• 1.

    Abbott, R. J. et al. Hybridization and speciation. J. Evol. Biol. 26, 229–246 (2013).

    CAS  PubMed  Google Scholar 

  • 2.

    Mallet, J. Hybrid speciation. Nature 446, 279–283 (2007).

    ADS  CAS  PubMed  Google Scholar 

  • 3.

    Schumer, M., Cui, R., Rosenthal, G. G. & Andolfatto, P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genet. 11, e1005041 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 4.

    Hoffmann, A. A. & Rieseberg, L. H. 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 (2008).

    PubMed  PubMed Central  Google Scholar 

  • 5.

    Buerkle, C. A., Morris, R. J., Asmussen, M. A. & Rieseberg, L. H. The likelihood of homoploid hybrid speciation. Heredity 84, 441–451 (2000).

    PubMed  Google Scholar 

  • 6.

    Marques, D. A., Meier, J. I. & Seehausen, O. A combinatorial view on speciation and adaptive radiation. Trends Ecol. Evol. 34, 531–544 (2019).

    PubMed  Google Scholar 

  • 7.

    Brennan, A. C., Hiscock, S. J. & Abbott, R. J. Completing the hybridization triangle: the inheritance of genetic incompatibilities during homoploid hybrid speciation in ragworts (Senecio). AoB Plants 11, ply078 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 8.

    Hermansen, J. S. et al. Hybrid speciation through sorting of parental incompatibilities in Italian sparrows. Mol. Ecol. 23, 5831–5842 (2015).

    Google Scholar 

  • 9.

    Rieseberg, L. H. et al. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301, 1211–1216 (2003).

    ADS  CAS  PubMed  Google Scholar 

  • 10.

    Schumer, M., Rosenthal, G. G. & Andolfatto, P. How common is homoploid hybrid speciation? Evolution 68, 1553–1560 (2014).

    PubMed  Google Scholar 

  • 11.

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

    PubMed  Google Scholar 

  • 12.

    Ravinet, M. et al. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J. Evol. Biol. 30, 1450 (2017).

    CAS  PubMed  Google Scholar 

  • 13.

    Gompert, Z. & Buerkle, A. Bayesian estimation of genomic clines. Mol. Ecol. 20, 2111–2127 (2011).

    PubMed  Google Scholar 

  • 14.

    Schumer, M. et al. High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species. eLife 3, e02535 (2014).

    PubMed Central  Google Scholar 

  • 15.

    Rigling, D. & Prospero, S. Cryphonectria parasitica, the causal agent of chestnut blight: Invasion history, population biology and disease control. Mol. Plant Pathol. 19, 7–20 (2018).

    CAS  PubMed  Google Scholar 

  • 16.

    Kuhlman, E. G. Chestnut Blight. Science 210, 1199–1200 (1980).

    ADS  CAS  PubMed  Google Scholar 

  • 17.

    Thompson, H. Plant science: the chestnut resurrection. Nature 490, 22–23 (2012).

    ADS  PubMed  Google Scholar 

  • 18.

    Gabriel, Popkin Can a transgenic chestnut restore a forest icon? Science 361, 830–831 (2018).

    Google Scholar 

  • 19.

    Huang, C., Zhang, Y. & Bruce, B. Fagaceae in Flora of China, Vol. 4 (eds Wu, Z. Y. & Peter, R. H.) 314–400 (Science Press, 1999).

  • 20.

    Liu, G. & Fang, J. Spatial patterns of chestnut (Castanea millissima) and its species geographical distribution in China. Acta Ecol. Sin. 21, 164–170 (2001).

    CAS  Google Scholar 

  • 21.

    Liu, G. B. et al. Study on the distant hybridization compatibility between Castanea mollissima and C. henryi. New Hortic. 15, 1–4 (2013).

    Google Scholar 

  • 22.

    Lang, P., Dane, F., Kubisiak, T. L. & Huang, H. Molecular evidence for an Asian origin and a unique westward migration of species in the genus Castanea via Europe to North America. Mol. Phylogenet. Evol. 43, 49–59 (2007).

    CAS  PubMed  Google Scholar 

  • 23.

    Lang, P. & Huang, H. Genetic diversity and geographic variation in natural populations of the endemic Castanea species in China. Acta Bot. Sin. 41, 651–657 (1999).

    CAS  Google Scholar 

  • 24.

    Clarke, J. et al. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Biotechnol. 4, 265 (2009).

    ADS  CAS  Google Scholar 

  • 25.

    Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 26.

    Xing, Y. et al. Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima). GigaScience 8, giz112 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 27.

    Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764 (2011).

    PubMed  PubMed Central  Google Scholar 

  • 28.

    Li, H. Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM. https://arxiv.org/abs/1303.3997v2 (2013).

  • 29.

    Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543–548 (2017).

    PubMed Central  Google Scholar 

  • 30.

    Staton, M. et al. The Chinese Chestnut Genome: A Reference for Species Restoration. https://www.biorxiv.org/content/10.1101/615047v1, 615047 (2019).

  • 31.

    Depristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 32.

    Alexander, D. H. & Lange, K. Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinforma. 12, 246 (2011).

    Google Scholar 

  • 33.

    Raj, A., Stephens, M. & PritchardJ. K. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573–589 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 34.

    Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinforma. 15, 356 (2014).

    Google Scholar 

  • 35.

    Blischak, P. D., Chifman, J., Wolfe, A. D. & Kubatko, L. S. HyDe: a python package for genome-scale hybridization detection. Syst. Biol. 67, 821–829 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 36.

    Martin, S. H., Davey, J. W. & Jiggins, C. D. Evaluating the use of ABBA–BABA statistics to locate introgressed loci. Mol. Biol. Evol. 32, 244–257, https://doi.org/10.1093/molbev/msu269 (2015).

    CAS  Article  PubMed  Google Scholar 

  • 37.

    Kubatko, L. S. & Chifman, J. An invariants-based method for efficient identification of hybrid species from large-scale genomic data. BMC Evol. Biol. 19, 112–124 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 38.

    Schumer, M. et al. Natural selection interacts with recombination to shape the evolution of hybrid genomes. Science 360, 656–660 (2018).

    ADS  CAS  PubMed  PubMed Central  Google Scholar 

  • 39.

    Yeaman, S. & Whitlock, M. C. The genetic architecture of adaptation under migration–selection balance. Evolution 65, 1897–1911 (2011).

    PubMed  Google Scholar 

  • 40.

    Akerman, A. & Bürger, R. The consequences of gene flow for local adaptation and differentiation: a two-locus two-deme model. J. Math. Biol. 68, 1135–1198 (2014).

    MathSciNet  PubMed  MATH  Google Scholar 

  • 41.

    Kim, B. Y., Huber, C. D. & Lohmueller, K. E. Deleterious variation shapes the genomic landscape of introgression. PLoS Genet. 14, e1007741 (2018).

    PubMed  PubMed Central  Google Scholar 

  • 42.

    Lamichhaney, S. et al. Rapid hybrid speciation in Darwin’s finches. Science 359, 224–228 (2018).

    ADS  CAS  PubMed  Google Scholar 

  • 43.

    Aeschbacher, S., Selby, J. P., Willis, J. H. & Coop, G. Population-genomic inference of the strength and timing of selection against gene flow. PNAS 114, 7061–7066 (2017).

    CAS  PubMed  Google Scholar 

  • 44.

    Chan, A. H., Jenkins, P. A. & Song, Y. S. Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genet. 8, e1003090 (2012).

    PubMed  PubMed Central  Google Scholar 

  • 45.

    Kamm, J. A., Spence, J. P., Chan, J. & Song, Y. S. Two-locus likelihoods under variable population size and fine-scale recombination rate estimation. Genetics 203, 1381 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 46.

    Martin, S., Davey, J., Salazar, C. & Jiggins, C. Recombination rate variation shapes barriers to introgression across butterfly genomes. PLoS Biol. 17, e2006288 (2019).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 47.

    Bouché, F., Lobet, G., Tocquin, P. & Périlleux, C. FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucleic Acids Res. 44, D1167–D1171 (2016).

    PubMed  Google Scholar 

  • 48.

    Jin, J. B. et al. The SUMO E3 ligase, AtSIZ1, regulates flowering by controlling a salicylic acid‐mediated floral promotion pathway and through affects on FLC chromatin structure. Plant J. 53, 530–540 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 49.

    Lu, F., Cui, X., Zhang, S., Liu, C. & Cao, X. JMJ14 is an H3K4 demethylase regulating flowering time in Arabidopsis. Cell Res. 20, 387–390 (2010).

    PubMed  Google Scholar 

  • 50.

    Jesús, M. et al. Speciation by hybridization in Heliconius butterflies. Nature 441, 868–871 (2006).

    Google Scholar 

  • 51.

    Berner, D. & Roesti, M. Genomics of adaptive divergence with chromosome‐scale heterogeneity in crossover rate. Mol. Ecol. 26, 6351–6369 (2017).

    CAS  PubMed  Google Scholar 

  • 52.

    Yeaman, S. & Whitlock, M. C. The genetic architecture of adaptation under migration-selection balance. Evolution 65, 1897–1911 (2011).

    PubMed  Google Scholar 

  • 53.

    Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 54.

    Moriya, Y., Itoh, M., Okuda, S., Yoshizawa, A. C. & Kanehisa, M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 35, W182–W185 (2007).

    PubMed  PubMed Central  Google Scholar 

  • 55.

    Li, H., Handsaker, B., Wysoker, A., Fennell, T. & Ruan, J. The sequence alignment-map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

  • 56.

    Kim, S. et al. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinforma. 12, 231 (2011).

    Google Scholar 

  • 57.

    Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 58.

    Hudson, R. R., Slatkin, M. & Maddison, W. P. Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583–589 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 59.

    Bhatia, G., Patterson, N., Sankararaman, S. & Price, A. L. Estimating and interpreting FST: the impact of rare variants. Genome Res. 23, 1514–1521 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 60.

    Wakeley, J. The variance of pairwise nucleotide differences in two populations with migration. Theor. Popul. Biol. 49, 39 (1996).

    CAS  PubMed  MATH  Google Scholar 

  • 61.

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

    PubMed  PubMed Central  Google Scholar 

  • 62.

    Excoffier, L. & Foll, M. Fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27, 1332–1334 (2011).

    CAS  PubMed  Google Scholar 

  • 63.

    Sun, Y. et al. Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai–Tibet Plateau: homoploid hybrid origin and Pleistocene expansion. Mol. Ecol. 23, 343–359 (2014).

    CAS  PubMed  Google Scholar 

  • 64.

    De La Torre, A. R., Li, Z., Van de Peer, Y. & Ingvarsson, P. K. Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. Mol. Biol. Evol. 34, 1363–1377 (2017).

    Google Scholar 

  • 65.

    Heng, L. & Richard, D. Inference of human population history from individual whole-genome sequences. Nature 475, 493 (2011).

    Google Scholar 

  • 66.

    Browning, S. R. & Browning, B. L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 67.

    Browning, B. L., Zhou, Y. & Browning, S. R. A one-penny imputed genome from next generation reference panels. Am. J. Hum. Genet. 103, 338–348 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 68.

    Sonal, S. et al. Stable recombination hotspots in birds. Science 350, 928–932 (2015).

    Google Scholar 

  • Source