Polyploid taxa represent excellent models to address the underpinnings of genome evolution and the building up of new species in heterogeneous environments. Here, we present an overview of recent works in the alpine Biscutella laevigata autopolyploid complex (Brassicaceae). Transcriptomics inferred recurrent whole genome duplication (WGD) events specific to clade of species and that were used to infer processes fostering genome evolution across different timescales: (i) After a 7-8 million years old WGD event, intense chromosomal repatterning selected for clusters of retained duplicates enriched in functions associated with responses to abiotic stresses. Low coverage genome sequencing unraveled the dynamics of several retrotransposons, supporting interplay between genome reorganization and environmental opportunities in shaping the evolution of paleopolyploids. (ii) Retrotransposons in autotetraploids having recolonized the Alps after the ice ages showed considerable dynamics going along with ecological radiation following this recent WGD. Ecological genomics involving transplant experiment indeed supported distinct autopolyploid gene pools firmly associated with contrasted habitats despite gene flow. These ecotypes demonstrated adaptive differentiation at loci whose functions match habitat requirements. WGDs thus recurrently fostered genome reorganization and adaptive recruitment of genes responding to environmental factors, indicating that similar proximate and ultimate factors of genome dynamics may consistently act through time.