E-mail:
  colin.hughes@plants.ox.ac.uk

Tel  +44 (0)1865 275836
Fax +44 (0)1865 275074

Last Modified: May 2012

Systematics and evolution

My research embraces both taxonomic monography and phylogenetics and underpins broader questions about the origins and maintenance of biodiversity as well as how to document that diversity. I am particularly interested in species-level problems in systematics including:
- species delimitation and classification
- interspecific hybridisation
- methods of phylogeny reconstruction, especially among closely related species, and including methods to disentangle divergent from reticulate relationships
- patterns of Neotropical species diversification
- early domestication and origins of crop plants
These problems are tackled using field, morphological and molecular data and I am actively involved in collaborative field research mainly in Latin America, herbarium specimen-based research to generate morphological data and delimit and describe species, and laboratory work to develop suitable DNA sequence regions for reconstructing relationships among closely related species.

Current projects focus on a number of Neotropical legume genera including Amicia, Mimosa, Leucaena and Lupinus (ca. 250 species). Species of the latter two genera have been the focus of both early indigenous domestication and modern crop breeding – Leucaena as a tropical forage and a native food plant in Mexico, and Lupinus as a protein crop in modern agriculture and an indigenous pulse crop in the Andes and the Mediterranean.

Leucaena.
Leucaena is a small genus of 25 species of small to medium-sized Neotropical trees. My previous work on Leucaena combined species delimitation and description with systematic analysis of species and generic relationships. In 1998, this research culminated in two major publications - a Taxonomic Monograph of the genus, and a Genetic Resources Handbook. A taxonomic and specimen database for Leucaena has been compiled, using the botanical database BRAHMS, where these data are available.

Recent research on Leucaena has focused on understanding hybrid and polyploid origins. This work has been carried out jointly with Donovan Bailey and Ashley Robertson. We have used a gene tree approach combining maternally and bi-parentally inherited cpDNA, nrDNA ITS and other nuclear markers to disentangle reticulate from divergent species relationships. This work revealed extensive nrDNA polymorphism within individuals including non-functional pseudogene copies, in part attributable to post-allopolyploidization gene silencing. This discovery prompted us to investigate nrDNA evolution and associated paralogy issues that impact on plant phylogeny reconstruction in greater depth. As part of that work, we developed a direct method to detect potential pseudogene sequences and tested this on published ITS data sets. The ITS region is the most widely used DNA locus for species-level phylogenetics. Our work demonstrates the importance of polymorphism and pseudogene detection for assessing ITS gene tree sampling and accurate species tree reconstruction.

To address the problem of lack of resolution in parts of the Leucaena cpDNA and ITS gene trees, we have developed a RAPD-based approach to identify sequence characterized amplified regions (SCARs) that might provide greater resolution among closely related species. The initial success of this novel approach is reported in a Featured Paper published in 2004 in Systematic Botany.

Several putative hybrids in Leucaena appear to have arisen spontaneously following juxtaposition of previously isolated species in cultivation in informal orchards in south-central Mexico. We are undertaking fieldwork to quantify the geographic and taxonomic extent of the artificial sympatry created by cultivation and to map the distribution of putative hybrids in detail, in order to gain insights into the extent and outcomes of the incipient indigenous domestication of Leucaena species as minor food plants in this part of Mexico.

Lupinus.
Lupinus comprises ca. 250 species, with 15 species distributed around the Mediterranean and the remainder in the New World concentrated in western North America and the Andes. Lupins have been widely introduced elsewhere as ornamentals and agricultural crops and are now invasive weeds in parts of New Zealand, Australia, northern Europe and elsewhere. Despite the high concentration of species in the Andes, the taxonomy of these species remains chaotic and their relationships within the genus are unknown..

Our work on Lupinus currently focuses on three specific questions – delimitation and description of the ca 70 Andean species, analysis of species relationships across the whole genus, and investigation of the origins of domestication of the Andean food crop L. mutabilis. Conventional ITS and cpDNA loci provide limited resolution within Lupinus prompting exploration of alternative more rapidly evolving DNA sequence regions. We are currently working with two low-copy nuclear genes, cycloidea and GPAT and have published a new phylogeny for the genus using these loci.

New Legume Taxa
Alongside field sampling of these two genera, more general legume collecting in recent years has resulted in discovery and description of a number of new taxa, including a new species of Parkinsonia, P. peruviana, two new species of Caesalpinia, and a new genus, Maraniona, all from the upper Maranon valley in northern Peru, as well as two new species of Mimosa and a new species of Leucochloron endemic to Bolivia.

Drummond, C.S, Eastwood, R.J, Miotto, S.T.S, Hughes, C.E. (2012) Multiple continental radiations and correlates of diversification in lupinus (leguminosae): Testing for key innovation with incomplete taxon sampling Systematic Biology. 61 (3): pp 443-460.
doi:10.1093/sysbio/syr126.

Sarkinen, T, Pennington, R.T, Lavin, M, Simon, M.F, Hughes, C.E. (2012) Evolutionary islands in the Andes: Persistence and isolation explain high endemism in Andean dry tropical forests Journal of Biogeography..
doi:10.1111/j.1365-2699.2011.02644.x.

Dahmer, N, Simon, M.F, Schifino-Wittmann, M.T, Hughes, C.E, Miotto, S.T.S, Giuliani, J.C. (2011) Chromosome numbers in the genus Mimosa L.: Cytotaxonomic and evolutionary implications Plant Systematics and Evolution. 291 (3): pp 211-220.
doi:10.1007/s00606-010-0382-2.

Govindarajulu, R, Hughes, C.E, Alexander, P.J, Donovan, Bailey C. (2011) The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (leguminosae; mimosoideae) American Journal of Botany. 98 (12): pp 2064-2076.
doi:10.3732/ajb.1100260.

Govindarajulu, R, Hughes, C.E, Donovan, Bailey C. (2011) Phylogenetic and population genetic analyses of diploid Leucaena (leguminosae; mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation American Journal of Botany. 98 (12): pp 2049-2063.
doi:10.3732/ajb.1100259.

Sarkinen, T.E, Marcelo-Pena, J.L, Daza, Yomona A, Simon, M.F, Toby, Pennington R, Hughes, C.E. (2011) Underestimated endemic species diversity in the dry inter-Andean valley of the Río Marañón, northern Peru: An example from Mimosa (Leguminosae, Mimosoideae) Taxon. 60 (1): pp 139-150

Lewis, G.P, Hughes, C.E, Yomona, A.D, Sotuyo, J.S, Simon, M.F. (2010) Three new legumes endemic to the Marañón Valley, Perú Kew Bulletin. 65 (2): pp 209-220.
doi:10.1007/s12225-010-9203-6.

Lewis, G.P, Hughes, C.E, Yomona, A.D, Sotuyo, J.S, Simon, M.F. (2010) Three new legumes endemic to the Maranon Valley, Peru Kew Bulletin. pp 1-12.
doi:10.1007/s12225-010-9203-6.

Penningtona, R.T, Lavin, M, Sarkinen, T, Lewis, G.P, Klitgaard, B.B, Hughes, C.E. (2010) Contrasting plant diversification histories within the Andean biodiversity hotspot Proceedings of the National Academy of Sciences of the United States of America. 107 (31): pp 13783-13787.
doi:10.1073/pnas.1001317107.

Simon, M.F, Hughes, C.E, Harris, S.A. (2010) Four new species of mimosa (leguminosae) from the central highlands of Brazil Systematic Botany. 35 (2): pp 277-288.
doi:10.1600/036364410X518793.

Simon, M.F, Grether, R, De, Queiroz L.P, Skemae, C, Pennington, R.T, Hughes, C.E. (2009) Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire Proceedings of the National Academy of Sciences of the United States of America. 106 (48): pp 20359-20364.
doi:10.1073/pnas.0903410106.

Hawthorne, W.D, Hughes, C.E. (2008) Optimising linear taxon sequences derived from phylogenetic trees - A reply to Haston & al. Taxon. 57 (3): pp 698-704

Hawkins, J.A, Boutaoui, N, Cheung, K.Y, Van, Klinken R.D, Hughes, C.E. (2007) Intercontinental dispersal prior to human translocation revealed in a cryptogenic invasive tree New Phytologist. 175 (3): pp 575-587.
doi:10.1111/j.1469-8137.2007.02125.x.

Hughes, C.E, Govindarajulu, R, Robertson, A, Filer, D.L, Harris, S.A, Bailey, C.D. (2007) Serendipitous backyard hybridization and the origin of crops Proceedings of the National Academy of Sciences of. 104 (36): pp 14389-14389.
doi:10.1073/pnas.0702193104.

Stepkowski, T, Hughes, C.E, Law, I.J, Markiewicz, L, Gurda, D, Chlebicka, A, Moulin, L. (2007) Diversification of lupine Bradyrhizobium strains: Evidence from nodulation gene trees Applied and Environmental Microbiology. 73 (10): pp 3254-3264.
doi:10.1128/AEM.02125-06.

Atahuachi, B. M, Hughes, C.E. (2006) Two new species of Mimosa (Fabaceae) endemic to Bolivia Brittonia. 58 (1): pp 59-65

Hughes, C, Eastwood, R. (2006) Island radiation on a continental scale: Exceptional rates of plant diversification after uplift of the Andes Proceedings of the National Academy of Sciences of the United States of America. 103 (27): pp 10334-10339.
doi:10.1073/pnas.0601928103.

Hughes, C.E, Eastwood, R.J, Bailey, C.D. (2006) From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction Philosophical Transactions of the Royal Society of London Series B Biological Sciences. 361 (1465): pp 211-225.
doi:10.1098/rstb.2005.1735.

Hughes, C.E, Atahuachi, B M. (2006) A new species of Leucochloron (Leguminosae: Mimosoideae) endemic to Bolivia Kew Bulletin. 61 (4): pp 559-563

Bailey, C.D, Hughes, C.E, Harris, S.A. (2004) Using RAPDs to Identify DNA Sequence Loci for Species Level Phylogeny Reconstruction: An Example from Leucaena (Fabaceae) Systematic Botany. 29 (1): pp 4-14

Hughes, C.E, Lewis, G.P, Yomona, A.D, Reynel, C. (2004) Maraniona. A new dalbergioid legume genus (Leguminosae, Papilionoideae) from Peru Systematic Botany. 29 (2): pp 366-374

Lavin, M, Schrire, B.P, Lewis, G, Pennington, R.T, Delgado-Salinas, A, Thulin, M, Hughes, C.E, Matos, A.B, Wojciechowski, M.F. (2004) Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes Philosophical Transactions of the Royal Society of London Series B Biological Sciences. 359 (1450): pp 1509-1522.
doi:10.1098/rstb.2004.1536.

Bailey, C.D, Carr, T.G, Harris, S.A, Hughes, C.E. (2003) Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes Molecular Phylogenetics and Evolution. 29 (3): pp 435-455.
doi:10.1016/j.ympev.2003.08.021.

Hughes, C.E, Yomona, A.D, Hawkins, J.A. (2003) A new Palo Verde (Parkinsonia - Leguminosae: Caesalpinioideae) from Peru Kew Bulletin. 58 (2): pp 467-472

Lavin, M, Wojciechowski, M.F, Gasson, P, Hughes, C, Wheeler, E. (2003) Phylogeny of robinioid legumes (Fabaceae) revisited: Coursetia and Gliricidia recircumscribed, and a biogeographical appraisal of the Caribbean endemics Systematic Botany. 28 (2): pp 387-409

Hughes, C.E, Donovan, Bailey C, Harris, S.A. (2002) Divergent and reticulate species relationships in Leucaena (Fabaceae) inferred from multiple data sources: Insights into polyploid origins and nrDNA polymorphism American Journal of Botany. 89 (7): pp 1057-1073

Ewel, J.J, O'Dowd, D.J, Bergelson, J, Daehler, C.C, D'Antonio, C.M, Gomez, L.D, Gordon, D.R, Hobbs, R.J, Holt, A, Hopper, K.R, Hughes, C.E, LaHart, M, Leakey, R.R.B, Lee, W.G, Loope, L.L, Lorence, D.H, Louda, S.M, Lugo, A.E, McEvoy, P.B, Richardson, D.M, Vitousek, P.M. (1999) Deliberate introductions of species: Research needs. Benefits can be reaped, but risks are high BioScience. 49 (8): pp 619-630

Hawkins, J.A, White, Olascoaga L, Hughes, C.E, Contreras, Jimenez J.-L.R, Mercado, Ruaro P. (1999) Investigation and documentation of hybridization between Parkinsonia aculeata and Cercidium praecox (Leguminosae: Caesalpinioideae) Plant Systematics and Evolution. 216: pp 49-68

Hughes, C.E, Harris, S.A. (1998) A second spontaneous hybrid in the genus Leucaena (Leguminosae, Mimosoideae) Plant Systematics and Evolution. 212: pp 53-77

Hughes, C.E. (1998) To be or not to be a botanical monographer? Archives des Sciences et Compte Rendu Seances de la Societe. 51 (3): pp 353-357

Hawkins, J.A, Hughes, C.E, Scotland, R.W. (1997) Primary Homology Assessment, Characters and Character States Cladistics. 13 (3): pp 275-283

Hughes, C.E. (1997) Variation in anther and pollen morphology in Leucaena Benth. (Leguminosae-Mimosoideae) Botanical Journal of the Linnean Society. 123 (3): pp 177-196.
doi:10.1006/bojl.1996.0083.

Chamberlain, J.R, Hughes, C.E, Galwey, N.W. (1996) Patterns of isozyme variation in the Leucaena shannonii alliance (Leguminosae: Mimosoideae) Silvae Genetica. 45 (1): pp 1-7

Hughes, C.E, Johnson, C.D. (1996) New host records and notes on Bruchidae (Coleoptera) from Leucaena Benth. (Leguminosae, Mimosoideae) from Mexico, Central and South America Journal of Applied Entomology. 120 (3): pp 137-141

Harris, S.A, Hughes, C.E, Abbott, R.J, Ingram, R. (1994) Genetic variation in Leucaena leucocephala (Lam) de Wit (Leguminosae: Mimosoideae) Silvae Genetica. 43: pp 159-166

Harris, S.A, Hughes, C.E, Ingram, R, Abbott, R.J. (1994) A phylogenetic analysis of Leucaena (Leguminosae: Mimosoideae) Plant Systematics and Evolution. 191: pp 1-26

Hughes, C.E. (1994) Risks of species introductions in tropical forestry Commonwealth Forestry Review. 73 (4): pp 243-252

Hughes, C.E, Harris, S.A. (1994) The characterisation and identification of a naturally occurring hybrid in the genus Leucaena (Leguminosae: Mimosoideae) Plant Systematics and Evolution. 192: pp 177-197

Hughes, C.E. (1987) Biological considerations in designing a seed collection strategy for Gliricidia sepium (Jacq.) Walp. ( Leguminosae). Commonwealth Forestry Review. 66 (1): pp 31-48

Burley, J, Hughes, C.E, Styles, B.T. (1986) Genetic systems of tree species for arid and semiarid lands Forest Ecology and Management. 16: pp 317-343

Spontaneous hybridization and indigenous domestication of Mexican Leucaena: Nov 2000 - Oct 2003 Leverhulme Trust

Field collection of Andean Lupins: Mar 2002 - Aug 2003 Stanley Smith Horticultural Trust

Plant phylogeny and rDNA evolution. Apr 2003 - Mar 2004 Royal Society

Dr. Julie Hawkins, University of Reading, UK - Sytematics of Parkinsonia
Dr. Donovan Bailey, New Mexico State University, USA - Leucaena hybrids and polyploids
Dr. Silvia Miotto & Dr.Maria-Teresa Schifino-Wittmann, UFRGS, Porto Alegre, Brasil - Lupinus phylogeny and cytogenetics