Species are usually defined by reproductive isolation and are characterized by their gene repertoire. These two aspects are consequences of events fixed during evolution, including whole genome duplications and other polyploidizations. Thanks to the recent progress in genome sequencing, new light has been shed on these events. In this review, we will summarize these findings and discuss the methodology involved. Evolutionary traces of such events have been evidenced in various lineages in plants, animals, fungi and protozoa. Comparative analysis of synteny is a powerful approach to unveil evolutionary footprints of these events. According to expectations, these events would facilitate speciation since some of them are thought to be at the base of major radiations such as teleostei or eudicotyledons. After an initial amplification, the gene repertoire would be shaped by constraints such as expression level and functional interactions that would tend to maintain only a tiny fraction of the duplicates over the long term. Functional innovation from duplication may be a secondary effect, enabled by these duplicate retention mechanisms.