Plants of southern Africa

Source: R/phyloregion-package.R

This dataset consists of a dated phylogeny of the woody plant species of southern Africa along with their geographical distributions. The dataset comes from a study that maps tree diversity hotspots in southern Africa (Daru et al. 2015). The study mapped five types of diversity hotspots including species richness (SR), phylogenetic diversity (PD), phylogenetic endemism (PE), species weighted endemism (CWE), and evolutionary distinctiveness and global endangerment (EDGE). The results revealed large spatial incongruence between biodiversity indices, resulting in unequal representation of PD, SR, PE, CWE and EDGE in hotspots and currently protected areas, suggesting that an integrative approach which considers multiple facets of biodiversity is needed to maximise the conservation of tree diversity in southern Africa. Specifically for this package, we arranged the dataset into four components: “comm”, “polys”, “phylo”, “mat”, “IUCN”.

Details

  • comm: This is a sparse community composition matrix of each species presences/absences within 50 × 50 km grid cells. A sparse matrix is a matrix with a high proportion of zero entries (Duff 1977), of which only the non-zero entries are stored and used for downstream analysis.

  • polys: These are the grid cells covering the geographic extent of study area. These can be created using the function fishnet. The polys object is of class SpatVector and has a column labeled “grids”, with the grid identities.

  • phylo: This corresponds to the phylogenetic tree which was estimated using Bayesian analysis of 1,400 species and 1,633 bp of chloroplast DNA sequences derived from a combination of matK and rbcLa, assuming an uncorrelated relaxed molecular clock model, using the program BEAST v.1.7.5 (Drummond & Rambaut, 2007). Branch lengths were calibrated in millions of years using a Bayesian MCMC approach by enforcing topological constraints assuming APG III backbone from Phylomatic v.3 (Webb & Donoghue, 2005) and 18 fossil calibration points from Bell et al. (2010).

  • mat: This is a distance matrix of phylogenetic beta diversity between all grid cells at the 50 × 50 km scale.

  • IUCN: This is a dataframe of IUCN conservation status of each woody species (LC, NT, VU, EN, CR). This is useful for analysis of Evolutionary Distinctiveness and Global Endangerment using the function EDGE.

References

Bell, C.D., Soltis, D.E., & Soltis, P.S. (2010). The age and diversification of the angiosperms re-revisited. American Journal of Botany 97, 1296–1303.

Daru, B.H., Van der Bank, M. & Davies, T.J. (2015) Spatial incongruence among hotspots and complementary areas of tree diversity in southern Africa. Diversity and Distributions 21, 769-780.

Drummond, A.J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology 7, 214.

Duff, I.S. (1977). A survey of sparse matrix research. Proceedings of the IEEE 65, 500–535.

Webb, C.O., & Donoghue, M.J. (2005). Phylomatic: Tree assembly for applied phylogenetics. Molecular Ecology Notes 5, 181–183.

Examples

data(africa)
names(africa)
#> [1] "comm"  "phylo" "mat"   "IUCN"  "K"     "theta" "omega" "trait"
# \donttest{
library(terra)
#> terra 1.7.55
#> 
#> Attaching package: ‘terra’
#> The following objects are masked from ‘package:ape’:
#> 
#>     rotate, trans, zoom
library(ape)
plot(africa$phylo)

# }