Research Interests


           As an evolutionary biologist focused on plant systems I am actively engaged in researching the evolutionary relationships among taxa, patterns of speciation and diversification, and the development of informative classifications.  Over the last ten years these interests have focused increasingly on homoploid and polyploid plant hybridization as important forms of plant-plant and plant-human evolutionary interactions in both wild and semi-domesticated plant species.   The variety of topics researched in my lab are selected to engage graduate and undergraduate students in aspects of molecular biology, integrative evolutionary biology, and plant taxonomy, with primary focus on members of the mustard and legume plant families (Brassicaceae and Fabaceae).  These systems include numerous western US and Mexican representatives, important semi-domesticated crop species, and endangered species that provide well-rounded projects involving studies derived from fieldwork, molecular biology, and morphology. 

Our current funded research projects derived from an NSF Plant Genome Research program Mid-Career Award entitled MCA-PGR: A Phylogenetically Informed Investigation of Transcriptome Evolution and Transcriptome Response of the Tropical Crop Genus Leucaena (Leguminosae) to Psyllid Herbivores. (February 2013-2016) Please see our developing page on the project for further details.

Past and ongoing research projects.

A) Legume systematics, polyploidy, hybridization, and crop origins.  NSF EF-0542228, PI D. Bailey, March 2006-2009.

One of the major research thrusts in the laboratory over the last seven years includes a project that began as part of my postdoctoral work at the University of Oxford.  Research in this area focuses on plant evolutionary biology and plant-plant and plant-human integrative biology involving hybridization, polyploidy, and human translocation on the evolutionary trajectory of plant lineages. Our recent published work (e.g., PNAS Hughes et al., 2007) has applied molecular phylogenetics, patterns of geographic distribution, as well as archeological information to illustrate the impact human translocation on the evolutionary trajectory of a plant lineage and semi-domesticate species.  We have since expanded this study through the inclusion of comprehensively sampled multilocus molecular phylogenetic and population genetic datasets that have revealed additional cryptic diploid species and diploid relationships consistent with a general pattern of allopatric speciation. In contrast, the application of multiple plastid and nuclear-encoded gene-trees suggests that the five polyploid species of Leucaena formed through a minimum of four unique allopolyploid speciation events, a form of sympatric speciation influenced by the human translocation of species suggested by the results in our 2007 paper.  Viewed in the context of related mimosoid plant taxa, we are now able to demonstrate that the evolutionary history of Leucaena has involved cyclic polyploidy, diploidization, allopatric diploid divergence, and sympatric allopolyploid speciation. 

B)  A model system revisited: phylogenetic relationships and species limits among diploid taxa of Boechera (Brassicaceae).  NSF DEB0817033, Lead PI D. Bailey with Co-PIs Michael Windham (Duke), Loreen Alphin (BYU), and Ihsan Al-Shehbaz (Mo. Bot. Garden). August 2008-2012

The second major project ongoing in my lab involves the use of a combined phylogenetic and population genetic framework, similar to that developed for Leucaena, to investigate the evolutionary history of the complex Brassicaceae genus Boechera (formerly most of N. American Arabis).  Boechera is a close relative of Arabidopsis, primary distributed in the western United States, whose species have become a prime subject for studies in evolutionary biology and ecology including investigations on aspects of plant breeding, plant-pathogen interactions, hybrid speciation, apomixis, polyploidy, population ecology, evolutionary ecology, phenotypic plasticity and adaptation, and the evolution of genomes.  Unfortunately, efforts to use Boechera as a model system are constrained by the lack of a robust and comprehensive understanding to relationships and patterns of diversification across the 80 diploid and 30 polyploid species. We are investigating the evolutionary history of Boechera through the application of an eight gene multilocus phylogeny and a 13 locus microsatellite study on diploid divergent taxa, including representatives of multiple populations of all 80 diploid species.  We are also demonstrating the impact of plant-plant hybridization as a result of shifts in geographic range.  This is in contrast to the human induced allopolyploidization events recovered in Leucaena.   Our ultimate objective is to both uncover the diversity of evolutionary mechanisms that have operated in this system and to develop a comprehensive and useful classification, online keys, etc. 

C)  Advances in phylogenetic theory and the development of new tools for the study of genetic divergence in plant systems.

In addition to conducting empirical studies in systematic biology and related areas, m lab has been and will continue to be involved with projects that advance systematic biology through the generation of new tools (e.g., Bailey and Doyle, 1999; Alexander et al., 2007; Lohithaswa et al., 2007; Bacon et al., 2008; Hasan et al., 2010) as well as data analysis and interpretation  (e.g., Simmons, Bailey, and Nixon, 2000; Bailey et al., 2003; Scotland et al., 2003; Bailey, Fain, and Houde, 2006).  Most recently, we have invested considerable time and effort in a collaboration (see with Dr. Brook Milligan and bioinformatics expert Alexander Tchourbanov through which we are developing a number of different 454-based approaches to extract large numbers of orthologous sequences from many individual samples at a low cost with the intention of being able investigate evolutionary relationships in non-model systems with data sources that far exceed what is currently accessible.  Our recent work primarily applies the technology to previously sequenced genomes to judge relative performance, but we are also expanding to non-model systems and both intra and interspecific problems in evolutionary biology. 



Alexander, P. J., G. Rajanikanth, C. Bacon, AND C. D. Bailey. 2007. Rapid inexpensive recovery of high quality plant DNA using a reciprocating saw and silica-based columns. Molecular Ecology Notes 7: 5-9.
Bacon, C. D., F. A. Feltus, A. H. Paterson, AND C. D. Bailey. 2008. Developing intron-spanning primer sets for low-copy nuclear genes: novel tools for Arecaceae systematics. Molecular Ecology Notes 8: 211-214.
Bailey, C. D., AND J. J. Doyle. 1999. Potential phylogenetic utility of the low-copy nuclear gene pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Molecular Phylogenetics and Evolution 13: 20-30.
Bailey, C. D., M. G. Fain, AND P. Houde. 2006. On conditioned reconstruction, gene content data, and the recovery of fusion genomes. Molecular Phylogenetics and Evolution 39: 263-270.
Bailey, C. D., T. G. Carr, S. A. Harris, AND C. E. Hughes. 2003. Characterization of angiosperm nrDNA polymorphism, paralogy, and pseudogenes. Molecular Phylogenetics and Evolution 29: 435-455.
Hasan, N. A., K. Mummenhoff, C. F. Quiros, C. D. Tay, AND C. D. Bailey. 2010. Polymorphic chloroplast microsatellite markers in octoploid Lepidium meyenii (Brassicaceae) and cross-species amplification in Lepidium. American Journal of Botany Primer Notes: doi:10.3732/ajb.1000225.
Hughes, C. E., R. Govindarajulu, A. Robertson, S. A. Harris, AND C. D. Bailey. 2007. Serendipitous backyard hybridization and the origin of crops. Proceedings of the National Academy of Sciences 104: 14389-14394.
Lohithaswa, H. C., F. A. Feltus, H. P. Singh, C. D. Bacon, C. D. Bailey, AND A. H. Paterson. 2007. Leveraging the rice genome sequence for monocot comparative and translational genomics. Theoretical and Applied Genetics 115: 237-243.
Scotland, R., C. E. Hughes, C. D. Bailey, AND A. Wortley. 2003. The Big Machine and the Much-Maligned Taxonomist. Systematics and Biodiversity 1: 139-143.
Simmons, M. P., C. D. Bailey, AND K. C. Nixon. 2000. Phylogeny reconstruction using duplicate genes. Molecular Biology and Evolution 17: 469-473.