Geotemporal patterns of plant species diversification and the causes of differences in species richness among clades and geographic areas remain poorly understood. We are investigating patterns and processes underlying the historical assembly of plant species diversity in the neotropics, the most diverse continent where several of the world’s hottest plant diversity hotspots occur. We are using time-calibrated species-level phylogenies for a number of legume study groups, alongside geographical and broad-scale ecological data to investigate the dynamics of diversification. Recent work has looked at plant diversification in the high elevation Andes, seasonally dry neotropical forests, and the Cerrado biome of central South America. Accurate delimitation of species, via revisionary taxonomy and taxonomic monography are pivotal for the large scale evolutionary studies that we are undertaking, and several taxonomic monographic projects are in progress.

• PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing
  Kovar, L; Nageswara-Rao, M; Ortega-Rodriguez, S; Dugas, DV; Straub, S; Cronn, R; Strickler, SR; Hughes, CE; Hanley, KA; Rodriguez, DN; Langhorst, BW; Dimalanta, ET; Bailey, CD
  GENOME BIOLOGY AND EVOLUTION, 10 (9):2501-2517; 10.1093/gbe/evy179 SEP 2018
• The acaulescent rosette species of Lupinus L. (Fabaceae) of Colombia and Ecuador including a new species from Colombia
  Contreras-Ortiz, N; Jara-Munoz, OA; Hughes, CE
  PHYTOTAXA, 364 (1):61-70; 10.11646/phytotaxa.364.1.3 AUG 7 2018
• DNA Sequence Variation among Conspecific Accessions of the Legume Coursetia caribaea Reveals Geographically Localized Clades Here Ranked as Species
  Lavin, M; Pennington, RT; Hughes, CE; Lewis, GP; Delgado-Salinas, A; de Stefano, RD; de Queiroz, LP; Cardoso, D; Wojciechowski, MF
  SYSTEMATIC BOTANY, 43 (3):664-675; 10.1600/036364418X697382 JUL-SEP 2018
• Pleistocene glacial cycles drive isolation, gene flow and speciation in the high-elevation Andes
  Nevado, B; Contreras-Ortiz, N; Hughes, C; Filatov, DA
  NEW PHYTOLOGIST 219(2): 779-793 DOI: 10.1111/nph.15243  JUL 2018
• Convergent evolution of high elevation plant growth forms and geographically structured variation in Andean Lupinus (Fabaceae)
  Contreras-Ortiz, Natalia; Atchison, Guy W.; Hughes, Colin E.; Madrinan, Santiago
  BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, 187 (1):118-136; 10.1093/botlinnean/box095 MAY 2018
• Are there many different routes to becoming a global biodiversity hotspot? 
  Hughes, Colin E. 
  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114 (17): 4275-4277 APR 25 2017 Editorial Material (Details)
• A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny 
  Azani, Nasim; Babineau, Marielle; Bailey, C. Donovan; et al. 
  TAXON, 66 (1): 44-77 FEB 2017 Article (Details)

• Systematics and biogeography of Legumes
• Taxonomic monographs of Leucaena & Lupinus
• Historical assembly of neotropical plant species diversity
• Polyploidy and hybridization in Leucaena
• Early crop domestication in Mesoamerica and the Andes

• Plant taxonomy
• Systematic botany
• Plant phylogenetics
• Multi-locus gene tree approaches to interspecific hybridization
• Historical biogeography
• Crop evolution and domestication