Our data sets used in this study were based on the gene sets of Brown et al. (2012) with some modifications of the taxa included (see supplementary table S1, Supplementary Material online, for the details).
Apart from fundamental implications for evolutionary processes, the present study has provided information and resources for detection, discrimination and potential modification of agronomically important endophyte taxa.
For species-level classification, Wilson and Reeder [52] (with minor modifications) was followed, so that the number of taxa that did not correctly associate with their taxonomic ranks was calculated and the percentage of correctly associated taxa was calculated.
If the "Modified Lineage" box in the setting-parameter page is checked, a default Lineage Modification file is used to report the convergence of taxa.
Cladistic approaches to evolutionary analysis seek to capture patterns of character states among a set of taxa that were created by descent with modification from ancestors through time (Freeman and Herron 2007).
Assume that we are given a set of taxa X that have evolved under a model of evolution that includes both speciation events and descent with modification, as usual, and, in addition, hybridization events.
Proof The proof is a modification of the proof for Theorem 2. The "good" taxa are placed in the same way and the bad taxa are placed onto any split corresponding to a conflicting split in.
For this reason, individual taxa or selections of taxa were selected using a random number generator.
Two datasets were defined by the level of taxonomic identification, all taxa or a subset of common taxa, and the level of taxa reduction; all taxa, taxa > 1% of total abundance, and taxa significantly contributing to variation.
These are useful for visual comparisons of taxa at various levels.
