Figure 1

(a) A species tree S for G ={1,2,3,4}. The three internal vertices of S are named A, B and C; (b) A gene tree T. A leaf label x indicates a gene copy in genome x. Internal vertices are labelled according to the LCA mapping between T and S. Flagged vertices are duplication vertices of T with respect to S (Section “LCA Mapping”); (c) A reconciliation R(T,S) of T and S. Dotted lines represent subtree insertions. The correspondence between vertices of R(T,S) and S is indicated by vertex labels. Flagged vertices are duplication vertices. All other internal vertices of R(T,S) are speciation vertices. This reconciliation reflects a history of the gene family with two gene duplications preceding the first speciation event, and 4 losses.