The evolutionary significance of whole-genome duplication (WGD), or polyploidy, has long been one of the central questions in plant evolutionary biology. For more than a century, researchers have grappled with the "polyploid paradox": although polyploid organisms are widespread in nature, only a limited number of ancient WGD events have persisted over evolutionary timescales (Van de Peer et al., 2017; Carretero-Paulet and Van de Peer, 2020). In this context, the recent study by Chen et al. (2026) of Van de Peer Lab in Cell provides compelling genomic evidence for when and why polyploid lineages became established, marking an important step toward resolving this long-standing paradox (Chen et al., 2026).

Analyzing 470 angiosperm genomes, Chen et al. (2026) identified 132 independent ancient WGD events, representing the largest dataset assembled to date for this question. Using Bayesian molecular clock analyses calibrated with 44 fossils, they showed that paleopolyploidization events are not randomly distributed through time. Instead, successful WGD establishment is concentrated around intervals of major environmental disruptions, including the Cretaceous–Paleogene (K–Pg) extinction (~66 Ma), the Paleocene–Eocene Thermal Maximum (~56 Ma), the Eocene–Oligocene transition (~34 Ma), the Middle Miocene disruption (~14 Ma), and multiple oceanic anoxic events. Through exponential-Gaussian mixture modeling and Monte Carlo randomization, the authors further demonstrated that this temporal clustering is unlikely to be explained by chance alone.

Chen et al.'s (2026) findings are especially significant in light of the long-running debate over whether polyploidy is an evolutionary dead end. Mayrose et al. (2011) argued that recently formed polyploid lineages diversify more slowly than their diploid relatives, largely because of elevated extinction rates (Mayrose et al., 2011). Soltis et al. (2014) challenged this conclusion, citing methodological limitations, sampling biases, and concerns over phylogenetic inference. In response, Mayrose et al. (2015) defended their analytical framework while acknowledging that deeper evolutionary timescales might reveal different patterns for ancient polyploid events. Recent genomic analyses of 11 chromosome-scale genomes across all nine Malvaceae subfamilies show that the extent of post-polyploid diploidization (PPD), quantified by descending dysploidy rate, strongly predicts taxonomic richness (Zhang et al., 2025). Zhang et al. (2025) thus argue that evolutionary success hinges not on polyploidization per se, but on the degree of subsequent chromosomal diploidization—exemplified by the highly diploidized and species-rich Malvoideae—shifting the focus from whether polyploidy is a dead end to under what PPD conditions it becomes a springboard. Rather than simply siding with one view, Chen et al. (2026) reframe the debate by showing that the evolutionary fate of polyploids is strongly context dependent: polyploid lineages may be disadvantaged under relatively stable conditions, yet gain a marked advantage during episodes of severe environmental change.

The association between polyploidy and the K–Pg boundary was proposed previously by Fawcett et al. (2009), who observed that nine ancient WGD events appeared to cluster around that mass extinction event. Vanneste et al. (2014) expanded this analysis to 41 plant genomes and provided further support for a wave of successful WGD events associated with the K–Pg transition. Zhang et al. (2020) presciently proposed an ancient wave of whole-genome duplications—τ (~120 Ma), γ (~117 Ma), λ (~110 Ma), and π (~100 Ma)—to facilitate angiosperm adaptation to Cretaceous environmental stress. Chen et al. (2026) now offer robust validation, with their COMO (121.31 Ma, τ) aligning with the OAE1a peak (~120 Ma) associated with massive volcanism and greenhouse warming, COEU (107.58 Ma, γ) and LAUR β (109.98 Ma, λ) with the OAE1c peak (~108 Ma) marked by high atmospheric CO₂ and elevated temperatures, and NYMP (100.82 Ma, π) with the OAE1d peak (~99 Ma) coinciding with major extinction pulses and pronounced climatic excursions indicative of aridification stress. These early studies were limited by restricted phylogenetic sampling, and later large-scale analyses did not always recover clear temporal clustering. By greatly expanding genomic sampling and applying updated dating approaches, Chen et al. (2026) substantially strengthen this hypothesis. Their results not only support the K–Pg association, but also reveal a broader series of WGD establishment pulses extending from the Lower Cretaceous to the Neogene, each linked to major episodes of environmental upheaval.

It is also important to contextualize these findings alongside their inherent uncertainties. The ~24 million years ago (Ma) WGD peak, for example, is the least robust of the identified pulses, as it lacks a clear association with a documented major extinction or oceanic anoxic event and its recovery is sensitive to the analytical method used. Similarly, the ~73 Ma peak, while prominent, does not align with a classical mass extinction—though it coincides with elevated genus-level extinction rates around the Campanian–Maastrichtian boundary. Furthermore, the diversity-dependent background regime is inferred from correlation rather than mechanistic proof; Chen et al. (2026) themselves rightly note that establishing a causal link between lineage diversity and WGD establishment rates will require diversification modeling beyond the scope of their study. These open questions do not detract from the central pattern, but rather highlight exciting avenues for integrating refined fossil calibrations, spatially explicit diversification models, and experimental ecological approaches to further dissect the mechanisms underlying polyploid establishment.

The mechanistic basis of this pattern has also been increasingly explored. Van de Peer et al. (2021) reviewed evidence that polyploidization can enhance mutational and environmental robustness through genetic redundancy, particularly under stressful conditions. More recently, Ebadi et al. (2023) used simulations of duplicated gene regulatory networks to show that genome duplication can systematically expand phenotypic variation along the same directional axis as the ancestral phenotype, effectively amplifying the accessible phenotypic landscape —a model-based prediction that awaits direct empirical validation in natural populations. Such increased variation may be especially beneficial under large environmental perturbations, when duplicated regulatory networks can facilitate access to adaptive peaks that may remain inaccessible to diploid progenitors.

One of the most thought-provoking aspects of Chen et al. (2026) is the proposal of two superimposed regimes of WGD establishment: a background rate shaped by diversity dependence—albeit inferred from correlation rather than demonstrated mechanistically and episodic pulses triggered by environmental crisis. The reported negative correlation between WGD establishment rate and species richness mirrors the broader diversity dependence observed for speciation, suggesting that ecological opportunity, rather than genomic potential alone, is a key determinant of polyploid success. This view is further substantiated by Kauai et al. (2026), who used spatially explicit individual-based simulations of an extended Felber model—calibrated with the Australian burrowing frog Neobatrachus autopolyploid complex—to show that polyploids can establish at expanding range fronts through ecological drift and assortative mating alone, with niche divergence emerging subsequently as a consequence of geographical segregation rather than a prerequisite for establishment (Kauai et al., 2026). This view shifts the emphasis from genome doubling as an inherently advantageous event to genome doubling as a conditional advantage whose success depends on historical and ecological context. In that sense, polyploidy should not be viewed simply as a recurrent genomic accident, but as a mechanism whose macroevolutionary consequences are revealed most clearly during periods of planetary instability. These macroevolutionary consequences are further elaborated in recent perspectives: Peeters and Van de Peer (2026) frame polyploidy as a macromutational force that reshapes genomes, phenotypes, and ecological interactions, with broad implications for sustainable bioeconomic applications across agriculture, aquaculture, and biotechnology; Oliver et al. (2026) survey stress-induced polyploidy across fungi, plants, and animals (including human cancers), demonstrating how diverse stresses converge on shared cell-cycle alterations to impact genomes, cells, and tissues, thereby bridging micro- and macroevolutionary scales. As the authors note, this perspective raises the intriguing possibility that, in the current Anthropocene, characterized by rapid anthropogenic climate change and habitat disruption, new "ancient" polyploidy events may now be in the making (Chen et al., 2026).

This framework also raises important questions. Chen et al. (2026) focus primarily on the timing of successful establishment, yet the subsequent diploidization trajectory—including fractionation, neofunctionalization, and subfunctionalization—likely shapes whether a polyploid lineage radiates, persists, or disappears. Notably, the incidence of ancient polyploidy varies markedly across lineages: for instance, eudicots harbor 95 independent ancient WGD events compared with 25 in monocots and only 5 in magnoliids, hinting at differential post-polyploid responses such as diploidization that may shape divergent long-term evolutionary outcomes among clades (Chen et al., 2026). Comparative analyses of gene retention and regulatory rewiring between ancient polyploid lineages that underwent substantial diversification and their diploid sister groups with low species richness may help identify the genomic forces that facilitate long-term success. These considerations are especially pertinent because the current Anthropocene may already be fostering new polyploid lineages with long-term evolutionary potential, echoing the dynamics observed in past epochs of planetary upheaval. More broadly, in the Anthropocene, can we predict which contemporary plant lineages are most likely to benefit from polyploidization under accelerating climatic and ecological disruption (Oliver et al., 2026; Peeters and Van de Peer, 2026)? Integrating ploidy surveys, population genomics, and ecological monitoring may eventually transform polyploidy from a retrospective evolutionary pattern into an actionable framework for biodiversity forecasting. Addressing these questions will require closer integration across comparative genomics, phylogenomics, experimental evolution, and global change biology.

Taken together, Chen et al. (2026) provide a timely and persuasive reappraisal of the evolutionary role of polyploidy. By linking the establishment of ancient WGDs to episodes of environmental upheaval, their study helps explain why genome doubling is both pervasive and paradoxically selective in its long-term outcomes. It marks an important advance in understanding how genomic redundancy, ecological opportunity, and planetary crisis interact to shape the evolutionary history of plants.

Acknowledgments

We thank Dr. Hengchi Chen from University of Göttingen for discussion.

CRediT authorship contribution statement

Tao Shi: Writing – original draft, Writing – review & editing. Tao Zhao: Writing – original draft, Writing – review & editing.

Declaration of competing interest

The author Tao Shi is an Editorial Board Member for Plant Diversity and was not involved in the editorial review or the decision to publish this article. The other authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.