Tree reconciliation example. Two alternative rootings of the same unrooted gene tree (thin black lines) imbedded in a species tree (thick grey lines) visualized with the tool PrIMETV . The gene tree is the maximum likelihood tree for a data set with 12 tentative consensus (TC) sequences assembled from ESTs from seven taxa (our cluster 13024). Bars indicate duplications within species (in-duplications) and black circles indicate out-duplications (those followed by a speciation event). A. The gene tree rooted to minimize the number of duplications required to reconcile the trees (two out-duplications required). B. The gene tree rooted using midpoint rooting, which places the root along the branch to the Arabidopsis sequences. This rooting is less optimal, requiring five out-duplications.