mantel_test_nbpartners function

Compute Mantel test

Compute Mantel test

This function tests for phylogenetic signal in species interactions in guild A using a Mantel test that keep constant the number of partners per species.

mantel_test_nbpartners(network, tree_A, tree_B = NULL, method="Jaccard_binary",
nperm = 1000, correlation = "Pearson")

Arguments

  • network: a matrix representing the bipartite interaction network with species from guild A in columns and species from guild B in rows. Row names (resp. columns names) must correspond to the tip labels of tree B (resp. tree A).
  • tree_A: a phylogenetic tree of guild A (the columns of the interaction network). It must be an object of class "phylo".
  • tree_B: (optional) a phylogenetic tree of guild B (the rows of the interaction network). It must be an object of class "phylo".
  • method: indicates which method is used to compute the phylogenetic signal in species interactions. If you want to perform a Mantel test between the phylogenetic distances and some ecological distances (do closely related species interact with similar partners?), you can choose "Jaccard_weighted" (default) for computing the ecological distances using Jaccard dissimilarities (or "Jaccard_binary" to not take into account the abundances of the interactions), "Bray-Curtis" for computing the Bray-Curtis dissimilarity, or "GUniFrac" for computing the weighted (or generalized) UniFrac distances ("UniFrac_unweighted" to not take into account the interaction abundances).
  • correlation: indicates which correlation (R) must be used among Pearson (default) and Spearman correlations.
  • nperm: a number of permutations to evaluate the significance of the correlation. By default, it equals 1000.

Returns

  • mantelr: Mantel correlation (R).

  • pval1: one-tailed p-value (null hypothesis: R <= 0).

  • pval2: one-tailed p-value (null hypothesis: R >= 0).

  • pval3: two-tailed p-value (null hypothesis: R = 0).

References

Perez-Lamarque B, Maliet O, Pichon B, Selosse M-A, Martos F, Morlon H. 2022. Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks. bioRxiv, 2021.08.30.458192, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology. https://doi.org/10.1101/2021.08.30.458192

Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27:209-220.

Author(s)

Benoît Perez-Lamarque

See Also

phylosignal_network

phylosignal_sub_network

mantel_test

Examples

# Measuring phylogenetic signal in species interactions using a Mantel test 
# with permutations keeping constant the number of partners per species

library(RPANDA)

# Load the data
data(mycorrhizal_network)

network <- mycorrhizal_network[[1]] # bipartite interaction matrix 
tree_orchids <- mycorrhizal_network[[2]] # phylogenetic tree (phylo object)

# mantel_test_nbpartners(network, tree_orchids, method="Jaccard_weighted", 
# correlation="Pearson",  nperm = 1000)
RPANDA packageRead PDF manual