Supplementary Figure S4

Supplementary Figure S4 Support for the four most common gene tree topologies for each marker type. Median bootstrap support (a-c) and the median number of substitutions under a parsimony criterion (d-f) for branches in gene tree topologies that conflict with the species tree are shown for each marker type. Letters below each group refer to topologies shown in (j), with numbers referring to branches labelled on those topologies. Reference lines in (a-c) are drawn at 50% bootstrap support. (g-i) Violin plots of ΔAIC for loci belonging to each AGT category for CNEEs (part g), introns (part h), and UCEs (part i). Values show the difference in AIC for sequence alignments given the majority rule extended consensus gene tree topology, relative to the AIC when sequence alignments are constrained to the species tree topology. A reference line is drawn at ΔAIC(gene tree–species tree)= -2, with values beneath this cut off indicating substantially stronger support in favor of the gene tree topology (Burnham and Anderson 2002).