version 9). CoMSES Computational Model Library. Retrieved from: https://www.openabm.org/model/3137/version/9