Fig. 6

Comparison of assignments in gene classifications by three methods. The Brassicaceae study (a) represents overlaps in gene classifications across four phylostrata of Brassicaceae. The Saccharomyces study (b) represents overlaps in gene classifications across six phylostrata, from the S. cerevisiae-specific orphan phylostrata, through the genes unique to each of the s5 to s2 internal clades, to the genes conserved across the Saccharomyces genus. The three methods of comparison are 1) standard which represents standard phylostratigraphy; 2) fagin default which is the default fagin behaviour of identifying phylostrata based on presence/absence of any AAic inferred ortholog; and 3) fagin strict which identifies phylostrata based on presence/absence of amino acid matches only to annotated target genes (similar to standard phylostratigraphy). All methods use the set of protein coding genes that were inferred through standard phylostratigraphy to be limited to the Brassicaceae or Saccharomyces clades. c and d are the species trees representing the target genomes used for Brassicaceae [52] and Saccharomyces [53], respectively. The numbers indicate the number of genes in each clade according to standard phylostratigraphy (from phylostratr for Saccharomyces [50]; [51] for Brassicaceae). Nodes on the Saccharomyces tree, orange text, are labeled as s5-s2 because there are no taxonomic names for these within-genus clades