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].