Phylogenetic analysis of Tenebrionoidea
Phylogenetic relationships of 90 species of mtgenomes (including 19
sequenced in this study) in Tenebrionoidea were deduced using three
datasets and two inference methods with Aiolocaria hexaspilotaand Henosepilachna vigintioctopunctata (Coleoptera:
Coccinelloidea) as outgroups. Taxonomic information for each species
investigated and mtgenome accession numbers are listed in Table 1. Three
datasets were concatenated using PhyloSuite platform: 1) amino acid
sequence of 13 PCGs (AA); 2) nucleotide sequence at 1st and 2nd codon
position of 13 PCGs (PCG12); 3) PCG12 + 2 rRNAs, respectively with
excluding start codon, stop codon. Nucleotide sequences of 13 PCGs were
aligned by codon-based multiple alignments using the L-INS-i algorithm
and the rRNAs were aligned using the Q-INS-i strategy in MAFFT v. 7.0
(Katoh & Standley, 2013), and ambiguously aligned positions were
excluded using Gblocks (Talavera & Castresana, 2007). The concatenation
of aligned sequences was performed using SequenceMatrix (Vaidya et
al. , 2011). The selection of best-fit partitioning schemes and
substitution models for each dataset were calculated using
PartitionFinder v. 2.0 (Lanfear et al. , 2016) with the settings:
branch lengths as linked, model election as AICc with the greedy
algorithm. Partitioning schemes and models are listed in Table S2. Two
methods, maximum likelihood (ML) and Bayesian inference (BI) were
employed for the deduce. ML-based phylogenetic analyses were conducted
using IQ-TREE v. 1.6.8 in PhyloSuite v. 1.2.2 (Zhang et al. ,
2020). Nodal support values were inferred with 1 000 bootstrapped
replicates (BPs) (Minh et al. , 2013). BI analysis was conducted
using MrBayes v. 3.2.6 (Ronquist et al. , 2012). A total of 2 000
000 generations with four chains were sampled every 1 000 generations.
Posterior probabilities (PPs) were computed after discarding the first
25% of trees as the burn-in phase. The estimated sample size (ESS)
> 200 and the average deviation of the split frequency of
less than 0.01 indicates that the runs had converged. The phylogenetic
tree was visualized using FigTree v. 1.4.4 and iTOL online tool (Letunic
and Bork, 2016).