Särkinen, T.S. & Hughes, C.E. (accepted pending revisions). Systematics and biogeography of Amicia (Leguminosae, Papilionoideae). Systematic Botany Monographs.
Hughes, C.E. (in press). Leucaena. Flora Mesoamericana
Hughes, C.E., Pennington, R.T. & Antonelli, A. 2013. Neotropical plant evolution: assembling the big picture. Botanical Journal of the Linnean Society 171: 1-18.
Koenen, E.J.M., de Vos, J.M., Atchison, G.W., Simon, M.F., Schrire, B.D., de Souza, E.R., de Queiroz, L.P. & Hughes, C.E. 2013. Exploring the tempo of species diversification in legumes. South African Journal of Botany 89: 19-30.
Gagnon, E., Lewis, G.P., Sotuyo, S., Hughes, C.E. & Bruneau, A. 2013. A molecular phylogeny of Caesalpinia sensu lato: increased sampling reveals new insights and more genera than expected. South African Journal of Botany 89 111-127.
Legume Phylogeny Working Group [Bruneau, A., Doyle, J., Herendeen P., Hughes, C., Kenicer, G., Lewis, G., Mackinder, B., Pennington, R.T., Sanderson, M. & Wojciechowski, M. et al.]. 2013. Legume phylogeny and classification in the 21st century: progress, prospects and lessons. Taxon 62: 217-248.
Legume Phylogeny Working Group [Borges, L., Bruneau, A., Cardoso, D., Crisp, M., Delgado-Salinas, A., Doyle, J., Egan, A., Herendeen, P., Hughes, C., Kenicer, G., Klitgaard, B., Koenen, E., Lavin, M., Lewis, G., Luckow, M., Mackinder, B., Malécot, V., Miller, J.T., Pennington, R.T., de Queiroz, L.P., Schrire, B., Simon, M.F., Steele, K., Torke, B., Wieringa, J.J., Wojciechowski, M.F.] 2013. Towards a new classification system for legumes: progress report from the ILC6. South African Journal of Botany 89: 3-9.
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 innovations with incomplete taxon sampling. Systematic Biology. doi: 10.1093/sysbio/syr126
Särkinen, T., Pennington, R.T., Lavin, M., Simon, M.F. & Hughes, C.E. 2011. Islands in the Andes: persistence and isolation explain endemic legume species richness in Andean dry tropical forest. Journal of Biogeography. doi: 10.1111/j.1365-2699.2011.02644.x
Simon, M.F., Grether, R., De Quieroz, L.P., Särkinen, T.E., Dutra, V.F. & Hughes, C.E. 2011. The evolutionary history of Mimosa (Leguminosae): towards a phylogeny of the sensitive plants. American Journal of Botany 98: 1201-1221. doi: 10.3732/ajb.1000520
Govindarajulu, R., Hughes, C.E. & Bailey, C.D. 2011. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae) reveal cryptic species diversity and patterns of allopatric divergent speciation. American Journal of Botany 98: 2049-2063. doi: 10.3732/ajb.1100259
Govindarajulu, R., Hughes, C.E., Alexander, P. & Bailey, C.D. 2011. The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae). American Journal of Botany 98: 2064-2076. doi: 10.3732/ajb.1100260
Dahmer, N., Simon, M.F., Schifino-Wittmann, M.T., Hughes, C.E., Miotto, S.T.S. & Guiliani, J.S. 2011. Chromosome numbers in the genus Mimosa L.: cytotaxonomic and evolutionary implications. Plant Systematics & Evolution 291: 211-220. doi: 10.1007/s00606-010-0382-2
Särkinen, T.S., Marcelo Peña, J.L., Yomona, A.D., Simon, M.F., Pennington, R.T. & Hughes, C.E. 2011. Underestimated endemic species diversity in the Marañon seasonally dry tropical forests of Peru – an example from Mimosa (Leguminosae: Mimosoideae). Taxon. 60: 139-150.
Pennington R.T., Lavin M., Särkinen 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, USA. 107: 13783-13787. doi:10.1073/pnas.1001317107
Lewis, G.P., Hughes, C.E., Daza Yomona, A., Solange Sutoyo, J. & Simon, M.F. 2010. Three new legumes endemic to the Marañon Valley, Peru. Kew Bulletin 65: 209-220. doi:10.1007/s12225-010-9203-6.
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: 277-288. doi:10.1600/036364410791638333
Simon, M.F., Grether, R., de Quieroz, L., Skema, 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 National Academy of Sciences 106: 20359-20364. doi:10.1073/pnas.0903410106
James, E.K., Elliott, G.N., Chen, W-M., Bontemps, C., Young, J.P.W., de Faria, S.M., dos Reis Jnr, F.B., Simon, M.F., Gross, E., Loureiro, M.F., Reis, V.M., Perin, L, Boddey, R.M., Hughes, C.E., Moulin, L., Prescott, A.R. & Sprent, J.I. 2008. Infection of legumes by beta-rhizobia. In: Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture. Eds. F.D. Dakora, S.B.M. Chimphango, A.J. Valentine, C. Elmerich and W.E. Newton. Springer, Dordrecht. 249-250.
Bontemps, C., Elliott, G.N., James, E.K., Sprent, J.I., Simon, M.F., Hughes, C.E., & Young, J.P.W. 2008. In search of beta-rhizobia: Exploring the symbionts of Mimosa in Brazil. In: Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture. Eds. F.D. Dakora, S.B.M. Chimphango, A.J. Valentine, C. Elmerich and W.E. Newton. Springer, Dordrecht. 251-252.
Hawthorne, W.D. & Hughes, C.E. 2008. Optimising linear taxon sequences derived from phylogenetic trees – a reply to Haston & al. Taxon 57: 698-704.
Eastwood, R.J. & Hughes, C.E. 2008. Origins of domestication of Lupinus mutabilis in the Andes. Pp. 373-379, in: Palta, J.A. & Burger, J.B. (Eds.) Lupins for Health & Wealth, Proceedings 12th International Lupin Conference, Fremantle, Australia, International Lupin Association, Canterbury, New Zealand.
Eastwood, R.J., Drummond, C.S., Schifino-Wittmann, M.T. & Hughes, C.E. 2008. Diversity and evolutionary history of lupins – insights from new phylogenies. Pp. 346-354, in: Palta, J.A. & Burger, J.B. (Eds.) Lupins for Health & Wealth, Proceedings 12th International Lupin Conference, Fremantle, Australia, International Lupin Association, Canterbury, New Zealand.
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 National Academy of Sciences 104: 14389-14394. doi:10.1073/pnas.0702193104
Stepkowski, T., Hughes, C.E., Law, I.J., Markiewiez, L., Gurda, D., Chlebicka, A. & Moulin, L. 2007. Diversification of lupin Bradyrhizobium strains: evidence from nodulation gene trees. Applied & Environmental Microbiology 73: 3254-3264. doi:10.1128/AEM.02125-06
Hawkins, J.A., Boutaoui, N., Cheung, K.Y., van Klinken, R. & Hughes, C.E. 2007. Intercontinental dispersal prior to human translocations revealed in a cryptogenic invasive tree. New Phytologist 175: 575-587. doi:10.1111/j.1469-8137.2007.02125.x
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. Series B 361: 211-225. doi:10.1098/rstb.2005.1735
Atahuachi, M. & Hughes, C.E. 2006. Two new species of Mimosa endemic to Bolivia. Brittonia 58: 59-65. doi:10.1663/0007-196X(2006)58[59:TNSOMF]2.0.CO;2
Hughes, C.E. & Eastwood, R.J. 2006. Island radiation on a continental scale: exceptional rates of plant diversification after uplift of the Andes. Proceedings National Academy of Sciences 103: 10334-10339. doi:10.1073/pnas.0601928103
Hughes, C.E. & Atahuachi, M. 2006. A new species of Leucochloron (Leguminosae: Mimosoideae) endemic to Bolivia. Kew Bulletin 61: 559-563.
Luckow, M., Hughes, C.,, Schrire, B., Pedley, L., Fagg, C.,, Fortunado, R., Hurter, J., Rico, L., Bruneau, A., Caccavari, M., Crisp, M., Delgado S., A., Doyle, J.J., Harris, S., Herendeen, P.S., Hernández, H.M., Hirsch, A.M., Jobson, R., Klitgaard, B.B., Simpson, B.B., Smith, G.F., Sousa S., M., Timberlake, J., Wills, C.K., Winter, P. & Wojciechowski, M.F. 2005. Acacia: the case against moving the type to Australia. Taxon 54: 513-519.
Bailey, C.D., Hughes, C.E. & Harris, S.A. 2004. Using RAPDs to develop DNA sequence loci for species-level phylogeny reconstruction: an example from Leucaena (Fabaceae). Systematic Botany 29: 4-14. doi: 10.1600/036364404772973483
Maunder, M. Hughes, C., Hawkins, J. & Culham, A. 2004. Hybridization in ex situ plant collections: conservation concerns, liabilities and opportunities. Pp. 325-364 In: Guerrant, E.O., Havens, K. and Maunder, M. (Eds.). Ex Situ Plant Conservation. Supporting Species Survival in the Wild. Island Press.
Hughes, C.E., Lewis, G.P., Daza Y., A. & Reynel, C. 2004. Maraniona. A new Dalbergioid legume genus (Leguminosae: Papilionoideae) from Peru. Systematic Botany 29: 366-374. doi:10.1600/036364404774195557
Lavin, M., Schrire, B., Lewis, G., Pennington, R.T., Delgado-Salinas, A., Thulin, M., Hughes, C., Beyra Matos, A. & Wojciechowski, M.F. 2004. Metacommunity process rather than continental tectonic history better explains geographically structured phylogenies in legumes. Philosophical Transactions of the Royal Society. Series B 359: 1509-1522. doi:10.1098/rstb.2004.1536
Hughes, C.E., Daza Y., A., & Hawkins, J.A. 2003. A new Palo Verde (Parkinsonia – Leguminosae: Caesalpinioideae) from Peru. Kew Bulletin 58: 467-472.
Scotland, R.W., Hughes, C.E., Bailey, C.D. & Wortley, A. 2003. The Big Machine and the much-maligned taxonomist. Systematics & Biodiversity 1: 139-143. doi:10.1017/S1477200003001178
Lavin, M, Wojiechowski, M.F., Gaason, P., Hughes, C.E. & Wheeler, E. 2003. Phylogeny of robinioid legumes (Fabaceae) revisited: Coursetia and Gliricidia recircumscribed, and a biogeographical appraisal of the Caribbean endemics. Systematic Botany 28: 387-409. doi/abs/10.1043/0363-6445-28.2.387
Hughes, C.E., Bailey, C.D. Krosnick, S. & Luckow, M.A. 2003. Relationships among genera of the informal Dichrostachys and Leucaena groups (Mimosoideae) inferred from nuclear ribosomal ITS sequences. Pp. 221-238, in: Klitgaard, B.B. and Bruneau, A. (Eds.). Advances in Legume Systematics Part 10. Higher Level Systematics. Royal Botanic Gardens Kew.
Bailey, C.D., Carr, T.G., Harris, S.A. & Hughes, C.E. 2003. Characterization of angiosperm nrDNA polymorphim, paralogy, and pseudogenes. Molecular Phylogenetics & Evolution 29: 435-455. doi:10.1016/j.ympev.2003.08.021
Hughes, C.E., Bailey, C.D. & 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: 1057-1073.
Bass, S; Hughes, C. & Hawthorne W. 2001. Forests, biodiversity and livelihoods: linking policy and practice. Pp. 23-73 in, Koziell I. and Saunders J. (Eds.) Living off Biodiversity. Exploring livelihoods and biodiversity issues in natural resources management. International Institute for Environment and Development. London.
Hughes, C.E. 2001. Gliricidia. Pp. 1013, In Stevens, W.D.; Ulloa Ulloa, C.; Pool, A. Montiel, O.M. (Eds.). Flora de Nicaragua. Monographs in Systematic Botany 85. Missouri Botanical Garden Press. St. Louis.
Hughes, C.E. & Jones, R.J. 1999. Environmental hazards of Leucaena. Pp. 61-70, in: Shelton, H.M.; Gutteridge, R.C.; Mullen, B.F. and Bray, R.A. (Eds.). Leucaena - Adaptation, quality and farming systems. Proceedings of a workshop, Hanoi, Vietnam, Feb. 1998. ACIAR Proceedings 86. Australian Centre for International Agricultural Research, Canberra.
Hawkins, J.A.; White O., L.; Hughes, C.E.; Contreras J., J.L. & Mercado R., P. 1999. Investigation and documentation of hybridization between Parkinsonia aculeata and Cercidium praecox (Caesalpinioideae: Leguminosae). Plant Systematics & Evolution 216: 49-68.
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., Loope, L., Lorence, D. Louda, S.M., Lugo, A.E., McEvoy, P.B. Richardson, D.M. & Vitousek, P.M. 1999. Deliberate introductions of species: research needs. Bioscience 49: 619-630.
Hughes, C.E. 1998. Leucaena. A Genetic Resources Handbook. Tropical Forestry Paper 37. Oxford Forestry Institute. 274pp. (also published in Spanish - Leucaena. Manual de Recursos Genéticos). pdf (TFP37 in English / TFP37S in Spanish)
Hughes, C.E. & Harris, S.A. 1998. A second spontaneous hybrid in the genus Leucaena (Leguminosae: Mimosoideae). Plant Systematics & Evolution 212: 53-77.
Hughes, C.E. 1998. Monograph of Leucaena (Leguminosae: Mimosoideae). Systematic Botany Monographs 55: 1-244.
Hughes, C.E. 1997. Variation in anther and pollen morphology in Leucaena Benth. (Leguminosae: Mimosoideae). Botanical Journal of the Linnean Society 123: 177-196. doi:10.1006/bojl.1996.0083
Hughes, C.E. 1997. Proposal to conserve the name Leucaena (Leguminosae) with a conserved type. Taxon 46: 355-356.
Hughes, C.E. 1997. Species delimitation and new taxa and combinations in Leucaena (Leguminosae). Contributions from the University of Michigan Herbarium 21: 277-290.
Bray, R.A.; Hughes, C.E.; Brewbaker, J.L. Hanson, J.; Thomas, B.D. & Ortiz, A. 1997. The World Leucaena Catalogue. Department of Agriculture, The University of Queensland, Brisbane. 48 pp. + PC diskette.
Hawkins, J.A.; Hughes, C.E. & Scotland, R.W. 1997. Primary homology assessment, characters and character states. Cladistics 13: 275-283.
Hughes, C.E. & Johnson, C.D. 1996. New host records and notes on Bruchidae (Coleoptera) from Leucaena (Leguminosae: Mimosoideae) from Mexico, Central and South America. Journal of Applied Entomology 120: 137-141.
Chamberlain, J.R., Hughes, C.E. & Galwey, N. 1996. Patterns of isozyme variation in the Leucaena shannonii (Leguminosae: Mimosoideae) alliance. Silvae Genetica 45: 1-7.
Harris, S.A., Chamberlain, J.L. & Hughes, C.E. 1996. New insights into the evolution of Leucaena. pp. 117-126, in: Pickersgill, B. and Lock J.M. (Eds.) Advances in Legume Systematics. Part 8. Legumes of Economic Importance Royal Botanic Gardens, Kew, UK.
Hughes, C.E. 1995. Protocols for plant introductions with particular reference to forestry: changing perspectives on risks to biodiversity and economic development. pp. 15-32 in Stirton, C.H. (Ed.). Weeds in a Changing World. British Crop Protection Council Symposium Proceedings No. 64.
Farjon A. & Hughes, C.E. 1995. Bigcone Pinyon pine: Pinus maximartinezii. In: Stone, R.D. (Ed.) Encyclopedia of Endangered Species. IUCN, Gland, Switzerland.
Hughes, C.E. & Harris, S.A. 1995. Systematics of Leucaena: recent findings and implications for breeding and conservation. pp. 54-65. in: Shelton. H.M., Piggin, C.M. and Brewbaker, J.L. (Eds.). Leucaena - Opportunities and Limitations. Proceedings of a Workshop, Bogor, Indonesia, January 1994. ACIAR Proceedings No. 57.
Harris, S.A., Hughes, C.E., Ingram, R. & Abbott, R.J. 1994. A phylogenetic analysis of Leucaena (Leguminosae: Mimosoideae). Plant Systematics & Evolution 191: 1-26.
Harris, S.A., Hughes, C.E., Abbott, R.J. & Ingram, R. 1994. Genetic diversity in Leucaena leucocephala (Lam.) de Wit (Leguminosae: Mimosoideae). Silvae Genetica 43: 159-167.
Hughes, C.E. & Harris, S.A. 1994. The identification and characterisation of a naturally occurring hybrid in Leucaena (Leguminosae: Mimosoideae). Plant Systematics & Evolution 192: 177-197.
Hughes, C.E. 1994. Risks of species introductions in tropical forestry. Commonwealth Forestry Review 73: 243-252.
Hellin, J.J. & Hughes, C.E. 1993. Leucaena salvadorensis: utilization and conservation in Central America. Serie Miscelanea de CONSEFORH 39-21/93, Siguatepeque, Honduras, C.A. (Also published in Spanish, Serie Miscelanea 15-15/92).
Hughes, C.E. 1991. Two new subspecies of Leucaena (Leguminosae, Mimosoideae) from Guatemala. Kew Bulletin 46: 547-557.
Lavin, M.; Mathews, S. & Hughes, C.E. 1991. Chloroplast DNA variation in Gliricidia sepium: intraspecific phylogeny and tokogeny. American Journal of Botany 78: 1576-1585.
Hughes, C.E. & Styles, B.T. 1989. The benefits and risks of woody legume introductions. In Stirton, C.H. and Zarruchi, J.L. (eds.) Advances in Legume Biology. Monographs in Systematic Botany, Missouri Botanical Garden 29: 505-531.
Hughes, C.E. 1988. Leucaena salvadorensis: status, distribution and genetic conservation. Leucaena Research Reports 9: 99-105.
Hughes, C.E. 1988. Exotic and native trees for social forestry. Appropriate Technology 15: 22-23.
Hughes, C.E. 1988. Abertura de los conos de Pinus caribaea con relacion a densidad y contenido de humedad. El Tatascan (Honduras) 14:4-11.
Hughes, C.E. 1987. Biological considerations in designing a seed collection strategy for Gliricidia sepium (Jacq.) Walp. (Leguminosae). Commonwealth Forestry Review 66: 31-48.
Hughes, C.E. 1986. A new Leucaena from Guatemala. Leucaena Research Reports 7:110-113. (Spanish translation Silvoenergia (Costa Rica) 20:1-4).
McCarter, P.S. & Hughes, C.E. 1984. Liquidambar styraciflua: a species of potential for the tropics. Commonwealth Forestry Review 63: 207-216.
Styles, B.T. & Hughes, C.E. 1983. Studies of variation in Central American Pines III. Notes on the taxonomy and nomenclature of the pines and related gymnosperms in Honduras and adjacent Latin American republics. Brenesia 21: 269-291.
Robbins, A.M.J. & Hughes, C.E. 1983. Provenance regions for Pinus caribaea and Pinus oocarpa within the Republic of Honduras. Tropical Forestry Paper 18, Oxford Forestry Institute, Oxford, UK. 93pp.
Hughes, C.E. & Robbins, A.M.J. 1982. Seed stand establishment procedures for Pinus oocarpa and Pinus caribaea in the natural forests of Central America. Commonwealth Forestry Review 61: 107-113.

Miscellaneous & book reviews

Hughes, C.E. 2005. Four new legumes in forty-eight hours. Oxford Plant Systematics Newsletter 12: 5-6.
Hughes, C.E. 2003. Breathless in the Andes. Oxford Plant Systematics Newsletter 10: 6-7.
Hughes, C.E. 2001. Conflict Trees. Book Review. Rogers, K.E. (2000) The Magnificent Mesquite. University of Texas Press, Austin. 159pp. Diversity & Distributions 7: 111-112.
Hughes, C.E. 1999. Book Review. Pennington, T.D. (1997). The genus Inga: Botany. Royal Botanic Gardens, Kew, 844pp. Edinburgh Journal of Botany 56: 151-153.
Hughes, C.E. 1998. Book Review. Oldfield, S.; Lusty, C. and MacKinven, A. (Eds.) (1998). The World List of Threatened Trees. World Conservation Press, Cambridge. 650pp. Commonwealth Forestry Review 77: 291-293.
Hughes, C.E. 1998. To be or not to be a botanical monographer? Archives de Sciences (Geneva) 51: 353-358.
Hughes, C.E. 1997. Book Review. Barneby, R.C. and Grimes, J.W. (1996). Silk Tree, Guanacaste, Monkey's Earring: A generic system for the synandrous Mimosaceae of the Americas. Memoirs of the New York Botanical Garden 74. Edinburgh Journal of Botany 54: 117-123.
Hughes, C.E. 1993. Obituary, Brian Thomas Styles. The Independent and Commonwealth Forestry Review.