Phylogenetic signal of traits

Measures how strongly closely related species resemble each other in each trait, with Blomberg's K (Blomberg et al. 2003) or Pagel's lambda (Pagel 1999), using phytools::phylosig(). K = 1 and lambda = 1 match Brownian-motion evolution; values near 0 mean no phylogenetic signal.

Usage

phylo_signal(
  traits,
  tree,
  species = species,
  cols = tidyselect::everything(),
  method = c("K", "lambda"),
  nsim = 999
)

Arguments

traits

A data frame with a species column and numeric traits.

tree

A phylogeny of class phylo (ape); tip labels must match species names.

species

<tidy-select> The species column of traits.

cols

<tidy-select> Numeric trait columns.

method

"K" or "lambda".

nsim

Number of randomisations for the test of K.

Value

A tibble with trait, method, n_species (with data and in the tree), statistic and p.value (randomisation test for K, likelihood-ratio test against lambda = 0 for lambda).

References

Blomberg, S. P., Garland, T. and Ives, A. R. (2003). Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57, 717-745. doi:10.1111/j.0014-3820.2003.tb00285.x

Pagel, M. (1999). Inferring the historical patterns of biological evolution. Nature, 401, 877-884. doi:10.1038/44766