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).