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Table 1 Summary of datasets and phylogenomic analyses

From: Museomics and phylogenomics with protein-encoding ultraconserved elements illuminate the evolution of life history and phallic morphology of flesh flies (Diptera: Sarcophagidae)

Analysis number Datamatrix Occupancy (%) UCE loci Sequence coding Model Analysis Topology
1 10_nt_ml 0.10 2018 Nucleotides GTRCAT concat. RAxML A
2 20_nt_ml 0.20 1778 Nucleotides GTRCAT concat. RAxML A
3 30_nt_ml 0.30 1634 Nucleotides GTRCAT concat. RAxML A
4 40_nt_ml 0.40 1524 Nucleotides GTRCAT concat. RAxML A
5 50_nt_ml 0.50 1417 Nucleotides GTRCAT concat. RAxML A
6 60_nt_ml 0.60 1271 Nucleotides GTRCAT concat. RAxML A
7 70_nt_ml 0.70 936 Nucleotides GTRCAT concat. RAxML int.
8 80_nt_ml 0.80 440 Nucleotides GTRCAT concat. RAxML int.
9 90_nt_ml 0.90 59 Nucleotides GTRCAT concat. RAxML B
10 10_nt_astral 0.10 2018 Nucleotides GTR + F + I + G4 coales. ASTRAL-III A
11 30_nt_astral 0.30 1634 Nucleotides GTR + F + I + G4 coales. ASTRAL-III A
12 60_nt_astral 0.60 1271 Nucleotides GTR + F + I + G4 coales. ASTRAL-III A
13 75_nt_astral 0.75 288 Nucleotides GTR + F + I + G4 coales. ASTRAL-III int.
14 10_aa_astral 0.10 2018 Amino acids HIVw + F + I + G4 coales. ASTRAL-III A
15 30_aa_astral 0.30 1634 Amino acids HIVw + F + I + G4 coales. ASTRAL-III A
16 60_aa_astral 0.60 1271 Amino acids HIVw + F + I + G4 coales. ASTRAL-III A
17 75_aa_astral 0.75 288 Amino acids HIVw + F + I + G4 coales. ASTRAL-III int.
  1. Topologies have been grouped into A, B and ‘int’ for intermediate according to their phylogenetic relationships