Fig. 1

Example of PNS for a 100-vertebrates tree. Here we show graphically the values of the phylogenetic novelty scores \(w_s\) from Eq. 1 for the tips of a tree of 100-vertebrate species. The tree is taken from the UCSC genome browser 100-way alignment of vertebrates to the human genome, downloaded from http://hgdownload.cse.ucsc.edu/goldenPath/hg38/multiz100way/hg38.100way.commonNames.nh. The scale bar indicates 0.25 expected substitutions per site. This tree was also used for simulations in this work. a The tree has all tips spaced uniformly on the horizontal axis, representing the case of no weighting scheme being used. b Tips are spaced horizontally according to their \(w_s\) weight. The weight of each tip can also be seen in the length of the colored bars. Notice how species in regions of the tree with many close relatives (e.g. mammal, primate and bird clades) have low PNSs, and so take up less space individually. This means the horizontal dimension of the plot now gives more equal representation of the novelty of each sequence and clade, instead of emphasising densely sampled clades. More divergent species with few close relatives (e.g. lamprey, coelacanth, frog and platypus) have higher PNSs and are given more horizontal space, representing the greater novelty of their sequences relative to other species in the tree. Cumulative ESN scores (clade-wise sum of PNSs) are also shown for some clades