Understanding the relationship between macro- and microevolutionary processes and their delimitation remains a challenge. This review focuses on the role of chromosomal rearrangements in plant population differentiation and lineage diversification resulting in speciation, helping bridge the gap between macro- and microevolution through chromosomal evolution. We focus on angiosperms, a group that comprises the majority of extant plant species diversity and exhibits the largest chromosomal and genomic variations. Here, we address the following questions: Are macroevolutionary patterns of chromosome evolution the result of accumulated microevolutionary changes, or do chromosomal dynamics drive larger shifts along the speciation continuum? At the macroevolutionary level, we investigated the association between karyotype diversity and diversification rates using evidence from comparative genomics, chromosomal evolution modelling across phylogenies, and the association with several traits across different angiosperm lineages. At the microevolutionary level, we explore if different karyotypes are linked to morphological changes and population genetic differentiation in the same lineages. Polyploidy (autopolyploidy and allopolyploidy) and dysploidy are known drivers of speciation, with karyotypic differences often leading to reproductive barriers. We found that dysploidy, involving gains and losses of single chromosomes with no significant change in overall content of the genome, appears to be relatively more frequent and persistent across macroevolutionary histories than polyploidy. Additionally, chromosomal rearrangements that do not entail change in chromosome number, such as insertions, deletions, inversions, and duplications of chromosome fragments, as well as translocations between chromosomes, are increasingly recognized for their role in local adaptation and speciation. We argue that there is more evidence linking chromosomal rearrangements with genetic and morphological trait differentiation at microevolutionary scales than at macroevolutionary ones. Our findings highlight the importance of selection across evolutionary scales, where certain chromosomal dynamics become fixed over macroevolutionary time. Consequently, at microevolutionary scales, chromosome rearrangements are frequent and diverse, serving as key drivers of plant diversification and adaptation by providing a pool of variation from which beneficial chromosomal changes can be selected and fixed by evolutionary forces.

Biodiversity Genomics Laboratory Institute of Biology University of Neuchâtel Neuchâtel Switzerland

Botany Area Department of Molecular Biology and Biochemical Engineering Universidad Pablo de Olavide Seville Spain

Botany Area Department of Plant Biology and Ecology Faculty of Biology University of Seville Seville Spain

Centre for Climate Change Impact University of Pisa Pisa Italy

Czech Academy of Sciences Institute of Botany Průhonice Czechia

Department of Biology Botany Unit University of Pisa Pisa Italy

Department of Botany Faculty of Science Charles University Prague Czechia

Department of Chromosome Biology Max Planck Institute for Plant Breeding Research Cologne Germany

Department of Microbial and Plant Interactions Plant Science and Biodiversity Centre Slovak Academy of Sciences Institute of Botany Bratislava Slovakia

Institute for Biodiversity and Ecosystem Dynamics Faculty of Science University of Amsterdam Amsterdam Netherlands

Royal Botanic Gardens Kew Richmond United Kingdom

Zobrazit více v PubMed

Abbott R., Albach D., Ansell S., Arntzen J. W., Baird S. J. E., Bierne N., et al. (2013). Hybridization and speciation. J. Evolutionary Biol. 26, 229–246. doi:  10.1111/j.1420-9101.2012.02599.x, PMID: PubMed DOI

Abbott R. J., Hegarty M. J., Hiscock S. J., Brennan A. C. (2010). Homoploid hybrid speciation in action. Taxon 59, 1375–1386. doi:  10.1002/tax.595005 DOI

Adams K. L., Wendel J. F. (2005). Polyploidy and genome evolution in plants. Curr. Opin. Plant Biol. 8, 135–141. doi:  10.1016/j.pbi.2005.01.001, PMID: PubMed DOI

Aguillon S. M., Dodge T. O., Preising G. A., Schumer M. (2022). Introgression. Curr. Biol. 32, 865–868. doi:  10.1016/j.cub.2022.07.004, PMID: PubMed DOI PMC

Akiyama R., Sun J., Hatakeyama M., Lischer H. E. L., Briskine R. V., Hay A., et al. (2020). Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species. New Phytol. 229, 3587–3601. doi:  10.1111/nph.17101, PMID: PubMed DOI PMC

Alix K., Gérard P. R., Schwarzacher T., Heslop-Harrison J. S. (2017). Polyploidy and interspecific hybridization: partners for adaptation, speciation and evolution in plants. Ann. Bot. 120, 183–194. doi:  10.1093/aob/mcx079, PMID: PubMed DOI PMC

Alsamir M., Mahmood T., Trethowan R., Ahmad N. (2021). An overview of heat stress in tomato ( PubMed DOI PMC

Álvarez-González L., Burden F., Doddamani D., Malinverni R., Leach E., Marín-García C., et al. (2022). 3D chromatin remodelling in the germ line modulates genome evolutionary plasticity. Nat. Commun. 13, 2608. doi:  10.1038/s41467-022-30296-6, PMID: PubMed DOI PMC

Anjali N., Ganga K. M., Nadiya F., Shefeek S., Sabu K. K. (2016). Intraspecific variations in cardamom ( PubMed DOI PMC

Archibald J. K., Mort M. E., Crawford D. J., Kelly J. K. (2005). Life history affects the evolution of reproductive isolation among species of Coreopsis (Asteraceae). Evolution 59, 2362–2369. doi:  10.1111/j.0014-3820.2005.tb00946.x, PMID: PubMed DOI

Arnold B., Kim S.-T., Bomblies K. (2015). Single geographic origin of a widespread autotetraploid PubMed DOI

Arrigo N., Barker M. S. (2012). Rarely successful polyploids and their legacy in plant genomes. Curr. Opin. Plant Biol. 15, 140–146. doi:  10.1016/j.pbi.2012.03.010, PMID: PubMed DOI

Arvanitis L., Wiklund C., Münzbergova Z., Dahlgren J. P., Ehrlén J. (2010). Novel antagonistic interactions associated with plant polyploidization influence trait selection and habitat preference. Ecol. Lett. 13, 330–337. doi:  10.1111/j.1461-0248.2009.01429.x, PMID: PubMed DOI

Ayala F. J., Coluzzi M. (2005). Chromosome speciation: humans, Drosophila, and mosquitoes. Proc. Natl. Acad. Sci. U.S.A. 102 Suppl 1, 6535–6542. doi:  10.1073/pnas.0501847102, PMID: PubMed DOI PMC

Balao F., Herrera J., Talavera S. (2011). Phenotypic consequences of polyploidy and genome size at the microevolutionary scale: A multivariate morphological approach. New Phytol. 192, 256–. doi:  10.1111/j.1469-8137.2011.03787.x, PMID: PubMed DOI

Balao F., Valente L. M., Vargas P., Herrera J., Talavera S. (2010). Radiative evolution of polyploid races of the Iberian carnation PubMed DOI

Barker M. S. (2013). “Karyotype and genome evolution in pteridophytes,” in Plant genome diversity, vol. 2 . Eds. Greilhuber J., Doležel J., Wendel J. F. (Springer, Vienna, Austria: ), 245–253.

Barker M. S., Arrigo N., Baniaga A. E., Zheng L., Levin D. A. (2016). On the relative abundance of autopolyploids and allopolyploids. New Phytol. 210, 391–398. doi:  10.1111/nph.13698, PMID: PubMed DOI

Barker M. S., Jiao Y., Glennon. K. L. (2024). Doubling down on polyploid discoveries: Global advances in genomics and ecological impacts of polyploidy. Am. J. Bot. 111, e16395. doi:  10.1002/ajb2.16395, PMID: PubMed DOI

Barrier M., Baldwin B. G., Robichaux R. H., Purugganan M. D. (1999). Interspecific hybrid ancestry of a plant adaptive radiation: allopolyploidy of the Hawaiian silversword alliance (Asteraceae) inferred from floral homeotic gene duplications. Mol. Bio. Evol. 16, 8, 1105–1113. doi:  10.1093/oxfordjournals.molbev.a026200, PMID: PubMed DOI

Bartolić P., Morgan E. J., Padilla-García N., Kolář F. (2024). Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow. Ann. Bot. 134, 537–550. doi:  10.1093/aob/mcae096, PMID: PubMed DOI PMC

Basit A., Lim K.-B. (2024). Systematic approach of polyploidy as an evolutionary genetic and genomic phenomenon in horticultural crops. Plant Sci. 348, 112236. doi:  10.1016/j.plantsci.2024.112236, PMID: PubMed DOI

Bell G. (1982). The masterpiece of nature: The evolution and genetics of sexuality (USA: University of California Press; ).

Bellinger M. R., Datlof E. M., Selph K. E., Gallaher T. J., Knope M. L. (2022). A genome for PubMed DOI PMC

Benton M. J., Wilf P., Sauquet H. (2021). The angiosperm terrestrial revolution and the origins of modern biodiversity. New Phytol. 233, 2017–2035. doi:  10.1111/nph.17822, PMID: PubMed DOI

Berdan E. L., Aubier T. G., Cozzolino S., Faria R., Feder J. L., Giménez M. D., et al. (2024). Structural variants and speciation: multiple processes at play. Cold Spring Harb. Perspect. Biol. 16, a041446. doi:  10.1101/cshperspect.a041446, PMID: PubMed DOI PMC

Birchler J. A., Veitia R. A. (2007). The gene balance hypothesis: from classical genetics to modern genomics. Plant Cell 19, 395–402. doi:  10.1105/tpc.106.049338, PMID: PubMed DOI PMC

Birchler J. A., Yao H., Chudalayandi S. (2007). Biological consequences of dosage dependent gene regulatory systems. Biochim. Biophys. Acta Gene Struct. Expr. 1769, 422–428. doi:  10.1016/j.bbaexp.2006.12.002, PMID: PubMed DOI PMC

Blaine Marchant D., Soltis D. E., Soltis P. S. (2016). Patterns of abiotic niche shifts in allopolyploids relative to their progenitors. New Phytol. 212, 708–718. doi:  10.1111/nph.14069, PMID: PubMed DOI

Bohutínská M., Petříková E., Booker T. R., Cobo C. V., Vlček J., Šrámková G., et al. (2024). Polyploids broadly generate novel haplotypes from trans-specific variation in PubMed DOI PMC

Bomblies K., Jones G., Franklin C., Zickler D., Kleckner N. (2016). The challenge of evolving stable polyploidy: could an increase in ‘crossover interference distance’ play a central role? Chromosoma 125, 287–300. doi:  10.1007/s00412-015-0571-4, PMID: PubMed DOI PMC

Bomblies K., Madlung A. (2014). Polyploidy in the PubMed DOI

Boore J. L. (2006). The use of genome-level characters for phylogenetic reconstruction. Trends Ecol. Evol. 21, 439–446. doi:  10.1016/j.tree.2006.05.009, PMID: PubMed DOI

Bretagnolle F., Thompson J. D. (1995). Tansley review no. 78. Gametes with the stomatic chromosome number: mechanisms of their formation and role in the evolution of autopolypoid plants. New Phytol. 129, 1–22. doi:  10.1111/j.1469-8137.1995.tb03005.x, PMID: PubMed DOI

Brown M. R., Abbott R. J., Twyford A. D. (2024). The emerging importance of cross-ploidy hybridisation and introgression. Mol. Ecol. 33, e17315. doi:  10.1111/mec.17315, PMID: PubMed DOI

Buerkle C. A., Morris R. J., Asmussen M. A., Rieseberg L. H. (2000). The likelihood of homoploid hybrid speciation. Heredity 84, 441–451. doi:  10.1046/j.1365-2540.2000.00680.x, PMID: PubMed DOI

Burak M. K., Monk J. D., Schmitz O. J. (2018). Eco-evolutionary dynamics: the predator-prey adaptive play and the ecological theater. Yale J. Biol. Med. 91, 481–489., PMID: PubMed PMC

Burdon J. J., Marshall D. R. (1981). Inter- and intraspecific diversity in the disease response of Glycine species to the leaf-rust fungus DOI

Burns R., Kulkarni A., Glushkevich A., Kolesnikova U. K., Kolář F., Scott A. D., et al. (2024). Diploid origins, adaptation to polyploidy, and the beginning of rediploidization in allotetraploid DOI

Burns R., Mandáková T., Gunis J., Soto-Jiménez L. M., Liu C., Lysak M. A., et al. (2021). Gradual evolution of allopolyploidy in Arabidopsis suecica. Nat. Ecol. Evol. 5, 1367–1381. doi:  10.1038/s41559-021-01525-w, PMID: PubMed DOI PMC

Carta A., Bedini G., Peruzzi L. (2020). A deep dive into the ancestral chromosome number and genome size of flowering plants. New Phytol. 228, 1097–1106. doi:  10.1111/nph.16668, PMID: PubMed DOI

Carta A., Escudero M. (2023). Karyotypic diversity: a neglected trait to explain angiosperm diversification? Evol. 77, pp.1158–1164. doi:  10.1093/evolut/qpad014, PMID: PubMed DOI

Carta A., Peruzzi L. (2016). Testing the large genome constraint hypothesis: plant traits, habitat and climate seasonality in Liliaceae. New Phytol. 210, 709–716. doi:  10.1111/nph.13769, PMID: PubMed DOI

Carvalho C. M. B., Lupski J. R. (2016). Mechanisms underlying structural variant formation in genomic disorders. Nat. Rev. Genet. 17, 224–238. doi:  10.1038/nrg.2015.25, PMID: PubMed DOI PMC

Čertner M., Fenclová E., Kúr P., Kolář F., Koutecký P., Krahulcová A., et al. (2017). Evolutionary dynamics of mixed-ploidy populations in an annual herb: dispersal, local persistence and recurrent origins of polyploids. Ann. Bot. 120, 303–315. doi:  10.1093/aob/mcx032, PMID: PubMed DOI PMC

Charron G., Marsit S., Hénault M., Martin H., Landry C. R. (2019). Spontaneous whole-genome duplication restores fertility in interspecific hybrids. Nat. Commun. 10, 4126. doi:  10.1038/s41467-019-12041-8, PMID: PubMed DOI PMC

Chase M. W., Samuel R., Leitch A. R., Guignard M. S., Conran J. G., Nollet F., et al. (2023). Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section. Suaveolentes (Solanaceae). Ann. Bot. 131, 123–142. doi:  10.1093/aob/mcac006, PMID: PubMed DOI PMC

Chelaifa H., Monnier A., Ainouche M. (2010). Transcriptomic changes following recent natural hybridization and allopolyploidy in the salt marsh species Spartina × townsendii and Spartina anglica (Poaceae). New Phytol. 186, 161–174. doi:  10.1111/j.1469-8137.2010.03179.x, PMID: PubMed DOI

Chen Z. J. (2007). Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu. Rev. Plant Biol. 58, 377–406. doi:  10.1146/annurev.arplant.58.032806.103835, PMID: PubMed DOI PMC

Chen J., Zhong Y., Zou P., Ni J., Liu Y., Dai S., et al. (2024). Identification of Genomic Regions Associated with Differences in Flowering Time and Inflorescence Architecture between PubMed DOI PMC

Cheng J., Li J., Zhang Z., Lu H., Chen G., Yao B., et al. (2021). Autopolyploidy-driven range expansion of a temperate-originated plant to pan-tropic under global change. Ecol. Monogr. 91, e01445. doi:  10.1002/ecm.1445 DOI

Cheng F., Wu J., Fang L., Sun S., Liu B., Lin K., et al. (2012). Biased gene fractionation and dominant gene expression among the subgenomes of PubMed DOI PMC

Chester M., Gallagher J. P., Symonds V. V., Cruz da Silva A. V., Mavrodiev E. V., Leitch A. R., et al. (2012). Extensive chromosomal variation in a recently formed natural allopolyploid species. Tragopogon miscellus (Asteraceae). PNAS 109, 1176–1181. doi:  10.1073/pnas.1112041109, PMID: PubMed DOI PMC

Chester M., Leitch A. R., Soltis P. S., Soltis D. E. (2010). Review of the application of modern cytogenetic methods (FISH/GISH) to the study of reticulation (Polyploidy/hybridisation). Genes 1, 166–192. doi:  10.3390/genes1020166, PMID: PubMed DOI PMC

Chumová Z., Monier Z., Šemberová K., Havlíčková E., Euston-Brown D., Muasya A., et al. (2024). Diploid and tetraploid cytotypes of the flagship Cape species PubMed DOI PMC

Clark J., Hidalgo O., Pellicer J., Liu H., Marquardt J., Robert Y., et al. (2016). Genome evolution of ferns: evidence for relative stasis of genome size across the fern phylogeny. New Phytol. 210, 1072–1082. doi:  10.1111/nph.13833, PMID: PubMed DOI

Clarkson J. J., Knapp S., Garcia V., Olmstead R. G., Chase M. W. (2004). Phylogenetic relationships in Nicotiana (Solanaceae) inferred from multiple plastid DNA regions. Mol. Phylogenet Evol. 33, 75–90. doi:  10.1016/j.ympev.2004.05.002, PMID: PubMed DOI

Clo J., Kolář F. (2021). Short- and long-term consequences of genome doubling: a meta-analysis. Am. J. Bot. 108, 2315–2322. doi:  10.1002/ajb2.1759, PMID: PubMed DOI

Cohen H., Fait A., Tel-Zur N. (2013). Morphological, cytological and metabolic consequences of autopolyploidization in PubMed DOI PMC

Comai L. (2005). The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 6, 836–846. doi:  10.1038/nrg1711, PMID: PubMed DOI

Costa L., Oliveira A., Carvalho-Sobrinho J., Souza G. (2017). Comparative cytomolecular analyses reveal karyotype variability related to biogeographic and species richness patterns in Bombacoideae (Malvaceae). Plant Syst. Evol. 303, 1131–1144. doi:  10.1007/s00606-017-1427-6 DOI

Coyne J. A., Orr H. A. (2004). Speciation (Sunderland: Sinauer; ).

Cozzolino S., Scopece G. (2008). Specificity in pollination and consequences for postmating reproductive isolation in deceptive Mediterranean orchids. Philos. Trans. R. Soc Lond. B Biol. Sci. 363, 3037–3046. doi:  10.1098/rstb.2008.0079, PMID: PubMed DOI PMC

Crespel L., Le Bras C., Relion D., Roman H., Morel P. (2015). Effect of high temperature on the production of 2n pollen grains in diploid roses and obtaining tetraploids via unilateral polyploidization. Plant Breed. 134, 356–364. doi:  10.1111/pbr.12271 DOI

Da Silva C. R. M., Souza T. B., Trevisan R., González-Elizondo M. S., Torezan J. M. D., de Souza R. F., et al. (2017). Genome differentiation, natural hybridisation and taxonomic relationships among DOI

Dixon J. R., Selvaraj S., Yue F., Kim A., Li Y., Shen Y., et al. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380. doi:  10.1038/nature11082, PMID: PubMed DOI PMC

Dobzhansky T. (1951). Genetics and the origin of species. 3rd Ed (New York: Columbia University Press; ).

Dobzhansky T., Sturtevant A. H. (1938). Inversions in the chromosomes of PubMed DOI PMC

Dodsworth S., Chase M. W., Leitch A. R. (2016). Is post-polyploidization diploidization the key to the evolutionary success of angiosperms? Bot. J. Linn. Soc 180, 1–5. doi:  10.1111/boj.12357 DOI

Edger P. P., Heidel-Fischer H. M., Bekaert M., Rota J., Glöckner G., Platts A. E., et al. (2015). The butterfly plant arms-race escalated by gene and genome duplications. PNAS 112, 8362–8366. doi:  10.1073/pnas.1503926112, PMID: PubMed DOI PMC

Edger P. P., Smith R., McKain M. R., Cooley A. M., Vallejo-Marin M., Yuan Y., et al. (2017). Subgenome dominance in an interspecific hybrid, synthetic allopolyploid, and a 140-year-old naturally established neo-allopolyploid monkeyflower. Plant Cell 29, 2150–2167. doi:  10.1105/tpc.17.00010, PMID: PubMed DOI PMC

Escudero M., Arroyo J., Sánchez-Ramírez S., Jordano P. (2024). Founder events and subsequent genetic bottlenecks underlie karyotype evolution in the Ibero-North African endemic PubMed DOI PMC

Escudero M., Hahn M., Brown B., Lueders K., Hipp A. (2016. b). Chromosomal rearrangements in holocentric organisms lead to reproductive isolation by hybrid dysfunction: the correlation between karyotype rearrangements and germination rates in sedges. Am. J. Bot. 103, 1529–1536. doi:  10.3732/ajb.1600051, PMID: PubMed DOI

Escudero M., Hahn M., Hipp A. L. (2018). RAD-seq linkage mapping and patterns of segregation distortion in sedges: meiosis as a driver of karyotypic evolution in organisms with holocentric chromosomes. J. Evol. Bio. 31, 833–843. doi:  10.1111/jeb.13267, PMID: PubMed DOI

Escudero M., Hipp A. (2013). Shifts in diversification rates and clade ages explain species richness in higher-level sedge taxa (Cyperaceae). Am. J. Bot. 100, 2403–2411. doi:  10.3732/ajb.1300162, PMID: PubMed DOI

Escudero M., Hipp A. L., Hansen T. F., Voje K. L., Luceño M. (2012). Selection and inertia in the evolution of holocentric chromosomes in sedges (Carex, Cyperaceae). New Phytol. 195, 237–247. doi:  10.1111/j.1469-8137.2012.04137.x, PMID: PubMed DOI

Escudero M., Hipp A. L., Luceño M. (2010). Karyotype stability and predictors of chromosome number variation in sedges: A study in PubMed DOI

Escudero M., Maguilla E., Luceño M. (2013. a). Selection by climatic regime and neutral evolutionary processes in holocentric chromosomes ( DOI

Escudero M., Márquez-Corro J. I., Hipp A. L. (2016. a). The phylogenetic origins and evolutionary history of holocentric chromosomes. Syst. Bot. 41, 580–585. doi:  10.1600/036364416X692442 DOI

Escudero M., Martín-Bravo S., Mayrose I., Fernández-Mazuecos M., Fiz-Palacios O., Hipp A. L., et al. (2014). Karyotypic Changes through Dysploidy Persist Longer over Evolutionary Time than Polyploid Changes. PLoS One 9, e85266. doi:  10.1371/journal.pone.0085266, PMID: PubMed DOI PMC

Escudero M., Weber J. A., Hipp A. L. (2013. b). Species coherence in the face of karyotype diversification in holocentric organisms: the case of a cytogenetically variable sedge (Carex scoparia, Cyperaceae). Ann. Bot. 112, 515–526. doi:  10.1093/aob/mct119, PMID: PubMed DOI PMC

Escudero M., Wendel J. F. (2020). The grand sweep of chromosomal evolution in angiosperms. New Phytol. 228, 805–808. doi:  10.1111/nph.16802, PMID: PubMed DOI

Estep M. C., McKain M. R., Diaz D. V., Zhong J. S., Hodge J. G., Hodkinson T. R., et al. (2014). Allopolyploidy, diversification, and the Miocene grassland expansion. Proc. Natl. Acad. Sci. U.S.A. 111, 15149–15154. doi:  10.1073/pnas.1404177111, PMID: PubMed DOI PMC

Ezoe A., Seki M. (2024). Exploring the complexity of genome size reduction in angiosperms. Plant Mol. Biol. 114, 121. doi:  10.1007/s11103-024-01518-w, PMID: PubMed DOI PMC

Farhat P., Hidalgo O., Robert T., Siljak-Yakovlev S., Leitch I. J., Adams R. P., et al. (2019). Polyploidy in the conifer genus PubMed DOI PMC

Farhat P., Siljak-Yakovlev S., Hidalgo O., Rushforth K., Bartel J. A., Valentin N., et al. (2022). Polyploidy in Cupressaceae: Discovery of a new naturally occurring tetraploid, DOI

Faria R., Navarro A. (2010). Chromosomal speciation revisited: rearranging theory with pieces of evidence. Trends Ecol. Evol. 25, 660–669. doi:  10.1016/j.tree.2010.07.008, PMID: PubMed DOI

Faria R., Neto S., Noor M., Navarro A. (2011). Role of Natural Selection in Chromosomal Speciation in eLS , (Ed.). doi:  10.1002/9780470015902.a0022850 DOI

Farminhão J. N. M., Verlynde S., Kaymak E., Droissart V., Simo-Droissart M., Collobert G., et al. (2021). Rapid radiation of angraecoids (Orchidaceae, Angraecinae) in tropical Africa characterised by multiple karyotypic shifts under major environmental instability. Mol. Phylogenet. Evol. 159, 107105. doi:  10.1016/j.ympev.2021.107105, PMID: PubMed DOI

Fehrer J., Bertrand Y. J. K., Hartmann M., Caklová P., Josefiová J., Bräutigam S., et al. (2022). Multigene phylogeny of native american hawkweeds ( PubMed DOI PMC

Fernández P., Hidalgo O., Juan A., Leitch I. J., Leitch A. R., Palazzesi L., et al. (2022). Genome Insights into Autopolyploid Evolution: A Case Study in PubMed DOI PMC

Fishman L., Stathos A., Beardsley P. M., Williams C. F., Hill J. P. (2013). Chromosomal rearrangements and the genetics of reproductive barriers in Mimulus (monkey flowers). Evol. 67, 2547–2560. doi:  10.1111/evo.12154, PMID: PubMed DOI

Fowler N. L., Levin D. A. (1984). Ecological constraints on the establishment of a novel polyploid in competition with its diploid progenitor. Amer. Nat. 124, 703–711. doi:  10.1086/284307 DOI

Franco M. F., Colabelli M. N., Petigrosso L. R., De Battista J. P., Echeverría M. M. (2015). Evaluation of infection with endophytes in seeds of forage species with different levels of ploidy. N. Z. J. Agric. Res. 58, 181–189. doi:  10.1080/00288233.2015.1011283 DOI

Freyman W. A., Höhna S. (2018). Cladogenetic and anagenetic models of chromosome number evolution: a Bayesian model averaging approach. Syst. Biol. 67, 195–215. doi:  10.1093/sysbio/syx065, PMID: PubMed DOI

Giraud D., Lima O., Rousseau-Gueutin M., Salmon A., Aïnouche M. (2021). Gene and transposable element expression evolution following recent and past polyploidy events in spartina (Poaceae). Front. Genet. 12. doi:  10.3389/fgene.2021.589160, PMID: PubMed DOI PMC

Glick L., Mayrose I. (2014). ChromEvol: assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny. Mol. Biol. Evol. 31, 1914–1922. doi:  10.1093/molbev/msu122, PMID: PubMed DOI

Goel M., Schneeberger K. (2022). Plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics 38, 2922–2926. doi:  10.1093/bioinformatics/btac196, PMID: PubMed DOI PMC

Goel M., Sun H., Jiao W. B., Schneeberger K. (2019). SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol. 20, 277. doi:  10.1186/s13059-019-1911-0, PMID: PubMed DOI PMC

Goldblatt P., Johnson D. E. (2010). The Index to Plant Chromosome Numbers. Ann. Missouri Bot. Gard. 98, 226–227. doi:  10.3417/2011027 DOI

Goldblatt P., Lowry P. P. (2011). The DOI

Grant V. (1958). “The regulation of recombination in plants,” in Exchange of genetic material: mechanisms and consequences, cold spring harbor symposium on quantitative biology, vol. 23. (Cold Spring Harbor, NY, USA: ), 337–363. PubMed

Grant V. (1981). Plant speciation. 2nd edn (NY, USA: Columbia University Press; ).

Griffiths A. G., Moraga R., Tausen M., Gupta V., Bilton T. P., Campbell, et al. (2019). Breaking free: the genomics of allopolyploidy-facilitated niche expansion in white clover. Plant Cell. 31, 1466–1487. doi:  10.1105/tpc.18.00606, PMID: PubMed DOI PMC

Gross B. L., Rieseberg L. H. (2005). The ecological genetics of homoploid hybrid speciation. J. Heredity 96, 241–252. doi:  10.1093/jhered/esi026, PMID: PubMed DOI PMC

Guan J., Xu Y., Yu Y., Fu J., Ren F., Guo J., et al. (2021). Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape. Genome Biol. 22, 13. doi:  10.1186/s13059-020-02239-1, PMID: PubMed DOI PMC

Guerra M. (2008). Chromosome numbers in plant cytotaxonomy: concepts and implications. Cytogenet. Genome Res. 120, 339–350. doi:  10.1159/000121083, PMID: PubMed DOI

Guerra M. (2016). Agmatoploidy and symploidy: a critical review. Genet. Mol. Biol. 39, 492–496. doi:  10.1590/1678-4685-GMB-2016-0103, PMID: PubMed DOI PMC

Guggisberg A., Mansion G., Kelso S., Conti E. (2006). Evolution of biogeographic patterns, ploidy levels, and breeding systems in a diploid–polyploid species complex of Primula. New Phytol. 171, 617–632. doi:  10.1111/j.1469-8137.2006.01722.x, PMID: PubMed DOI

Guignard M. S., Nichols R. A., Knell R. J., Macdonald A., Romila C. A., Trimmer M., et al. (2016). Genome size and ploidy influence angiosperm species’ biomass under nitrogen and phosphorus limitation. New Phytol. 210, 1195–1206. doi:  10.1111/nph.13881, PMID: PubMed DOI PMC

Gundel P. E., Dirihan S., Helander M., Zabalgogeazcoa I., Väre H., Saikkonen K. (2014). Systemic fungal endophytes and ploidy level in Festuca vivipara populations in North European Islands. Pl. Syst. Evol. 300, 1683–1691. doi:  10.1007/s00606-014-0994-z DOI

Haufler C. H. (1987). Electrophoresis is modifying our concepts of evolution in homosporous pteridophytes. Am. J. Bot. 74, 953–966. doi:  10.1002/j.1537-2197.1987.tb08700.x DOI

Haufler C. H., Soltis D. E. (1986). Genetic evidence suggests that homosporous ferns with high chromosome numbers are diploid. Proc. Nat. Acad. Sci. U.S.A. 83, 4389–4393. doi:  10.1073/pnas.83.12.4389, PMID: PubMed DOI PMC

Hegarty M. J., Hiscock S. J. (2008). Genomic clues to the evolutionary success of review polyploid plants. Curr. Biol. 18, R435–R444. doi:  10.1016/j.cub.2008.03.043, PMID: PubMed DOI

Heilborn O. (1924). Chromosome numbers and dimensions, species formation and phylogeny in the genus DOI

Hipp A. L., Rothrock P. E., Roalson E. H. (2009). The evolution of chromosome arrangements in DOI

Hipp A. L., Rothrock P. E., Whitkus R., Weber J. A. (2010). Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges, a group with holocentric chromosomes. Mol. Evol. 19, 3124–3138. doi:  10.1111/j.1365-294X.2010.04741.x, PMID: PubMed DOI

Hoencamp C., Dudchenko O., Elbatsh A. M., Brahmachari S., Raaijmakers J. A., van Schaik T., et al. (2021). 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science 372, 984–989. doi:  10.1126/science.abe2218, PMID: PubMed DOI PMC

Hoffmann A. A., Rieseberg L. H. (2008). Revisiting the impact of inversions in evolution: from population genetic markers to drivers of adaptive shifts and speciation? Annu. Rev. Ecol. Evol. Syst. 39, 21–42. doi:  10.1146/annurev.ecolsys.39.110707.173532, PMID: PubMed DOI PMC

Hou C., Li L., Qin Z. S., Corces V. G. (2012). Gene density, transcription, and insulators contribute to the partition of the Drosophila genome into physical domains. Mol. Cell 48, 471–484. doi:  10.1016/j.molcel.2012.08.031, PMID: PubMed DOI PMC

Huang Y., Guo X., Zhang K., Mandáková T., Cheng F., Lysak M. A. (2023). The meso-octoploid PubMed DOI

Huang K., Rieseberg L. H. (2020). Frequency, origins, and evolutionary role of chromosomal inversions in plants. Front. P. Sci. 11. doi:  10.3389/fpls.2020.00296, PMID: PubMed DOI PMC

Huettel B., Kreil D. P., Matzke M., Matzke A. J. (2008). Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana. PLoS Genet. 4, e1000226. doi:  10.1371/journal.pgen.1000226, PMID: PubMed DOI PMC

Jayakodi M., Lu Q., Pidon H., Rabanus-Wallace M. T., Bayer M., Lux T., et al. (2024). Structural variation in the pangenome of wild and domesticated barley. Nature 636, 654–662. doi:  10.1038/s41586-024-08187-1, PMID: PubMed DOI PMC

Jersáková J., Castro S., Sonk N., Milchreit K., Schödelbauerová I., Tolasch T., et al. (2010). Absence of pollinator-mediated premating barriers in mixed-ploidy populations of DOI

Jiang J. (2019). Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res. 27, 153–165. doi:  10.1007/s10577-019-09607-z, PMID: PubMed DOI

Jiao Y., Leebens-Mack J., Ayyampalayam S., Bowers J. E., McKain M. R., McNeal J., et al. (2012). A genome triplication associated with early diversification of the core eudicots. Genome Biol. 26, R3. doi:  10.1186/gb-2012-13-1-r3, PMID: PubMed DOI PMC

Jiao Y., Wickett N., Ayyampalayam S., Chanderbali A. S., Landherr L., Ralph P. E., et al. (2011). Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100. doi:  10.1038/nature09916, PMID: PubMed DOI

Jin S., Han Z., Hu Y., Si Z., Dai F., He L., et al. (2023). Structural variation (SV)-based pan-genome and GWAS Reveal the Impacts of SVs on the speciation and diversification of allotetraploid cottons. Mol. Plant 16, 678–693. doi:  10.1016/j.molp.2023.02.004, PMID: PubMed DOI

Johnen L., de Souza T. B., Rocha D. M., Parteka L. M., González-Elizondo M. S., Trevisan R., et al. (2020). Allopolyploidy and genomic differentiation in holocentric species of the DOI

Johnson M. T. J., Smith S. D., Rausher M. D. (2009). Plant sex and the evolution of plant defenses against herbivores. Proc. Natl. Acad. Sci. U.S.A. 106, 18079–18084. doi:  10.1073/pnas.0904695106, PMID: PubMed DOI PMC

Jørgensen M. H., Ehrich D., Schmickl R., Koch M. A., Brysting A. K. (2011). Interspecific and interploidal gene flow in Central European PubMed DOI PMC

Julca I., Marcet-Houben M., Vargas P., Gabaldón T. (2018). Phylogenomics of the olive tree ( PubMed DOI PMC

Kantor A., Kučera J., Šlenker M., Breidy J., Dönmez A. A., Marhold K., et al. (2023). Evolution of hygrophytic plant species in the Anatolia–Caucasus region: insights from phylogenomic analyses of PubMed DOI PMC

Kauai F., Bafort Q., Mortier F., Montagu M. V., Bonte D., Van de Peer Y. (2024). Interspecific transfer of genetic information through polyploid bridges. PNAS. 121, (21), e2400018121. doi:  10.1073/pnas.2400018121, PMID: PubMed DOI PMC

Kearns A. M., Restani M., Szabo I., Schrøder-Nielsen A., Kim J. A., Richardson H. M., et al. (2018). Genomic evidence of speciation reversal in ravens. Nat. Commun. 9, 906. doi:  10.1038/s41467-018-03294-w, PMID: PubMed DOI PMC

Kelly L. J., Leitch A. R., Clarkson J. J., Knapp S., Chase M. W. (2013). Reconstructing the complex evolutionary origin of wild allopolyploid tobaccos ( PubMed DOI

Kinosian S., Barker M. S. (2024). Meiotic drive and genome evolution in vascular land plants. EcoevoRxiv. doi:  10.32942/X2RD0K DOI

Kirkpatrick M., Barton N. (2006). Chromosome inversions, local adaptation and speciation. Genetics 173, 419–434. doi:  10.1534/genetics.105.047985, PMID: PubMed DOI PMC

Klekowski E. J., Jr., Baker H. G. (1966). Evolutionary significance of polyploidy in the pteridophyta. Sci. 153, 305–307. doi:  10.1126/science.153.3733.305, PMID: PubMed DOI

Knight C. A., Molinari N., Petrov D. A. (2005). The large genome constraint hypothesis: evolution, ecology and phenotype. Ann. Bot. 95, 177–190. doi:  10.1093/aob/mci011, PMID: PubMed DOI PMC

Koch M. A. (2019). The plant model system PubMed DOI

Koella J. C. (1993). Ecological correlates of chiasma frequency and recombination index of plants. Biol. J. Linn. Soc 48, 227–238. doi:  10.1111/j.1095-8312.1993.tb00889.x DOI

Köhler C., Scheid O. M., Erilova A. (2010). The impact of the triploid block on the origin and evolution of polyploid plants. Trends Genet. 26, 142–148. doi:  10.1016/j.tig.2009.12.006, PMID: PubMed DOI

Kolář F., Čertner M., Suda J., Schönswetter P., Husband B. C. (2017). Mixed-ploidy species: progress and opportunities in polyploid research. Trends Plant Sci. 22, 1041–1055. doi:  10.1016/j.tplants.2017.09.011, PMID: PubMed DOI

Kolář F., Lučanová M., Záveská E., Fuxová G., Mandáková T., Španiel S., et al. (2016). Ecological segregation does not drive the intricate parapatric distribution of diploid and tetraploid cytotypes of the DOI

Kolesnikova U. K., Scott A. D., Van de Velde J. D., Burns R., Tikhomirov N. P., Pfordt U., et al. (2023). Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid PubMed DOI PMC

Kollar L. M., Stanley L. E., Raju S. K. K., Lowry D. B., Niederhuth C. E. (2024). The evolutionary dynamics of locally adaptive chromosome inversions in PubMed DOI

Krak K., Caklová P., Chrtek J., Fehrer J. (2013). Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae). Hered. 110, 138–151. doi:  10.1038/hdy.2012.100, PMID: PubMed DOI PMC

Krakos K. N., Johnson M. G., Hoch P. C., Wagner W. L., Huang P., Raven P. H. (2022). Molecular phylogenetics reveals multiple transitions to self-compatibility in a primary subclade of DOI

Kumar S., Kaur S., Seem K., Kumar S., Mohapatra T. (2021). Understanding 3D genome organization and its effect on transcriptional gene regulation under environmental stress in plant: A chromatin perspective. Front. Cell Dev. Biol. 9. doi:  10.3389/fcell.2021.774719, PMID: PubMed DOI PMC

Lafon-Placette C., Johannessen I. M., Hornslien K. S., Ali M. F., Bjerkan K. N., Bramsiepe J., et al. (2017). Endosperm-based hybridization barriers explain the pattern of gene flow between PubMed DOI PMC

Landis J. B., Soltis D. E., Li Z., Marx H. E., Barker M. S., Tank D. C., et al. (2018). Impact of whole-genome duplication events on diversification rates in angiosperms. Am. J. Bot. 105, 348–363. doi:  10.1002/ajb2.1060, PMID: PubMed DOI

Larridon I., Zuntini A. R., Léveillé-Bourret É., Barrett R. L., Starr J. R., Muasya A. M., et al. (2021). A new classification of Cyperaceae (Poales) supported by phylogenomic data. J. Syst. Evol. 59, 852–895. doi:  10.1111/jse.12757 DOI

Lee Y. W., Fishman L., Kelly J. K., Willis J. H. (2016). A segregating inversion generates fitness variation in yellow monkeyflower ( PubMed DOI PMC

Leitch I. J., Bennett M. D. (1997). Polyploidy in angiosperms. Trends Plant Sci. 12, 470–476. doi:  10.1016/S1360-1385(97)01154-0 DOI

Leitch I. J., Hanson L. (2002). DNA C-values in seven families fill phylogenetic gaps in the basal angiosperms. Bot. J. Linn. 140, 175–179. doi:  10.1046/j.1095-8339.2002.00096.x DOI

Leitch A., Leitch I. J. (2008). Genomic plasticity and the diversity of polyploid plants. Science 320, 48–483. doi:  10.1126/science.1153585, PMID: PubMed DOI

Leitch A. R., Leitch I. J. (2012). Ecological and genetic factors linked to contrasting genome dynamics in seed plants. New Phytol. 194, 629–646. doi:  10.1111/j.1469-8137.2012.04105.x, PMID: PubMed DOI

Leitch I. J., Leitch A. R. (2013). “Genome size diversity and evolution in land plants,” in Plant genome diversity, vol. 2, physical structure, behaviour and evolution of plant genomes. Eds. Leitch I. J., Greilhuber J., Doležel J., Wendel J. F. (Springer-Verlag, Wien, Austria: ), 307–322.

Le Scouarnec S., Gribble S. (2012). Characterising chromosome rearrangements: recent technical advances in molecular cytogenetics. Heredity 108, 75–85. doi:  10.1038/hdy.2011.100, PMID: PubMed DOI PMC

Levin D. A. (2002). The role of chromosomal change in plant evolution (New York, NY, USA: OUP; ).

Li Z., Kinosian S. P., Zhan S. H., Barker M. S. (2024). Ancient polyploidy and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns. bioRxiv. doi:  10.1101/2024.09.23.614530 DOI

Li Z., McKibben M. T. W., Finch G. S., Blischak P. D., Sutherland B. L., Barker M. S. (2021). Patterns and processes of diploidization in land plants. Annu. Rev. Plant Biol. 72, 387–410. doi:  10.1146/annurev-arplant-050718-100344, PMID: PubMed DOI

Li H., Wang S., Chai S., Yang Z., Zhang Q., Xin H., et al. (2022). Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber. Nat. Commun. 13, 682. doi:  10.1038/s41467-022-28362-0, PMID: PubMed DOI PMC

Li X., Wang J., Yu Y., Li G., Wang J., Li C., et al. (2023). Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae). BMC Biol. 21, 56. doi:  10.1186/s12915-023-01560-y, PMID: PubMed DOI PMC

Lin Y., Rajan V., Moret B. M. (2012). Bootstrapping phylogenies inferred from rearrangement data. Algorithms Mol. Biol. 7, 21. doi:  10.1186/1748-7188-7-21, PMID: PubMed DOI PMC

Liu Y., Li D., Zhang Q., Song C., Zhong C., Zhang X., et al. (2017). Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two-layer mode of species diversification. New Phytol. 215, 877–890. doi:  10.1111/nph.14607, PMID: PubMed DOI

López-González N., Bobo-Pinilla J., Padilla-García N., Loureiro J., Castro S., Rojas-Andrés B. M., et al. (2021). Genetic similarities versus morphological resemblance: unraveling a polyploid complex in a Mediterranean biodiversity hotspot. Mol. Phylogenet. Evol. 155, 107006. doi:  10.1016/j.ympev.2020.107006, PMID: PubMed DOI

Lowry D. B., Willis J. H. (2010). A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation. PLoS Biol. 8, e1000500. doi:  10.1371/journal.pbio.1000500, PMID: PubMed DOI PMC

Lucek K., Augustijnen H., Escudero M. (2022). A holocentric twist to chromosomal speciation? Trends Ecol. Evol. 37, 655–662. doi:  10.1016/j.tree.2022.04.002, PMID: PubMed DOI

Lucek K., Giménez M. D., Joron M., Rafajlovic M., Searle J. B., Walden N., et al. (2023). The impact of chromosomal rearrangements in Speciation: From Micro-to Macroevolution. Cold Spring Harb. Perspect. Biol. 15, a041447. doi:  10.1101/cshperspect.a041447, PMID: PubMed DOI PMC

Luceño M., Castroviejo S. (1991). Agmatoploidy in Carex laevigata (Cyperaceae). Fusion and fission of chromosomes as the mechanism of cytogenetic evolution in Iberian populations. Pl. Syst. Evol. 177, 149–159. doi:  10.1007/BF00937952 DOI

Luceño M., Guerra M. (1996). Numerical variations in species exhibiting holocentric chromosomes: a nomenclatural proposal. Caryologia 49, 301–309. doi:  10.1080/00087114.1996.10797374 DOI

Luo M. C., Deal K. R., Akhunov E. D., Akhunova A. R., Anderson O. D., Anderson J. A., et al. (2009). Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae. Proc. Natl. Acad. Sci. U.S.A. 106, 15780–15785. doi:  10.1073/pnas.0908195106, PMID: PubMed DOI PMC

Lysak M. A., Berr A., Pecinka A., Schmidt R., McBreen K., Schubert I. (2006). Mechanisms of chromosome number reduction in PubMed DOI PMC

Lysak M. A., Schubert I. (2012). “Mechanisms of chromosome rearrangements,” in Plant Genome Diversity, vol. 2 . Eds. Greilhuber J., Dolezel J., Wendel J. (Springer, Vienna: ). doi:  10.1007/978-3-7091-1160-4_9 DOI

Maguilla E., Escudero M., Ruíz-Martín J., Arroyo J. (2021). Origin and diversification of flax and their relationship with heterostyly across the range. J. Biogeog. 48, 1994–2007. doi:  10.1111/jbi.14129 DOI

Maheshwari S., Barbash D. A. (2011). The genetics of hybrid incompatibilities. Annu. Rev. Genet. 45, 331–355. doi:  10.1146/annurev-genet-110410-132514, PMID: PubMed DOI

Mallet J. (2007). Hybrid speciation. Nature 446, 279–283. doi:  10.1038/nature05706, PMID: PubMed DOI

Mandáková T., Gloss A. D., Whiteman N. K., Lysak M. A. (2016). How diploidization turned a tetraploid into a pseudotriploid. Am. J. Bot. 103, 1187–1196. doi:  10.3732/ajb.1500452, PMID: PubMed DOI

Mandáková T., Guo X., Özüdoğru B., Mummenhoff K., Lysak M. A. (2018). Hybridization-facilitated genome merger and repeated chromosome fusion after 8 million years. TPJ 96, 748–760. doi:  10.1111/tpj.14065, PMID: PubMed DOI

Mandáková T., Heenan P. B., Lysak M. A. (2010. a). Island species radiation and karyotypic stasis in Pachycladon allopolyploids. BMC Evol. Biol. 10, 367. doi:  10.1186/1471-2148-10-367, PMID: PubMed DOI PMC

Mandáková T., Joly S., Krzywinski M., Mummenhoff K., Lysak M. A. (2010. b). Fast diploidization in close mesopolyploid relatives of PubMed DOI PMC

Mandáková T., Lysak M. A. (2008). Chromosomal phylogeny and karyotype evolution in x=7 crucifer species (Brassicaceae). Plant Cell 20, 2559–2570. doi:  10.1105/tpc.108.062166, PMID: PubMed DOI PMC

Mandáková T., Lysak M. A. (2018). Post-polyploid diploidization and diversification through dysploid changes. Plant Biol. 42, 55–65. doi:  10.1016/j.pbi.2018.03.001, PMID: PubMed DOI

Mandáková T., Pouch M., Harmanová K., Zhan S. H., Mayrose I., Lysak M. A. (2017). Multispeed genome diploidization and diversification following ancient allopolyploidization. Mol. Ecol. 26, 6445–6462. doi:  10.1111/mec.14379, PMID: PubMed DOI

Marburger S., Monnahan P., Seear P. J., Martin S. H., Koch J., Paajanen P., et al. (2019). Interspecific introgression mediates adaptation to whole genome duplication. Nat. Commun. 10, 1–11. doi:  10.1038/s41467-019-13159-5, PMID: PubMed DOI PMC

Marks R. A., Delgado P., Makonya G. M., Cooper K., VanBuren R., Farrant J. M. (2024). Higher order polyploids exhibit enhanced desiccation tolerance in the grass PubMed DOI PMC

Márquez-Corro J. I., Escudero M., Luceño M. (2018). Do holocentric chromosomes represent an evolutionary advantage? A study of paired analyses of diversification rates of lineages with holocentric chromosomes and their monocentric closest relatives. Chromosome Res. 26, 139–152. doi:  10.1007/s10577-017-9566-8, PMID: PubMed DOI

Márquez-Corro J. I., Martín-Bravo S., Blanco-Pastor J. L., Luceño M., Escudero M. (2024). The holocentric chromosome microevolution: From phylogeographic patterns to genomic associations with environmental gradients. Mol. Ecol. 33, e17156. doi:  10.1111/mec.17156, PMID: PubMed DOI PMC

Márquez-Corro J. I., Martín-Bravo S., Jiménez-Mejías P., Hipp A. L., Spalink D., Naczi R. F., et al. (2021). Macroevolutionary insights into sedges ( DOI

Márquez-Corro J. I., Martín-Bravo S., Pedrosa-Harand A., Hipp A. L., Luceño M., Escudero M. (2019). Karyotype Evolution In Holocentric Organisms (Chichester: eLS. John Wiley and Sons, Ltd; ). doi:  10.1002/9780470015902.a0028758 DOI

Mata J. K., Martin S. L., Smith T. W. (2023). Global biodiversity data suggest allopolyploid plants do not occupy larger ranges or harsher conditions compared with their progenitors. Ecol. Evol. 13, e10231. doi:  10.1002/ece3.10231, PMID: PubMed DOI PMC

Mayrose I., Barker M. S., Otto S. P. (2010). Probabilistic models of chromosome number evolution and the inference of polyploidy. Syst. Biol. 59, 132–144. doi:  10.1093/sysbio/syp083, PMID: PubMed DOI

Mayrose I., Lysak M. A. (2021). The evolution of chromosome numbers: mechanistic models and experimental approaches. Genome Biol. Evol. 13, evaa220. doi:  10.1093/gbe/evaa220, PMID: PubMed DOI PMC

Mayrose I., Zhan S. H., Rothfels C. J., Arrigo N., Barker M. S., Rieseberg L. H., et al. (2014). Methods for studying polyploid diversification and the dead end hypothesis: A reply to Soltis et al. New Phytol. 206, 27–35. doi:  10.1111/nph.13192, PMID: PubMed DOI

McCarthy E. W., Arnold S. E., Chittka L., Le Comber S. C., Verity R., Dodsworth S., et al. (2015). The effect of polyploidy and hybridization on the evolution of floral colour in Nicotiana (Solanaceae). Ann. Bot. 115, 1117–1131. doi:  10.1093/aob/mcv048, PMID: PubMed DOI PMC

McHale N. A. (1983). Environmental induction of high frequency 2n pollen formation in diploid Solanum. Can. J. Genet. Cytol. 25, 609–615. doi:  10.1139/g83-091 DOI

McKibben M. T. W., Finch G., Barker M. S. (2024). Species-tree topology impacts the inference of ancient whole-genome duplications across the angiosperm phylogeny. Am. J. Bot. 111, e16378. doi:  10.1002/ajb2.16378, PMID: PubMed DOI

Meier J. I., Marques D. A., Mwaiko S., Wagner C. E., Excoffier L., Seehausen O. (2017). Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nat. Commun. 8, 14363. doi:  10.1038/ncomms14363, PMID: PubMed DOI PMC

Michael T. P. (2014). Plant genome size variation: bloating and purging DNA. Brief Funct. Genomics 13, 308–317. doi:  10.1093/bfgp/elu005, PMID: PubMed DOI

Ming R., Bendahmane A., Renner S. S. (2011). Sex chromosomes in land plants. Annu. Rev. Plant Biol. 62, 485–514. doi:  10.1146/annurev-arplant-042110-103914, PMID: PubMed DOI

Mohan A. V., Escuer P., Cornet C., Lucek K. (2024). A three-dimensional genomics view for speciation research. Trends Genet. 40, 638–641. doi:  10.1016/j.tig.2024.05.009, PMID: PubMed DOI

Monnahan P., Kolář F., Baduel P., Sailer C., Koch J., Horvath R., et al. (2019). Pervasive population genomic consequences of genome duplication in PubMed DOI

Moret B., Warnow T. (2005). “Advances in phylogeny reconstruction from gene order and content data,” in Methods In Enzymology, Molecular Evolution: Producing The Biochemical Data, Part B. Vol. 395. Ed. Roalson Z. (Amsterdam: Elsevier; ), 673–700., PMID: PubMed

Morgan E. J., Čertner M., Lučanová M., Deniz U., Kubíková K., Venon A., et al. (2021). Disentangling the components of triploid block and its fitness consequences in natural diploid–tetraploid contact zones of Arabidopsis arenosa. New Phytol. 232, 1449–1462. doi:  10.1111/nph.17357, PMID: PubMed DOI

Moura R. F., Queiroga D., Vilela E., Moraes A. P. (2021). Polyploidy and high environmental tolerance increase the invasive success of plants. J. Plant Res. 134, 105–114. doi:  10.1007/s10265-020-01236-6, PMID: PubMed DOI

Mutti J. S., Bhullar R. K., Gill K. S. (2017). Evolution of gene expression balance among homeologs of natural polyploids. G3: Genes Genomes Genet. 7, 1225–1237. doi:  10.1534/g3.116.038711, PMID: PubMed DOI PMC

Naiki A. (2012). Heterostyly and the possibility of its breakdown by polyploidization. Plant Species Biol. 27, 3–29. doi:  10.1111/j.1442-1984.2011.00363.x DOI

Nieto Feliner G., Casacuberta J., Wendel F. J. (2020). Genomics of evolutionary novelty in hybrids and polyploids. Front. Genet. 11. doi:  10.3389/fgene.2020.00792, PMID: PubMed DOI PMC

Nijalingappa B. H. M. (1974). Cytological studies in

Nokkala S., Kuznetsova V. G., Maryanska-Nadachowska A., Nokkala C. (2004). Holocentric chromosomes in meiosis. I. Restriction of the number of chiasmata in bivalents. Chromosome Res. 12, 733–739. doi:  10.1023/B:CHRO.0000045797.74375.70, PMID: PubMed DOI

Novikova P. Y., Hohmann N., Van de Peer Y. (2018). Polyploid PubMed DOI

Novikova P. Y., Tsuchimatsu T., Simon S., Nizhynska V., Voronin V., Burns R., et al. (2017). Genome sequencing reveals the origin of the allotetraploid PubMed DOI PMC

Novikova P., Yu, Kolesnikova U. K., Scott A. D. (2023). Ancestral self-compatibility facilitates the establishment of allopolyploids in Brassicaceae. Plant Reprod. 36, 125–138. doi:  10.1007/s00497-022-00451-6, PMID: PubMed DOI PMC

Nuismer S. L., Thompson J. N. (2001). Plant polyploidy and non-uniform effects on insect herbivores. Proc. R. Soc Lond. B. 268, 1937–1940. doi:  10.1098/rspb.2001.1760, PMID: PubMed DOI PMC

Orians C. M. (2000). The effects of hybridization in plants on secondary chemistry: implications for the ecology and evolution of plant-herbivore interactions. Am. J. Bot. 87, 1749–1756. doi:  10.2307/2656824, PMID: PubMed DOI

Osborn T. C., Pires J. C., Birchler J. A., Auger D. L., Chen Z. J., Lee H. S., et al. (2003). Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19, 141–147. doi:  10.1016/S0168-9525(03)00015-5, PMID: PubMed DOI

Ostevik K. L., Samuk K., Rieseberg L. H. (2020). Ancestral reconstruction of karyotypes reveals an exceptional rate of nonrandom chromosomal evolution in sunflowers. Genetics 214, 1031–1045. doi:  10.1534/genetics.120.303026, PMID: PubMed DOI PMC

Oswald B. P., Nuismer S. L. (2011). A unified model of autopolyploid establishment and evolution. Am. Nat. 178, 687–700. doi:  10.1086/662673, PMID: PubMed DOI PMC

Otto S. P. (2007). The evolutionary consequences of polyploidy. Cell 131, 452–462. doi:  10.1016/j.cell.2007.10.022, PMID: PubMed DOI

Otto S. P., Whitton J. (2000). Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437. doi:  10.1146/annurev.genet.34.1.401, PMID: PubMed DOI

Ouyang W., Xiong D., Li G., Li X. (2020). Unraveling the 3D genome architecture in plants: present and future. Mol. Plant 13, 1676–1693. doi:  10.1016/j.molp.2020.10.002, PMID: PubMed DOI

Owens G. L., Rieseberg L. H. (2014). Hybrid incompatibility is acquired faster in annual than in perennial species of sunflower and tarweed. Evol. 68, 893–900. doi:  10.1111/evo.12297, PMID: PubMed DOI

Paape T., Briskine R. V., Halstead-Nussloch G., Lischer H. E. L., Shimizu-Inatsugi R., Hatakeyama M., et al. (2018). Patterns of polymorphism and selection in the subgenomes of the allopolyploid PubMed DOI PMC

Pandit M. K., Pocock M. J. O., Kunin W. E. (2011). Ploidy influences rarity and invasiveness in plants. J. Ecol. 99, 1108–1115. doi:  10.1111/j.1365-2745.2011.01838.x DOI

Parent C., Patton A., Pfennig K., Rubinoff D., Schluter D., Seehausen O., et al. (2020). Comparing adaptive radiations across space, time, and taxa. J. Hered. 111, 1–20. doi:  10.1093/jhered/esz064, PMID: PubMed DOI PMC

Parisod C., Broennimann O. (2016). Towards unified hypotheses of the impact of polyploidy on ecological niches. New Phytol. 212, 540–542. doi:  10.1111/nph.14133, PMID: PubMed DOI

Parisod C., Holderegger R., Brochmann C. (2010). Evolutionary consequences of autopolyploidy. New Phytol. 186, 5–17. doi:  10.1111/j.1469-8137.2009.03142.x, PMID: PubMed DOI

Paterson A. H., Wang X., Li J., Tang H. (2012). “Ancient and recent polyploidy in monocots,” in Polyploidy and genome evolution. Eds. Soltis P. S., Soltis D. E. (Springer, Berlin, Germany: ), 93–108.

Patterson T. B., Givnish T. J. (2004). Geographic cohesion, chromosomal evolution, parallel adaptive radiations, and consequent floral adaptations in DOI

Pease J. B., Haak D. C., Hahn M. W., Moyle L. C. (2016). Phylogenomics reveals three sources of adaptive variation during a rapid radiation. PLoS Biol. 14, e1002379. doi:  10.1371/journal.pbio.1002379, PMID: PubMed DOI PMC

Pécrix Y., Rallo G., Folzer H., Cigna M., Gudin S., Bris M. L. (2011). Polyploidization mechanisms: temperature environment can induce diploid gamete formation in Rosa sp. J. Exp. Bot. 62, 3587–3597. doi:  10.1093/jxb/err052, PMID: PubMed DOI

Pegoraro L., Vos J. M., Cozzolino S., Scopece G. (2019). Shift in flowering time allows diploid and autotetraploid DOI

Pei L., Li G., Lindsey K., Zhang X., Wang M. (2021). Plant 3D genomics: the exploration and application of chromatin organization. New Phytol. 230, 1772–1786. doi:  10.1111/nph.17262, PMID: PubMed DOI PMC

Pellicer J., Hidalgo O., Dodsworth S., Leitch I. J. (2018). Genome size diversity and its impact on the evolution of land plants. Genes 9, 88. doi:  10.3390/genes9020088, PMID: PubMed DOI PMC

Peskoller A., Silbernagl L., Hülber K., Sonnleitner M., Schönswetter P. (2021). Do pentaploid hybrids mediate gene flow between tetraploid Senecio disjunctus and hexaploid DOI

Pikaard C. S. (2001). Genomic change and gene silencing in polyploids. Trend Genet. 17, 675–677. doi:  10.1016/S0168-9525(01)02545-8, PMID: PubMed DOI

Pimentel M., Escudero M., Sahuquillo E., Minaya M.Á., Catalán P. (2017). Are diversification rates and chromosome evolution in the temperate grasses (Pooideae) associated with major environmental changes in the Oligocene-Miocene? PeerJ. 5, e3815. doi:  10.7717/peerj.3815, PMID: PubMed DOI PMC

Qian H., Jin Y. (2016). An updated megaphylogeny of plants, a tool for generating plant phylogenies and an analysis of phylogenetic community structure. J. Plant Ecol. 9, 233–239. doi:  10.1093/jpe/rtv047 DOI

Qiao X., Li Q., Yin H., Qi K., Li L., Wang R., et al. (2019). Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants. Genome Biol. 20, 38. doi:  10.1186/s13059-019-1650-2, PMID: PubMed DOI PMC

Qiu T., Liu Z., Liu B. (2020). The effects of hybridization and genome doubling in plant evolution via allopolyploidy. Mol. Biol. Rep. 47, 5549–5558. doi:  10.1007/s11033-020-05597-y, PMID: PubMed DOI

Ramsey J., Schemske D. W. (1998). Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 29, 467–501. doi:  10.1146/annurev.ecolsys.29.1.467 DOI

Ravinet M., Faria R., Butlin R. K., Galindo J., Bierne N., Rafajlović M., et al. (2017). Interpreting the genomic landscape of speciation: A road map for finding barriers to gene flow. J. Evol. Biol. 30, 1450–1477. doi:  10.1111/jeb.13047, PMID: PubMed DOI

Rezende L., Suzigan J., Amorim F. W., Moraes A. P. (2020). Can plant hybridization and polyploidy lead to pollinator shift? Acta Bot. Bras. 34, 229–242. doi:  10.1590/0102-33062020abb0025 DOI

Rice A., Glick L., Abadi S., Einhorn M., Kopelman N. M., Salman-Minkov A., et al. (2015). The Chromosome Counts Database (CCDB) – a community resource of plant chromosome numbers. New Phytol. 206, 19–26. doi:  10.1111/nph.13191, PMID: PubMed DOI

Rice A., Mayrose I. (2023). “The chromosome counts database (CCDB),” in Plant Genomic and Cytogenetic Databases, vol. 2703 . Eds. Garcia S., Nualart N. (Humana, New York: ). doi:  10.1007/978-1-0716-3389-2_10, PMID: PubMed DOI

Rieseberg L. H. (2001. a). Chromosomal rearrangements and speciation. Trends Ecol. Evol. 16, 351–358. doi:  10.1016/S01695347(01)02187-5 PubMed DOI

Rieseberg L. H. (2001. b). Polyploid evolution: Keeping the peace at genomic reunions. Curr. Biol. 11, R925–R928. doi:  10.1016/S0960-9822(01)00556-5, PMID: PubMed DOI

Rieseberg L. H., Van Fossen C., Desrochers A. (1995). Hybrid speciation accompanied by genomic reorganization in wild sunflowers. Nature 375, 313–316. doi:  10.1038/375313a0 DOI

Roalson E. H. (2008). A synopsis of chromosome number variation in the Cyperaceae. Bot. Rev. 74, 209–393. doi:  10.1007/s12229-008-9011-y DOI

Rodionov A. V. (2023). Eupolyploidy as a mode in plant speciation. Russ. J. Genet. 59, 419–443. doi:  10.1134/S1022795423050113 DOI

Rosche C., Broennimann O., Novikov A., Mrázová V., Boiko G. V., Danihelka J., et al. (2025). Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe. New Phytol. 245, 392–405. doi:  10.1111/nph.20212, PMID: PubMed DOI PMC

Rurik I., Melichárková A., Gbúrová Štubová E., Kučera J., Kochjarová J., Paun O., et al. (2024). Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus PubMed DOI

Sader M. A., Amorim B. S., Costa L., Souza G., Pedrosa-Harand A. (2019). The role of chromosome changes in the diversification of DOI

Scarrow M., Wang Y., Sun G. (2020). Molecular regulatory mechanisms underlying the adaptability of polyploid plants. Biol. Rev. 96, 394–407. doi:  10.1111/brv.12661, PMID: PubMed DOI

Schmickl R., Jørgensen M. H., Brysting A. K., Koch M. A. (2010). The evolutionary history of the PubMed DOI PMC

Schmickl R., Vallejo Marín M., Hojka J., Gorospe J. M., Haghighatnia M. J., İltaş Ö., et al. (2024). Polyploidy-induced floral changes lead to unexpected pollinator behavior in DOI

Schmickl R., Yant L. (2021). Adaptive introgression: how polyploidy reshapes gene flow landscapes. New Phytol. 230, 457–461. doi:  10.1111/nph.17204, PMID: PubMed DOI

Schoener T. W. (1990). “Ecological interactions,” in Analytical Biogeography. Eds. Myers A. A., Giller P. S. (Springer, Dordrecht: ). doi:  10.1007/978-94-009-0435-4_9 DOI

Schranz M. E., Osborn T. C. (2000). Novel flowering time variation in the resynthesized polyploid Brassica napus. J. Hered. 91, 242–246. doi:  10.1093/jhered/91.3.242, PMID: PubMed DOI

Schumer M., Rosenthal G. G., Andolfatto P. (2014). How common is homoploid hybrid speciation? Evol. 68, 1553–1560. doi:  10.1111/evo.12399, PMID: PubMed DOI

Scopece G., Lecer C., Widmer A., Cozzolino S. (2010). Polymorphism of postmating reproductive isolation within plant species. Taxon 59, 1367–1374. doi:  10.2307/20774034 DOI

Scott A. D., Kolesnikova U., Glushkevich A., Steinmann L., Tikhomirov N., Pfordt U., et al. (2024). Multiple polyploidizations in PubMed DOI PMC

Scott A. D., Stenz N. W. M., Ingvarsson P. K., Baum D. A. (2016). Whole genome duplication in coast redwood ( PubMed DOI

Seehausen O. (2004). Hybridization and adaptive radiation. Trends Ecol. Evol. 19, 198–207. doi:  10.1016/j.tree.2004.01.003, PMID: PubMed DOI

Segraves K. A., Anneberg T. J. (2016). Species interaction and plant polyploidy. Am. J. Bot. 103, 1326–1335. doi:  10.3732/ajb.1500529, PMID: PubMed DOI

Servick S., Visger C. J., Gitzendanner M. A., Soltis P. S., Soltis D. E. (2015). Population genetic variation, geographic structure, and multiple origins of autopolyploidy in Galax urceolata. Am. J. Bot. 102, 973–982. doi:  10.3732/ajb.1400554, PMID: PubMed DOI

Seymour D. K., Koenig D., Hagmann J., Becker C., Weigel D. (2014). Evolution of DNA methylation patterns in the brassicaceae is driven by differences in genome organization. PLoS Genet. 10, e1004785. doi:  10.1371/journal.pgen.1004785, PMID: PubMed DOI PMC

Shi F. X., Li M. R., Li Y. L., Jiang P., Zhang C., Pan Y. Z., et al. (2015). The impacts of polyploidy, geographic and ecological isolations on the diversification of Panax (Araliaceae). BMC Plant Biol. 15, 297. doi:  10.1186/s12870-015-0669-0, PMID: PubMed DOI PMC

Shu J.-P., Wang H., Shen H., Wang R.-J., Fu Q., Wang Y.-D., et al. (2022). Phylogenomic analysis reconstructed the order matoniales from paleopolyploidy veil. Plants. 11, 1529. doi:  10.3390/plants11121529, PMID: PubMed DOI PMC

Skopalíková J., Leong-Škorničková J., Šída O., Newman M., Chumová Z., Fér T., et al. (2023). Ancient hybridization in PubMed DOI

Šlenker M., Kantor A., Marhold K., Schmickl R., Mandáková T., Lysak M. A., et al. (2021). Allele sorting as a novel approach to resolving the origin of allotetraploids using hyb-Seq data: A case study of the balkan mountain endemic PubMed DOI PMC

Slovák M., Melichárková A., Gbúrová Štubňová E., Kučera J., Mandáková T., Smyčka J., et al. (2023). Pervasive introgression during rapid diversification of the european mountain genus PubMed DOI PMC

Soltis P. S., Liu X., Marchant D. B., Visger C. J., Soltis D. E. (2014). Polyploidy and novelty: Gottlieb’s legacy. Philos. Trans. R. Soc Lond. B Biol. Sci. 369, 20130351. doi:  10.1098/rstb.2013.0351, PMID: PubMed DOI PMC

Soltis P. S., Ma D. B., Van de Peer Y., Soltis D. E. (2015). Polyploidy and genome evolution in plants. Curr. Opin. Genet. Dev. 35, 119–125. doi:  10.1016/j.gde.2015.11.003, PMID: PubMed DOI

Soltis D. E., Soltis P. S. (1989). Genetic consequences of autopolyploidy in Tolmiea (Saxifragaceae). Evol. 43, 586–594. doi:  10.1111/j.1558-5646.1989.tb04254.x, PMID: PubMed DOI

Soltis P. S., Soltis D. E. (2009). The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60, 561–588. doi:  10.1146/annurev.arplant.043008.092039, PMID: PubMed DOI

Soltis D. E., Soltis P. S., Bennett M. D., Leitch I. J. (2013). Evolution of genome size in the angiosperms. Am. J. Bot. 90, 1596–1603. doi:  10.3732/ajb.90.11.1596, PMID: PubMed DOI

Stankowski S., Streisfeld M. A. (2015). Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers. Proc. R. Soc B: Biol. Sci. 282, 20151666. doi:  10.1098/rspb.2015.1666, PMID: PubMed DOI PMC

Stathos A. M., Fishman L. (2014). Chromosomal rearrangements directly cause underdominant F1 pollen sterility in PubMed DOI

Stebbins G. L. (1947). Types of polyploids: their classification and significance. Adv. Genet. 1, 403–429. doi:  10.1016/S0065-2660(08)60490-3, PMID: PubMed DOI

Stebbins G. L. (1957). The hybrid origin of microspecies in the

Stebbins G. L. (1958). The inviability, weakness, and sterility of interspecific hybrids. Adv. Genet. 9, 147–215. doi:  10.1016/S0065-2660(08)60162-5, PMID: PubMed DOI

Stebbins G. L. (1971). Chromosomal evolution in higher plants (London, UK: Edward Arnold; ).

Stebbins G. L. (1984). Mosaic evolution, mosaic selection and angiosperm phylogeny. Bot. Jour. Linn. Soc 88, 149–164. doi:  10.1111/j.1095-8339.1984.tb01568.x DOI

Sturtevant A. H. (1921). A case of rearrangement of genes in Drosophila. Proc. Nat. Acad. Sci. 7, 235–237. doi:  10.1073/pnas.7.8.235, PMID: PubMed DOI PMC

Suarez-Gonzalez A., Lexer C., Cronk Q. C. B. (2018). Adaptive introgression: A plant perspective. Biol. Lett. 14, 20170688. doi:  10.1098/rsbl.2017.0688, PMID: PubMed DOI PMC

Suda J., Krahulcová A., Trávníček P., Rosenbaumová R., Peckert T., Krahulec F. (2007). Genome size variation and species relationships in PubMed DOI PMC

Svardal H., Quah F. X., Malinsky M., Ngatunga B. P., Miska E. A., Salzburger W., et al. (2020). Ancestral hybridization facilitated species diversification in the Lake Malawi cichlid fish adaptive radiation. Mol. Biol. Evol. 37, 1100–1113. doi:  10.1093/molbev/msz294, PMID: PubMed DOI PMC

Tang H., Bowers J. E., Wang X., Ming R., Alam M., Paterson A. H. (2008). Synteny and collinearity in plant genomes. Science 320, 486–488. doi:  10.1126/science.1153917, PMID: PubMed DOI

Tate J. A., Douglas E. S., Soltis P. S. (2005). “Polyploidy in plants,” in The evolution of the genome. Ed. Gregory T. R. (San Diego: Elsevier Academic Press; ), 371–426.

Tayalé A., Parisod C. (2013). Natural pathways to polyploidy in plants and consequences for genome reorganization. Cytogenet. Genome Res. 140, 79–96. doi:  10.1159/000351318, PMID: PubMed DOI

Taylor S. A., Larson E. L. (2019). Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat. Ecol. Evol. 3, 170–177. doi:  10.1038/s41559-018-0777-y, PMID: PubMed DOI

Te Beest M., Le Roux J. J., Richardson D. M., Brysting A. K., Suda J., Kubešová M., et al. (2012). The more the better? The role of polyploidy in facilitating plant invasions. Ann. Bot. 109, 19–45. doi:  10.1093/aob/mcr277, PMID: PubMed DOI PMC

Thébault A., Gillet F., Müller-Schärer H., Buttler A. (2011). Polyploidy and invasion success: trait trade-offs in native and introduced cytotypes of two Asteraceae species. Plant Ecol. 212, 315–325. doi:  10.1007/s11258-010-9824-8 DOI

Thompson J. N. (2009). The coevolving web of life. Am. Nat. 173, 125–140. doi:  10.1086/595752, PMID: PubMed DOI

Thompson J. N., Nuismer S. L., Merg. K. (2004). Plant polyploidy and the evolutionary ecology of plant/animal interactions. Biol. J. Linn Soc 82, 511–519. doi:  10.1111/j.1095-8312.2004.00338.x DOI

Todesco M., Owens G. L., Bercovich N., Légaré J. S., Soudi S., Burge D. O., et al. (2020). Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584, 602–607. doi:  10.1038/s41586-020-2467-6, PMID: PubMed DOI

Todesco M., Pascual M. A., Owens G. L., Ostevik K. L., Moyers B. T., Hübner S., et al. (2016). Hybridization and extinction. Evol. Appl. 9, 892–908. doi:  10.1111/eva.12367, PMID: PubMed DOI PMC

Tomlin C. M., Rajaraman S., Sebesta J. T., Scheen A.-C., Bendiksby M., Wen Low Y., et al. (2024). Allopolyploid origin and diversification of the Hawaiian endemic mints. Nat. Commun. 15, 3109. doi:  10.1038/s41467-024-47247-y, PMID: PubMed DOI PMC

Tribble C. M., Márquez-Corro J. I., May M. R., Hipp A. L., Escudero M., Zenil-Ferguson R. (2025). Macroevolutionary inference of complex modes of chromosomal speciation in a cosmopolitan plant lineage. New Phytol. 24, 2350–2361. doi:  10.1111/nph.20353, PMID: PubMed DOI

Trickett A. J., Butlin R. K. (1994). Recombination suppressors and the evolution of new species. Heredity. 73, 339–345. doi:  10.1038/hdy.1994.180, PMID: PubMed DOI

Turcotte M. M., Kaufmann N., Wagner K. L., Zallek T. A., Ashman T.-L. (2024). Neopolyploidy increases stress tolerance and reduces fitness plasticity across multiple urban pollutants: support for the “general-purpose” genotype hypothesis. Evol. Lett. 8, 416–426. doi:  10.1093/evlett/qrad072, PMID: PubMed DOI PMC

Valdés-Florido A., González-Toral C., Maguilla E., Cires E., Díaz-Lifante Z., Andrés-Camacho C., et al. (2024. a). Polyploidy and hybridization in the Mediterranean: unraveling the evolutionary history of PubMed DOI PMC

Valdés-Florido A., Tan L., Maguilla E., Simón-Porcar V. I., Zhou Y.-H., Arroyo J., et al. (2023). Drivers of diversification in PubMed DOI PMC

Valdés-Florido A., Valcárcel V., Maguilla E., Díaz-Lifante Z., Andrés-Camacho C., Zeltner L., et al. (2024. b). The interplay between climatic niche evolution, polyploidy and reproductive traits explains plant speciation in the Mediterranean Basin: a case study in PubMed DOI PMC

Van de Peer Y., Ashman T. L., Soltis P. S., Soltis D. E. (2021). Polyploidy: an evolutionary and ecological force in stressful times. Plant Cell 33, 11–26. doi:  10.1093/plcell/koaa015, PMID: PubMed DOI PMC

Van de Peer Y., Mizrachi E., Marchal K. (2017). The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424. doi:  10.1038/nrg.2017.26, PMID: PubMed DOI

Van der Heijden E., Näsvall K., Seixas F. A., Becerra Nobre C. E., Campos D. Maia A., Salazar-Carrión P., et al. (2024). Genomics of Neotropical biodiversity indicators: two butterfly radiations with rampant chromosomal rearrangements and hybridisation. BioRxiv. doi:  10.1101/2024.07.07.602206, PMID: PubMed DOI PMC

Van Drunen W. E., Husband B. C. (2019). Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms. New Phytol. 224, 1266–1277. doi:  10.1111/nph.15999, PMID: PubMed DOI

Vanrell M. A., Novaes L. R., Afonso A., Arroyo J., Simón-Porcar V. (2024). Ecological correlates of population genetics in Linum suffruticosum, an heterostylous polyploid and taxonomic complex endemic to the Western Mediterranean Basin. AoB Plants 16, plae027. doi:  10.1093/aobpla/plae027, PMID: PubMed DOI PMC

Vereecken N. J., Cozzolino S., Schiestl F. P. (2010). Hybrid floral scent novelty drives pollinator shift in sexually deceptive orchids. BMC Evol. Biol. 10, 103. doi:  10.1186/1471-2148-10-103, PMID: PubMed DOI PMC

Vlček J., Hämälä T., Cobo C. V., Curran E., Šrámková G., Slotte T., et al. (2025). Whole-genome duplication increases genetic diversity and load in outcrossing PubMed DOI PMC

Vleugels T., Cnops G., Van Bockstaele E. (2013). Screening for resistance to clover rot (Sclerotinia spp.) among a diverse collection of red clover populations (Trifolium pratense L.). Euphytica. 194, 371–382. doi:  10.1007/s10681-013-0949-4 DOI

Wan J., Oduor A. M., Pouteau R., Wang B., Chen L., Yang B., et al. (2020). Can polyploidy confer invasive plants with a wider climatic tolerance? A test using PubMed DOI PMC

Wang J., Li D., Shang F., Kang X. (2017). High temperature-induced production of unreduced pollen and its cytological effects in Populus. Sci. Rep. 7, 5281. doi:  10.1038/s41598-017-05661-x, PMID: PubMed DOI PMC

Wang C., Liu L., Yin M., Eller F., Brix H., Wang T., et al. (2024). Genome-wide analysis tracks the emergence of intraspecific polyploids in PubMed DOI PMC

Wang X., Morton J. A., Pellicer J., Leitch I. J., Leitch A. R. (2021). Genome downsizing after polyploidy: mechanisms, rates and selection pressures. Plant J. 107, 1003–1015. doi:  10.1111/tpj.15363, PMID: PubMed DOI

Wang M., Wang P., Lin M., Ye Z., Li G., Tu L., et al. (2018). Evolutionary dynamics of 3D genome architecture following polyploidization in cotton. Nat. Plants 4, 90–97. doi:  10.1038/s41477-017-0096-3, PMID: PubMed DOI

Weiss-Schneeweiss H., Schneeweiss G. M. (2013). “Karyotype diversity and evolutionary trends in angiosperms,” in Plant Genome Diversity vol.2: Physical Structure, Behaviour and Evolution of Plant Genomes vol. 2. Eds. Greilhuber J., Dolezel J., Wendel J. F. (Springer, Vienna: ), 209–230.

Wendel J. F. (2015). The wondrous cycles of polyploidy in plants. Am. J. Bot. 102, 1753–1756. doi:  10.3732/ajb.1500320, PMID: PubMed DOI

Wendel J. F., Jackson S. A., Meyers B. C., Wing R. A. (2016). Evolution of plant genome architecture. Genome Biol. 17, 1–14. doi:  10.1186/s13059-016-0908-1, PMID: PubMed DOI PMC

Wendel J. F., Lisch D., Hu G., Mason A. S. (2018). The long and short of doubling down: polyploidy, epigenetics, and the temporal dynamics of genome fractionation. Curr. Opin. Genet. Dev. 49, 1–7. doi:  10.1016/j.gde.2018.01.004, PMID: PubMed DOI

Whitkus R. (1988). Experimental hybridizations among chromosome races of DOI

Wolf P. G., Haufler C. H., Sheffield E. (1987). Electrophoretic evidence for genetic diploidy in the bracken fern (Pteridium aquilinum). Science 236, 947–949. doi:  10.1126/science.236.4804.947, PMID: PubMed DOI

Wray G. A., Hahn M. W., Abouheif E., Balhoff J. P., Pizer M., Rockman M. V., et al. (2003). The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20, 1377–1419. doi:  10.1093/molbev/msg140, PMID: PubMed DOI

Wu F., Tanksley S. D. (2010). Chromosomal evolution in the plant family Solanaceae. BMC Genomics 11, 182. doi:  10.1186/1471-2164-11-182, PMID: PubMed DOI PMC

Yakimowski S. B., Rieseberg L. H. (2014). The role of homoploid hybridization in evolution: A century of studies synthesizing genetics and ecology. Am. J. Bot. 101, 1247–1258. doi:  10.3732/ajb.1400201, PMID: PubMed DOI

Yant L., Hollister J. D., Wright K. M., Arnold B. J., Higgins J. D., Franklin F. C. H., et al. (2013). Meiotic adaptation to genome duplication in PubMed DOI PMC

Yona A. H., Manor Y. S., Herbst R. H., Romano G. H., Mitchell A. M., Kupiec M., et al. (2012). Chromosomal duplication is a transient evolutionary solution to stress. Proc. Natl. Acad. Sci. 109, 21010–21015. doi:  10.1073/pnas.1211150109, PMID: PubMed DOI PMC

Yuan Y., Bayer P. E., Batley J., Edwards D. (2021). Current status of structural variation studies in plants. Plant Biotechnol. J. 19, 2153–2163. doi:  10.1111/pbi.13646, PMID: PubMed DOI PMC

Zanne A. E., Tank D. C., Cornwell W. K., Eastman J. M., Smith S. A., FitzJohn R. G., et al. (2014). Three keys to the radiation of angiosperms into freezing environments. Nature. 506, 89–92. doi:  10.1038/nature12872, PMID: PubMed DOI

Zhan S., Otto S., Barker M. (2021). Broad variation in rates of polyploidy and dysploidy across flowering plants is correlated with lineage diversification. BioRxiv. doi:  10.1101/2021.03.30.436382 DOI

Zhang K., Wang X., Cheng P. (2019). Plant polyploidy: origin, evolution, and its influence on crop domestication. Hortic. Plant Journ. 5, 231–239. doi:  10.1016/j.hpj.2019.11.003 DOI

Zhang X., Wang G., Zhang S., Chen S., Wang Y., Wen P., et al. (2020). Genomes of the banyan tree and pollinator wasp provide insights into fig-wasp coevolution. Cell. 183, 875–889.e17. doi:  10.1016/j.cell.2020.09.043, PMID: PubMed DOI

Zhao J., Bayer P. E., Ruperao P., Saxena R. K., Khan A. W., Golicz A. A., et al. (2020). Trait associations in the pangenome of pigeon pea ( PubMed DOI PMC

Zhao J., Feng Q., Lu H., Li Y., Wang A., Tian Q., et al. (2018). Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat. Genet. 50, 278–284. doi:  10.1038/s41588-018-0041-z, PMID: PubMed DOI

Zheng L., Kinosian S. P., Zhan S. H., Barker M. S. (2024). Ancient polyploid and low rate of chromosome loss explain the high chromosome numbers of homosporous ferns. BioRxiv. doi:  10.1101/2024.09.23.614530 DOI

Zhong S., Li B., Chen W., Wang L., Guan J., Wang Q., et al. (2022). The chromosome-level genome of PubMed DOI