Abundance of established polyploid lineages varies across lineages, evolutionary time, and geography, suggesting both genetics and environment play a role in polyploid persistence. We show Arabidopsis lyrata is the most polyploid-rich species complex in the Arabidopsis genus, with multiple origins of autotetraploidy. This is revealed by genomic data from over 400 A. lyrata samples across Eurasia. We found over 30 previously undescribed autotetraploid populations in Siberia with a minimum of two separate origins, independent of those previously reported in Central Europe. The establishment of Siberian tetraploids is mediated by meiotic adaptation at the same genes as in European tetraploid A. lyrata and Arabidopsis arenosa, despite their genomic divergence and geographical separation. Haplotype analysis based on synthetic long-read assemblies supports the long-range introgression of adaptive alleles from the tetraploid interspecific pool of European A. lyrata and A. arenosa to tetraploid Siberian A. lyrata. Once adaptations to polyploidy emerge, they promote the establishment of new polyploid lineages through adaptive inter- and intraspecific introgression.

Department of Botany Faculty of Science Charles University Prague Czech Republic

Department of Chromosome Biology Max Planck Institute for Plant Breeding Research Cologne 50829 Germany

Department of Plant Sciences University of Cambridge Cambridge UK

Herbarium Faculty of Biology M 5 Lomonosov Moscow State University Moscow 119991 Russia

Institute of Botany The Czech Academy of Sciences Průhonice Czech Republic

See more in PubMed

Alexander  DH, Novembre  J, Lange  K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009:19(9):1655–1664. 10.1101/gr.094052.109. PubMed DOI PMC

Alonge  M, Lebeigle  L, Kirsche  M, Jenike  K, Ou  S, Aganezov  S, Wang  X, Lippman  ZB, Schatz  MC, Soyk  S. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 2022:23(1):258. 10.1186/s13059-022-02823-7. PubMed DOI PMC

Ansell  SW, Stenøien  HK, Grundmann  M, Schneider  H, Hemp  A, Bauer  N, Russell  SJ, Vogel  JC. Population structure and historical biogeography of European PubMed DOI

Arnold  B, Kim  ST, Bomblies  K. Single geographic origin of a widespread autotetraploid PubMed DOI

Barakate  A, Higgins  JD, Vivera  S, Stephens  J, Perry  RM, Ramsay  L, Colas  I, Oakey  H, Waugh  R, Franklin  FCH, et al.  The synaptonemal complex protein ZYP1 is required for imposition of meiotic crossovers in barley. Plant Cell. 2014:26(2):729–740. 10.1105/tpc.113.121269. PubMed DOI PMC

Barker  MS, Arrigo  N, Baniaga  AE, Li  Z, Levin  DA. On the relative abundance of autopolyploids and allopolyploids. New Phytol. 2016:210(2):391–398. 10.1111/nph.13698. PubMed DOI

Blischak  PD, Sajan  M, Barker  MS, Gutenkunst  RN. Demographic history inference and the polyploid continuum. Genetics. 2023:224(4):iyad107. 10.1093/genetics/iyad107. PubMed DOI PMC

Bohutínská  M, Alston  M, Monnahan  P, Mandáková  T, Bray  S, Paajanen  P, Kolář  F, Yant  L. Novelty and convergence in adaptation to whole genome duplication. Mol Biol Evol. 2021a:38(9):3910–3924. 10.1093/molbev/msab096. PubMed DOI PMC

Bohutínská  M, Handrick  V, Yant  L, Schmickl  R, Kolář  F, Bomblies  K, Paajanen  P. De novo mutation and rapid protein (co-)evolution during meiotic adaptation in PubMed DOI PMC

Bohutínská  M, Petříková  E, Booker  TR, Cobo  CV, Vlček  J, Šrámková  G, Poštulková  A, Hojka  J, Marhold  K, Yant  L, et al. Mosaic haplotypes underlie repeated adaptation to whole genome duplication in DOI

Bohutínská  M, Petříková  E, Booker  TR, Vives Cobo  C, Vlček  J, Šrámková  G, Poupětová  A, Hojka  J, Marhold  K, Yant  L, et al.  Polyploids broadly generate novel haplotypes from trans-specific variation in PubMed DOI PMC

Bomblies  K. Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis. Plant Reprod. 2023:36(1):107–124. 10.1007/s00497-022-00448-1. PubMed DOI PMC

Bomblies  K, Higgins  JD, Yant  L. Meiosis evolves: adaptation to external and internal environments. New Phytol. 2015:208(2):306–323. 10.1111/nph.13499. PubMed DOI

Bomblies  K, Jones  G, Franklin  C, Zickler  D, Kleckner  N. The challenge of evolving stable polyploidy: could an increase in “crossover interference distance” play a central role?  Chromosoma. 2016:125(2):287–300. 10.1007/s00412-015-0571-4. PubMed DOI PMC

Broad Institute . Picard. [accessed 2024 Aug 27]. Available from: http://broadinstitute.github.io/picard/

Brochmann  C, Brysting  AK, Alsos  IG, Borgen  L, Grundt  HH, Scheen  AC, Elven  R. Polyploidy in Arctic plants. Biol J Linn Soc Lond. 2004:82(4):521–536. 10.1111/j.1095-8312.2004.00337.x. DOI

Buchfink  B, Xie  C, Huson  DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015:12(1):59–60. 10.1038/nmeth.3176. PubMed DOI

Burns  R, Mandáková  T, Gunis  J, Soto-Jiménez  LM, Liu  C, Lysak  MA, Novikova  PY, Nordborg  M. Gradual evolution of allopolyploidy in PubMed DOI PMC

Bushnell  B. BB tools software package; 2014. [accessed 2024 Jan 8]. Available from: http://bbtools.jgi.doe.gov.

Camacho  C, Coulouris  G, Avagyan  V, Ma  N, Papadopoulos  J, Bealer  K, Madden  TL. BLAST+: architecture and applications. BMC Bioinformatics. 2009:10(1):421. 10.1186/1471-2105-10-421. PubMed DOI PMC

Capilla-Pérez  L, Durand  S, Hurel  A, Lian  Q, Chambon  A, Taochy  C, Solier  V, Grelon  M, Mercier  R. The synaptonemal complex imposes crossover interference and heterochiasmy in Arabidopsis. Proc Natl Acad Sci U S A.  2021:118(12):e2023613118. 10.1073/pnas.2023613118. PubMed DOI PMC

Castric  V, Bechsgaard  J, Schierup  MH, Vekemans  X. Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genet. 2008:4(8):e1000168. 10.1371/journal.pgen.1000168. PubMed DOI PMC

Castric  V, Vekemans  X. Plant self-incompatibility in natural populations: a critical assessment of recent theoretical and empirical advances. Mol Ecol. 2004:13(10):2873–2889. 10.1111/j.1365-294X.2004.02267.x. PubMed DOI

Chao  DY, Dilkes  B, Luo  H, Douglas  A, Yakubova  E, Lahner  B, Salt  DE. Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science. 2013:341(6146):658–659. 10.1126/science.1240561. PubMed DOI PMC

Charlesworth  D, Mable  BK, Schierup  MH, Bartolomé  C, Awadalla  P. Diversity and linkage of genes in the self-incompatibility gene family in PubMed DOI PMC

Clauss  MJ, Mitchell-Olds  T. Population genetic structure of PubMed DOI

Comai  L, Tyagi  AP, Winter  K, Holmes-Davis  R, Reynolds  SH, Stevens  Y, Byers  B. Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids. Plant Cell. 2000:12(9):1551–1568. 10.1105/tpc.12.9.1551. PubMed DOI PMC

Dart  S, Kron  P, Mable  BK. Characterizing polyploidy in DOI

David  KT. Global gradients in the distribution of animal polyploids. Proc Natl Acad Sci U S A.  2022:119(48):e2214070119. 10.1073/pnas.2214070119. PubMed DOI PMC

De Storme  N, Copenhaver  GP, Geelen  D. Production of diploid male gametes in Arabidopsis by cold-induced destabilization of postmeiotic radial microtubule arrays. Plant Physiol. 2012:160(4):1808–1826. 10.1104/pp.112.208611. PubMed DOI PMC

Ehlers  J, Gibbard  PL, Hughes  PDM, editors. Quaternary glaciations—extent and chronology: volume 15: a closer look. London (England): Elsevier Science; 2011.

Eidesen  PB, Ehrich  D, Bakkestuen  V, Alsos  IG, Gilg  O, Taberlet  P, Brochmann  C. Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity. New Phytol. 2013:200(3):898–910. 10.1111/nph.12412. PubMed DOI

Excoffier  L, Marchi  N, Marques  DA, Matthey-Doret  R, Gouy  A, Sousa  VC. Fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics. 2021:37(24):4882–4885. 10.1093/bioinformatics/btab468. PubMed DOI PMC

Genete  M, Castric  V, Vekemans  X. Genotyping and de novo discovery of allelic variants at the Brassicaceae self-incompatibility locus from short-read sequencing data. Mol Biol Evol. 2020:37(4):1193–1201. 10.1093/molbev/msz258. PubMed DOI

Goodstein  DM, Shu  S, Howson  R, Neupane  R, Hayes  RD, Fazo  J, Mitros  T, Dirks  W, Hellsten  U, Putnam  N, et al.  Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012:40(D1):D1178–D1186. 10.1093/nar/gkr944. PubMed DOI PMC

Gregory  TR, Mable  BK. CHAPTER 8—polyploidy in animals. In: Gregory  TR, editor. The evolution of the genome. Burlington: Academic Press; 2005. p. 427–517.

Guindon  S, Dufayard  J-F, Lefort  V, Anisimova  M, Hordijk  W, Gascuel  O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010:59(3):307–321. 10.1093/sysbio/syq010. PubMed DOI

Gutenkunst  RN, Hernandez  RD, Williamson  SH, Bustamante  CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 2009:5(10):e1000695. 10.1371/journal.pgen.1000695. PubMed DOI PMC

Hämälä  T, Mattila  TM, Leinonen  PH, Kuittinen  H, Savolainen  O. Role of seed germination in adaptation and reproductive isolation in PubMed DOI

Heckmann  S, Feng  C, Lorenz  J, Dreissig  S, Schubert  V, Wang  B, Hartmann  F, Cuacos  M, Fernández-Jiménez  N, Câmara  AS, et al. The novel synaptonemal complex central element SCEP3 interlinks synapsis initiation and crossover formation in PubMed PMC

Higgins  JD, Sanchez-Moran  E, Armstrong  SJ, Jones  GH, Franklin  FCH. The Arabidopsis synaptonemal complex protein ZYP1 is required for chromosome synapsis and normal fidelity of crossing over. Genes Dev. 2005:19(20):2488–2500. 10.1101/gad.354705. PubMed DOI PMC

Hijmans  RJ. raster: Geographic data analysis and modeling; 2023. [accessed 2024 Jan 8]. Available from: https://CRAN.R-project.org/package=raster

Hoang  DT, Chernomor  O, von Haeseler  A, Minh  BQ, Vinh  LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018:35(2):518–522. 10.1093/molbev/msx281. PubMed DOI PMC

Hoff  KJ, Lomsadze  A, Borodovsky  M, Stanke  M. Whole-genome annotation with BRAKER. Methods Mol Biol. 2019:1962:65–95. 10.1007/978-1-4939-9173-0_5. PubMed DOI PMC

Hoff  KJ, Stanke  M. Predicting genes in single genomes with AUGUSTUS. Curr Protoc Bioinformatics. 2019:65(1):e57. 10.1002/cpbi.57. PubMed DOI

Hohmann  N, Koch  MA. An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes. BMC Genomics. 2017:18(1):810. 10.1186/s12864-017-4220-6. PubMed DOI PMC

Hollister  JD, Arnold  BJ, Svedin  E, Xue  KS, Dilkes  BP, Bomblies  K. Genetic adaptation associated with genome-doubling in autotetraploid Arabidopsis arenosa. PLoS Genet. 2012:8(12):e1003093. 10.1371/journal.pgen.1003093. PubMed DOI PMC

Huson  DH, Bryant  D. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 2006:23(2):254–267. 10.1093/molbev/msj030. PubMed DOI

Joo  JH, Kang  HA, Kim  KP, Hong  S. Meiotic prophase roles of Pds5 in recombination and chromosome condensation in budding yeast. J Microbiol. 2022:60(2):177–186. 10.1007/s12275-022-1635-9. PubMed DOI

Jørgensen  MH, Ehrich  D, Schmickl  R, Koch  MA, Brysting  AK. Interspecific and interploidal gene flow in central European Arabidopsis (Brassicaceae). BMC Evol Biol. 2011:11(1):346. 10.1186/1471-2148-11-346. PubMed DOI PMC

Katche  EI, Schierholt  A, Schiessl  S-V, He  F, Lv  Z, Batley  J, Becker  HC, Mason  AS. Genetic factors inherited from both diploid parents interact to affect genome stability and fertility in resynthesized allotetraploid PubMed DOI PMC

Katoh  K, Kuma  K-I, Toh  H, Miyata  T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005:33(2):511–518. 10.1093/nar/gki198. PubMed DOI PMC

Kauai  F, Mortier  F, Milosavljevic  S, Van de Peer  Y, Bonte  D. Neutral processes underlying the macro eco-evolutionary dynamics of mixed-ploidy systems. Proc Biol Sci. 2023:290(1995):20222456. 10.1098/rspb.2022.2456. PubMed DOI PMC

Khoshoo  TN. Polyploidy in gymnosperms. Evolution. 1959:13(1):24–39. 10.2307/2405943. DOI

Kolberg  L, Raudvere  U, Kuzmin  I, Adler  P, Vilo  J, Peterson  H. G:Profiler-interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update). Nucleic Acids Res. 2023:51(W1):W207–W212. 10.1093/nar/gkad347. PubMed DOI PMC

Kolesnikova  UK, Scott  AD, Van de Velde  JD, Burns  R, Tikhomirov  NP, Pfordt  U, Clarke  AC, Yant  L, Seregin  AP, Vekemans  X, et al.  Transition to self-compatibility associated with dominant S-allele in a diploid Siberian progenitor of allotetraploid PubMed DOI PMC

Korunes  KL, Samuk  K. pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Mol Ecol Resour. 2021:21(4):1359–1368. 10.1111/1755-0998.13326. PubMed DOI PMC

Kreiner  JM, Kron  P, Husband  BC. Frequency and maintenance of unreduced gametes in natural plant populations: associations with reproductive mode, life history and genome size. New Phytol. 2017a:214(2):879–889. 10.1111/nph.14423. PubMed DOI

Kreiner  JM, Kron  P, Husband  BC. Evolutionary dynamics of unreduced gametes. Trends Genet. 2017b:33(9):583–593. 10.1016/j.tig.2017.06.009. PubMed DOI

Lafon-Placette  C, Johannessen  IM, Hornslien  KS, Ali  MF, Bjerkan  KN, Bramsiepe  J, Glockle  BM, Rebernig  CA, Brysting  AK, Grini  PE, et al.  Endosperm-based hybridization barriers explain the pattern of gene flow between PubMed DOI PMC

Lafon-Placette  C, Kohler  C. Endosperm-based postzygotic hybridization barriers: developmental mechanisms and evolutionary drivers. Mol Ecol. 2016:25(11):2620–2629. 10.1111/mec.13552. PubMed DOI

Le Veve  A, Burghgraeve  N, Genete  M, Lepers-Blassiau  C, Takou  M, De Meaux  J, Mable  BK, Durand  E, Vekemans  X, Castric  V. Long-term balancing selection and the genetic load linked to the self-incompatibility locus in PubMed DOI PMC

Li  H. Protein-to-genome alignment with miniprot. Bioinformatics. 2023:39(1):btad014. 10.1093/bioinformatics/btad014. PubMed DOI PMC

Li  H, Durbin  R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009:25(14):1754–1760. 10.1093/bioinformatics/btp324. PubMed DOI PMC

Li  H, Handsaker  B, Wysoker  A, Fennell  T, Ruan  J, Homer  N, Marth  G, Abecasis  G, Durbin  R; 1000 Genome Project Data Processing Subgroup . The sequence alignment/map format and SAMtools. Bioinformatics. 2009:25(16):2078–2079. 10.1093/bioinformatics/btp352. PubMed DOI PMC

Llaurens  V, Billiard  S, Leducq  J-B, Castric  V, Klein  EK, Vekemans  X. Does frequency-dependent selection with complex dominance interactions accurately predict allelic frequencies at the self-incompatibility locus in PubMed DOI

Lohaus  R, Van de Peer  Y. Of dups and dinos: evolution at the K/Pg boundary. Curr Opin Plant Biol. 2016:30:62–69. 10.1016/j.pbi.2016.01.006. PubMed DOI

Mable  BK, Beland  J, Di Berardo  C. Inheritance and dominance of self-incompatibility alleles in polyploid PubMed DOI

Mable  BK, Schierup  MH, Charlesworth  D. Estimating the number, frequency, and dominance of S-alleles in a natural population of PubMed DOI

Manzaneda  AJ, Rey  PJ, Bastida  JM, Weiss-Lehman  C, Raskin  E, Mitchell-Olds  T. Environmental aridity is associated with cytotype segregation and polyploidy occurrence in PubMed DOI PMC

Marburger  S, Monnahan  P, Seear  PJ, Martin  SH, Koch  J, Paajanen  P, Bohutínská  M, Higgins  JD, Schmickl  R, Yant  L. Interspecific introgression mediates adaptation to whole genome duplication. Nat Commun. 2019:10(1):5218. 10.1038/s41467-019-13159-5. PubMed DOI PMC

Martin  SH, Van Belleghem  SM. Exploring evolutionary relationships across the genome using topology weighting. Genetics. 2017:206(1):429–438. 10.1534/genetics.116.194720. PubMed DOI PMC

Mason  AS, Nelson  MN, Yan  G, Cowling  WA. Production of viable male unreduced gametes in Brassica interspecific hybrids is genotype specific and stimulated by cold temperatures. BMC Plant Biol. 2011:11(1):103. 10.1186/1471-2229-11-103. PubMed DOI PMC

Mason  AS, Pires  JC. Unreduced gametes: meiotic mishap or evolutionary mechanism?  Trends Genet. 2015:31(1):5–10. 10.1016/j.tig.2014.09.011. PubMed DOI

Mattila  TM, Tyrmi  J, Pyhajarvi  T, Savolainen  O. Genome-wide analysis of colonization history and concomitant selection in PubMed DOI

McKenna  A, Hanna  M, Banks  E, Sivachenko  A, Cibulskis  K, Kernytsky  A, Garimella  K, Altshuler  D, Gabriel  S, Daly  M, et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010:20(9):1297–1303. 10.1101/gr.107524.110. PubMed DOI PMC

Monnahan  P, Kolář  F, Baduel  P, Sailer  C, Koch  J, Horvath  R, Laenen  B, Schmickl  R, Paajanen  P, Šrámková  G, et al.  Pervasive population genomic consequences of genome duplication in PubMed DOI

Morgan  C, White  MA, Franklin  FCH, Zickler  D, Kleckner  N, Bomblies  K. Evolution of crossover interference enables stable autopolyploidy by ensuring pairwise partner connections in PubMed DOI PMC

Morgan  C, Zhang  H, Henry  CE, Franklin  FCH, Bomblies  K. Derived alleles of two axis proteins affect meiotic traits in autotetraploid PubMed DOI PMC

Morgan  CH, Zhang  H, Bomblies  K. Are the effects of elevated temperature on meiotic recombination and thermotolerance linked via the axis and synaptonemal complex?  Philos Trans R Soc Lond B Biol Sci. 2017:372(1736):20160470. 10.1098/rstb.2016.0470. PubMed DOI PMC

Muller  M-H, Leppälä  J, Savolainen  O. Genome-wide effects of postglacial colonization in PubMed DOI

Nei  M. Genetic distance between populations. Am Nat. 1972:106(949):283–292. 10.1086/282771. DOI

Nei  M, Li  WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A.  1979:76(10):5269–5273. 10.1073/pnas.76.10.5269. PubMed DOI PMC

Neuffer  B, Bechsgaard  J, Paetsch  M, Titel  C, Wesse  C, Bona  E, Schimpf  R, Žerdoner Čalasan  A, Hurka  H. S-alleles and mating system in natural populations of DOI

Nguyen  L-T, Schmidt  HA, von Haeseler  A, Minh  BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015:32(1):268–274. 10.1093/molbev/msu300. PubMed DOI PMC

Novikova  PY, Hohmann  N, Nizhynska  V, Tsuchimatsu  T, Ali  J, Muir  G, Guggisberg  A, Paape  T, Schmid  K, Fedorenko  OM, et al.  Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat Genet. 2016:48(9):1077–1082. 10.1038/ng.3617. PubMed DOI

Novikova  PY, Hohmann  N, Van de Peer  Y. Polyploid Arabidopsis species originated around recent glaciation maxima. Curr Opin Plant Biol. 2018:42:8–15. 10.1016/j.pbi.2018.01.005. PubMed DOI

Parisod  C, Holderegger  R, Brochmann  C. Evolutionary consequences of autopolyploidy. New Phytol. 2010:186(1):5–17. 10.1111/j.1469-8137.2009.03142.x. PubMed DOI

Pebesma  E. Simple features for R: standardized support for spatial vector data. R J. 2018:10(1):439. 10.32614/RJ-2018-009. DOI

Pembleton  LW, Cogan  NOI, Forster  JW. StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations. Mol Ecol Resour. 2013:13(5):946–952. 10.1111/1755-0998.12129. PubMed DOI

Pickrell  JK, Pritchard  JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012:8(11):e1002967. 10.1371/journal.pgen.1002967. PubMed DOI PMC

Polatschek  A. Cytotaxonomische Beiträge zur Flora der Ostalpenländer, I. Österreichische Botanische Zeitschrift. 1966:113(1):1–46. 10.1007/BF01373246. DOI

Pradillo  M, Knoll  A, Oliver  C, Varas  J, Corredor  E, Puchta  H, Santos  JL. Involvement of the cohesin cofactor PDS5 (SPO76) during meiosis and DNA repair in Arabidopsis thaliana. Front Plant Sci. 2015:6:1034. 10.3389/fpls.2015.01034. PubMed DOI PMC

Rawat  V, Abdelsamad  A, Pietzenuk  B, Seymour  DK, Koenig  D, Weigel  D, Pecinka  A, Schneeberger  K. Improving the annotation of PubMed DOI PMC

R Core Team . R: a language and environment for statistical computing; 2022. Available from: https://www.R-project.org/

Rice  A, Šmarda  P, Novosolov  M, Drori  M, Glick  L, Sabath  N, Meiri  S, Belmaker  J, Mayrose  I. The global biogeography of polyploid plants. Nat Ecol Evol. 2019:3(2):265–273. 10.1038/s41559-018-0787-9. PubMed DOI

Ross-Ibarra  J, Wright  SI, Foxe  JP, Kawabe  A, DeRose-Wilson  L, Gos  G, Charlesworth  D, Gaut  BS. Patterns of polymorphism and demographic history in natural populations of PubMed DOI PMC

Schmickl  R, Jørgensen  MH, Brysting  AK, Koch  MA. The evolutionary history of the PubMed DOI PMC

Schmickl  R, Koch  MA. Arabidopsis hybrid speciation processes. Proc Natl Acad Sci U S A.  2011:108(34):14192–14197. 10.1073/pnas.1104212108. PubMed DOI PMC

Schmickl  R, Marburger  S, Bray  S, Yant  L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. J Exp Bot. 2017:68(20):5453–5470. 10.1093/jxb/erx297. PubMed DOI

Schmickl  R, Yant  L. Adaptive introgression: how polyploidy reshapes gene flow landscapes. New Phytol. 2021:230(2):457–461. 10.1111/nph.17204. PubMed DOI

Schmid  M, Evans  BJ, Bogart  JP. Polyploidy in Amphibia. Cytogenet Genome Res. 2015:145(3-4):315–330. 10.1159/000431388. PubMed DOI

Scott  AD, Van de Velde  JD, Novikova  PY. Inference of polyploid origin and inheritance mode from population genomic data. Methods Mol Biol. 2023:2545:279–295. 10.1007/978-1-0716-2561-3_15. PubMed DOI

Seear  PJ, France  MG, Gregory  CL, Heavens  D, Schmickl  R, Yant  L, Higgins  JD. A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid PubMed DOI PMC

Seregin  A. Moscow University Herbarium (MW). Version 1.391. Lomonosov Moscow State University. Occurrence dataset; 2025. [accessed 2025 Jul 21]. 10.15468/cpnhcc accessed via GBIF.org DOI

Servick  S, Visger  CJ, Gitzendanner  MA, Soltis  PS, Soltis  DE. Population genetic variation, geographic structure, and multiple origins of autopolyploidy in PubMed DOI

Shimizu  KK, Fujii  S, Marhold  K, Watanabe  K, Kudoh  H. DOI

Shimizu-Inatsugi  R, Lihová  J, Iwanaga  H, Kudoh  H, Marhold  K, Savolainen  O, Watanabe  K, Yakubov  VV, Shimizu  KK. The allopolyploid PubMed DOI

Simão  FA, Waterhouse  RM, Ioannidis  P, Kriventseva  EV, Zdobnov  EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015:31(19):3210–3212. 10.1093/bioinformatics/btv351. PubMed DOI

Slowikowski  K. ggrepel: Automatically Position Non-Overlapping Text Labels with “ggplot2”; 2023. [accessed 2024 Jan 8]. Available from: https://CRAN.R-project.org/package=ggrepel

Soltis  DE, Buggs  RJA, Barbazuk  WB, Schnable  PS, Soltis  PS. On the origins of species: does evolution repeat itself in polyploid populations of independent origin?  Cold Spring Harb Symp Quant Biol. 2009:74:215–223. 10.1101/sqb.2009.74.007. PubMed DOI

Song  M, Zhai  B, Yang  X, Tan  T, Wang  Y, Yang  X, Tan  Y, Chu  T, Cao  Y, Song  Y, et al.  Interplay between Pds5 and Rec8 in regulating chromosome axis length and crossover frequency. Sci Adv. 2021:7(11):eabe7920. 10.1126/sciadv.abe7920. PubMed DOI PMC

Sora  D, Kron  P, Husband  BC. Genetic and environmental determinants of unreduced gamete production in PubMed DOI PMC

Stanke  M, Schöffmann  O, Morgenstern  B, Waack  S. Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. BMC Bioinformatics. 2006:7(1):62. 10.1186/1471-2105-7-62. PubMed DOI PMC

Stift  M, Kolář  F, Meirmans  PG. STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations. Heredity (Edinb). 2019:123(4):429–441. 10.1038/s41437-019-0247-6. PubMed DOI PMC

Tajima  F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989:123(3):585–595. 10.1093/genetics/123.3.585. PubMed DOI PMC

Takou  M, Hämälä  T, Koch  EM, Steige  KA, Dittberner  H, Yant  L, Genete  M, Sunyaev  S, Castric  V, Vekemans  X, et al.  Maintenance of adaptive dynamics and no detectable load in a range-edge outcrossing plant population. Mol Biol Evol. 2021:38(5):1820–1836. 10.1093/molbev/msaa322. PubMed DOI PMC

The 1001 Genomes Consortium . 1,135 genomes reveal the global pattern of polymorphism in PubMed DOI PMC

Van de Peer  Y, Mizrachi  E, Marchal  K. The evolutionary significance of polyploidy. Nat Rev Genet. 2017:18(7):411–424. 10.1038/nrg.2017.26. PubMed DOI

Viera  A, Berenguer  I, Ruiz-Torres  M, Gómez  R, Guajardo  A, Barbero  JL, Losada  A, Suja  JA. PDS5 proteins regulate the length of axial elements and telomere integrity during male mouse meiosis. EMBO Rep. 2020:21(6):e49273. 10.15252/embr.201949273. PubMed DOI PMC

Vlček  J, Hämälä  T, Cobo  CV, Curran  E, Šrámková  G, Slotte  T, Schmickl  R, Yant  L, Kolář  F. Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis. bioRxiv 2025.01.12.632621. https://www.biorxiv.org/content/10.1101/2025.01.12.632621v1.abstract, 15 January 2025, preprint: not peer reviewed. PubMed DOI PMC

Walden  N, Lucek  K, Willi  Y. Lineage-specific adaptation to climate involves flowering time in north American PubMed DOI

Wang  O, Chin  R, Cheng  X, Wu  MKY, Mao  Q, Tang  J, Sun  Y, Anderson  E, Lam  HK, Chen  D, et al.  Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Res. 2019a:29(5):798–808. 10.1101/gr.245126.118. PubMed DOI PMC

Wang  S, Veller  C, Sun  F, Ruiz-Herrera  A, Shang  Y, Liu  H, Zickler  D, Chen  Z, Kleckner  N, Zhang  L. Per-nucleus crossover covariation and implications for evolution. Cell. 2019b:177(2):326–338.e16. 10.1016/j.cell.2019.02.021. PubMed DOI PMC

Weiß  CL, Pais  M, Cano  LM, Kamoun  S, Burbano  HA. Nquire: a statistical framework for ploidy estimation using next generation sequencing. BMC Bioinformatics. 2018:19(1):122. 10.1186/s12859-018-2128-z. PubMed DOI PMC

Weisenfeld  NI, Kumar  V, Shah  P, Church  DM, Jaffe  DB. Direct determination of diploid genome sequences. Genome Res. 2017:27(5):757–767. 10.1101/gr.214874.116. PubMed DOI PMC

Westermann  J, Srikant  T, Gonzalo  A, Tan  HS, Bomblies  K. Defective pollen tube tip growth induces neo-polyploid infertility. Science. 2024:383(6686):eadh0755. 10.1126/science.adh0755. PubMed DOI

Wickham  H, Averick  M, Bryan  J, Chang  W, McGowan  LD, François  R, Grolemund  G, Hayes  A, Henry  L, Hester  J, et al.  Welcome to the tidyverse. J Open Source Softw. 2019:4(43):1686. 10.21105/joss.01686. DOI

Willi  Y, Lucek  K, Bachmann  O, Walden  N. Recent speciation associated with range expansion and a shift to self-fertilization in North American Arabidopsis. Nat Commun. 2022:13(1):7564. 10.1038/s41467-022-35368-1. PubMed DOI PMC

Wright  KM, Arnold  B, Xue  K, Šurinová  M, O’Connell  J, Bomblies  K. Selection on meiosis genes in diploid and tetraploid PubMed DOI PMC

Yant  L, Hollister  JD, Wright  KM, Arnold  BJ, Higgins  JD, Franklin  FCH, Bomblies  K. Meiotic adaptation to genome duplication in PubMed DOI PMC

Zhang  Z, Ren  Q, Yang  H, Conrad  MN, Guacci  V, Kateneva  A, Dresser  ME. Budding yeast PDS5 plays an important role in meiosis and is required for sister chromatid cohesion: PDS5 and meiotic chromatids cohesion. Mol Microbiol. 2005:56(3):670–680. 10.1111/j.1365-2958.2005.04582.x. PubMed DOI

Zhou  X, Mo  X, Gui  M, Wu  X, Jiang  Y, Ma  L, Shi  Z, Luo  Y, Tang  W. Cytological, molecular mechanisms and temperature stress regulating production of diploid male gametes in PubMed DOI

Zhukova  PG, Petrovsky  VV, Plieva  TV. The chromosome numbers and taxonomy of some plant species from Siberia and Far East. Bot Z. 1973:58:1331–1342. 10.17581/bp.2017.06103. DOI