Academic publications

74. Rowena Hill, Quentin Levicky, Frances Pitsillides, Amy Junnonen, Elena Arrigoni, J Miguel Bonnin, Anthony Kermode, Sahr Mian, Ilia J Leitch, Alan G Buddie, Richard J. A. Buggs, Ester Gaya (2023) Tapping culture collections for fungal endophytes: first genome assemblies for three genera and five species in the Ascomycota. Genome Biology and Evolution Full text

73. Richard J. A. Buggs (2022) The challenge of demonstrating contemporary natural selection on polygenic quantitative traits in the wild. Molecular Ecology 31(24):6383-6386 Full Text

72. Oliver White, Manosh Biswas, Wendawek M. Abebe, Yann Dussert, Firew Kebede, Richard Nichols, Richard J. A. Buggs, Sebsebe Demissew, Feleke Woldeyes, Alexander S.T. Papadopulos, Trude Schwarzacher, Pat J.S. Heslop-Harrison, Paul Wilkin, James S. Borrell (2022) Maintenance and expansion of genetic and trait variation following domestication in a clonal crop EcoEvoRxiv Full text

71. Carey L. Metheringham, William J. Plumb, Jonathan J. Stocks, Laura J. Kelly, Miguel Nemesio Gorriz, Justin Moat, Richard J. A. Buggs, Richard A. Nichols (2022) Rapid polygenic adaptation in a wild population of ash trees under a novel fungal epidemic bioRxiv Full text

70. Gabriele Nocchi, Jing Wang, Long Yang, Junyi Ding, Ying Gao, Richard J. A. Buggs, Nian Wang (2023) Genomic signals of local adaptation and hybridization in Asian white birch. Molecular Ecology 32(3): 595-612 Full Text

69. Chris Rampersad, Tesfu Geto, Tarekegn Samuel, Meseret Abebe, Marybel Soto Gomez, Samuel Pironon, Lucie Büchi, Jeremy Haggar, Jonathan Stocks, Philippa Ryan, Richard Buggs, Sebsebe Demissew, Paul Wilkin, Wendawek M. Abebe, James S. Borrell (2022) Introduced crops supplement rather than replace indigenous crops in an African center of agrobiodiversity bioRxiv Full Text

68. Rowena Hill, Richard J.A. Buggs, Dang Toan Vu, and Ester Gaya (2022) Lifestyle transitions in Fusarioid fungi are frequent and lack clear genomic signatures. Molecular Biology and Evolution, 39(4): msac085. Full text

67. Richard J. A. Buggs (2022) Reconfiguring Darwin’s abominable mystery. Nature Plants, 8:194–195 . Full text

66. Louise A. P. Gathercole, Gabriele Nocchi, Nathan Brown, Timothy L. R. Coker, William J. Plumb, Jonathan J. Stocks, Richard A. Nichols, Sandra Denman, and Richard J. A. Buggs (2021) Evidence for the Widespread Occurrence of Bacteria Implicated in Acute Oak Decline from Incidental Genetic Sampling. Forests 12: 1683. Full Text

65. Federico Rossi, Alessandro Crnjar, Federico Comitani, Rodrigo Feliciano, Leonie Jahn, George Malim, Laura Southgate, Emily Kay, Rebecca Oakey, Richard J. A. Buggs, Andy Moir, Logan Kistler, Ana Rodriguez Mateos, Carla Molteni, and Reiner Schulz (2021) Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling. PLoS ONE 16(11): e0254971. Full Text

64. Matt Huff, Josiah Seaman, Di Wu, Tetyana Zhebentyayeva, Laura J. Kelly, Nurul Faridi, Charles Dana Nelson ,Endymion Cooper, Teodora Best, Kim Steiner, Jennifer Koch, Jeanne Romero Severson, John E. Carlson, Richard J. A. Buggs and Margaret Staton (2022) A high quality reference genome for Fraxinus pennsylvanica for ash species restoration and research. Molecular Ecology Resources 22(4): 1284-1302 Full text

63. Carly Cowell, Alan Paton, James S. Borrell, China Williams, Paul Wilkin, Alexandre Antonelli, William J. Baker, Richard J. A. Buggs, Michael F. Fay, Roberta Gargiulo, Olwen M. Grace, Benedikt G. Kuhnhäuser, Yannick Woudstra and Paul J. Kersey (2021) Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections. Plants, People, Planet 4(1):33-43 Full text

62. Gabriele Nocchi, Nathan Brown, Timothy L. R. Coker, William J. Plumb, Jonathan J. Stocks, Sandra Denman and Richard J. A. Buggs (2022) Genomic structure and diversity of oak populations in British parklands. Plants, People, Planet 4(2): 167-181 Full-text

61. Nihal Oztolan-Erol, Andrew J. Helmstetter, Asuman Inan, Richard J. A. Buggs and Stuart J. Lucas (2021) Unraveling genetic diversity amongst European Hazelnut (Corylus avellana L.) varieties in Turkey. Frontiers in Plant Science 12 Abstract

60. Nian Wang, Laura J. Kelly, Hugh A. McAllister, Jasmin Zohren, Richard J. A. Buggs (2021) Resolving phylogeny and polyploid parentage using genus-wide genome-wide sequence data from birch trees. Molecular Phylogenetics and Evolution 160: 107126 Full text

59. Richard J. A. Buggs (2021) The origin of Darwin’s “abominable mystery”. American Journal of Botany 108(1): 22-36 Abstract Full Text

58. Junyi Ding, Donglai Hua, James S. Borrell, Richard J. A. Buggs, Luwei Wang, Feifei Wang, Zheng Li and Nian Wang (2021) Introgression between Betula tianshanica and Betula microphylla and its implications for conservation. Plants, People, Planet 3(4): 363-374 Full text

57. Richard J. A. Buggs (2020) The origin of novel genes. Inference 5 (3) Full text

56. Laura J. Kelly, William J. Plumb, David W. Carey, Mary E. Mason, Endymion D. Cooper, William Crowther, Alan T. Whittemore, Stephen J. Rossiter, Jennifer L. Koch and Richard J. A. Buggs (2020) Convergent molecular evolution among ash species resistant to the emerald ash borer. Nature Ecology and Evolution 4: 1116-1128 Full text

55. Josiah Seaman and Richard J. A. Buggs (2020) FluentDNA: Nucleotide Visualization of Whole Genomes, Annotations, and Alignments. Frontiers in Genetics 11:292 Full text

54. Richard J. A. Buggs (2020) Editorial: Changing perceptions of tree resistance research. Plants People Planet 2(1): 2-4 Full text

53. Jonathan J. Stocks, Carey L. Metheringham, William Plumb, Steve J. Lee, Laura J. Kelly, Richard A. Nichols and Richard J. A. Buggs (2019) Genomic basis of European ash tree resistance to ash dieback fungus. Nature Ecology & Evolution 3: 1686–1696 Full text

52. David N. Showalter, Robert J. Saville, Elizabeth S. Orton, Richard J. A. Buggs, Pierluigi Bonello and James K. M. Brown (2020) Resistance of European ash (Fraxinus excelsior) saplings to larval feeding by the emerald ash borer (Agrilus planipennis) Plants People Planet 2(1):41-46 Full text

51. Stuart J. Lucas, Kadriye Kahraman, Bihter Avşar, Richard J. A. Buggs, Ipek Bilge (2020). A chromosome-scale genome assembly of European Hazel (Corylus avellana L.) reveals targets for crop improvement. The Plant Journal Full text

50. Andrew J. Helmstetter, Richard J. A. Buggs, Stuart J. Lucas (2019). Repeated long-distance dispersal and convergent evolution in hazel Scientific Reports 9: 16016 Full text

49. James S. Borrell, Jasmin Zohren, Richard A. Nichols, Richard J. A. Buggs (2020). Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow Evolutionary Applications 31(1): 161-175 Full text

48. Andrew J. Helmstetter, Nihal Oztolan-Erol, Stuart J. Lucas and Richard J. A. Buggs (2020). Genetic diversity and domestication of hazelnut (Corylus avellana L.) in Turkey. Plants People Planet Full text

47. William J. Plumb, Timothy L. R. Coker, Jonathan J. Stocks, Paul Woodcock, Christopher P. Quine, Miguel Nemesio‐Gorriz, Gerry C. Douglas, Laura J. Kelly and Richard J. A. Buggs (2020). The viability of a breeding programme for ash in the British Isles in the face of ash dieback. Plants People Planet 2(1): 29-40 Full text

46. Yanan Hu, Lei Zhao, Richard J. A. Buggs, Xuemin Zhang, Jun Li and Nian Wang (2019). Population structure of Betula albosinensis and Betula platyphylla: evidence for hybridization and a cryptic lineage. Annals of Botany 123(7):1179-1189 Full text

45. Tim L. R. Coker, Jiří Rozsypálek, Anne Edwards, Tony P. Harwood, Louise A. Butfoy and Richard J. A. Buggs (2018). Estimating mortality rates of European ash (Fraxinus excelsior) under the ash dieback (Hymenoscyphus fraxineus) epidemic. Plants People Planet 1:48-58
Full text

44. Maryam Rafiqi, Diane Saunders, Mark McMullan, Richard Oliver, Ruth Bone, Helen Fones, Sarah Gurr, Delphine Vincent, Timothy Coker and Richard J. A. Buggs (2018). Plant-killers: Fungal threats to ecosystems. In: K. J. Willis (ed.), State of the World’s Fungi. Report. Royal Botanic Gardens, Kew. pp. 56–61.
Full text

43. James S. Borrell, Nian Wang, Richard A. Nichols and Richard J. A. Buggs (2018) Genetic diversity maintained among fragmented populations of a tree undergoing range contraction. Heredity 121:304–318
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42. Elizabeth S. A. Sollars and Richard J. A. Buggs (2018). Genome-wide epigenetic variation among ash trees differing in susceptibility to a fungal disease. BMC Genomics 19:502
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41. Christine M. Sambles, Deborah L. Salmon, Hannah Florance, Thomas P. Howard, Nicholas Smirnoff, Lene R. Nielsen, Lea V. McKinney, Erik D. Kjær, Richard J. A. Buggs David J. Studholme and Murray Grant (2017). Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease. Scientific Data 4: 170190
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40. Jonathan J. Stocks, Richard J. A. Buggs and Steve J. Lee (2017). A first assessment of Fraxinus excelsior (common ash) susceptibility to Hymenoscyphus fraxineus (ash dieback) throughout the British Isles. Scientific Reports 7: 16546
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39. Paul Woodcock, Joan E. Cottrell, Richard J. A. Buggs and Chris P. Quine (2017). Mitigating pest and pathogen impacts using resistant trees: a framework and overview to inform development and deployment in Europe and North America. Forestry 91(1):1-16
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38. Richard J. A. Buggs (2017) The deepening of Darwin’s abominable mystery. Nature Ecology & Evolution 1: 0169
Full text   Blog

37. Richard J. A. Buggs, Timothy L. R. Coker, Christopher Dennis, Don Walker, Julian Smith, David Mota-Sanchez and Matthew J.W. Cock (2017) Plant Health: State of Research. State of the World’s Plants 2017 pp. 64-71. Ed. Kathy J. Willis. Report. Royal Botanic Gardens Kew
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36. Elizabeth S. A. Sollars, Andrea L. Harper, Laura J. Kelly, Christine M. Sambles, Ricardo H. Ramirez-Gonzalez, David Swarbreck, Gemy Kaithakottil, Endymion D. Cooper, Cristobal Uauy, Lenka Havlickova, Gemma Worswick, David J. Studholme, Jasmin Zohren, Deborah L. Salmon, Bernardo J. Clavijo, Yi Li, Zhesi He, Alison Fellgett, Lea Vig McKinney, Lene Rostgaard Nielsen, Gerry C. Douglas, Erik Dahl Kjær, J. Allan Downie, David Boshier, Steve Lee, Jo Clark, Murray Grant, Ian Bancroft, Mario Caccamo and Richard J. A. Buggs (2017) Genome sequence and genetic diversity of European ash trees. Nature 541: 212–216
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35. Elizabeth S. A. Sollars and Richard J. A. Buggs (2016) Emerging genomics of Angiosperm trees, in Comparative and Evolutionary Genomics of Angiosperm Trees Eds. Quentin Cronk and Andrew Groover, Springer.
Full text

34. Jasmin Zohren, Nian Wang, Igor Kardailsky, James S. Borrell, Anika Joecker, Richard A. Nichols and Richard J. A. Buggs (2016) Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by RAD markers. Molecular Ecology 25: 2413–2426
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33. Paul A. Nelson and Richard J. A. Buggs (2016) Next-generation apomorphy: the ubiquity of taxonomically restricted genes, pp 237-264 in Next Generation Systematics Eds. Peter D. Olson, Joseph Hughes and James A. Cotton, Cambridge University Press.
Book   Chapter

32. Nian Wang, Hugh A. McAllister, Paul Bartlett and Richard J. A. Buggs (2016) Molecular phylogeny and genome sizes of the genus Betula L. (Betulaceae). Annals of Botany 117: 1023-1035

31. Andrea L. Harper, Lea Vig McKinney, Lene Rostgaard Nielsen, Lenka Havlickova, Yi Li, Martin Trick, Fiona Fraser, Lihong Wang, Alison Fellgett, Elizabeth S. A. Sollars, Sophie H. Janacek, J. Allan Downie, Richard. J. A. Buggs , Erik Dahl Kjær and Ian Bancroft. (2016) Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics. Scientific Reports 6, Article number: 19335

30. Andrew Matthews, Katie Emelianova, Abubakar A. Hatimy, Michael Chester, Jaume Pellicer, Khawaja Shafique Ahmad, Maité S. Guignard, Germinal Rouhan, Douglas E. Soltis, Pamela S. Soltis, Ilia J. Leitch, Andrew R. Leitch, Evgeny V. Mavrodiev and Richard J. A. Buggs. (2015) 250 years of hybridisation between two biennial herb species without speciation. AoB Plants 7: plv081

29. Mario Vallejo-Marin, Richard J. A. Buggs, Arielle Cooley and Joshua Puzey. (2015) Speciation by genome duplication: Repeated origins and genomic composition of the recently formed allopolyploid species Mimulus peregrinus. Evolution 69: 1487-1500

28. David Boshier and Richard J. A. Buggs. (2014) The potential for field studies and genomic technologies to enhance resistance and resilience of British tree populations to pests and pathogens. Forestry 88: 27-40

27. Nian Wang, James S. Borrell and Richard J. A. Buggs. (2014) Is the Atkinson discriminant function a reliable method for distinguishing between Betula pendula and B. pubescens? New Journal of Botany 4: 90-94

26. Nian Wang, James S. Borrell, William J. A. Bodles, Ana Kuttapitiya, Richard A. Nichols and Richard J. A. Buggs. (2014) Molecular footprints of the Holocene retreat of dwarf birch in Britain. Molecular Ecology 23: 2771-2782
Abstract   Press Release

25. Richard J. A. Buggs, Jonathan F. Wendel, Jeffrey J. Doyle, Douglas E. Soltis, Pamela S. Soltis and Jeremy Coate. (2014) The legacy of diploid progenitors in allopolyploid gene expression patterns. Philosophical Transactions of the Royal Society B 369

24. Nian Wang, Marian Thomson, William J. A. Bodles, Robert M. M. Crawford, Harriet V. Hunt, Alan Watson Featherstone, Jaume Pellicer and Richard J. A. Buggs. (2013) Genome sequence of dwarf birch (Betula nana) and cross-species RAD markers. Molecular Ecology 11: 3098-3111
Abstract   Press Release   Sunday Times    BBC

23. Richard J. A. Buggs. (2012) Perspective: Monkeying around with ploidy. Molecular Ecology 21: 5159-5161

22. Richard J. A. Buggs. (2013) Commentary: Unravelling gene expression of complex crop genomes. Heredity 110: 97–98
Abstract   PDF

21. The FroSpects Gregynog Workshop (Richard Abbott, Dirk Albach, Stephen Ansell, Jan Arntzen, Stuart J.E. Baird, Nicolas Bierne, Jenny Boughman, Alan Brelsford, C. Alex Buerkle, Richard Buggs, Roger Butlin, Ulf Dieckmann, Fabrice Eroukhmanoff, Andrea Grill, Sara Helms Cahan, Jo Skeie Hermansen, Godfrey Hewitt, Alan G. Hudson, Chris Jiggins, Julia Jones, Barbara Keller, Tobias Maczewski, Jim Mallet, Paloma Martinez-Rodriguez, Markus Möst, Sean Mullen, Richard Nichols, Arne W. Nolte, Christian Parisod, Karin Pfennig, Amber Rice, Michael G Ritchie, Bernhardt Seifert, Carole Smadja, Rike Stelkens, Jacek M. Szymura, Risto Väinölä, Jochen B. W. Wolf and Dietmar Zinner)(2013) Hybridization and speciation. Journal of Evolutionary Biology 26: 229-246
Abstract   PDF

20. Richard J. A. Buggs, Srikar Chamala, Wei Wu, Jennifer A. Tate, Patrick S. Schnable, Douglas E. Soltis, Pamela S. Soltis, W. Brad Barbazuk (2012) Rapid, repeated and clustered loss of duplicate genes in allopolyploid plant populations of independent origin. Current Biology 22: 248-252
Abstract   Press Release

19. Douglas E. Soltis, Richard J. A. Buggs, W. Brad Barbazuk, Srikar Chamala, Michael Chester, Joseph P. Gallagher, Patrick S. Schnable, Pamela S. Soltis (2012). Rapid and repeated evolution in the early stages of polyploidy: genomic and cytogenetic studies of recent polyploidy in Tragopogon. In: P. S. Soltis and D. E. Soltis (eds). Polyploidy and Genome Evolution. Springer. pp. 271-292

18. Richard J. A. Buggs, Simon Renny-Byfield, Michael Chester, Ingrid E. Jordan-Thaden, Lyderson F. Viccini, Srikar Chamala, Andrew R. Leitch, Patrick S. Schnable, W. Brad Barbazuk, Pamela S. Soltis and Douglas E. Soltis (2012) Next-generation sequencing and genome evolution in allopolyploids American Journal of Botany 99:372-382

17. Richard J. A. Buggs, Linjing Zhang, Nicholas Miles, Lu Gao, Wei Wu, Patrick S. Schnable, W. Brad Barbazuk, Pamela S. Soltis and Douglas E. Soltis (2011) Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant Current Biology 21:551-556
Abstract   Commentary   Press Release   ABC News

16. Richard J. A. Buggs, Pamela S. Soltis and Douglas E. Soltis (2011) Biosystematic relationships and the formation of polyploids Taxon 60:324-332

15. Douglas E. Soltis, Richard J. A. Buggs, Jeff J. Doyle and Pamela S. Soltis (2010) What we still don’t know about polyploidy Taxon 59: 1387-1403

14. Richard J. A. Buggs, Natalie M. Elliott, Linjing Zhang, Jin Koh, Lyderson F. Viccini, Douglas E. Soltis and Pamela S. Soltis (2010) Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus New Phytologist 186: 175-183
Abstract   PDF

13. Richard J. A. Buggs, Srikar Chamala, Wei Wu, Lu Gao, Gregory D. May, Patrick S. Schnable, Douglas E. Soltis, Pamela S. Soltis and W. Brad Barbazuk (2010) Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom MassARRAY genotyping Molecular Ecology 19 (Suppl. 1, Next Generation Molecular Ecology): 132-146
Abstract   PDF

12. Douglas E. Soltis, Richard J. A. Buggs, W. Brad Barbazuk, Patrick S. Schnable and Pamela S. Soltis (2009) On the origins of species: does evolution repeat itself in polyploid populations of independent Origin? Cold Spring Harbor Symposia on Quantitative Biology 74: 215-223

11. Richard J. A. Buggs, Pamela S. Soltis and Douglas E. Soltis (2009) Does hybridization between divergent progenitors drive whole-genome duplication? Molecular Ecology 18: 3334-3339
Abstract   PDF

10. Richard J. A. Buggs, Andrew N. Doust, Jennifer A. Tate, Jin Koh, Kerry Soltis, F. Alex Feltus, Andrew Paterson, Pamela S. Soltis and Douglas E. Soltis (2009) Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids. Heredity 103: 73-81
Abstract   PDF   Commentary

9. Jennifer A. Tate, V. Vaughan Symonds, Andrew N. Doust, Richard J. A. Buggs, Evgeny V. Mavrodiev, Lucas Majure, Pamela S.
Soltis and Douglas E. Soltis (2009) Synthetic polyploids of Tragopogon miscellus and T. mirus (Asteraceae): 60 years after Ownbey’s discovery. American Journal of Botany 96: 979-988

8. Richard J. A. Buggs, Pamela S.
Soltis, Evgeny V. Mavrodiev, V. Vaughan Symonds and Douglas E. Soltis (2008) Does phylogenetic distance between parental genomes govern the success of polyploids? Castanea 73:74-93
Abstract Full text   PDF

7. Richard J. A. Buggs. (2008) Perspective: Towards natural polyploid model organisms. Molecular Ecology 17:1875-1876
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6. Richard J. A. Buggs. (2007) Empirical study of hybrid zone movement. Heredity 99:301-312
Abstract PDF Supplementar data

Richard J. A. Buggs and John R. Pannell. (2007) Ecological differentiation and diploid superiority across a moving ploidy contact zone. Evolution 61 (1): 125-140
Abstract Full text   PDF

4. Darren J. Obbard, Stephen A. Harris, Richard J. A. Buggs and John R. Pannell. (2006) Hybridization and the evolution of sexual systems and polyploidy in Mercurialis (Euphorbiaceae). Evolution 60: 1801-1815

3. Richard J. A. Buggs and John R. Pannell. (2006) Rapid displacement of a monoecious plant lineage is due to pollen swamping by a dioecious relative. Current Biology 16: 996-1000
Abstract Full text   PDF Supplementary data    Commentary Press release

2. Matthew J. Hegarty, Joanna M. Jones, Ian D. Wilson, Gary L. Barker, Jane A. Coghill, Patricia Sanchez-Baracaldo, Guoqing Liu, Richard J. A. Buggs, Richard J. Abbott, Keith J. Edwards and Simon J. Hiscock. (2005) Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Molecular Ecology 14 (8): 2493-2510

1. John R. Pannell, Darren J. Obbard, Richard J. A. Buggs. (2004) Polyploidy and the sexual system: what can we learn from Mercurialis annuaBiological Journal of the Linnean Society 82 (4): 547-560