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Summary Recently formed allopolyploid species offer unprecedented insights into the early stages of polyploid evolution. This review examines seven well‐studied neopolyploids (we use ‘neopolyploid’ to refer to very recently formed polyploids, i.e. during the past 300 years), spanning different angiosperm families, exploring commonalities and differences in their evolutionary trajectories. Each neopolyploid provides a unique case study, demonstrating both shared patterns, such as rapid genomic and phenotypic changes, and unique responses to hybridization and genome doubling. While previous studies of these neopolyploids have improved our understanding of polyploidy, significant knowledge gaps remain, highlighting the need for further research into the varied impacts of whole‐genome duplication on gene expression, epigenetic modifications, and ecological interactions. Notably, all of these neopolyploids have spontaneously arisen due to human activity in natural environments, underscoring the profound consequences of polyploidization in a rapidly changing world. Understanding the immediate effects of polyploidy is crucial not only for evolutionary biology but also for applied practices, as polyploidy can lead to novel traits, as well as stress tolerance and increased crop yields. Future research directions include investigating the genetic and epigenetic mechanisms underlying polyploid evolution, as well as exploring the potential of neopolyploids for crop improvement and environmental adaptation. 

Abstract By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts. We show that many of the events show a relative rate of duplicate gene loss before the first postpolyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate postpolyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with 2 distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is, therefore, possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass reciprocal gene loss barriers. 

Summary Drought stress substantially impacts crop physiology resulting in alteration of growth and productivity. Understanding the genetic and molecular crosstalk between stress responses and agronomically important traits such as fibre yield is particularly complicated in the allopolyploid species, upland cotton (Gossypium hirsutum), due to reduced sequence variability between A and D subgenomes. To better understand how drought stress impacts yield, the transcriptomes of 22 genetically and phenotypically diverse upland cotton accessions grown under well‐watered and water‐limited conditions in the Arizona low desert were sequenced. Gene co‐expression analyses were performed, uncovering a group of stress response genes, in particular transcription factors GhDREB2A‐A and GhHSFA6B‐D, associated with improved yield under water‐limited conditions in an ABA‐independent manner. DNA affinity purification sequencing (DAP‐seq), as well as public cistrome data from Arabidopsis, were used to identify targets of these two TFs. Among these targets were two lint yield‐associated genes previously identified through genome‐wide association studies (GWAS)‐based approaches,GhABP‐DandGhIPS1‐A. Biochemical and phylogenetic approaches were used to determine thatGhIPS1‐Ais positively regulated by GhHSFA6B‐D, and that this regulatory mechanism is specific toGossypiumspp. containing the A (old world) genome. Finally, an SNP was identified within the GhHSFA6B‐D binding site inGhIPS1‐Athat is positively associated with yield under water‐limiting conditions. These data lay out a regulatory connection between abiotic stress and fibre yield in cotton that appears conserved in other systems such as Arabidopsis.