Rapid homoploid hybrid speciation in British gardens: The origin of Oxford ragwort (Senecio squalidus)
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Hybridisation can lead to homoploid hybrid speciation, i.e., the origin of new species without change in chromosome number between parents and offspring. Central to homoploid hybrid speciation is the role of hybridisation in the establishment of reproductive isolation between the hybrid and the parental species in the early stages of speciation, when typically all species occur at least partly in sympatry. In this work we analyse genome‐wide polymorphism data obtained by transcriptome sequencing of the British hybrid species Oxford ragwort (Senecio squalidus,Asteraceae), its two Italian parental species (S. aethnensis and S. chrysanthemifolius)and their naturally occurring hybrids on Mt Etna (Italy). We show that Oxford ragwort most likely originated from de novo hybridisation between its two Italian parental species whilst they were in cultivation in British gardens at the turn of the 18th century. Reproductive isolation between the new hybrid species and its parental species probably resulted from inheritance of genetic incompatibilities between the two parental species and subsequent ecological segregation – both of which have been shown in previous studies. Our results imply that S. squalidus meets the most stringent criteria set forth to identify homoploid hybrid speciation, and call attention to the creative role of hybridisation in responding to novel environmental conditions.
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Other examples come from studies of adaptive introgression or homoploid hybrid speciation, in which alleles or SVs critical to RI have been identified in parental populations.
“Other examples come from studies of adaptive introgression or homoploid hybrid speciation (see Speciation with gene flow, introgression, and hybrid speciation), in which alleles or SVs critical to RI have been identified in parental populations (Nevado et al., 2020; Todesco et al., 2020; Wang et al., 2021b).”
From Genomics of plant speciation (2023) · cites this paper as Nevado et al., 2020
The Introduction and Discussion (§4.2; page numbers unavailable) support Oxford ragwort as an example of homoploid hybrid speciation and discuss inherited genetic incompatibilities as a possible basis for reproductive isolation. But §4.2 explicitly says this study does not address the mechanism of isolation; it does not identify particular alleles or structural variants critical to it in the parental populations. (LLM, conf=0.88)
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607 · see citing works
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895 · see citing works
genepop ’007: a complete re‐implementation of the genepop software for Windows and Linux
Rousset, F. (2007) · Molecular Ecology Resources · doi:10.1111/j.1471-8286.2007.01931.x · Cited by 8,514 · see citing works
Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., et al. (2013) · Nature Protocols · doi:10.1038/nprot.2013.084 · Cited by 8,464 · see citing works
adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
Jombart, T., & Ahmed, I. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr521 · Cited by 3,233 · see citing works
Approximate Bayesian computation in population genetics
Beaumont, M. A., Zhang, W., & Balding, D. J. (2002) · Genetics · doi:10.1093/genetics/162.4.2025 · Cited by 2,932 · see citing works
Self-citationGenerating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,397 · see citing works
Abbott, R., Albach, D., Ansell, S., Arntzen, J. W., Baird, S. J. E., Bierne, N., Boughman, J., Brelsford, A., Buerkle, C. A., Buggs, R., et al. (2013) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2012.02599.x · Cited by 2,194 · see citing works
Scheet, P. A., & Stephens, M. (2006) · The American Journal of Human Genetics · doi:10.1086/502802 · Cited by 1,949 · see citing works
Natural Hybridization and Evolution
Arnold, M. L. (1997) · doi:10.1093/oso/9780195099744.001.0001 · Cited by 1,819 · see citing works
Grant, V. (1981) · Columbia University Press eBooks · doi:10.7312/gran92318 · Cited by 1,765 · see citing works
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
Raj, A., Stephens, M., & Pritchard, J. K. (2014) · Genetics · doi:10.1534/genetics.114.164350 · Cited by 1,666 · see citing works
Major Ecological Transitions in Wild Sunflowers Facilitated by Hybridization
Rieseberg, L. H., Raymond, O., Rosenthal, D. M., Lai, Z., Livingstone, K. D., Nakazato, T., Durphy, J. L., Schwarzbach, A. E., Donovan, L. A., & Lexer, C. (2003) · Science · doi:10.1126/science.1086949 · Cited by 1,247 · see citing works
Hybrid origins of plant species
Rieseberg, L. H. (1997) · Annual Review of Ecology and Systematics · doi:10.1146/annurev.ecolsys.28.1.359 · Cited by 1,246 · see citing works
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors
Bryant, D. M., Johnson, K. A., DiTommaso, T., Tickle, T. L., Couger, M. B., Payzin‐Dogru, D., Lee, T. J., Leigh, N. D., Kuo, T., Davis, F. G., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2016.12.063 · Cited by 958 · see citing works
abc: an R package for approximate Bayesian computation (ABC)
Csilléry, K., François, O., & Blum, M. G. B. (2012) · Methods in Ecology and Evolution · doi:10.1111/j.2041-210x.2011.00179.x · Cited by 709 · see citing works
Hybrid Zones and the Genetic Architecture of a Barrier to Gene Flow Between Two Sunflower Species
Rieseberg, L. H., Whitton, J., & Gardner, K. A. (1999) · Genetics · doi:10.1093/genetics/152.2.713 · Cited by 600 · see citing works
Speciation by hybridization in Heliconius butterflies
Mavárez, J., Salazar, C. A., Bermingham, E., Salcedo, C., Jiggins, C. D., & Linares, M. (2006) · Nature · doi:10.1038/nature04738 · Cited by 454 · see citing works
Role of Gene Interactions in Hybrid Speciation: Evidence from Ancient and Experimental Hybrids
Rieseberg, L. H., Sinervo, B., Linder, C. R., Ungerer, M. C., & Arias, D. M. (1996) · Science · doi:10.1126/science.272.5262.741 · Cited by 434 · see citing works
Reliable ABC model choice via random forests
Pudlo, P., Marin, J., Estoup, A., Cornuet, J., Gautier, M., & Robert, C. P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv684 · Cited by 387 · see citing works
The Ecological Genetics of Homoploid Hybrid Speciation
Gross, B. L., & Rieseberg, L. H. (2004) · Journal of Heredity · doi:10.1093/jhered/esi026 · Cited by 385 · see citing works
Hybrid speciation accompanied by genomic reorganization in wild sunflowers
Rieseberg, L. H., Fossen, C. V., & Desrochers, A. M. (1995) · Nature · doi:10.1038/375313a0 · Cited by 375 · see citing works
HOW COMMON IS HOMOPLOID HYBRID SPECIATION?: PERSPECTIVE
Schumer, M., Rosenthal, G. G., & Andolfatto, P. (2014) · Evolution · doi:10.1111/evo.12399 · Cited by 360 · see citing works
Lack of confidence in approximate Bayesian computation model choice
Robert, C. P., Cornuet, J.-M., Marin, J.-M., & Pillai, N. S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1102900108 · Cited by 317 · see citing works
Understanding the onset of hybrid speciation
Nolte, A. W., & Tautz, D. (2010) · Trends in Genetics · doi:10.1016/j.tig.2009.12.001 · Cited by 239 · see citing works
Yakimowski, S. B., & Rieseberg, L. H. (2014) · American Journal of Botany · doi:10.3732/ajb.1400201 · Cited by 219 · see citing works
Lai, Z., Nakazato, T., Salmaso, M., Burke, J. M., Tang, S., Knapp, S. J., & Rieseberg, L. H. (2005) · Genetics · doi:10.1534/genetics.105.042242 · Cited by 217 · see citing works
Rapid hybrid speciation in wild sunflowers
Ungerer, M. C., Baird, S. J. E., Pan, J. J., & Rieseberg, L. H. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.20.11757 · Cited by 217 · see citing works
Doorduin, L. J., Gravendeel, B., Lammers, Y., et al. (2011) · DNA Research · doi:10.1093/dnares/dsr002 · Cited by 203 · see citing works
Flora of Great Britain and Ireland
Sell, P. D., Murrell, G., & Walters, S. M. (2006) · Cambridge University Press eBooks · doi:10.1017/cbo9780511541841 · Cited by 180 · see citing works
James, J. K., & Abbott, R. J. (2005) · Evolution · doi:10.1111/j.0014-3820.2005.tb00967.x · Cited by 161 · see citing works
The genomic mosaicism of hybrid speciation
Elgvin, T. O., Trier, C. N., Tørresen, O. K., Hagen, I. J., Lien, S., Nederbragt, A. J., Ravinet, M., Jensen, H., & Sætre, G. (2017) · Science Advances · doi:10.1126/sciadv.1602996 · Cited by 148 · see citing works
Altitudinal gradients, plant hybrid zones and evolutionary novelty
Abbott, R. J., & Brennan, A. C. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0346 · Cited by 111 · see citing works
Genomic Divergence during Speciation Driven by Adaptation to Altitude
Chapman, M. A., Hiscock, S. J., & Filatov, D. A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst168 · Cited by 104 · see citing works
Self-citationCROSSING RELATIONSHIPS AMONG ANCIENT AND EXPERIMENTAL SUNFLOWER HYBRID LINEAGES
Rieseberg, L. H. (2000) · Evolution · doi:10.1111/j.0014-3820.2000.tb00086.x · Cited by 88 · see citing works
Abbott, R. J., Brennan, A. C., James, J. K., et al. (2008) · Biological Invasions · doi:10.1007/s10530-008-9382-3 · Cited by 82 · see citing works
Self-incompatibility in Senecio squalidus L. (Asteraceae)
Hiscock, S. J. (2000) · Annals of Botany · doi:10.1006/anbo.1999.1058 · Cited by 78 · see citing works
Self-citationHYBRID SPECIATION IN WILD SUNFLOWERS1
Rieseberg, L. H. (2006) · Annals of the Missouri Botanical Garden · doi:10.3417/0026-6493(2006)93[34:hsiws]2.0.co;2 · Cited by 70 · see citing works
Hybrid origin of the Oxford Ragwort Senecio squalidus L
Abbott, R. J., James, J., Irwin, J. A., et al. (2000) · New Journal of Botany · Cited by 61 · see citing works
Extreme changes to gene expression associated with homoploid hybrid speciation
Hegarty, M., Barker, G., Brennan, A. C., Edwards, K. J., Abbott, R. J., & Hiscock, S. J. (2009) · Molecular Ecology · doi:10.1111/j.1365-294x.2008.04054.x · Cited by 57 · see citing works
Self-citationDetermining epistatic selection in admixed populations
Schumer, M., & Brandvain, Y. (2016) · Molecular Ecology · doi:10.1111/mec.13641 · Cited by 57 · see citing works
Outcrossing rate and self-incompatibility in the colonizing species Senecio squalidus
Abbott, R. J., & Forbes, D. G. (1993) · Heredity · doi:10.1038/hdy.1993.119 · Cited by 51 · see citing works
Introduction of Oxford ragwort, Senecio squalidus L. (Asteraceae), to the United Kingdom
Harris, S. A. (2002) · Cited by 50 · see citing works
Self-citationBrennan, A. C., Barker, D., Hiscock, S. J., & Abbott, R. J. (2011) · Heredity · doi:10.1038/hdy.2011.46 · Cited by 48 · see citing works
Self-citationRapid Speciation with Gene Flow Following the Formation of Mt. Etna
Osborne, O. G., Batstone, T., Hiscock, S. J., & Filatov, D. A. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt127 · Cited by 45 · see citing works
Self-citationChapman, M. A., Hiscock, S. J., & Filatov, D. A. (2015) · Journal of Evolutionary Biology · doi:10.1111/jeb.12765 · Cited by 37 · see citing works
Self-citationCytotaxonomic studies in the section annui of Senecio
Crisp, P. (1972) · OpenGrey (Institut de l'Information Scientifique et Technique) · Cited by 37 · see citing works
Brennan, A. C., Hiscock, S. J., & Abbott, R. J. (2014) · Heredity · doi:10.1038/hdy.2014.14 · Cited by 36 · see citing works
Self-citationBrennan, A. C., Hiscock, S. J., & Abbott, R. J. (2019) · AoB Plants · doi:10.1093/aobpla/ply078 · Cited by 27 · see citing works
Self-citationBrennan, A. C., Harris, S. A., & Hiscock, S. J. (2012) · Evolution · doi:10.1111/evo.12033 · Cited by 20 · see citing works
Self-citationWong, E. L. Y., Nevado, B., Osborne, O. G., Papadopulos, A. S. T., Bridle, J. R., Hiscock, S. J., & Filatov, D. A. (2019) · Molecular Ecology · doi:10.1111/mec.15319 · Cited by 15 · see citing works
Self-citationCROSSING RELATIONSHIPS AMONG ANCIENT AND EXPERIMENTAL SUNFLOWER HYBRID LINEAGES
Rieseberg, L. H. (2000) · Evolution · doi:10.1554/0014-3820(2000)054[0859:craaae]2.3.co;2 · Cited by 9 · see citing works
Barbero (2014) · doi:10.1016/j · Cited by 1 · see citing works
Flagged first, then by citations
Research works printed but not linked: 5
- [21]21. Druce, G. C. (1927). The flora of Oxfordshire (2nd ed.). Clarendon Press.
- [25]25. Haas, B. J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P. D., Bowden, J., Couger, M. B., Eccles, D., Li, B., Lieber, M., & Regev, A. (2013). De novo transcript sequence reconstruction from RNA-Seq: Reference generation and analysis with Trinity. Nature Protocols, 8(8). https://doi.org/10.1038/nprot.2013.1084 · DOI
- [32]32. Kent, D. H. (1956). Senecio squalidus L. in the British Isles. 1. Early records (to 1877). Proceedings of the Botanical Society of the British Isles, 2, 115-118.
- [33]33. Kent, D. H. (1960). Senecio squalidus L. in the British Isles. 2. The spread from Oxford (1879-1939). Proceedings of the Botanical Society of the British Isles, 3, 375-379.
- [52]52. Ross, R. I. C. (2010). Local adaptation and adaptive divergence in a hybrid species complex in Senecio. Doctor of Philosophy PhD, University of Oxford.
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Bock, D. G., Cai, Z., Elphinstone, C., González-Segovia, E., Hirabayashi, K., Huang, K., Keais, G. L., Kim, A., Owens, G. L., & Rieseberg, L. H. (2023) · Plant Communications · doi:10.1016/j.xplc.2023.100599 · Cited by 84 · see citing works
“…genomic studies have confirmed the hybrid origin of the Oxford ragwort (Senecio squalidus) from the two Senecio species on Mt. Etna described above (Nevado et al., 2020), identified several potential new cases of homoploid hybrid speciation (e.g., Gr€unig et al., 2021; Wang et al., 2021b; Wang et…”
Influential
- Authors
- Nevado, B., Harris, S. A., Beaumont, M. A., & Hiscock, S. J.
- Affiliations
- University of Oxford (GB)
- University of Bristol (GB)
- Corresponding author
- Nevado, Bruno
- Venue
- Molecular Ecology
- Publisher
- Wiley
- Published
- 2020-09-26
- Volume
- 29
- Issue
- 21
- Pages
- 4221-4233
- ISSN
- 0962-1083 (ISSN-L)
- 1365-294X
- OpenAlex
- W3086640053
- Semantic Scholar
- c1fd546f14932fe41e49af83d601750eb76b17c4
- Cited by
- 26
- References
- 54
- Citations by year
- 2025: 7 · 2024: 4 · 2023: 6 · 2022: 6 · 2021: 2 · 2020: 1
- FWCI
- 2.42
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Ecology (publishedVersion)
- PubMed (publishedVersion)
- Explore Bristol Research (publishedVersion)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
- Bristol Research (University of Bristol) (submittedVersion)
- Funders
- John Fell Fund, University of Oxford (162/091)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Taxonomy and Phylogenetics
- Keywords
- homoploid hybrid speciation, Senecio squalidus, hybridization, reproductive isolation, genetic incompatibility, ecological segregation, garden plants, Mount Etna, Asteraceae, genome-wide polymorphism
- MeSH terms
- Gardens, Hybridization, Genetic, Italy, Senecio, Genetic Speciation
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