Whole genome duplications (WGD) have been a frequent occurrence during the evolution of angiosperms, providing all gene families the opportunity to grow and diversify. Most of this potential growth has not been realized, since each WGD has been followed by massive gene losses. The likelihood of survival of gene duplicates after a WGD has been shown to depend on their function, as is also the case for single gene duplications. These two modes of growth have different functional and evolutionary implications and have had a markedly divergent impact on the evolution of different gene families. Despite duplications, gene losses, and translocations it is still possible in many cases to reconstruct the history of angiosperm genomic segments, sometimes back to the last ancestor of monocots and eudicots. This segmental phylogeny can in turn shed light on the evolution of the genes that form part of those segments. Position-based phylogeny can improve the resolution and correct artifacts created by phylogenies based on gene sequences, although a number of questions need to be resolved for its full potential to be fulfilled.