Professor of Biology
Biologist, Oklahoma Biological Survey
Phone: (405)325-5357RM/Lab:Biological Survey 150
Dr. Broughton's web page
Current Research Interests and Subject Areas Available for Graduate Research
My research involves using molecular characters to understanding evolution at several levels of organization including nucleotide change in genes and genomes, divergence of populations and species, and phylogenetic patterns among species and higher taxa. Taxonomically, I am broadly interested in ray-finned fishes and more specifically in North American freshwater fishes, however I am also involved in projects on several other animal groups. Another major focus is development of methodological/computational approaches for improving phylogenetic inference by extracting historical signal from background noise in DNA sequences.
Current Research Projects
1. Comparative studies of vertebrate mitochondrial genomes and phylogeny of actinopterygian fishes. This involves sequencing complete mitochondrial genomes using a high-throughput shotgun cloning approach. These data are being used to reconstruct the phylogeny of major groups of ray-finned fishes, evaluate the amount of data needed to recover accurate phylogenetic patterns under various evolutionary conditions, and to discover new methodological approaches for molecular phylogenetic analysis (see next).
2. Patterns of nucleotide change and character quality in phylogenetic analysis. In particular, this involves assessing the relative historical information content of characters that conflict on phylogenetic trees (homoplasy). I am developing methods that indicate, when homoplasy is misleading, when homoplasy is not misleading, and how we recognize the difference and make use of this information.
3. Development of "high through-put phylogenetics". Or, toward a true "phylogenomics". This involves sequencing a very large number of genes from many taxa. Thus far we have focused on vertebrate genes that are readily amplified in all taxa, phylogenetically informative, and of functional interest.
4. Using genealogical patterns to understand processes of population divergence and speciation. What do gene genealogies reveal about the historical, demographic, and selective factors cause or arise from speciation in natural populations?
5. Systematics, biogeography, and conservation of fishes with emphasis on species native to central and southwestern North America. Includes molecular population genetic and phylogenetic studies of native species and field surveys of the distribution and abundance of fishes in Oklahoma.
To learn more about this research, visit Dr. Broughton's web page
Ph.D., Arizona State University
M.S., California State University, Chico
B.A.., California State University, Chico
Broughton, R.E., and R.G. Harrison. 2003. Nuclear gene genealogies reveal historical, demographic, and selective factors associated with speciation in field crickets. Genetics 163: 1389-1401.
Broughton, R.E., L.B. Stewart, and J.R. Gold. 2002. Microsatellite variation suggests substantial gene flow among Gulf of Mexico and Atlantic Ocean populations of king mackerel (Scomberomorus cavalla). Fisheries Research 54: 305-316.
Broughton, R.E., J.E. Milam, and B.A. Roe. 2001. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Research 11: 1958-1967.
Broughton, R.E., S.E. Stanley, and R.T. Durrett. 2000. Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis. Systematic Biology 49: 617-627.
Broughton, R.E., and J.R. Gold. 2000. Phylogenetic relationships in the North American cyprinid genus Cyprinella (Actinopterygii: Cyprinidae) based on mitochondrial ND2 and ND4L gene sequences. Copeia 2000: 1-10.