Fig. 5
From: Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses
Effect of paralog splitting criteria on the inference of gene flux. a Species-wise comparison of the total gene flux (gains and losses along the species tree, left), the ratio between gene turnover and gene sequence evolution (middle), and total gain vs loss ratio (right) inferred from synteny- and orthology-based OGC. The method-dependent uncertainty is equal to 1 − R2. b Flux per gene per functional category inferred from orthology- (top) and synteny-based (middle) OGC. Each data point corresponds to one species; boxes span the 25–75 percentiles; the central line indicates the median; whiskers extend to the most extreme data points that are not outliers; isolated points denote outliers. The bar plot at the bottom shows the inconsistency between methods, quantified as one minus the squared rank correlation. Abbreviations of functional categories as in Fig. 4. c Median flux per gene per category, calculated over all the species, for orthology-based (x-axis) and synteny-based (y-axis) OGC. Similar trends are observed for gains, losses, and the combination of both