Current research in my lab examines historical patterns of diversification among genes, genomes, and organisms. We use transcriptome sequences (RNA-seq), ddRAD-seq and sequences of genes and genomes to study evolution at multiple levels of organization. Taxonomically, we are interested in all fishes with particular emphasis on North American freshwater fishes; however, several projects involve other animal groups. We are also interested in application of high performance computing to analysis of molecular data, and methods of phylogenetic inference.

Current projects:

• The Fish Tree of Life – Assembling a phylogeny of all fishes and understanding the evolution of fish adaptations
• Evolution of the oxidative phosphorylation system in relation to organismal energetics
• Geographical and environmental genomics – genetic mechanisms involved in population divergence and contemporary evolution and their relevance for adaptation and speciation
• Systematics, biogeography, and conservation of fishes – particularly species native to central and southwestern North America

• Zhang, F and RE Broughton.  2015.  Heterogeneous natural selection on oxidative phosphorylation genes among fishes with extreme high and low aerobic performance.  BMC Evolutionary Biology 15:173, doi: 10.1186/s12862-015-0453-7.

• Cureton, J C and RE Broughton.  2014.  Rapid morphological divergence of a stream fish in response to changes in water flow.  Biology Letters 10: 20140352.  http://dx.doi.org/10.1098/rsbl.2014.0352

• Zhang, F and RE Broughton.  2013.  Mito-nuclear Interactions: Compensatory Evolution or Relaxed Selection? Variable Substitution Rates of Vertebrate Oxidative Phosphorylation Genes.  Genome Biology and Evolution 5:1781–1791; doi:10.1093/gbe/evt129.

• Broughton, RE, R Betancur, C Li, G Arratia and G Ortí.  2013.  Multilocus phylogenetic analysis reveals the pattern and tempo of bony fish evolution.  Plos Currents –Tree of Life, doi: 10.1371/currents.tol.2ca8041495ffafd0c92756e75247483e.  

• Betancur, R., R E Broughton, E O Wiley, K Carpenter, J A López, C Li, N Holcroft, D. Arcila, M Sanciangco, J C Cureton, F Zhang, T Buser, M Campbell, J Ballesteros, A Roa-Varon, S Willis, W C Borden, T Rowley, P Reneau, D Hough, G Lu, T Grande, G Arratia, and G Ortí.  2013.  The tree of life and a new classification of bony fishes. Plos Currents – Tree of Life, doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.

• Broughton, R.E., K.C. Vedala, T.M. Crowl and L.L. Ritterhouse.  2011.  Current and historical hybridization with differential introgression among three species of cyprinid fishes (genus Cyprinella).  Genetica 139:699-707.

• Broughton, R.E.  2010.  Phylogeny of teleosts based on mitochondrial genome sequences.  Pp. 61-76 in Origin and phylogenetic interrelationships of teleosts honoring Gloria Arratia, J.S. Nelson, H.-P. Schultze and M.V.H. Wilson (eds.).  Munchen, Verlag Dr. Friedrich Pfeil.

• Richter, S.C., B.I. Crother, and R.E. Broughton.  2009.  Genetic consequences of population reduction and geographic isolation in the critically endangered frog, Rana sevosa.  Copeia 2009: 799-806.

• Wellborn, G.A., and R.E. Broughton.  2008.  Diversification on an ecologically constrained adaptive landscape.  Molecular Ecology 17:2927–2936.