2.6 Phylogenetic analysis of Hypocrealean species
To determine the phylogenetic relationships of the cordyceps species among the Hypocreales order, 19 mitogenomes were downloaded from the NCBI database and subjected to Maximum Likelihood (ML) and Bayesian phylogenetic analysis using the aforementioned 14 PCGs and rps3 . Rhizopogon salebrosus and Rhizopogon vinicolor were used as outgroups for the analyses (Table S1). Single mitochondrial genes were first aligned using MAFFT v7.037 [49] and these alignments were then concatenated using SequenceMatrix v1.7.8 (http://www.softpedia.com/get/Science-CAD/Sequence-Matrix.shtml) [50]. The ML tree was then calculated for the combined gene set using RAxML v8.0.0 [51], while Bayesian inference (BI) analysis was performed with MrBayes v3.2.6 [52]. Other analyses and evaluation methods were conducted based on previously described protocols [9].