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These analyses were carried out for three kinds of tree sets obtained by individual analyses of each of the three regions: (1) all most parsimonious trees recovered in maximum parsimony analyses, (2) all most likely trees recovered in maximum likelihood analyses, and (3) 100 bayesian trees recovered in Bayesian inference of phylogeny.
The maximum parsimony analyses produced 50 of the most parsimonious trees with 1,435 steps.
Maximum likelihood and maximum parsimony analyses recovered two phylogenetic hypotheses that differed in the placement of one of the areas.
Numbers at left and right above the branches represent bootstrap values (50% or more) of ML and maximum parsimony analyses, respectively, based on 1000 replicates.
Bayesian and maximum parsimony analyses revealed identical topologies.
Maximum parsimony analyses were conducted using Paup* v.4.0b10a [34].
Maximum parsimony analyses (MP) were conducted with WinClada [65] and NONA [76].
A total of 1000 bootstrap replicates were performed for each maximum parsimony analyses.
Neighbor-joining distance and maximum parsimony analyses were performed with PAUPV4b10 [58], with indels coded as missing data.
A few more were identified following closer examination of sequences on long branches in preliminary maximum parsimony analyses.
Maximum parsimony analyses using the rbcL + trnL-F reference database compiled in this study successfully identified samples as Dryopteris dilatata, Athyrium filix-femina or Thelypteris palustris.
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