My students and I study evolution, molecular ecology and conservation genetics. Although my taxonomic expertise is with freshwater invertebrates, graduate students in the lab have studied a wide variety of animals using genetic markers.  Our lab techniques currently include microsatellites, ISSRs, and mtDNA and nDNA genotyping and sequencing.  Each project focuses on interpreting patterns of genetic variation to 1) determine the relationships among different evolutionary lineages, 2) estimate historical and contemporary connectivity among populations, and 3) make management and conservation recommendations.

• I have long-standing interests in estimating dispersal and gene flow, particularly in freshwater invertebrates (reviewed in Bohonak 1999a, Bohonak and Roderick 2001, Bohonak and Jenkins 2003). Nearly all of my published research relates to this topic in some way.
  
  
• With a number of faculty and student collaborators, I have worked on software development for population genetic analysis. Current efforts are focused on the web-based IBDWS software (Jensen et al. 2005).
  
  
• I have studied predation, population genetics and hatching requirements in the fairy shrimp Branchinecta coloradensis in temporary ponds in the Colorado Rockies. Ambystoma tiger salamanders are the top predators in these ponds, controlling zooplankton and insect community composition.  Ironically, they also seem to be the dominant vector for dispersing fairy shrimp eggs among ponds (Whiteman et al. 1994, Bohonak 1998, Bohonak and Whiteman 1999).
  
  
• I am studying genetic variation in the San Diego fairy shrimp Branchinecta sandiegonensis, a federally endangered species. I have also consulted with military and USFWS personnel on activities that impact this species (such as military training). We are also working on genetic techniques for identifying species from the cyst stage, and on the hatching requirement for this species. This information aids recovery planning for this species (e.g., Bohonak 2002-2004). Marie Simovich (at the University of San Diego) is a close collaborator on these projects.
  
  
• Tephritid flies are invasive agricultural pests throughout the world. I collaborated on projects aimed at learning as much as possible from patterns of genetic variation in medflies.  Can we use genetic differentiation to infer the source of invading individuals?  Can we infer past dispersal and colonization patterns from now established populations? (Bohonak et al. 2001, Mun et al. 2003)
  
  
• Two previous graduate students and two current students have studied genetic variation in marine vertebrates, such as sharks, dolphins and porpoises (Lewallen 2007, Viaud-Martinez et al. 2007).
  
  
• A series of projects has focused on water mites in the genus Arrenurus.  These (fresh)water mites are free-living as adults, but larvae parasitize insects such as dragonflies or mosquitoes.  Parasitism is obligate: mites which fail to find the appropriate host die.  I am interested in how host use in each species relates to genetic patterns and evolutionary diversification. In addition, some populations have a life history similar to "direct development" in marine invertebrates.  In direct developers, extra large eggs hatch into larvae that skip the parasitic phase.  Under what conditions is parasitism lost in this way?  What happens to evolutionary lineages of direct developers?  What are the consequences of direct development for genetic variation?  (Bohonak 1999b, Bohonak et al. 2004). I collaborate with Bruce Smith (Ithaca College) on these studies.
  
  
• Recent graduate and undergraduate students have studied stream invertebrates in San Diego county (e.g., Zickovich and Bohonak in press). On some projects, we work with the San Diego Stream Team, a volunteer organization that uses insects for freshwater bioassessment.
  
  
• Recent graduate and undergraduate students have worked with the San Diego Tracking Team, a volunteer organization that monitors (terrestrial vertebrate) wildlife in San Diego County. Two students have conducted DNA fingerprinting on mule deer scat to help understand how deer move within and among wildlife corridors.
  

Student research opportunities

Graduate and undergraduate students interested in research opportunities should email me at bohonak"at"sciences.sdsu.edu.

Undergraduate research in my laboratory could involve:

• DNA sequencing and analysis
• field work on freshwater insects in San Diego County
• assisting graduate students with other genetic and conservation-oriented research projects
  
  

• Conservation genetics
• Empirical population genetics
• Computational population genetics / application development
• Systematics
• Freshwater invertebrate population ecology

At San Diego State University, the Biology department offers Master's degrees in six areas of Biology, and Doctoral degrees in two areas. I mentor Master's students in the Evolutionary Biology Program Area and the Ecology Program Area. I advise doctoral candidates in the Ecology Program Area.

Please email me prior to applying, and note the application instructions on the following Biology Department web pages:

• Applying to the Evolutionary Biology Master's program?
  
  
• Applying to the Ecology Master's program?
  
  
• Applying to the Ecology PhD program?
  

The application deadlines and general information on these 3 pages is more current than the instructions on the University' graduate application web page. Doctoral applications are usually due in December for the following fall. Prospective Master's students are advised to get all application materials submitted by January 31.