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Table 1 Summary of initial conditions and results obtained in phylogenetic reconstructions and model testing.

From: Molecular phylogenetics and evolutionary history of ariid catfishes revisited: a comprehensive sampling

Analysis Mitochondrial Nuclear Combined
  129 taxa, 2866 bp 73 taxa, 978 bp 73 taxa, 3844 bp
MP    
RA replicates 100 5 100
Bootstrap replicates 1000 (10 RA rep.) _ 1000 (10 RA rep.)
Optimal trees retained 8 >5 × 104 36
Optimal tree score (steps) 11208 387 9002
Consistency index 0.188 0.749 0.25
Consensus type strict 50% majority rule 90% majority rule
Initial model (ML and BI)    
Akaike information criterion GTR+I+Γ HKY+I+Γ GTR+I+Γ
Number of substitution rate parameters 6 2 6
ML – Garli    
Search replicates 10 5 10
Automatic termination* (generations) 1 × 104 1 × 104 1 × 104
Optimal tree score (lnL) -52003.50 -3791.51 -43666.78
Bootstrap _ _ _
ML – RAxML    
Search replicates 10 5 5
Partitions none none none
Optimal tree score (lnL) -52145.37 -3790.72 -43726.10
Bootstrap replicates** 150 400 200
BI    
Search replicates 3 3 3
Partitions none none none
Generations 1 × 107 6 × 106 6 × 106
Burn-in 2.5 × 106 1.5 × 106 1.5 × 106
Post-burn-in trees (combined searches) ~2.15 × 105 ~1.35 × 105 ~1.35 × 105
Mean lnL -52160 -4119.14 -43760
Efective Sample Size (all parameters) >200 >200 >200
Consensus type 50% majority rule 50% majority rule 50% majority rule
  1. RA, random addition
  2. *genthreshfortopoterm command
  3. **rapid bootstrapping algorithm via automatic termination
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