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Figure 1 | BMC Evolutionary Biology

Figure 1

From: Duplications and functional divergence of ADP-glucose pyrophosphorylase genes in plants

Figure 1

Reconciled large and small subunit trees. A) Amino acid tree of the large and small subunits from angiosperms, Physcomitrella patens and Chlamydomonas reinhardtii. The topology of the tree was determined by ML using aligned amino acid sequences using PhyML. Branch lengths reflect numbers of amino acid substitutions per site. The branches within groups have been replaced by the grey triangles. ML bootstrap values are indicated above branches, and the bar shows the number of amino acid substitutions per site. B) Angiosperm large subunit reconciled tree. C) Angiosperm small subunit reconciled tree. The topology of the trees shown in B) and C) was determined by ML using aligned cDNA sequences using GARLI. Branch lengths reflect numbers of amino acid substitutions per site as estimated by AAML and the scale bar shows the number of amino acid substitutions per site. ML bootstrap values > 50% are indicated above branches. Reconciled tree analyses (using the gene trees shown and the species tree shown in Additional file 1) were conducted using GENETREE. Black boxes at nodes indicate duplication events. The arrow in B) indicates the divergence of Physcomitrella patens from angiosperms. The trees in B) and C) were rooted with the AGPase large and small subunit from Chlamydomonas reinhardtii respectively. Thicker lines indicate branches that follow duplication events and have KS < 0.1 (based upon ML estimates of synonymous branch lengths).

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