Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.

Department of Forest Sciences University of Helsinki 00014 Helsinki Finland

Faculty of Environmental Sciences Czech University of Life Sciences Prague Kamýcká 129 16521 Prague Czech Republic

Organismal and Evolutionary Biology Research Program Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre University of Helsinki P O Box 65 00014 Helsinki Finland

Physiology and Environmental Toxicology Department of Organismal Biology Uppsala University Norbyvägen 18A 75236 Uppsala Sweden

Plant Ecology and Evolution Department of Ecology and Genetics Uppsala University Norbyvägen 18D 75236 Uppsala Sweden

School of Biological Sciences Nanyang Technological University 60 Nanyang Drive Singapore 637551 Singapore

Science for Life Laboratory Uppsala University 75237 Uppsala Sweden

Zobrazit více v PubMed

Albertin  W., Marullo  P.  2012. Polyploidy in fungi: evolution after whole-genome duplication. Proc. R Soc. B. Biol. Sci. 279:2497–2509. PubMed PMC

Amborella Genome Project. 2013. The Amborella genome and the evolution of flowering plants. Science  342:1241089. PubMed

Anamthawat-Jónsson  K., Tomasson  T.  1990. Cytogenetics of hybrid introgression in Icelandic birch. Hereditas  112:65–70.

Anamthawat-Jónsson  K., Thór Thórsson  A.  2003. Natural hybridisation in birch: triploid hybrids between

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

Arnold  B.J., Lahner  B., DaCosta  J.M., Weisman  C.M., Hollister  J.D., Salt  D.E., Bomblies  K., Yant  L.  2016. Borrowed alleles and convergence in serpentine adaptation. Proc. Natl. Acad. Sci. U.S.A. 113:8320–8325. PubMed PMC

Ashburner  K., McAllister  H.A.  2013. The genus

Atkinson  M.D.  1992.

Aury  J.-M., Jaillon  O., Duret  L., Noel  B., Jubin  C., Porcel  B.M., Ségurens  B., Daubin  V., Anthouard  V., Aiach  N., Arnaiz  O., Billaut  A., Beisson  J., Blanc  I., Bouhouche  K., Câmara  F., Duharcourt  S., Guigo  R., Gogendeau  D., Katinka  M., Keller  A.-M., Kissmehl  R., Klotz  C., Koll  F., Le Mouël  A., Lepère  G., Malinsky  S., Nowacki  M., Nowak  J.K., Plattner  H., Poulain  J., Ruiz  F., Serrano  V., Zagulski  M., Dessen  P., Bétermier  M., Weissenbach  J., Scarpelli  C., Schächter  V., Sperling  L., Meyer  E., Cohen  J., Wincker  P.  2006. Global trends of whole-genome duplications revealed by the ciliate PubMed

Baack  E., Melo  M.C., Rieseberg  L.H., Ortiz-Barrientos  D.  2015. The origins of reproductive isolation in plants. New Phytol. 207:968–984. PubMed

Baduel  P., Bray  S., Vallejo-Marin  M., Kolář  F., Yant  L.  2018. The “Polyploid Hop”: shifting challenges and opportunities over the evolutionary lifespan of genome duplications. Front. Ecol. Evol. 6:1–19.

Bagherieh-Najjar  M.B., de Vries  O.M.H., Hille  J., Dijkwel  P.P.  2005. Arabidopsis RecQl4A suppresses homologous recombination and modulates DNA damage responses. Plant J. 43:789–798. PubMed

Bao  S., Tibbetts  R.S., Brumbaugh  K.M., Fang  Y., Richardson  D.A., Ali  A., Chen  S.M., Abraham  R.T., Wang  X.-F.  2001. ATR/ATM-mediated phosphorylation of human Rad17 is required for genotoxic stress responses. Nature  411:969–974. PubMed

Barker  M.S., Arrigo  N., Baniaga  A.E., Li  Z., Levin  D.A.  2016. On the relative abundance of autopolyploids and allopolyploids. New Phytol. 210:391–398. PubMed

Barton  N.H., Hewitt  G.M.  1989. Adaptation, speciation and hybrid zones. Nature  341:497–503. PubMed

Beaumont  M.A., Zhang  W., Balding  D.J.  2002. Approximate Bayesian computation in population genetics. Genetics. 162:2025–2035. PubMed PMC

Beaumont  M.A.  2019. Approximate Bayesian computation. Annu. Rev. Stat. Appl. 6:379–403.

Berthelot  C., Brunet  F., Chalopin  D., Juanchich  A., Bernard  M., Noël  B., Bento  P., Da Silva  C., Labadie  K., Alberti  A., Aury  J.-M., Louis  A., Dehais  P., Bardou  P., Montfort  J., Klopp  C., Cabau  C., Gaspin  C., Thorgaard  G.H., Boussaha  M., Quillet  E., Guyomard  R., Galiana  D., Bobe  J., Volff  J.-N., Genêt  C., Wincker  P., Jaillon  O., Crollius  H.R., Guiguen  Y.  2014. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat. Commun. 5:3657. PubMed PMC

Bertrand  Y.J.K., Scheen  A.-C., Marcussen  T., Pfeil  B.E., de Sousa  F., Oxelman  B.  2015. Assignment of homoeologs to parental genomes in allopolyploids for species tree inference, with an example from PubMed

Bleeker  W., Hurka  H.  2001. Introgressive hybridization in PubMed

Bleeker  W.  2003. Hybridization and PubMed

Blischak  P.D., Mabry  M.E., Conant  G.C., Pires  J.C.  2018. Integrating networks, phylogenomics, and population genomics for the study of polyploidy. Annu. Rev. Ecol. Evol. Syst. 49:253–278.

Bomblies  K., Higgins  J.D., Yant  L.  2015. Meiosis evolves: adaptation to external and internal environments. New Phytol. 208:306–323. PubMed

Bomblies  K.  2023. Learning to tango with four (or more): the molecular basis of adaptation to polyploid meiosis. Plant Reprod. 36:107–124. PubMed PMC

Bowers  J.E., Chapman  B.A., Rong  J., Paterson  A.H.  2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature  422:433–438. PubMed

Braasch  I., Postlethwait  J.H.  2012. Polyploidy in fish and the teleost genome duplication. In: Soltis  P.S., Soltis  D.E., editors. Polyploidy and genome evolution. Berlin, Heidelberg: Springer. p. 341–383.

Brown  I.R., Al-Dawoody  D.  1979. Observations on meiosis in three cytotypes of

Bryant  D., Moulton  V.  2004. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21:255–265. PubMed

Burns  R., Mandáková  T., Gunis  J., Soto-Jiménez  L.M., Liu  C., Lysak  M.A., Novikova  P.Y., Nordborg  M.  2021. Gradual evolution of allopolyploidy in PubMed PMC

Caldwell  K.S., Michelmore  R.W.  2009. PubMed PMC

Cao  H., Bowling  S.A., Gordon  A.S., Dong  X.  1994. Characterization of an arabidopsis mutant that is nonresponsive to inducers of systemic acquired resistance. Plant Cell. 6:1583–1592. PubMed PMC

Cerca  J., Armstrong  E.E., Vizueta  J., Fernández  R., Dimitrov  D., Petersen  B., Prost  S., Rozas  J., Petrov  D., Gillespie  R.G.  2021. The PubMed PMC

Chalhoub  B., Denoeud  F., Liu  S., Parkin  I.A.P., Tang  H., Wang  X., Chiquet  J., Belcram  H., Tong  C., Samans  B., Corréa  M., Da Silva  C., Just  J., Falentin  C., Koh  C.S., Le Clainche  I., Bernard  M., Bento  P., Noel  B., Labadie  K., Alberti  A., Charles  M., Arnaud  D., Guo  H., Daviaud  C., Alamery  S., Jabbari  K., Zhao  M., Edger  P.P., Chelaifa  H., Tack  D., Lassalle  G., Mestiri  I., Schnel  N., Le Paslier  M.-C., Fan  G., Renault  V., Bayer  P.E., Golicz  A.A., Manoli  S., Lee  T.-H., Thi  V.H.D., Chalabi  S., Hu  Q., Fan  C., Tollenaere  R., Lu  Y., Battail  C., Shen  J., Sidebottom  C.H.D., Wang  X., Canaguier  A., Chauveau  A., Bérard  A., Deniot  G., Guan  M., Liu  Z., Sun  F., Lim  Y.P., Lyons  E., Town  C.D., Bancroft  I., Wang  X., Meng  J., Ma  J., Pires  J.C., King  G.J., Brunel  D., Delourme  R., Renard  M., Aury  J.-M., Adams  K.L., Batley  J., Snowdon  R.J., Tost  J., Edwards  D., Zhou  Y., Hua  W., Sharpe  A.G., Paterson  A.H., Guan  C., Wincker  P.  2014. Early allopolyploid evolution in the post-Neolithic PubMed

Chen  X., Lu  L., Mayer  K.S., Scalf  M., Qian  S., Lomax  A., Smith  L.M., Zhong  X.  2016. POWERDRESS interacts with HISTONE DEACETYLASE 9 to promote aging in PubMed PMC

Chen  S., Wang  Y., Yu  L., Zheng  T., Wang  S., Yue  Z., Jiang  J., Kumari  S., Zheng  C., Tang  H., Li  J., Li  Y., Chen  J., Zhang  W., Kuang  H., Robertson  J.S., Zhao  P.X., Li  H., Shu  S., Yordanov  Y.S., Huang  H., Goodstein  D.M., Gai  Y., Qi  Q., Min  J., Xu  C., Wang  S., Qu  G.-Z., Paterson  A.H., Sankoff  D., Wei  H., Liu  G., Yang  C.  2021. Genome sequence and evolution of PubMed PMC

Cheng  H., Liu  J., Wen  J., Nie  X., Xu  L., Chen  N., Li  Z., Wang  Q., Zheng  Z., Li  M., Cui  L., Liu  Z., Bian  J., Wang  Z., Xu  S., Yang  Q., Appels  R., Han  D., Song  W., Sun  Q., Jiang  Y.  2019. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biol. 20:136. PubMed PMC

Chenuil  A., Galtier  N., Berrebi  P.  1999. A test of the hypothesis of an autopolyploid vs. allopolyploid origin for a tetraploid lineage: application to the genus Barbus (Cyprinidae). Heredity  82 Pt 4:373–380. PubMed

Chester  M., Gallagher  J.P., Symonds  V.V., Cruz da Silva  A.V., Mavrodiev  E.V., Leitch  A.R., Soltis  P.S., Soltis  D.E.  2012. Extensive chromosomal variation in a recently formed natural allopolyploid species, PubMed PMC

Cifuentes  M., Grandont  L., Moore  G., Chèvre  A.M., Jenczewski  E.  2010. Genetic regulation of meiosis in polyploid species: new insights into an old question. New Phytol. 186:29–36. PubMed

Cingolani  P., Platts  A., Wang  L.L., Coon  M., Nguyen  T., Wang  L., Land  S.J., Lu  X., Ruden  D.M.  2012. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly  6:80–92. PubMed PMC

Clark  L.V., Stewart  J.R., Nishiwaki  A., Toma  Y., Kjeldsen  J.B., Jørgensen  U., Zhao  H., Peng  J., Yoo  J.H., Heo  K., Yu  C.Y., Yamada  T., Sacks  E.J.  2015. Genetic structure of PubMed PMC

Comai  L.  2005. The advantages and disadvantages of being polyploid. Nat. Rev. Genet. 6:836–846. PubMed

Cornish-Bowden  A.  1985. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 13:3021–3030. PubMed PMC

Danecek  P., Bonfield  J.K., Liddle  J., Marshall  J., Ohan  V., Pollard  M.O., Whitwham  A., Keane  T., McCarthy  S.A., Davies  R.M., Li  H.  2021. Twelve years of SAMtools and BCFtools. GigaScience. 10:1–4. PubMed PMC

Dasmahapatra  K.K., Walters  J.R., Briscoe  A.D., Davey  J.W., Whibley  A., Nadeau  N.J., Zimin  A.V., Hughes  D.S.T., Ferguson  L.C., Martin  S.H., Salazar  C., Lewis  J.J., Adler  S., Ahn  S.-J., Baker  D.A., Baxter  S.W., Chamberlain  N.L., Chauhan  R., Counterman  B.A., Dalmay  T., Gilbert  L.E., Gordon  K., Heckel  D.G., Hines  H.M., Hoff  K.J., Holland  P.W.H., Jacquin-Joly  E., Jiggins  F.M., Jones  R.T., Kapan  D.D., Kersey  P., Lamas  G., Lawson  D., Mapleson  D., Maroja  L.S., Martin  A., Moxon  S., Palmér  W.J., Papa  R., Papanicolaou  A., Pauchet  Y., Ray  D.A., Rosser  N., Salzberg  S.L., Supple  M.A., Surridge  A., Tenger-Trolander  A., Vogel  H., Wilkinson  P.A., Wilson  D., Yorke  J.A., Yuan  F., Balmuth  A.L., Eland  C., Gharbi  K., Thomson  M., Gibbs  R.A., Han  Y., Jayaseelan  J.C., Kovar  C., Mathew  T., Muzny  D.M., Ongeri  F., Pu  L.-L., Qu  J., Thornton  R.L., Worley  K.C., Wu  Y.-Q., Linares  M., Blaxter  M.L., ffrench-Constant  R.H., Joron  M., Kronforst  M.R., Mullen  S.P., Reed  R.D., Scherer  S.E., Richards  S., Mallet  J., Owen McMillan  W., Jiggins  C.D., The Heliconius Genome Consortium. 2012. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature. 487:94–98. PubMed PMC

De Bodt  S., Maere  S., Van de Peer  Y.  2005. Genome duplication and the origin of angiosperms. Trends Ecol. Evol. 20:591–597. PubMed

de Groot  W.J., Thomas  P.A., Wein  R.W.  1997.

Dehal  P., Boore  J.L.  2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3:e314. PubMed PMC

Ding  J., Zhang  B., Li  Y., André  D., Nilsson  O.  2021. Phytochrome B and PHYTOCHROME INTERACTING FACTOR8 modulate seasonal growth in trees. New Phytol. 232:2339–2352. PubMed

Dong  M.A., Farré  E.M., Thomashow  M.F.  2011. CIRCADIAN CLOCK-ASSOCIATED 1 and LATE ELONGATED HYPOCOTYL regulate expression of the C-REPEAT BINDING FACTOR (CBF) pathway in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 108:7241–7246. PubMed PMC

Dowling  T.E., Secor  C.L.  1997. The role of hybridization and introgression in the diversification of animals. Annu. Rev. Ecol. Syst. 28:593–619.

Eidesen  P.B., Alsos  I.G., Brochmann  C.  2015. Comparative analyses of plastid and AFLP data suggest different colonization history and asymmetric hybridization between PubMed

Ellstrand  N.C.  2014. Is gene flow the most important evolutionary force in plants? Am. J. Bot. 101:737–753. PubMed

Enns  L.C., Kanaoka  M.M., Torii  K.U., Comai  L., Okada  K., Cleland  R.E.  2005. Two callose synthases, GSL1 and GSL5, play an essential and redundant role in plant and pollen development and in fertility. Plant Mol. Biol. 58:333–349. PubMed

Excoffier  L., Foll  M., Petit  R.J.  2009. Genetic consequences of range expansions. Annu. Rev. Ecol. Evol. Syst. 40:481–501.

Excoffier  L., Dupanloup  I., Huerta-Sánchez  E., Sousa  V.C., Foll  M.  2013. Robust demographic inference from genomic and SNP data. PLoS Genet. 9:e1003905. PubMed PMC

Felber  F.  1991. Establishment of a tetraploid cytotype in a diploid population: effect of relative fitness of the cytotypes. J. Evol. Biol. 4:195–207.

Filiault  D.L., Wessinger  C.A., Dinneny  J.R., Lutes  J., Borevitz  J.O., Weigel  D., Chory  J., Maloof  J.N.  2008. Amino acid polymorphisms in PubMed PMC

Fletcher  W., Yang  Z.  2009. INDELible: a flexible simulator of biological sequence evolution. Mol. Biol. Evol. 26:1879–1888. PubMed PMC

Fontaine  M.C., Pease  J.B., Steele  A., Waterhouse  R.M., Neafsey  D.E., Sharakhov  I.V., Jiang  X., Hall  A.B., Catteruccia  F., Kakani  E., Mitchell  S.N., Wu  Y.-C., Smith  H.A., Love  R.R., Lawniczak  M.K., Slotman  M.A., Emrich  S.J., Hahn  M.W., Besansky  N.J.  2015. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science  347:1258524. PubMed PMC

Fraïsse  C., Popovic  I., Mazoyer  C., Spataro  B., Delmotte  S., Romiguier  J., Loire  E., Simon  A., Galtier  N., Duret  L., Bierne  N., Vekemans  X., Roux  C.  2021. DILS: demographic inferences with linked selection by using ABC. Mol. Ecol. Resour. 21:2629–2644. PubMed

Freyman  W.A., Johnson  M.G., Rothfels  C.J.  2023. homologizer: phylogenetic phasing of gene copies into polyploid subgenomes. Methods Ecol. Evol. 14:1230–1244. PubMed

Fujiwara  S., Oda  A., Yoshida  R., Niinuma  K., Miyata  K., Tomozoe  Y., Tajima  T., Nakagawa  M., Hayashi  K., Coupland  G., Mizoguchi  T.  2008. Circadian clock proteins LHY and CCA1 regulate SVP protein accumulation to control flowering in PubMed PMC

Gaeta  R.T., Chris Pires  J.  2010. Homoeologous recombination in allopolyploids: the polyploid ratchet. New Phytol. 186:18–28. PubMed

Grant  P.R., Grant  B.R.  1992. Hybridization of bird species. Science  256:193–197. PubMed

Grant  P.R., Grant  B.R.  2020. Triad hybridization via a conduit species. Proc. Natl. Acad. Sci. U.S.A. 117:7888–7896. PubMed PMC

Gutenkunst  R.N., Hernandez  R.D., Williamson  S.H., Bustamante  C.D.  2009. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet. 5:e1000695. PubMed PMC

Hajdu  A., Ádám  E., Sheerin  D.J., Dobos  O., Bernula  P., Hiltbrunner  A., Kozma-Bognár  L., Nagy  F.  2015. High-level expression and phosphorylation of phytochrome B modulates flowering time in PubMed

Hardigan  M.A., Laimbeer  F.P.E., Newton  L., Crisovan  E., Hamilton  J.P., Vaillancourt  B., Wiegert-Rininger  K., Wood  J.C., Douches  D.S., Farré  E.M., Veilleux  R.E., Buell  C.R.  2017. Genome diversity of tuber-bearing PubMed PMC

Hartung  F., Suer  S., Knoll  A., Wurz-Wildersinn  R., Puchta  H.  2008. Topoisomerase 3α and RMI1 suppress somatic crossovers and are essential for resolution of meiotic recombination intermediates in PubMed PMC

Heitzeberg  F., Chen  I.-P., Hartung  F., Orel  N., Angelis  K.J., Puchta  H.  2004. The Rad17 homologue of PubMed

Heled  J., Drummond  A.J.  2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570–580. PubMed PMC

Higgins  J.D., Ferdous  M., Osman  K., Franklin  F.C.H.  2011. The RecQ helicase AtRECQ4A is required to remove inter-chromosomal telomeric connections that arise during meiotic recombination in PubMed

Hohmann  N., Schmickl  R., Chiang  T.-Y., Lučanová  M., Kolář  F., Marhold  K., Koch  M.A.  2014. Taming the wild: resolving the gene pools of non-model PubMed PMC

Hohmann  N., Koch  M.A.  2017. An Arabidopsis introgression zone studied at high spatio-temporal resolution: interglacial and multiple genetic contact exemplified using whole nuclear and plastid genomes. BMC Genom. 18:1–18. PubMed PMC

Howland  D.E., Oliver  R.P., Davy  A.J.  1995. Morphological and molecular variation in natural populations of

Hu  Q., Zhang  C., Xue  Z., Ma  L., Liu  W., Shen  Y., Ma  B., Cheng  Z.  2018. OsRAD17 is required for meiotic double-strand break repair and plays a redundant role with OsZIP4 in synaptonemal complex assembly. Front. Plant Sci. 9:1236. PubMed PMC

Husband  B.C.  2004. The role of triploid hybrids in the evolutionary dynamics of mixed-ploidy populations. Biol. J. Linn. Soc. 82:537–546.

Huson  D.H., Bryant  D.  2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254–267. PubMed

Ingvarsson  P.K., Garcia  M.V., Luquez  V., Hall  D., Jansson  S.  2008. Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 Locus in European Aspen ( PubMed PMC

Jadwiszczak  K.A., Banaszek  A., Jabłońska  E., Sozinov  O.V.  2012. Chloroplast DNA variation of

Järvinen  P., Palmé  A., Morales  L.O., Lännenpää  M., Keinänen  M., Sopanen  T., Lascoux  M.  2004. Phylogenetic relationships of PubMed

Jeffers, R. M.  1971. Research at the Institute of Forest Genetics, Rhinelander, Wisconsin. USDA Forest Service, Research Paper NC-67, p. 17.

Jiang  X., Song  Q., Ye  W., Chen  Z.J.  2021. Concerted genomic and epigenomic changes accompany stabilization of PubMed PMC

Johnsson  H.  1944. Triploidy in

Jombart  T., Devillard  S., Balloux  F.  2010. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 11:94–15. PubMed PMC

Jones  G., Sagitov  S., Oxelman  B.  2013. Statistical inference of allopolyploid species networks in the presence of incomplete lineage sorting. Syst. Biol. 62:467–478. PubMed

Jørgensen  M.H., Ehrich  D., Schmickl  R., Koch  M.A., Brysting  A.K.  2011. Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae). BMC Evol. Biol. 11:346. PubMed PMC

Joubès  J., Raffaele  S., Bourdenx  B., Garcia  C., Laroche-Traineau  J., Moreau  P., Domergue  F., Lessire  R.  2008. The VLCFA elongase gene family in PubMed

Jung  J.-H., Domijan  M., Klose  C., Biswas  S., Ezer  D., Gao  M., Khattak  A.K., Box  M.S., Charoensawan  V., Cortijo  S., Kumar  M., Grant  A., Locke  J.C.W., Schäfer  E., Jaeger  K.E., Wigge  P.A.  2016. Phytochromes function as thermosensors in PubMed

Kaczorowski  K.A., Quail  P.H.  2003. Arabidopsis PSEUDO-RESPONSE REGULATOR7 is a signaling intermediate in phytochrome-regulated seedling deetiolation and phasing of the circadian clock. Plant Cell  15:2654–2665. PubMed PMC

Kamm  J., Terhorst  J., Durbin  R., Song  Y.S.  2020. Efficiently inferring the demographic history of many populations with allele count data. J. Am. Stat. Assoc. 115:1472–1487. PubMed PMC

Keightley  P.D., Jackson  B.C.  2018. Inferring the probability of the derived vs. the ancestral allelic state at a polymorphic site. Genetics  209:897–906. PubMed PMC

Keller  I., Wagner  C.E., Greuter  L., Mwaiko  S., Selz  O.M., Sivasundar  A., Wittwer  S., Seehausen  O.  2013. Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Mol. Ecol. 22:2848–2863. PubMed

Kellis  M., Birren  B.W., Lander  E.S.  2004. Proof and evolutionary analysis of ancient genome duplication in the yeast PubMed

Kim  H.-J., Kim  Y.-K., Park  J.-Y., Kim  J.  2002. Light signalling mediated by phytochrome plays an important role in cold-induced gene expression through the C-repeat/dehydration responsive element (C/DRE) in PubMed

Kim  M., Cui  M.-L., Cubas  P., Gillies  A., Lee  K., Chapman  M.A., Abbott  R.J., Coen  E.  2008. Regulatory genes control a key morphological and ecological trait transferred between species. Science  322:1116–1119. PubMed

Kim  Y., Park  S., Gilmour  S.J., Thomashow  M.F.  2013. Roles of CAMTA transcription factors and salicylic acid in configuring the low-temperature transcriptome and freezing tolerance of PubMed

Kim  Y.J., Wang  R., Gao  L., Li  D., Xu  C., Mang  H., Jeon  J., Chen  X., Zhong  X., Kwak  J.M., Mo  B., Xiao  L., Chen  X.  2016. POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 113:14858–14863. PubMed PMC

Koch  M.A., Matschinger  M.  2007. Evolution and genetic differentiation among relatives of PubMed PMC

Koch  M.A.  2019. The plant model system PubMed

Koropachinskii  I.Y.  2013. Natural hybridization and taxonomy of birches in North Asia. Contemp. Probl. Ecol. 6:350–369.

Krehenwinkel  H., Tautz  D.  2013. Northern range expansion of European populations of the wasp spider PubMed

Lafon-Placette  C., Johannessen  I.M., Hornslien  K.S., Ali  M.F., Bjerkan  K.N., Bramsiepe  J., Glöckle  B.M., Rebernig  C.A., Brysting  A.K., Grini  P.E., Köhler  C.  2017. Endosperm-based hybridization barriers explain the pattern of gene flow between PubMed PMC

Lamichhaney  S., Berglund  J., Almén  M.S., Maqbool  K., Grabherr  M., Martinez-Barrio  A., Promerová  M., Rubin  C.-J., Wang  C., Zamani  N., Grant  B.R., Grant  P.R., Webster  M.T., Andersson  L.  2015. Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature  518:371–375. PubMed

Lashermes  P., Hueber  Y., Combes  M.-C., Severac  D., Dereeper  A.  2016. Inter-genomic DNA exchanges and homeologous gene silencing shaped the nascent allopolyploid coffee genome ( PubMed PMC

Lautenschlager  U., Wagner  F., Oberprieler  C.  2020. AllCoPol: inferring allele co-ancestry in polyploids. BMC Bioinf. 21:441. PubMed PMC

Leal  J.L., Milesi  P., Salojärvi  J., Lascoux  M.  2023. Phylogenetic analysis of allotetraploid species using polarized genomic sequences. Syst. Biol. 72:372–390. PubMed PMC

Legris  M., Klose  C., Burgie  E.S., Rojas  C.C.R., Neme  M., Hiltbrunner  A., Wigge  P.A., Schäfer  E., Vierstra  R.D., Casal  J.J.  2016. Phytochrome B integrates light and temperature signals in PubMed

Li  J., Shoup  S., Chen  Z.  2005. Phylogenetics of

Li  J., Shoup  S., Chen  Z.  2007. Phylogenetic relationships of diploid species of

Li  H., Durbin  R.  2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics  25:1754–1760. PubMed PMC

Li  F., Fan  G., Lu  C., Xiao  G., Zou  C., Kohel  R.J., Ma  Z., Shang  H., Ma  X., Wu  J., Liang  X., Huang  G., Percy  R.G., Liu  K., Yang  W., Chen  W., Du  X., Shi  C., Yuan  Y., Ye  W., Liu  X., Zhang  X., Liu  W., Wei  H., Wei  S., Huang  G., Zhang  X., Zhu  S., Zhang  H., Sun  F., Wang  X., Liang  J., Wang  J., He  Q., Huang  L., Wang  J., Cui  J., Song  G., Wang  K., Xu  X., Yu  J.Z., Zhu  Y., Yu  S.  2015. Genome sequence of cultivated Upland cotton ( PubMed

Li  Z., Tiley  G.P., Galuska  S.R., Reardon  C.R., Kidder  T.I., Rundell  R.J., Barker  M.S.  2018a. Multiple large-scale gene and genome duplications during the evolution of hexapods. Proc. Natl. Acad. Sci. U.S.A. 115:4713–4718. PubMed PMC

Li  X., Yu  H., Jiao  Y., Shahid  M.Q., Wu  J., Liu  X.  2018b. Genome-wide analysis of DNA polymorphisms, the methylome and transcriptome revealed that multiple factors are associated with low pollen fertility in autotetraploid rice. PLoS One  13:e0201854. PubMed PMC

Li  L., Milesi  P., Tiret  M., Chen  J., Sendrowski  J., Baison  J., Chen  Z., Zhou  L., Karlsson  B., Berlin  M., Westin  J., Garcia-Gil  M.R., Wu  H.X., Lascoux  M.  2022. Teasing apart the joint effect of demography and natural selection in the birth of a contact zone. New Phytol. 236:1976–1987. PubMed PMC

Lihová  J., Kučera  J., Perný  M., Marhold  K.  2007. Hybridization between two polyploid Cardamine (Brassicaceae) species in North-western Spain: discordance between morphological and genetic variation patterns. Ann. Bot. 99:1083–1096. PubMed PMC

Lim  C.J., Park  J., Shen  M., Park  H.J., Cheong  M.S., Park  K.S., Baek  D., Bae  M.J., Ali  A., Jan  M., Lee  S.Y., Lee  B., Kim  W.-Y., Pardo  J.M., Yun  D.-J.  2020. The histone-modifying complex PWR/HOS15/HD2C epigenetically regulates cold tolerance. Plant Physiol. 184:1097–1111. PubMed PMC

Liu  Z., Hall  J.D., Mount  D.W.  2001. Arabidopsis UVH3 gene is a homolog of the PubMed

Lloyd  A., Bomblies  K.  2016. Meiosis in autopolyploid and allopolyploid PubMed

Lloyd  A., Blary  A., Charif  D., Charpentier  C., Tran  J., Balzergue  S., Delannoy  E., Rigaill  G., Jenczewski  E.  2018. Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop. New Phytol. 217:367–377. PubMed

Ma  L.-J., Ibrahim  A.S., Skory  C., Grabherr  M.G., Burger  G., Butler  M., Elias  M., Idnurm  A., Lang  B.F., Sone  T., Abe  A., Calvo  S.E., Corrochano  L.M., Engels  R., Fu  J., Hansberg  W., Kim  J.-M., Kodira  C.D., Koehrsen  M.J., Liu  B., Miranda-Saavedra  D., O’Leary  S., Ortiz-Castellanos  L., Poulter  R., Rodriguez-Romero  J., Ruiz-Herrera  J., Shen  Y.-Q., Zeng  Q., Galagan  J., Birren  B.W., Cuomo  C.A., Wickes  B.L.  2009. Genomic analysis of the basal lineage fungus PubMed PMC

Macqueen  D.J., Johnston  I.A.  2014. A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification. Proc. Biol. Sci. 281:20132881. PubMed PMC

Maddison  W.P., Knowles  L.L.  2006. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 55:21–30. PubMed

Mallet  J.  2005. Hybridization as an invasion of the genome. Trends Ecol. Evol. 20:229–237. PubMed

Mallet  J.  2007. Hybrid speciation. Nature  446:279–283. PubMed

Mallet  J., Besansky  N., Hahn  M.W.  2016. How reticulated are species? Bioessays  38:140–149. PubMed PMC

Mallo  D., De Oliveira Martins  L., Posada  D.  2016. SimPhy: phylogenomic simulation of gene, locus, and species trees. Syst. Biol. 65:334–344. PubMed PMC

Mandel  J.R., Barker  M.S., Bayer  R.J., Dikow  R.B., Gao  T.-G., Jones  K.E., Keeley  S., Kilian  N., Ma  H., Siniscalchi  C.M., Susanna  A., Thapa  R., Watson  L., Funk  V.A.  2017. The Compositae Tree of Life in the age of phylogenomics. J. Syst. Evol. 55:405–410.

Marburger  S., Monnahan  P., Seear  P.J., Martin  S.H., Koch  J., Paajanen  P., Bohutínská  M., Higgins  J.D., Schmickl  R., Yant  L.  2019. Interspecific introgression mediates adaptation to whole genome duplication. Nat. Commun. 10:5218. PubMed PMC

Marhold  K., Lihová  J.  2006. Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae. Plant Syst. Evol. 259:143–174.

Maruyama  K., Takeda  M., Kidokoro  S., Yamada  K., Sakuma  Y., Urano  K., Fujita  M., Yoshiwara  K., Matsukura  S., Morishita  Y., Sasaki  R., Suzuki  H., Saito  K., Shibata  D., Shinozaki  K., Yamaguchi-Shinozaki  K.  2009. Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol. 150:1972–1980. PubMed PMC

McCormack  J.E., Huang  H., Knowles  L.L.  2009. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Syst. Biol. 58:501–508. PubMed

McDonald  D.B., Parchman  T.L., Bower  M.R., Hubert  W.A., Rahel  F.J.  2008. An introduced and a native vertebrate hybridize to form a genetic bridge to a second native species. Proc. Natl. Acad. Sci. U.S.A. 105:10837–10842. PubMed PMC

McKenna  A., Hanna  M., Banks  E., Sivachenko  A., Cibulskis  K., Kernytsky  A., Garimella  K., Altshuler  D., Gabriel  S., Daly  M., DePristo  M.A.  2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297–1303. PubMed PMC

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. PubMed PMC

Merret  R., Descombin  J., Juan  Y., Favory  J.-J., Carpentier  M.-C., Chaparro  C., Charng  Y., Deragon  J.-M., Bousquet-Antonelli  C.  2013. XRN4 and LARP1 are required for a heat-triggered mRNA decay pathway involved in plant acclimation and survival during thermal stress. Cell Rep. 5:1279–1293. PubMed

Minh  B.Q., Schmidt  H.A., Chernomor  O., Schrempf  D., Woodhams  M.D., von Haeseler  A., Lanfear  R.  2020. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37:1530–1534. PubMed PMC

Mirarab  S., Bayzid  M.S., Warnow  T.  2016. Evaluating summary methods for multilocus species tree estimation in the presence of incomplete lineage sorting. Syst. Biol. 65:366–380. PubMed

Monnahan  P., Kolář  F., Baduel  P., Sailer  C., Koch  J., Horvath  R., Laenen  B., Schmickl  R., Paajanen  P., Šrámková  G., Bohutínská  M., Arnold  B., Weisman  C.M., Marhold  K., Slotte  T., Bomblies  K., Yant  L.  2019. Pervasive population genomic consequences of genome duplication in PubMed

Morgan  C., White  M.A., Franklin  F.C.H., Zickler  D., Kleckner  N., Bomblies  K.  2021. Evolution of crossover interference enables stable autopolyploidy by ensuring pairwise partner connections in PubMed PMC

Muñoz-Rodríguez  P., Carruthers  T., Wood  J.R.I., Williams  B.R.M., Weitemier  K., Kronmiller  B., Ellis  D., Anglin  N.L., Longway  L., Harris  S.A., Rausher  M.D., Kelly  S., Liston  A., Scotland  R.W.  2018. Reconciling conflicting phylogenies in the origin of sweet potato and dispersal to polynesia. Curr. Biol. 28:1246–1256.e12. PubMed

Nibau  C., Gonzalo  A., Evans  A., Sweet-Jones  W., Phillips  D., Lloyd  A.  2022. Meiosis in allopolyploid PubMed PMC

Nieto Feliner  G., Casacuberta  J., Wendel  J.F.  2020. Genomics of evolutionary novelty in hybrids and polyploids. Front. Genet. 11:1–21. PubMed PMC

Nossa  C.W., Havlak  P., Yue  J.-X., Lv  J., Vincent  K.Y., Brockmann  H.J., Putnam  N.H.  2014. Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication. GigaScience  3:2047–217X-3–9. PubMed PMC

Novikova  P.Y., Tsuchimatsu  T., Simon  S., Nizhynska  V., Voronin  V., Burns  R., Fedorenko  O.M., Holm  S., Säll  T., Prat  E., Marande  W., Castric  V., Nordborg  M.  2017. Genome sequencing reveals the origin of the Allotetraploid PubMed PMC

Novikova  P.Y., Brennan  I.G., Booker  W., Mahony  M., Doughty  P., Lemmon  A.R., Lemmon  E.M., Roberts  J.D., Yant  L., de Peer  Y.V., Keogh  J.S., Donnellan  S.C.  2020. Polyploidy breaks speciation barriers in Australian burrowing frogs PubMed PMC

Oberprieler  C., Wagner  F., Tomasello  S., Konowalik  K.  2017. A permutation approach for inferring species networks from gene trees in polyploid complexes by minimising deep coalescences. Methods Ecol. Evol. 8:835–849.

Opgenoorth  L., Dauphin  B., Benavides  R., Heer  K., Alizoti  P., Martínez-Sancho  E., Alía  R., Ambrosio  O., Audrey  A., Auñón  F., Avanzi  C., Avramidou  E., Bagnoli  F., Barbas  E., Bastias  C.C., Bastien  C., Ballesteros  E., Beffa  G., Bernier  F., Bignalet  H., Bodineau  G., Bouic  D., Brodbeck  S., Brunetto  W., Buchovska  J., Buy  M., Cabanillas-Saldaña  A.M., Carvalho  B., Cheval  N., Climent  J.M., Correard  M., Cremer  E., Danusevičius  D., Del Caño  F., Denou  J.-L., di Gerardi  N., Dokhelar  B., Ducousso  A., Eskild Nilsen  A., Farsakoglou  A.-M., Fonti  P., Ganopoulos  I., García del Barrio  J.M., Gilg  O., González-Martínez  S.C., Graf  R., Gray  A., Grivet  D., Gugerli  F., Hartleitner  C., Hollenbach  E., Hurel  A., Issehut  B., Jean  F., Jorge  V., Jouineau  A., Kappner  J.-P., Kärkkäinen  K., Kesälahti  R., Knutzen  F., Kujala  S.T., Kumpula  T.A., Labriola  M., Lalanne  C., Lambertz  J., Lascoux  M., Lejeune  V., Le-Provost  G., Levillain  J., Liesebach  M., López-Quiroga  D., Meier  B., Malliarou  E., Marchon  J., Mariotte  N., Mas  A., Matesanz  S., Meischner  H., Michotey  C., Milesi  P., Morganti  S., Nievergelt  D., Notivol  E., Ostreng  G., Pakull  B., Perry  A., Piotti  A., Plomion  C., Poinot  N., Pringarbe  M., Puzos  L., Pyhäjärvi  T., Raffin  A., Ramírez-Valiente  J.A., Rellstab  C., Remi  D., Richter  S., Robledo-Arnuncio  J.J., San Segundo  S., Savolainen  O., Schueler  S., Schneck  V., Scotti  I., Semerikov  V., Slámová  L., Sønstebø  J.H., Spanu  I., Thevenet  J., Tollefsrud  M.M., Turion  N., Vendramin  G.G., Villar  M., von Arx  G., Westin  J., Fady  B., Myking  T., Valladares  F., Aravanopoulos  F.A., Cavers  S.  2021. The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species. GigaScience  10:giab010. PubMed PMC

Oxelman  B., Brysting  A.K., Jones  G.R., Marcussen  T., Oberprieler  C., Pfeil  B.E.  2017. Phylogenetics of allopolyploids. Annu. Rev. Ecol. Evol. Syst. 48:543–557.

Palmé  A.E., Su  Q., Palsson  S., Lascoux  M.  2004. Extensive sharing of chloroplast haplotypes among European birches indicates hybridization among PubMed

Pardo-Diaz  C., Salazar  C., Baxter  S.W., Merot  C., Figueiredo-Ready  W., Joron  M., McMillan  W.O., Jiggins  C.D.  2012. Adaptive introgression across species boundaries in PubMed PMC

Pickrell  J.K., Pritchard  J.K.  2012. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 8:e1002967. PubMed PMC

Pritchard  J.K., Stephens  M., Donnelly  P.  2000. Inference of population structure using Multilocus genotype data. Genetics  155:945–959. PubMed PMC

Rabiee  M., Sayyari  E., Mirarab  S.  2019. Multi-allele species reconstruction using ASTRAL. Mol. Phylogenet. Evol. 130:286–296. PubMed

Ramsey  J., Schemske  D.W.  1998. Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu. Rev. Ecol. Syst. 29:467–501.

Ramsey  J., Schemske  D.W.  2002. Neopolyploidy in flowering plants. Annu. Rev. Ecol. Syst. 33:589–639.

Renard  J., Niñoles  R., Martínez-Almonacid  I., Gayubas  B., Mateos-Fernández  R., Bissoli  G., Bueso  E., Serrano  R., Gadea  J.  2020. Identification of novel seed longevity genes related to oxidative stress and seed coat by genome-wide association studies and reverse genetics. Plant Cell Environ. 43:2523–2539. PubMed

Rieseberg  L.H., Archer  M.A., Wayne  R.K.  1999. Transgressive segregation, adaptation and speciation. Heredity  83 ( Pt 4):363–372. PubMed

Rieseberg  L.H., Willis  J.H.  2007. Plant speciation. Science  317:910–914. PubMed PMC

Rius  M., Darling  J.A.  2014. How important is intraspecific genetic admixture to the success of colonising populations? Trends Ecol. Evol. 29:233–242. PubMed

Robertson  F.M., Gundappa  M.K., Grammes  F., Hvidsten  T.R., Redmond  A.K., Lien  S., Martin  S.A.M., Holland  P.W.H., Sandve  S.R., Macqueen  D.J.  2017. Lineage-specific rediploidization is a mechanism to explain time-lags between genome duplication and evolutionary diversification. Genome Biol. 18:111. PubMed PMC

Rothfels  C.J.  2021. Polyploid phylogenetics. New Phytol. 230:66–72. PubMed

Roux  C., Pannell  J.R.  2015. Inferring the mode of origin of polyploid species from next-generation sequence data. Mol. Ecol. 24:1047–1059. PubMed

Salojärvi  J., Smolander  O.-P., Nieminen  K., Rajaraman  S., Safronov  O., Safdari  P., Lamminmäki  A., Immanen  J., Lan  T., Tanskanen  J., Rastas  P., Amiryousefi  A., Jayaprakash  B., Kammonen  J.I., Hagqvist  R., Eswaran  G., Ahonen  V.H., Serra  J.A., Asiegbu  F.O., de Dios Barajas-Lopez  J., Blande  D., Blokhina  O., Blomster  T., Broholm  S., Brosché  M., Cui  F., Dardick  C., Ehonen  S.E., Elomaa  P., Escamez  S., Fagerstedt  K.V., Fujii  H., Gauthier  A., Gollan  P.J., Halimaa  P., Heino  P.I., Himanen  K., Hollender  C., Kangasjärvi  S., Kauppinen  L., Kelleher  C.T., Kontunen-Soppela  S., Koskinen  J.P., Kovalchuk  A., Kärenlampi  S.O., Kärkönen  A.K., Lim  K.-J., Leppälä  J., Macpherson  L., Mikola  J., Mouhu  K., Mähönen  A.P., Niinemets  U., Oksanen  E., Overmyer  K., Palva  E.T., Pazouki  L., Pennanen  V., Puhakainen  T., Poczai  P., Possen  B.J.H.M., Punkkinen  M., Rahikainen  M.M., Rousi  M., Ruonala  R., van der Schoot  C., Shapiguzov  A., Sierla  M., Sipilä  T.P., Sutela  S., Teeri  T.H., Tervahauta  A.I., Vaattovaara  A., Vahala  J., Vetchinnikova  L., Welling  A., Wrzaczek  M., Xu  E., Paulin  L.G., Schulman  A.H., Lascoux  M., Albert  V.A., Auvinen  P., Helariutta  Y., Kangasjärvi  J.  2017. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat. Genet. 49:904–912. PubMed

Salojärvi  J., Rambani  A., Yu  Z., Guyot  R., Strickler  S., Lepelley  M., Wang  C., Rajaraman  S., Rastas  P., Zheng  C., Muñoz  D.S., Meidanis  J., Paschoal  A.R., Bawin  Y., Krabbenhoft  T., Wang  Z.Q., Fleck  S., Aussel  R., Bellanger  L., Charpagne  A., Fournier  C., Kassam  M., Lefebvre  G., Métairon  S., Moine  D., Rigoreau  M., Stolte  J., Hamon  P., Couturon  E., Tranchant-Dubreuil  C., Mukherjee  M., Lan  T., Engelhardt  J., Stadler  P., Lemos  S.M.C.D., Suzuki  S.I., Sumirat  U., Man  W.C., Dauchot  N., Orozco-Arias  S., Garavito  A., Kiwuka  C., Musoli  P., Nalukenge  A., Guichoux  E., Reinout  H., Smit  M., Carretero-Paulet  L., Filho  O.G., Braghini  M.T., Padilha  L., Sera  G.H., Ruttink  T., Henry  R., Marraccini  P., de Peer  Y.V., Andrade  A., Domingues  D., Giuliano  G., Mueller  L., Pereira  L.F., Plaisance  S., Poncet  V., Rombauts  S., Sankoff  D., Albert  V.A., Crouzillat  D., de Kochko  A., Descombes  P.  2023. The genome and population genomics of allopolyploid PubMed PMC

Schenk  M.F., Thienpont  C.-N., Koopman  W.J.M., Gilissen  L.J.W.J., Smulders  M.J.M.  2008. Phylogenetic relationships in

Schmickl  R., Marburger  S., Bray  S., Yant  L.  2017. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. J. Exp. Bot. 68:5453–5470. PubMed

Schmickl  R., Yant  L.  2021. Adaptive introgression: how polyploidy reshapes gene flow landscapes. New Phytol. 230:457–461. PubMed

Schwager  E.E., Sharma  P.P., Clarke  T., Leite  D.J., Wierschin  T., Pechmann  M., Akiyama-Oda  Y., Esposito  L., Bechsgaard  J., Bilde  T., Buffry  A.D., Chao  H., Dinh  H., Doddapaneni  H., Dugan  S., Eibner  C., Extavour  C.G., Funch  P., Garb  J., Gonzalez  L.B., Gonzalez  V.L., Griffiths-Jones  S., Han  Y., Hayashi  C., Hilbrant  M., Hughes  D.S.T., Janssen  R., Lee  S.L., Maeso  I., Murali  S.C., Muzny  D.M., Nunes da Fonseca  R., Paese  C.L.B., Qu  J., Ronshaugen  M., Schomburg  C., Schönauer  A., Stollewerk  A., Torres-Oliva  M., Turetzek  N., Vanthournout  B., Werren  J.H., Wolff  C., Worley  K.C., Bucher  G., Gibbs  R.A., Coddington  J., Oda  H., Stanke  M., Ayoub  N.A., Prpic  N.-M., Flot  J.-F., Posnien  N., Richards  S., McGregor  A.P.  2017. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution. BMC Biol. 15:62. PubMed PMC

Seear  P.J., France  M.G., Gregory  C.L., Heavens  D., Schmickl  R., Yant  L., Higgins  J.D.  2020. A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid PubMed PMC

Seehausen  O.  2006. African cichlid fish: a model system in adaptive radiation research. Proc. Biol. Sci. 273:1987–1998. PubMed PMC

Séguéla-Arnaud  M., Crismani  W., Larchevêque  C., Mazel  J., Froger  N., Choinard  S., Lemhemdi  A., Macaisne  N., Van Leene  J., Gevaert  K., De Jaeger  G., Chelysheva  L., Mercier  R.  2015. Multiple mechanisms limit meiotic crossovers: TOP3α and two BLM homologs antagonize crossovers in parallel to FANCM. Proc. Natl. Acad. Sci. U.S.A. 112:4713–4718. PubMed PMC

Seo  M., Hanada  A., Kuwahara  A., Endo  A., Okamoto  M., Yamauchi  Y., North  H., Marion-Poll  A., Sun  T., Koshiba  T., Kamiya  Y., Yamaguchi  S., Nambara  E.  2006. Regulation of hormone metabolism in PubMed

Serra  H., Lambing  C., Griffin  C.H., Topp  S.D., Nageswaran  D.C., Underwood  C.J., Ziolkowski  P.A., Séguéla-Arnaud  M., Fernandes  J.B., Mercier  R., Henderson  I.R.  2018. Massive crossover elevation via combination of PubMed PMC

Shen  H., Luong  P., Huq  E.  2007. The F-box protein MAX2 functions as a positive regulator of photomorphogenesis in arabidopsis. Plant Physiol. 145:1471–1483. PubMed PMC

Shi  X., Sun  X., Zhang  Z., Feng  D., Zhang  Q., Han  L., Wu  J., Lu  T.  2015. GLUCAN SYNTHASE-LIKE 5 (GSL5) plays an essential role in male fertility by regulating callose metabolism during microsporogenesis in rice. Plant Cell Physiol. 56:497–509. PubMed

Sicard  A., Kappel  C., Josephs  E.B., Lee  Y.W., Marona  C., Stinchcombe  J.R., Wright  S.I., Lenhard  M.  2015. Divergent sorting of a balanced ancestral polymorphism underlies the establishment of gene-flow barriers in Capsella. Nat. Commun. 6:7960. PubMed PMC

Slotte  T., Huang  H., Lascoux  M., Ceplitis  A.  2008. Polyploid speciation did not confer instant reproductive isolation in capsella (Brassicaceae). Mol. Biol. Evol. 25:1472–1481. PubMed

Solís-Lemus  C., Bastide  P., Ané  C.  2017. PhyloNetworks: a package for phylogenetic networks. Mol. Biol. Evol. 34:3292–3298. PubMed

Soltis  P.S., Soltis  D.E.  2009. The role of hybridization in plant speciation. Annu. Rev. Plant Biol. 60:561–588. PubMed

Somers  D.E., Devlin  P.F., Kay  S.A.  1998. Phytochromes and cryptochromes in the entrainment of the PubMed

Spoelhof  J.P., Soltis  P.S., Soltis  D.E.  2017. Pure polyploidy: closing the gaps in autopolyploid research. J. Syst. Evol.. 55:340–352.

Stebbins  G.L.  1956. Cytogenetics and evolution of the grass family. Am. J. Bot. 43:890–905.

Stebbins  G.  1971. Chromosomal evolution in higher plants. London: Edward Arnold Ltd.

Stern  K.  1965. Tetrasome spaltung bei

Suarez-Gonzalez  A., Hefer  C.A., Lexer  C., Douglas  C.J., Cronk  Q.C.B.  2018. Introgression from PubMed

Sun  F., Fan  G., Hu  Q., Zhou  Y., Guan  M., Tong  C., Li  J., Du  D., Qi  C., Jiang  L., Liu  W., Huang  S., Chen  W., Yu  J., Mei  D., Meng  J., Zeng  P., Shi  J., Liu  K., Wang  X., Wang  X., Long  Y., Liang  X., Hu  Z., Huang  G., Dong  C., Zhang  H., Li  J., Zhang  Y., Li  L., Shi  C., Wang  J., Lee  S.M.-Y., Guan  C., Xu  X., Liu  S., Liu  X., Chalhoub  B., Hua  W., Wang  H.  2017. The high-quality genome of PubMed

Tavaré  S., Balding  D.J., Griffiths  R.C., Donnelly  P.  1997. Inferring coalescence times from DNA sequence data. Genetics  145:505–518. PubMed PMC

Than  C., Ruths  D., Nakhleh  L.  2008. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinf. 9:322. PubMed PMC

Thórsson  ÆH.T., Salmela  E., Anamthawat-Jónsson  K.  2001. Morphological, cytogenetic, and molecular evidence for introgressive hybridization in birch. J. Hered. 92:404–408. PubMed

Truong  C., Palmé  A.E., Felber  F.  2007. Recent invasion of the mountain birch PubMed

Tsuda  Y., Semerikov  V., Sebastiani  F., Vendramin  G.G., Lascoux  M.  2017. Multispecies genetic structure and hybridization in the PubMed

Van de Peer  Y., Mizrachi  E., Marchal  K.  2017. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18:411–424. PubMed

Wagner  N.D., He  L., Hörandl  E.  2020. Phylogenomic relationships and evolution of polyploid salix species revealed by RAD sequencing data. Front. Plant Sci. 11:1077. PubMed PMC

Walters  S.M.  1968.

Wang  N., Borrell  J.S., Bodles  W.J.A., Kuttapitiya  A., Nichols  R.A., Buggs  R.J.A.  2014. Molecular footprints of the Holocene retreat of dwarf birch in Britain. Mol. Ecol. 23:2771–2782. PubMed PMC

Wang  N., McAllister  H.A., Bartlett  P.R., Buggs  R.J.A.  2016. Molecular phylogeny and genome size evolution of the genus PubMed PMC

Wang  Z., Miao  H., Liu  J., Xu  B., Yao  X., Xu  C., Zhao  S., Fang  X., Jia  C., Wang  J., Zhang  J., Li  J., Xu  Y., Wang  J., Ma  W., Wu  Z., Yu  L., Yang  Y., Liu  C., Guo  Y., Sun  S., Baurens  F.-C., Martin  G., Salmon  F., Garsmeur  O., Yahiaoui  N., Hervouet  C., Rouard  M., Laboureau  N., Habas  R., Ricci  S., Peng  M., Guo  A., Xie  J., Li  Y., Ding  Z., Yan  Y., Tie  W., D’Hont  A., Hu  W., Jin  Z.  2019. PubMed PMC

Wang  N., Kelly  L.J., McAllister  H.A., Zohren  J., Buggs  R.J.A.  2021. Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees. Mol. Phylogenet. Evol. 160:107126. PubMed

Wen  D., Yu  Y., Zhu  J., Nakhleh  L.  2018. Inferring phylogenetic networks using PhyloNet. Syst. Biol. 67:735–740. PubMed PMC

Whitney  K.D., Randell  R.A., Rieseberg  L.H.  2006. Adaptive introgression of herbivore resistance traits in the weedy sunflower PubMed

Winkler  M., Escobar García  P., Gattringer  A., Sonnleitner  M., Hülber  K., Schönswetter  P., Schneeweiss  G.M.  2017. A novel method to infer the origin of polyploids from Amplified Fragment Length Polymorphism data reveals that the alpine polyploid complex of PubMed

Wolfe  K.H., Shields  D.C.  1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature  387:708–713. PubMed

Wood  T.E., Takebayashi  N., Barker  M.S., Mayrose  I., Greenspoon  P.B., Rieseberg  L.H.  2009. The frequency of polyploid speciation in vascular plants. Proc. Natl. Acad. Sci. U.S.A. 106:13875–13879. PubMed PMC

Wu  Y., Lin  F., Zhou  Y., Wang  J., Sun  S., Wang  B., Zhang  Z., Li  G., Lin  X., Wang  X., Sun  Y., Dong  Q., Xu  C., Gong  L., Wendel  J.F., Zhang  Z., Liu  B.  2021. Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids. Natl. Sci. Rev. 8:nwaa277. PubMed PMC

Xiong  Z., Gaeta  R.T., Edger  P.P., Cao  Y., Zhao  K., Zhang  S., Pires  J.C.  2021. Chromosome inheritance and meiotic stability in allopolyploid PubMed PMC

Yan  Z., Cao  Z., Liu  Y., Ogilvie  H.A., Nakhleh  L.  2022. Maximum parsimony inference of phylogenetic networks in the presence of polyploid complexes. Syst. Biol. 71:706–720. PubMed PMC

Yano  R., Nakamura  M., Yoneyama  T., Nishida  I.  2005. Starch-related α-glucan/water dikinase is involved in the cold-induced development of freezing tolerance in arabidopsis. Plant Physiol. 138:837–846. PubMed PMC

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

Yoshida  K., Schuenemann  V.J., Cano  L.M., Pais  M., Mishra  B., Sharma  R., Lanz  C., Martin  F.N., Kamoun  S., Krause  J., Thines  M., Weigel  D., Burbano  H.A.  2013. The rise and fall of the PubMed PMC

Zhang  C., Ogilvie  H.A., Drummond  A.J., Stadler  T.  2018a. Bayesian inference of species networks from multilocus sequence data. Mol. Biol. Evol. 35:504–517. PubMed PMC

Zhang  C., Rabiee  M., Sayyari  E., Mirarab  S.  2018b. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinf. 19:153. PubMed PMC

Zhang  T., Jing  J.-L., Liu  L., He  Y.  2021. ZmRAD17 is required for accurate double-strand break repair during maize male meiosis. Front. Plant Sci. 12:1–9. PubMed PMC

Zhou  B.-B.S., Elledge  S.J.  2000. The DNA damage response: putting checkpoints in perspective. Nature. 408:433–439. PubMed

Zohren  J., Wang  N., Kardailsky  I., Borrell  J.S., Joecker  A., Nichols  R.A., Buggs  R.J.A.  2016. Unidirectional diploid–tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers. Mol. Ecol. 25:2413–2426. PubMed PMC

Whole-genome duplication increases genetic diversity and load in outcrossing Arabidopsis arenosa

Overcoming Ploidy Barriers: The Role of Triploid Bridges in the Genetic Introgression of Cardamine amara

Polyploids broadly generate novel haplotypes from trans-specific variation in Arabidopsis arenosa and Arabidopsis lyrata