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Academic Positions

2015 - present Assistant Dean of Graduate Affairs, San Diego State University
2008 - 2015 Vice chair and Director of Undergraduate Advising and Curriculum, San Diego State University, Department of Biology
2011 - present Professor, San Diego State University, Department of Biology
2006 - 2011 Associate professor, San Diego State University, Department of Biology
2007 - 2008 Coordinator, Evolutionary Biology Program Area, San Diego State University, Department of Biology
2000 - 2006 Assistant professor, San Diego State University, Department of Biology
1999 - 2000 Postdoctoral fellow, University of California, Berkeley, Division of Insect Biology
1998 - 1999Postdoctoral fellow, University of Hawaii, Center for Conservation Research and Training


Education

1998Ph.D. Cornell University, Ecology and Evolutionary Biology
1991B.S.   Allegheny College, Biology


Publications     
(*SDSU graduate student, **SDSU undergraduate, ***High school student)      Google Scholar link

*Spoon, K., *J. Beemer, J. C. Whitmer, J. Fan, J. P. Frazee, J. Stronach, A. J. Bohonak and R. A. Levine. Accepted. Random forests for evaluating pedagogy and informing personalized learning. Journal of Educational Data Mining.

pdf *Lewallen, E. A., A. J. Bohonak, C. A. Bonin, A. J. van Wijnen, R. L. Pitman and N. R. Lovejoy. 2016. Population genetic structure of the tropical two-wing flyingfish (Exocoetus volitans). PLoS ONE 11: e0163198.

pdf *Coates, J. H., K. A. Hovel, J. L. Butler and A. J. Bohonak. 2014. Recruitment and recovery of pink abalone (Haliotis corrugata) in a historically overexploited kelp forest: are local populations self-sustaining? Journal of Experimental Marine Biology and Ecology 460: 184-192

pdf *Andrews, J. M., A. J. Bohonak and M. A. Simovich. 2014. Isolation and characterization of polymorphic microsatellite loci in the endangered San Diego fairy shrimp (Branchinecta sandiegonensis). Conservation Genetics Resources 6: 401-403.

pdf *Carney, L. T., A. J. Bohonak, M. S. Edwards and F. Alberto. 2013. Genetic and experimental evidence for a mixed age, mixed origin bank of kelp microscopic stages in southern California. Ecology 94: 1955-1965.

pdf Simovich, M. A., K. A. Davis and A. J. Bohonak. 2013. Landscape homogenization threatens the genetic integrity of the endangered San Diego fairy shrimp Branchinecta sandiegonensis (Branchiopoda: Anostraca). Journal of Crustacean Biology 33: 730-740.

pdf *Friedman, J., A. J. Bohonak and R. A. Levine. 2013. When are two pieces better than one: Fitting and testing OLS and RMA regressions. Environmetrics 24: 306-316.

pdf Bohonak, A. J. and A. G. Vandergast. 2011. The value of DNA sequence data for studying landscape genetics. Molecular Ecology 20: 2477-2479.

pdf Bohonak, A. J. and E. T. Bauder. 2011. Accuracy of a hydrogeomorphic guidebook for functional assessment of vernal pools in Southern California. Pages 131-144 in D. Alexander, and R. Schlising, editors. Research and Recovery in Vernal Pool Landscapes. Studies from the Herbarium, Number 16. California State University, Chico. CA.

pdf *Robles-Sikisaka, R., A. J. Bohonak, L. R. McClenaghan, Jr.and A. K. Dhar. 2010. Genetic signature of rapid IHHNV (Infectious Hypodermal and Hematopoeitic Necrosis Virus) expansion in wild Penaeus shrimp populations. PLoS ONE 5: e11799.

HGM link Bauder, E. T., A. J. Bohonak, B. Hecht, M. A. Simovich, D. Shaw, D. G. Jenkins, and M. Rains. 2009. A draft regional guidebook for applying the Hydrogeomorphic approach to assessing wetland functions of vernal pool depressional wetlands in southern California. San Diego State University, San Diego, CA.

pdf *Steele, A. N., M. A. Simovich, D. Pepino, K. McNamara Schroeder, A. G. Vandergast and A. J. Bohonak. 2009. Optimized DNA extraction methods for encysted embryos of the endangered fairy shrimp, Branchinecta sandiegonensis. Conservation Genetics 10: 1777-1781.

pdf *Holzman, J. P., A. J. Bohonak, L. R. Kirkendall, D. Gottlieb, A. R. Harari, and S. T. Kelley. 2009. Inbreeding variability and population structure in the invasive haplodiploid palm-seed borer (Coccotrypes dactyliperda). Journal of Evolutionary Biology 22: 1076-1087.

pdf *Turner, J. L., S. T. Kelley, J. S. Otto, F. Valafar and A. J. Bohonak. 2009. Parallelization and optimization of genetic analyses in Isolation by Distance Web Service. BMC Genetics 10: 29.

pdf Vandergast, A. G., *E. A. Lewallen, **J. Deas, A. J. Bohonak, D. B. Weissman, and R. N. Fisher. 2009. Loss of genetic connectivity and diversity in urban microreserves in a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus “santa monica”). Journal of Insect Conservation 13: 329-345.

pdf Vandergast, A. G., D. A. Wood, M. A. Simovich and A. J. Bohonak. 2009. Identification of co-occurring Branchinecta fairy shrimp species from encysted embryos using multiplex PCR. Molecular Ecology Resources 9: 767-770.

pdf Bohonak, A. J. 2008. Genetic drift in human populations. in Handbook of Human Molecular Evolution, cross-listed in Encyclopedia of Life Sciences. John Wiley and Sons, Ltd.

pdf Vandergast, A. G., A. J. Bohonak, S. A. Hathaway, **J. Boys and R. N. Fisher. 2008. Are hotspots of evolutionary potential adequately protected in southern California? Biological Conservation 141: 1648-1664.

pdf *Viaud-Martinez, K. A., R. L. Brownell, Jr., A. Komnenou and A. J. Bohonak. 2008. Genetic isolation and morphological divergence of Black Sea bottlenose dolphins. Biological Conservation 141: 1600-1611.

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*Lewallen, E. A., T. W. Anderson and A. J. Bohonak. 2007. Genetic structure of leopard shark (Triakis semifasciata) populations in California waters. Marine Biology 152: 599-609.

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Vandergast, A. G., A. J. Bohonak, D. B. Weissman and R. N. Fisher. 2007. Understanding the genetic effects of recent habitat fragmentation in the context of evolutionary history: phylogeography and landscape genetics of a southern California endemic Jerusalem cricket (Orthoptera: Stenopelmatidae: Stenopelmatus). Molecular Ecology 16: 977-992.

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*Viaud-Martinez, K. A., *M. Martinez Vergara, P. E. Gol’din, V. Ridoux, A. A. Öztürk, B. Öztürk, P. E. Rosel, A. Frantzis, A. Komnenou and A. J. Bohonak. 2007. Morphological and genetic differentiation of the Black Sea harbour porpoise Phocoena phocoena. Marine Ecology Progress Series 338: 281-294.

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*Zickovich, J. M. and A. J. Bohonak. 2007. Dispersal ability and genetic structure in aquatic invertebrates: a comparative study in southern California streams and reservoirs. Freshwater Biology 52: 1982-1996.

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Bohonak, A. J., M. D. Holland, B. Santer, M. Zeller, C. M. Kearns and N. G. Hairston, Jr. 2006. The population genetic consequences of diapause in Eudiaptomus copepods. Archiv für Hydrobiologie 167: 183-202.

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Bohonak, A. J. 2005. Genetic drift. in Encyclopedia of Life Sciences. John Wiley and Sons, Ltd.

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***Jensen, J. L., A. J. Bohonak and S. T. Kelley. 2005. Isolation by Distance Web Service. BMC Genetics 6: 13. visit IBDWS web site

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Bohonak, A. J., B. P. Smith and M. Thornton. 2004. Distributional, morphological and genetic consequences of dispersal for temporary pond water mites. Freshwater Biology 49: 170-180.

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Mun, J., A. J. Bohonak and G. K. Roderick. 2003. Population structure of the pumpkin fruit fly Bactrocera depressa (Tephritidae) in Korea and Japan: Pliocene allopatry or recent invasion? Molecular Ecology 12: 2941-2951.

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Bohonak, A. J. and D. G. Jenkins. 2003. Ecological and evolutionary significance of dispersal by freshwater invertebrates. Ecology Letters 6: 783-796.   Invited Review

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Bohonak, A. J. 2002. IBD (Isolation By Distance): A program for analyses of isolation by distance. Journal of Heredity 93: 153-154.   download software

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Bohonak, A. J., N. Davies, F. X. Villablanca, and G. K. Roderick. 2001. Invasion genetics of New World medflies: testing alternative colonization scenarios. Biological Invasions 3: 103-111.

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Bohonak, A. J., and G. K. Roderick. 2001. Dispersal of invertebrates among temporary ponds: are genetic estimates accurate? Israel Journal of Zoology 47: 367-386.  (Special Issue: Ecology of temporary pools)

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Bohonak, A. J. 1999. Dispersal, gene flow and population structure. Quarterly Review of Biology 74: 21-45.

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Bohonak, A. J. and H. H. Whiteman. 1999. Dispersal of the fairy shrimp Branchinecta coloradensis (Anostraca): effects of hydroperiod and salamanders. Limnology and Oceanography 44: 487-493.

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Bohonak, A. J. 1999. Effect of insect-mediated dispersal on the genetic structure of postglacial water mite populations. Heredity 82: 451-461.

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Hairston, N. G., Jr., L. J. Perry, A. J. Bohonak, M. Q. Fellows, C. M. Kearns and D. R. Engstrom. 1999. Population biology of a failed invasion: paleolimnology of Daphnia exilis in upstate New York. Limnology and Oceanography 44: 477-486.

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Wissinger, S. A., A. J. Bohonak, H. H. Whiteman and W. S. Brown. 1999. Subalpine wetlands in Colorado: habitat permanence, salamander predation, and invertebrate communities. Pages 757-790 in D. P. Batzer, R. B. Rader and S. A. Wissinger, editors. Invertebrates in Freshwater Wetlands of North America: Ecology and Management. John Wiley and Sons, New York.

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Bohonak, A. J. 1998. Genetic population structure of the fairy shrimp Branchinecta coloradensis (Anostraca) in the Rocky Mountains of Colorado. Canadian Journal of Zoology 76: 2049-2057.

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Bohonak, A. J., N. Davies, G. K. Roderick and F. X. Villablanca. 1998. Is population genetics mired in the past? Trends in Ecology and Evolution 13: 360.

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Hairston, N. G., Jr., and A. J. Bohonak. 1998. Copepod reproductive strategies: life-history theory, phylogenetic pattern and invasion of inland waters. Proceedings of the Sixth International Conference on Copepoda. Journal of Marine Systems 15: 23-34.


Roderick, G. K., N. Davies, A. J. Bohonak and F. X. Villablanca. 1998. The interface of population genetics and systematics: invasion genetics of the Mediterranean fruit fly (Ceratatis capitata). Pages 489-499 in M. P. Zalucki, R. A. I. Drew and G. G. White, editors. Proceedings of the 6th Australasian Applied Entomological Research Conference, University of Queensland, Brisbane, Australia. University of Queensland Printery.


Roderick, G. K., N. Davies , A. J. Bohonak and F. X. Villablanca. 1998. Origins of Medflies trapped in California. Pages 21-25 in J. G. Morse and R. V. Dowell, editors. Proceedings of the Exotic Fruit Fly Research Symposium. Regents of the University of California, Riverside, California.

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McClure, M. and A. J. Bohonak. 1995. Non-selectivity in extinction of bivalves in the late Cretaceous of the Atlantic and Gulf Coastal Plain of North America. Journal of Evolutionary Biology 8: 779-794.

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Whiteman, H. H., S. A. Wissinger and A. J. Bohonak. 1994. Seasonal movement patterns in a subalpine population of the tiger salamander, Ambystoma tigrinum nebulosum. Canadian Journal of Zoology 72: 1780-1787.


Selected Technical Reports     (* SDSU graduate student)
Franson, S. E., J. W. Bickham, A. J. Bohonak, D. M. Marsh and A. G. Vandergast. 2008. Expert panel recommendations for designing a genetic monitoring program to assess long-term effects of pesticides and plant incorporated protectants on non-target organisms. U.S. Environmental Protection Agency, National Exposure Research Laboratory, Ecological Exposure Research Division, Molecular Ecology Research Branch. Cincinnati, Ohio.

Bohonak, A. J. and A. G. Vandergast. 2006. Biodiversity in the southern California coastal ecoregion: Phylogeographic congruence and evolutionary processes. California State Parks. December 20, 2006.

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Bohonak, A. J. 2005. Genetic testing of the endangered fairy shrimp species Branchinecta sandiegonensis. Final report to City of San Diego and US Fish and Wildlife Service. (Appendix to the City of San Diego's Vernal Pool Inventory). August 12,2005.

*Viaud, K. A., A. J. Bohonak, R. L. Brownell, Jr., A. Komnenou and L. M. Mukhametov. 2004. Conservation status of Black Sea bottlenose dolphin (Tursiops truncatus): Assessment using morphological and genetic variation. Report to ACCOBAMS scientific committee (Agreement on the Conservation of Cetaceans of the Black Sea, Mediterranean Sea and contiguous Atlantic area, concluded under the auspices of the Convention on the Conservation of Migratory Species of Wild Animals (CMS)). September 3, 2004.


Computer Programs
Documentation
Platform
Citation


IBDWS / formerly IBD
pdf
web-based
***Jensen, J. L., A. J. Bohonak and S. T. Kelley. 2005. Isolation by Distance Web Service. BMC Genetics 6: 13.
Also performs Mantel Tests and partial Mantel Tests on any data set
Visit web site   Download pdf of reference

pdf
Download Macintosh softwareDownload Windows software
Bohonak, A. J. 2002. IBD (Isolation By Distance): A program for analyses of isolation by distance. Journal of Heredity 93: 153-154.   Download pdf of reference
Download v. 1.52




Others
pdf
Download Macintosh software
Bohonak, A. J. 2003. ESP: Evolution in Simulated Populations. documented in Bohonak et al. (2001) Biological Invasions 3: 103-111.   Download pdf of reference
Download v. 1.16

pdf
Download Macintosh softwareDownload windows software
Java logo
Bohonak, A. J. 2002. RMA: Software for Reduced Major Axis Regression.
Download v. 1.17


Collaborator Home Pages

Marie A. Simovich, University of San Diego

Amy G. Vandergast, U.S. Geological Survey

 



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