Supplementary Material 4. Best partition scheme and nucleotide substituion models based on BIC in IQTREE
(-m TESTMERGE) starting from 39 partitions (by 13 genes and by 3 codon sites)

-q command in IQTREE (edge-linked partition model)

#nexus
begin sets;
  charset atp6_cod1_coob_cod1_nad3_cod1 = 1-669\3  814-1944\3  6877-7227\3;
  charset atp8_cod1_nad2_cod1_nad6_cod1_atp8_cod2 = 670-813\3  5872-6876\3  10243-10731\3  671-813\3;
  charset cox1_cod1_cox2_cod1_cox3_cod1 = 1945-3471\3  3472-4152\3  4153-4932\3;
  charset nad1_cod1_nad4_cod1_nad5_cod1_nadl_cod1 = 4933-5871\3  7228-8556\3  8557-10242\3  10732-11016\3;
  charset atp6_cod2_coob_cod2_nad2_cod2_nad3_cod2_nad6_cod2 = 2-669\3  815-1944\3  5873-6876\3  6878-7227\3  10244-10731\3;
  charset cox1_cod2_cox2_cod2_cox3_cod2 = 1946-3471\3  3473-4152\3  4154-4932\3;
  charset nad1_cod2_nad4_cod2_nad5_cod2_nadl_cod2 = 4934-5871\3  7229-8556\3  8558-10242\3  10733-11016\3;
  charset atp6_cod3_atp8_cod3_coob_cod3_cox1_cod3_cox2_cod3_cox3_cod3_nad2_cod3_nad3_cod3_nad6_cod3 = 3-669\3  672-813\3  816-1944\3  1947-3471\3  3474-4152\3  4155-4932\3  5874-6876\3  6879-7227\3  10245-10731\3;
  charset nad1_cod3_nad4_cod3_nad5_cod3_nadl_cod3 = 4935-5871\3  7230-8556\3  8559-10242\3  10734-11016\3;
  charpartition mymodels =
    GTR+F+I+G4: atp6_cod1_coob_cod1_nad3_cod1,
    HKY+F+I+G4: atp8_cod1_nad2_cod1_nad6_cod1_atp8_cod2,
    GTR+F+I+G4: cox1_cod1_cox2_cod1_cox3_cod1,
    GTR+F+I+G4: nad1_cod1_nad4_cod1_nad5_cod1_nadl_cod1,
    GTR+F+I+G4: atp6_cod2_coob_cod2_nad2_cod2_nad3_cod2_nad6_cod2,
    HKY+F+I+G4: cox1_cod2_cox2_cod2_cox3_cod2,
    GTR+F+I+G4: nad1_cod2_nad4_cod2_nad5_cod2_nadl_cod2,
    GTR+F+I+G4: atp6_cod3_atp8_cod3_coob_cod3_cox1_cod3_cox2_cod3_cox3_cod3_nad2_cod3_nad3_cod3_nad6_cod3,
    GTR+F+I+G4: nad1_cod3_nad4_cod3_nad5_cod3_nadl_cod3;
end;

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-ssp command in IQTREE (allowing partition-specific rates)

#nexus
begin sets;
  charset atp6_cod1_atp8_cod1_coob_cod1_nad2_cod1_nad3_cod1_nad6_cod1_atp8_cod2 = 1-669\3  670-813\3  814-1944\3  5872-6876\3  6877-7227\3  10243-10731\3  671-813\3;
  charset cox1_cod1_cox2_cod1_cox3_cod1 = 1945-3471\3  3472-4152\3  4153-4932\3;
  charset nad1_cod1_nad4_cod1_nad5_cod1_nadl_cod1 = 4933-5871\3  7228-8556\3  8557-10242\3  10732-11016\3;
  charset atp6_cod2_coob_cod2_nad2_cod2_nad3_cod2_nad6_cod2 = 2-669\3  815-1944\3  5873-6876\3  6878-7227\3  10244-10731\3;
  charset cox1_cod2_cox2_cod2_cox3_cod2 = 1946-3471\3  3473-4152\3  4154-4932\3;
  charset nad1_cod2_nad4_cod2_nad5_cod2_nadl_cod2 = 4934-5871\3  7229-8556\3  8558-10242\3  10733-11016\3;
  charset atp6_cod3_atp8_cod3_coob_cod3_cox1_cod3_cox2_cod3_cox3_cod3_nad2_cod3_nad3_cod3_nad6_cod3 = 3-669\3  672-813\3  816-1944\3  1947-3471\3  3474-4152\3  4155-4932\3  5874-6876\3  6879-7227\3  10245-10731\3;
  charset nad1_cod3_nad4_cod3_nad5_cod3_nadl_cod3 = 4935-5871\3  7230-8556\3  8559-10242\3  10734-11016\3;
  charpartition mymodels =
    GTR+F+I+G4: atp6_cod1_atp8_cod1_coob_cod1_nad2_cod1_nad3_cod1_nad6_cod1_atp8_cod2,
    GTR+F+G4: cox1_cod1_cox2_cod1_cox3_cod1,
    GTR+F+I+G4: nad1_cod1_nad4_cod1_nad5_cod1_nadl_cod1,
    GTR+F+G4: atp6_cod2_coob_cod2_nad2_cod2_nad3_cod2_nad6_cod2,
    GTR+F+I+G4: cox1_cod2_cox2_cod2_cox3_cod2,
    GTR+F+I+G4: nad1_cod2_nad4_cod2_nad5_cod2_nadl_cod2,
    HKY+F+I+G4: atp6_cod3_atp8_cod3_coob_cod3_cox1_cod3_cox2_cod3_cox3_cod3_nad2_cod3_nad3_cod3_nad6_cod3,
    HKY+F+I+G4: nad1_cod3_nad4_cod3_nad5_cod3_nadl_cod3;
end;