Topologies for five proximal γ ancestral loci that contain three collinear Vitis genes. Vitis gene names are abbreviated as “[chromosome].[gene index]” for graphing. Each tree was rooted using one best-matching moss gene, identified by JGI protein accession number. The numbers above branches are bootstrap values in the phylogenetic reconstruction. There are a total of 10 local blocks that have more than five triplets in Carica and Vitis that are studied in the same way. Phylogenetic analysis was performed using PHYLIP version 3.67 (Retief 2000). The analysis was carried out using the protdist program (default parameters) followed by neighbor-joining using neighbor. We used the seqboot program to simulate 100 bootstrap replicates and the consense program to retrieve one consensus tree.
