Lotsy, J. P. Evolution by Means of Hybridization (Martinus Nijhoff, 1916).
Abbott, R. J. et al. Hybridization and speciation. J. Evol. Biol. 26, 229–246 (2013).
Google Scholar
Schumer, M., Rosenthal, G. G. & Andolfatto, P. How common is homoploid hybrid speciation? Evolution 68, 1553–1560 (2014).
Google Scholar
Payseur, B. A. & Rieseberg, L. H. A genomic perspective on hybridization and speciation. Mol. Ecol. 25, 2337–2360 (2016).
Google Scholar
Wang, Z. F. et al. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. Mol. Plant 14, 208–222 (2021).
Google Scholar
Müntzing, A. Outlines to a genetic monograph for the genus Galeopsis: with special reference to the nature and inheritance of partial sterility. Hereditas 13, 185–341 (1930).
Google Scholar
Schumer, M., Cui, R., Rosenthal, G. G. & Andolfatto, P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. Plos. Genet. 11, e1005041 (2015).
Google Scholar
Taylor, S. A. & Larson, E. L. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat. Ecol. Evol. 3, 170–177 (2019).
Google Scholar
Kong, S. & Kubatko, L. S. Comparative performance of popular methods for hybrid detection using genomic data. Syst. Biol. 70, 891–907 (2021).
Google Scholar
Goulet, B. E., Roda, F. & Hopkins, R. Hybridization in plants: old ideas, new techniques. Plant Physiol. 173, 65–78 (2016).
Google Scholar
Jiang, Y. F. et al. Differentiating homoploid hybridization from ancestral subdivision in evaluating the origin of the D lineage in wheat. N. Phytol. 228, 409–414 (2020).
Google Scholar
Rokas, A. & Holland, P. Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15, 454–459 (2000).
Google Scholar
Bapteste, E. & Philippe, H. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol. Biol. Evol. 19, 972–977 (2002).
Google Scholar
Mavárez, J. et al. Speciation by hybridization in Heliconius butterflies. Nature 441, 868–871 (2006).
Google Scholar
Lamichhaney, S. et al. Rapid hybrid speciation in Darwin’s finches. Science 359, 224–228 (2018).
Google Scholar
Zhang, B. W. et al. Phylogenomics reveals an ancient hybrid origin of the Persian walnut. Mol. Biol. Evol. 36, 2451–2461 (2019).
Google Scholar
Guo, X., Thomas, D. C. & Saunders, R. M. K. Gene tree discordance and coalescent methods support ancient intergeneric hybridisation between Dasymaschalon and Friesodielsia (Annonaceae). Mol. Phylogenet. Evol. 127, 14–29 (2018).
Google Scholar
Winkler, H. Betulaceae. In: Pflanzenreich IV (Verlag von Wilhelm Engelmann, 1904).
Li, P. Q. & Skvortsov, A. K. Betulaceae. In: Flora of China (Science Press & Missouri Botanical Garden Press, 1999).
Crane, P. R. Betulaceous leaves and fruits from the British Upper Palaeocene. Bot. J. Linn. Soc. 83, 103–136 (1981).
Google Scholar
Li, P. Q. & Cheng, S. X. Betulaceae. In: Flora Reipublicae Popularis Sinicae (Science Press, 1979).
Yoo, K. O. & Wen, J. Phylogeny and biogeography of Carpinus and subfamily Coryloideae (Betulaceae). Int. J. Plant Sci. 163, 641–650 (2002).
Google Scholar
Li, J. H. Sequences of low-copy nuclear gene support the monophyly of Ostrya and paraphyly of Carpinus (Betulaceae). J. Sys. Evol. 46, 333–340 (2008).
Yang, X. Y. et al. Plastomes of Betulaceae and phylogenetic implications. J. Sys. Evol. 57, 508–518 (2019).
Google Scholar
Yang, Y. Z. et al. Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana. Nat. Commun. 9, 5449 (2018).
Google Scholar
Yang, X. Y. et al. A chromosome-level reference genome of the hornbeam, Carpinus fangiana. Sci. Data 7, 24 (2020).
Google Scholar
Li, Y. et al. The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding. Hortic. Res. 8, 54 (2021).
Google Scholar
Salojärvi, J. et al. Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat. Genet. 49, 904–912 (2017).
Google Scholar
Tajima, F. Evolutionary relationship of DNA-sequences in finite populations. Genetics 105, 437–460 (1983).
Google Scholar
Durand, E. Y., Patterson, N., Reich, D. & Slatkin, M. Testing for ancient admixture between closely related populations. Mol. Biol. Evol. 28, 2239–2252 (2011).
Google Scholar
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).
Google Scholar
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 (2019).
Google Scholar
Baack, E., Melo, M. C., Rieseberg, L. H. & Ortiz-Barrientos, D. The origins of reproductive isolation in plants. N. Phytol. 207, 968–984 (2015).
Google Scholar
Sobel, J. M. & Chen, G. F. Unification of methods for estimating the strength of reproductive isolation. Evolution 68, 1511–1522 (2014).
Google Scholar
Imura, Y. et al. CRYPTIC PRECOCIOUS/MED12 is a novel flowering regulator with multiple target steps in Arabidopsis. Plant Cell Physiol. 53, 287–303 (2012).
Google Scholar
Kim, S.-J. & Bassham, D. C. TNO1 is involved in salt tolerance and vacuolar trafficking in Arabidopsis. Plant Physiol. 156, 514–526 (2011).
Google Scholar
Zhang, F. et al. Control of leaf blade outgrowth and floral organ development by LEUNIG, ANGUSTIFOLIA3 and WOX transcriptional regulators. N. Phytol. 223, 2024–2038 (2019).
Google Scholar
Liu, Z. C., Franks, R. G. & Klink, V. P. Regulation of gynoecium marginal tissue formation by LEUNIG and AINTEGUMENTA. Plant Cell 12, 1879–1891 (2000).
Google Scholar
Sitaraman, J., Bui, M. & Liu, Z. LEUNIG_HOMOLOG and LEUNIG perform partially redundant functions during Arabidopsis embryo and floral development. Plant Physiol. 147, 672–681 (2008).
Google Scholar
Chen, C. L. et al. Phylotranscriptomics reveals extensive gene duplication in the subtribe Gentianinae (Gentianaceae). J. Sys. Evol. 59, 1198–1208 (2021).
Google Scholar
Morales-Briones, D. F. et al. Disentangling sources of gene tree discordance in phylogenomic data sets: testing ancient hybridizations in Amaranthaceae s.l. Syst. Biol. 70, 219–235 (2021).
Google Scholar
Yang, Y. Z. et al. Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nat. Plants 6, 215–222 (2020).
Google Scholar
Stull, G. W. et al. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. Nat. Plants 7, 1015–1025 (2021).
Google Scholar
Luo, X. et al. Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor. Mol. Ecol. 26, 3037–3049 (2017).
Google Scholar
Grover, C. E. et al. Re-evaluating the phylogeny of allopolyploid Gossypium L. Mol. Phylogenet. Evol. 92, 45–52 (2015).
Google Scholar
Edger, P. P., McKain, M. R., Bird, K. A. & VanBuren, R. Subgenome assignment in allopolyploids: challenges and future directions. Curr. Opin. Plant Biol. 42, 76–80 (2018).
Google Scholar
Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small amounts of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. Plos ONE 9, e112963 (2014).
Google Scholar
Servant, N. et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 16, 259 (2015).
Google Scholar
Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).
Google Scholar
Chen, N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinf. 5, 4.10.1–4.10.14 (2004).
Google Scholar
Haas, B. J. et al. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).
Google Scholar
Stanke, M. et al. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, W435–W439 (2006).
Google Scholar
Birney, E., Clamp, M. & Durbin, R. GeneWise and genomewise. Genome Res. 14, 988–995 (2004).
Google Scholar
Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).
Google Scholar
Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28, 45–48 (2000).
Google Scholar
Marchler-Bauer, A. et al. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 39, D225–D229 (2011).
Google Scholar
Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211–D215 (2009).
Google Scholar
Conesa, A. & Götz, S. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008, 619832 (2008).
Google Scholar
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).
Google Scholar
Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).
Google Scholar
Ye, G. et al. De novo genome assembly of the stress tolerant forest species Casuarina equisetifolia provides insight into secondary growth. Plant J. 97, 779–794 (2019).
Google Scholar
Marrano, A. et al. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. GigaScience 9, giaa050 (2020).
Google Scholar
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
Google Scholar
Löytynoja, A. Phylogeny-aware alignment with PRANK. In: Multiple Sequence Alignment Methods, Methods in Molecular Biology (Humana Press, 2014).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Google Scholar
Wang, Y. P. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012).
Google Scholar
Kielbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487–493 (2011).
Google Scholar
Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19, 153 (2018).
Google Scholar
Sukumaran, J. & Holder, M. T. DendroPy: a Python library for phylogenetic computing. Bioinformatics 26, 1569–1571 (2010).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Google Scholar
Malinsky, M., Matschiner, M. & Svardal, H. Dsuite—Fast D-statistics and related admixture evidence from VCF files. Mol. Ecol. Resour. 21, 584–595 (2021).
Google Scholar
Hudson, R. R., Kreitman, M. & Aguadé, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153–159 (1987).
Google Scholar
Source: Ecology - nature.com
