The study investigates the evolutionary effects of polyploidy on gene functions in *Arabidopsis thaliana* by analyzing functional genomics data for duplicated gene pairs formed by ancient polyploidy events. The analysis reveals that genes retained in duplicate are not evenly distributed among functional categories, indicating a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, while those involved in DNA repair have been preferentially lost. Despite the initial identical transcription profiles of the two paralogs, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. The study also identifies cases where groups of duplicated gene pairs have diverged concertedly, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. Additionally, the rate of protein sequence evolution has been significantly asymmetric in over 20% of duplicate pairs. These findings suggest that functional diversification of surviving duplicated genes is a major feature of the long-term evolution of polyploids.The study investigates the evolutionary effects of polyploidy on gene functions in *Arabidopsis thaliana* by analyzing functional genomics data for duplicated gene pairs formed by ancient polyploidy events. The analysis reveals that genes retained in duplicate are not evenly distributed among functional categories, indicating a nonrandom process of gene loss. Genes involved in signal transduction and transcription have been preferentially retained, while those involved in DNA repair have been preferentially lost. Despite the initial identical transcription profiles of the two paralogs, less than half of the pairs formed by the most recent polyploidy event still retain significantly correlated profiles. The study also identifies cases where groups of duplicated gene pairs have diverged concertedly, forming two parallel networks, each containing one member of each gene pair. In these cases, the expression of each gene is strongly correlated with the other nonhomologous genes in its network but poorly correlated with its paralog in the other network. Additionally, the rate of protein sequence evolution has been significantly asymmetric in over 20% of duplicate pairs. These findings suggest that functional diversification of surviving duplicated genes is a major feature of the long-term evolution of polyploids.