ReproPhylo: An Environment for Reproducible Phylogenomics
Fig 3
Exploratory phylogenomic analysis of a Lepidoptera dataset.
(A) A nucleotide dataset from 26 species from Kawahara and Breinholt [40] was reanalyzed. Loci were sorted by their median, 75 percentile and 25 percentile entropy values (centre panel). For each locus, a box plot was generated. The medians are denoted by brown dots. The boxes (blue) represent the 25–75 percentiles. Whiskers (black) represent values that are found within a range outside the box, 1.5 times as long as the box (which is null, when the box itself has a null range) Trees (insets A 1–6) were reconstructed from 200-locus windows with 50 locus overlap between neighbouring windows. The windows are represented by black and gray horizontal bars, each with an arrow pointing to the tree generated from it. In trees 1–6, dark blue highlights denote Rhopalocera (butterfly) taxa, and light blue, gray and yellow highlights denote clades I, III and IV respectively (sensu Kawahara and Breinholt [40]). Bullets on nodes represent Bootstrap percentages (BP). Blue bullets represent maximal support. Other support values above 80% are denoted by gray bullets. (B-D) Three pairwise tree divergence metrics were calculated and presented as heatmaps, with the most divergent tree pairs denoted by dark blue and identical tree pairs by a white box. While the scales are not comparable among the metrics, the relative differences are. The metrics are (B) the Symmetric Distance of Robinson-Foulds [44], (C) the Branch Distance [45] and (D) evolutionary rate corrected Branch Distance [45].