Misconstruing scenario's. Misconstruing scenario's: genes C0/L0 (reddish) and Ca/La (greenish) co-duplicate, forming two orthologous groups in two species S0 and S1. a. Gene La.1 is lost in species S1 (gray). On a COG basis, gene L0.2 in species S1 is the only gene with gene-order conservation. Based on LOFT, this scenario is correctly interpreted. b. Gene La.1 is lost in species S1, while gene La.2 is lost in species S0 (differential gene-loss). As a result, gene La.2 in species S1 is erroneously assigned to LOFT cluster La.1 causing gene L0.2 in species S1 to appear the gene with gene order conservation (while using COG or LOFT).