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.

• The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event
  Koenen, Erik J. M.; Ojeda, Dario, I; Bakker, Freek T.; Wieringa, Jan J.; Kidner, Catherine; Hardy, OJ; Pennington, RT; Herendeen, PS; Bruneau, A; Hughes, CE
  Systematic Biology, 10.1093/sysbio/syaa041, MAY 2021
• Hybrid capture of 964 nuclear genes resolves evolutionary relationships in the mimosoid legumes and reveals the polytomous origins of a large pantropical radiation
  Koenen, Erik J. M.; Kidner, Catherine; de Souza, Elvia R.; Simon, Marcelo F.; Iganci, Joao R.; et al.
  American Journal Of Botany, 10.1002/ajb2.1568,  DEC 2020
• The origin of the Legumes is a complex paleopolyploid phylogenomic tangle closely associated with the Cretaceous-Paleogene (K-Pg) mass extinction event.
  Koenen, EJ, Ojeda, DI, Bakker, FT, Wieringa, JJ, Kidner, C, Hardy, OJ, Pennington, RT, Herendeen, PS, Bruneau, A and Hughes, CE.
  Systematic Biology. 2020. https://doi.org/10.1093/sysbio/syaa041
• Diversification in evolutionary arenas-Assessment and synthesis
  Nuerk, Nicolai M.; Linder, H. Peter; Onstein, Renske E.; Larcombe, Matthew J.; Hughes, Colin E.; et al.
  Ecology And Evolution  10.1002/ece3.6313 JUN 2020
• Biomes as evolutionary arenas: Convergence and conservatism in the trans-continental succulent biome
  Ringelberg, Jens J.; Zimmermann, Niklaus E.; Weeks, Andrea; Lavin, Matt; Hughes, Colin E.
  Global Ecology And Biogeography  DOI: 10.1111/geb.13089 Published: JUL 2020
• Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies
  Koenen, Erik J. M.; Ojeda, Dario, I; Steeves, Royce; Migliore, Jeremy; Bakker, Freek T.; Wieringa, Jan J.; Kidner, Catherine; Hardy, Olivier J.; Pennington, R. Toby; Bruneau, Anne; Hughes, Colin E
  New Phytologist,  DOI: 10.1111/nph.16290
• Extrafloral nectaries in Leguminosae: phylogenetic distribution, morphological diversity and evolution
  Marazzi, Brigitte; Maria Gonzalez, Ana; Delgado-Salinas, Alfonso; Luckow, Melissa A.; Ringelberg, Jens J.; Hughes CE
  Australian Systematic Botany,  DOI: 10.1071/SB19012
• Island woodiness underpins accelerated disparification in plant radiations
  Nurk, NM; Atchison, GW; Hughes, CE
  NEW PHYTOLOGIST, 224 (1):518-531; 10.1111/nph.15797 OCT 2019
• The evolutionary history of Leucaena: Recent research, new genomic resources and future directions
  Abair, A; Hughes, CE; Bailey, CD
  TROPICAL GRASSLANDS-FORRAJES TROPICALES, 7 (2):65-73; 1 10.17138/TGFT(7)65-73 FEB-MAY 2019
• Global Succulent Biome phylogenetic conservatism across the pantropical Caesalpinia Group (Leguminosae)
  Gagnon, E; Ringelberg, JJ; Bruneau, A; Lewis, GP; Hughes, CE
  NEW PHYTOLOGIST, 222 (4):1994-2008; 10.1111/nph.15633 JUN 2019
• Island woodiness underpins accelerated disparification in plant radiations
  NM Nürk, GW Atchison, CE Hughes
  New Phytologist https://doi.org/10.1111/nph.15797 2019
• …

• 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