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Conservation of gene order in vertebrates is evident after hundreds of millions of years of divergence^,, but comparisons of the Arabidopsis thaliana sequence to partial gene orders of other angiosperms (flowering plants) sharing common ancestry ∼170–235 million years ago yield conflicting results^,,,,,,. This difference may be largely due to the propensity of angiosperms to undergo chromosomal duplication (‘polyploidization’) and subsequent gene loss (‘diploidization’); these evolutionary mechanisms have profound consequences for comparative biology. Here we integrate a phylogenetic approach (relating chromosomal duplications to the tree of life) with a genomic approach (mitigating information lost to diploidization) to show that a genome-wide duplication^,,,,, post-dates the divergence of Arabidopsis from most dicots. We also show that an inferred ancestral gene order for Arabidopsis reveals more synteny …