Given the increasing interest in quantifying the phylogenetic diversity and dispersion in communities and the increasing use of phylogenetic supertrees to conduct such measurements, it is critical that we quantify the potential biases and the potential loss of statistical power introduced by this approach.
Despite this interest in quantifying the phylogenetic diversity and dispersion of communities, many methodological hurdles remain.
In recent decades ecologists, evolutionists and conservationists have become increasingly interested in quantifying the phylogenetic diversity and phylogenetic dispersion of communities [1] [3], [6], [9], [11] [12], [21] [22].
Despite this interest, quantifying the phylogenetic diversity and dispersion of communities often necessitates utilizing phylogenetic supertrees that contain multiple unresolved nodes.
While these two measures are still often reported and analyzed, conservationists and community ecologist have become increasingly interested in quantifying the phylogenetic diversity and phylogenetic dispersion of communities [1] [12].
Testing hypotheses about diversity requires a reliable technique for quantifying the phylogenetic relationships amongst shotgun metagenomic sequencing reads.
Townsend's phylogenetic informativeness (PI) method provides a quantitative measure of the phylogenetic signal in markers by quantifying the probability that a character changes at a certain position of a tree, and does not undergo further change [ 48].
Conservation biologists and community ecologists have increasingly begun to quantify the phylogenetic diversity and phylogenetic dispersion in species assemblages.
We also quantify the phylogenetic signals of N fixation and each successional index, which indicate the evolutionary conservatism of each trait.
We also quantified the phylogenetic support for each taxon in the bootstrap trees using quartet distances (e.g. [ 59]).
