NJ-consensus phylogeny of AFLP data and major effects revealed with HET.
The NJ consensus topology is based on Jaccard’s distances [62] of 3312 nc loci. Nodes affected by homoplasious effects are designated with letters A-M and indicated by open, red circles. Numbers at nodes refer to bootstrap-values (BS 500 replicates) and a 100% BS support is indicated by filled, black circles. Geographic distribution of taxa is depicted vertically on the right and colour shaded in the tree (Lake Tanganyika: yellow; Lake Malawi orange; rivers: grey). Major effects detected with HET and inference of cyto-nuclear discordances are delineated in coloured boxes on the left and correspond to those in Fig 6 and Fig 8. Arrows and coloured branches point to clades which especially introduce homoplasy in the dataset. Strong alternative signal (BS support >30) is denoted with dotted lines on the left.
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