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
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
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
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. in press
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
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.
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 in press
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
This paper is the first report of the sequencing of a birch tree genome, and the testing of restriction site associated DNA markers in birch. The dwarf birch (Betula nana) genome is composed of 450 million bases. We sequenced it using Illumina technology. This generated millions of short DNA reads in pairs separated by gaps of various lengths. Enough DNA was sequenced to cover the genome sixty-six times. This data set was assembled on high performance computers at Queen Mary University of London. Restriction site associated DNA (RAD) markers were developed in collaboration with scientists at the University of Edinburgh. These allowed us to examine thousands of sites in the genome of different trees, both in dwarf birch and downy birch (Betula pubescens).
23. Richard J. A. Buggs. (2012) Perspective: Monkeying around with ploidy. Molecular Ecology 21: 5159-5161
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
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
This paper contains the first test in a young polyploid of the gene-dosage hypothesis for the loss/retention of duplicated genes, with the surprising finding that even in 40 generations of evolution patterns of gene loss can be to some extent predicted, and seem to fit with patterns seen in putative ancient polyploids. Repeated patterns of duplicated-gene loss were also found among independently formed populations of the new allopolyploid species Tragopogon miscellus.
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
This paper forms part of a special issue of American Journal of Botany on “Methods and applications of next-generation sequencing in botany”. In it, the authors review recent work in our labs on genome evolution in Tragopogon and Nicotiana allopolyploids, including work on duplicated gene loss, changes in repetitive element composition, chromosome structural changes and changes to gene expression. This work was done using Illumina and 454 sequencing technologies and the Sequenom MassArray platform.
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
We discovered that tissue-specific gene expression in diploid parents is relaxed upon hybridization but re-emerges in the early generations of allopolyploidy; this fits with new hypotheses about the effects of hybridisation on small-RNA-mediated regulation of gene expression.
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
This study, which started as an undergraduate project by Natalie Elliott, provides new insights into polyploid evolution as one of the first studies to: distinguish between homeologs and among tissues, examine young naturally occurring polyploids, and examine patterns of expression in ancestral diploid species found in the same location.
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
This study explored new methods for investigating allopolyploid genome evolution. A review in Philosophical Transactions of the Royal Society, cited this paper in this sentence: “First studies exploring the potential of RNAseq in non-model organisms…are promising and document the dawning of an era where high-resolution transcript-profiling in non-model organisms will become commonplace”.
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
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
This paper documents the rapid loss of duplicated genes in the plant species Tragopogon miscellus (see publication 9 below). A good summary of our results and their implications, written by other scientists in the field, can be found here.
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
Plant species Tragopogon miscellus and T, mirus are classic examples of recent allopolyploidization. They formed about 80 years ago in the northwestern United States, through hybridization between the introduced speces T. dubius and T. pratensis. Genome duplication made them unable to interbreed with their parental species and hence new species. This paper reports the re-synthesis of both species in the greenhouses of the University of Florida.
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
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 annua? Biological Journal of the Linnean
Society 82 (4): 547-560