25. Richard J. A. Buggs, Jonathan F. Wendel, Jeffrey J. Doyle, Douglas E. Soltis, Pamela S. Soltis and Jeremy Coate (in press) The legacy of diploid progenitors in allopolyploid gene expression patterns. Philosophical Transactions of the Royal Society B
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
22. Richard J. A. Buggs. (2013) Commentary: Unravelling gene expression of complex crop genomes. Heredity 110: 97–98
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
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
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
The first in a series of special invited reviews published by the journal of the Southern Appalacian Botanical Society. This study tests an long-standing hypothesis: that polyploids are less likely to form if their parents are very closely related, compared to when they are the products of hybridisation between more distant species. Using molecular phylogenies from several genera, we found no overall support for the hypothesis. We argue that this fits well with current theory. Several other groups have recently become interested in this issue, so this is unlikely to be the last word on the topic!
7. Richard J. A. Buggs. (2008) Perspective: Towards natural polyploid model organisms. Molecular Ecology 17:1875-1876
Full text PDF
A short summary of the current prospects for good model organisms for the study of polyploidy (presence of more than two genome sets in the cells of an organism). The best models will be natural species whose evolution is traceable in detail, and should also have abundant genetic sequence data available on public databases. This was an invited perspective on a research paper in the same Issue documenting a newly discovered polyploid species.
6. Richard J. A. Buggs. (2007) Empirical study of hybrid zone movement. Heredity 99:301-312
Abstract PDF Supplementary data
This reviews many cases of hybrid zone movement in both plant and animal systems. Hybrid zones occur when the geographic ranges of two closely-related species meet and hybridise. Movements can occur under a variety of conditions. I argue that these provide excellent examples of evolution in action, and also raise important issues for species conservation. This paper develops several new and old ideas, perhaps the most significant being that introgression of genetic markers can be used to trace past movements. I wrote this paper independently in the time between graduating with my doctorate and getting my first postdoc position.
5. 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
This second major paper from my DPhil research reports a series of reciprocal transplant experiments and glasshouse drought experiments on diploid and hexaploid Mercurialis annua. We expected to find that the hexaploid would be better adapted to the dry conditions where it is found in southern Spain, than the diploid which has a more northerly distribution. Instead we found that the diploid was better adapted than the hexaploid to all enviroments that we tested it in, and is more drought tolerant. This provides an additional reason for the movement of a hybrid zone between the two ploidal levels (see 3.)
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
This is a phylogenetic reconstruction of the genus Mercurialis, carried out by Darren Obbard as part of his doctoral research. I was responsible for the genome size estimates reported here.
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
This was the first major paper to come from my DPhil research. It shows that when diploid and hexaploid Mercurialis annua meet, the diploids have a huge pollination advantage due to a sexual system difference with the hexaploids. This fits with historical data showing that diploids have rapidly advanced down the east coast of Spain over the past few decades. This is one of the most recent, rapid hybrid zone movements known to science.
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
I carried out flow cytometry in a small but crucial contribution to this work.
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
This provides a comprehensive review of the Mercurialis annua system, providing the background for much of the work carried out in my supervisor's lab over the next three years, including my DPhil. This was an invited paper and formed part of an Issue devoted to polyploidy.