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Table 4 Maximum-parsimony tree and evolutionary model parameters, Bayesian burn-in specifications for both individual data partitions and for the combined dataset

From: Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes

Partition ND2 Fib5 Concatenated
Score of MP trees 1578 174 1610
Consistency index of MP trees 0.407 0.759 0.475
Retention index of MP trees 0.844 0.883 0.779
Best evolutionary model (-lnL) TrN+G (7887.1631) HKY+G (1937.5226 n/a
Base frequencies (A, C, G) 0.3089, 0.3089, 0.0922 0.2902, 0.1695, 0.2296 n/a
Transition/transversion ratio n/a 2.4813 n/a
Substitution rate matrix (AC, AG, AT, CG, CT) 1, 29.4411, 1, 1, 15.1094 n/a n/a
Gamma shape parameter 0.2632 0.3180 n/a
Proportion of invariable sites 0 0 n/a
Burn-in of Bayesian analysis 100,000 10,000 75,000
  1. Abbreviations: MP – most-parsimonious, n/a – not applicable