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Fig. 1 | Algorithms for Molecular Biology

Fig. 1

From: Evolution through segmental duplications and losses: a Super-Reconciliation approach

Fig. 1

(i) Two genomes A and B; three gene families (red, green and blue) grouped into two syntenies \(A_1, A_2\) in A and two syntenies \(B_1, B_2\) in B. (ii) Ignoring node labels and dotted lines, T, \(T'\) and \(T''\) are the corresponding gene trees and \(\tilde{T}\), \(\tilde{T}'\) and \(\tilde{T}''\) are the corresponding synteny trees. The reconciled gene trees R, \(R'\) and \(R''\) are the same trees but including node labels and dotted lines. Nodes identified by circles are speciations, those represented by rectangles are duplications, and dotted lines represent lost branches. (iii) The reconciled trees embedded into the species tree S. (iv) A Super-Reconciliation \({\mathcal {R}}\), representing a more realistic evolutionary history from a common ancestral synteny. Each ancestral node is identified by the synteny, the event and the segment of the synteny affected by the event. Square nodes represent Dup events, round nodes Spe events, brackets pLoss events and dotted lines fLoss (see text)

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