Additional file 2 of Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)
Creators: name: Zhang, Qi
name: Lu, Yi-Wen
name: Liu, Xin-Yu
name: Li, Ye
name: Gao, Wei-Nan
name: Sun, Jing-Tao
name: Hong, Xiao-Yue
name: Shao, Renfu
name: Xue, Xiao-Feng
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1. The 54 mitochondrial gene arrangement patterns (Pattern 1–Pattern 54) from 153 eriophyoid mite species in this study. Genes underlined have opposite transcription orientation to those not underlined. Translocated or inverted genes are colour‐coded (blue: inversion and translocation; green: translocation; orange: inversion). Abbreviations of protein‐coding genes are atp6 and atp8 for ATP synthase subunits 6 and 8; cox1–3 for cytochrome oxidase subunits 1–3; cob for cytochrome b; nad1–6 and nad4L for NADH dehydrogenase subunits 1–6 and 4L; rrnL and rrnS for large and small rRNA subunits; tRNA genes are indicated by the single‐letter IUPAC‐IUB abbreviations for their corresponding amino acids. The shared rearranged mt gene clusters of each sample were denoted by underneath lines in different colors as the same as Fig. 1. Fig. S2. Mitochondrial gene arrangements of representative samples in the Eriophyoidea. Two samples were selected as representatives of each clade. Shared rearranged mt gene clusters of each sample were denoted by underneath lines in different colors. Underlined genes are encoded in the N‐strand. Translocated or inverted genes are colour-coded (blue: inversion and translocation; green: translocation; orange: inversion). Abbreviations of protein‐coding genes are atp6 and atp8 for ATP synthase subunits 6 and 8; cox1–3 for cytochrome oxidase subunits 1–3; cob for cytochrome b; nad1–6 and nad4L for NADH dehydrogenase subunits 1–6 and 4L; rrnL and rrnS for large and small rRNA subunits; tRNA genes are indicated by the single‐letter IUPAC‐IUB abbreviations for their corresponding amino acids.Fig. S3. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences using maximum likelihood method with partition by gene and GTRGAMMAI model. Fig. S4. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences (without the 3rd codon positions of PCGs) using maximum likelihood method with partition by gene and GTRGAMMAI model. Fig. S5. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences using maximum likelihood method with partition by codon and GTRGAMMAI model. Fig. S6. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences (without the 3rd codon positions of PCGs) using maximum likelihood method with partition by codon and GTRGAMMAI model. Fig. S7. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences using maximum likelihood method with partition by PartitionFinder and GTRGAMMAI model. Fig. S8. The phylogenetic tree inferred from mitochondrial genome amino acid sequences using maximum likelihood method with partition by gene and GAMMA model. Fig. S9. The phylogenetic tree inferred from mitochondrial genome amino acid sequences using maximum likelihood method with partition by PartitionFinder and GAMMA model. Fig. S10. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences using maximum likelihood method with partition by gene and GTRCAT model. Fig. S11. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences (without the 3rd codon positions of PCGs) using maximum likelihood method with partition by gene and GTRCAT model. Fig. S12. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences using maximum likelihood method with partition by codon and GTRCAT model. Fig. S13. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences (without 3rd codon positions of PCGs) using maximum likelihood method with partition by codon and GTRCAT model. Fig. S14. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences using maximum likelihood method with partition by PartitionFinder and GTRCAT model. Fig. S15. The phylogenetic tree inferred from mitochondrial genome amino acid sequences using maximum likelihood method with partition by gene and GTRCAT model. Fig. S16. The phylogenetic tree inferred from mitochondrial genome amino acid sequences using maximum likelihood method with partition by PartitionFinder and GTRCAT model. Fig. S17. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences (without 3rd codon positions of PCGs) using Bayesian method and partition by gene. Fig. S18. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences using Bayesian method and partition by codon. Fig. S19. The phylogenetic tree inferred from mitochondrial genome nucleotide sequences (without 3rd codon positions of PCGs) using Bayesian method and partition by codon. Fig. S20. The phylogenetic tree inferred from mitochondrial amino acid sequences using PMSF method in IQ-TREE with LG + C20+F+ G” model. Fig. S21. The relevant Navajo (sensitivity) plots to the 12 internal nodes of the RCP grade in Fig. 2. Fig. S22. (a) Box plots ofKa (nonsynonymous substitutions per nonsynonymous site) in different arachnid lineages, marked by different colours. (b) Box plots of Bp (breakpoints) in different arachnid lineages, marked by different colours.