My students and I study evolutionary biology, primarily below the species level (molecular ecology, population genetics, 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 has worked with microsatellites, ISSRs, mtDNA and nDNA genotyping and sequencing, and the current students are now moving into genomics.  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, Bohonak and Vandergast 2011). Much of my published research relates to this topic in some way.
  
  
• With faculty and student collaborators, I worked for many years on software development for population genetic analysis (e.g., the web-based IBDWS software: Jensen et al. 2005).
  
  
• I collaborated with Amy Vandergast at the US Geological Survey on a comparative GIS-based analysis of landscape genetics in southern California (Vandergast et al. 2008). This study focused on the conservation status of "evolutionary hotspots" in this region. We have also collaborated on studies of fairy shrimp and Jerusalem crickets (Vandergast et al. 2007, 2009).
  
  
• 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).
  
  
• With many students and lab technicians, I studied genetic variation in the San Diego fairy shrimp Branchinecta sandiegonensis, a federally endangered species. I have also consulted with a variety of agencies regarding the anthropogenic activities that impact this species. We have developed a variety of genetic tools for working with this species (Steele et al. 2009, Vandergast et al. 2009), and morphological tools for hybrid analysis (Simovich et al. 2013). This information aids recovery planning for this species (e.g., Bohonak 2002-2004). Marie Simovich (at the University of San Diego) was a close collaborator and sometimes lead on these projects.
  
  
• Previous and current graduate students and have studied microevolutionary processes in a wide variety of organisms, including marine, freshwater and terrestrial vertebrates, invertebrates and plants (student projects).
  
  
• A series of projects 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 collaborated with Bruce Smith (Ithaca College) on these studies.
  
  
• Graduate and undergraduate students have worked with the San Diego Tracking Team, a volunteer organization that monitors (terrestrial vertebrate) wildlife in San Diego County. Several 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 abohonak@sdsu.edu

Undergraduate research in my laboratory could involve:

• DNA extraction, genotyping, 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 three areas. I mentor students in both the Evolutionary Biology Program Area and 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 Evolutionary Biology PhD program?
  
  
• Applying to the Ecology Master's program?
  
  
• Applying to the Ecology PhD program?
  

The application deadlines and general information on the 4 pages linked from above is more current than the instructions on the University's graduate application web page. Use the above links. Doctoral applications are usually due December 1 for the following fall. Prospective Master's students are advised to get all application materials submitted by the third week of January.