Watson C.T., Steinberg K.M., Huddleston J., Sudmant P., Warren R.L., Malig M., Schein J., Willsey J.A., Joy J.B., Scott J.K., Graves T., Wilson R.K., Holt R.A., Eichler E.E. and F. Breden. 2013. Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variants. American Journal of Human Genetics. In press

Sandkam, B. A., Joy, J. B., Watson, C. T., Gabor, C. R., Gonzales-Bendicksen, P. and F. Breden. 2013. Hybridization leads to sensory repertoire expansion in a gynogenetic fish, the Amazon molly (Poecilia formosa): a test of the hybrid-sensory expansion hypothesis. Evolution 67(1):120-30

Watson C.T., Disanto G., Breden F., Giovannoni G. and S.V. Ramagopalan. 2012. Estimating the proportion of variation in susceptibility to multiple sclerosis captured by common SNPs. Sci Rep. 22:770

Watson C.T., Disanto G., Sandve G.R., Breden F., Giovannoni G. and S.V. Ramagopalan. 2012. Age-associated hyper-methylated regions in the human brain overlap with bivalent chromatin domains. PLoS One. 2012;7(9):e43840

Gorman, K. F., Pohl, K., Ali, F., Bandwait, K., and Felix Breden. 2012. Model teleosts for the study of idiopathic-type spinal curvatures: potential biomedical applications (miniReview). Journal of Applied Ichthyology 28:353-359.

Watson, C. T. and F. Breden. 2012. The immunoglobulin heavy chain locus: genetic variation, missing data and implications for human disease. Genes and Immunity 13:363-373.

Tam, K. J., Watson, C. T., Massah, S., Kolybaba, A. M., Breden, F., Prefontaine, G. G. and T. Beischlag. 2011. Regulatory function of conserved sequences upstream of the long-wave sensitive opsin genes in teleost fishes. Vision Research 51:2295-303.

Gaudet, R. G., Breden, F., Plummer, F., and J. D. Berry. 2011. Molecular characterization of the cervical and systemic IgVH repertoire in an HIV-1 resistant individual reveals unique, yet overlapping immune compartments. MAbs 3:181-91.

Gorman, K. F., Christians, J. K., Parent, J., Ahmadi, R., Dreyer, C., Weigel, D., and F. Breden. 2011. A major QTL controls susceptibility to spinal curvature in the curveback guppy. BMC Genetics 12:16.

Breden, F., Lepik, C., Longo, N. S., Montero, M., Lipsky, P. E., and J. K. Scott. 2011. Comparison of antibody repertoires produced by HIV-1 infection, other chronic and acute infections, and systemic autoimmune disease. PLoS ONE 3:e16857.

Watson, C. T., Para, A. E., Lincoln, M. R., Ramagopalan, S. V., Orton, S. M., Morrison, K. M., Handunnetthi, L., Handel, A. E., Chao, M. J., Morahan, J., Sadovnick, A. D., Breden, F., and G. C. Ebers. 2011. Revisiting the T cell receptor alpha/delta locus and possible associations with multiple sclerosis. Genes and Immunity 12:59-66.

Watson, C. T., Gray, S. M., Hoffmann, M., Lubieniecki, K. P., Joy, J. B., Sandkam, B. A., Weigel, D., Loew, E., Dreyer, C., Davidson, W. S., and F. Breden. 2011. Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata. Journal of Molecular Evolution 72:240-52.

Breden, F. and A. Lindholm. 2011. Genetic Variation in Natural Populations. In: Ecology and Evolution of Poeciliid Fishes (eds. Jonathan Evans, Andrea Pilastro, and Ingo Schlupp) University of Chicago Press, Chicago.

Pavey, S. A., Nielsen, J. L., Mackas, R. H., Hamon, T. R., and F. Breden. 2010. Contrasting ecology shapes juvenile lake-type and riverine sockeye salmon. Transactions of the American Fisheries Society 139:1584-1594.

Wade, M. J., Wilson, D. S., and 16 other authors. 2010. Multilevel and kin selection in a connected world. Nature 463: E8-E9.

Watson, C. T., Lubieniecki, K. P., Loew, E., Davidson, W. S., and F. Breden. 2010. Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri. BMC Evolutionary Biology 10:87.

Gorman, K. F., Handrigan, G. R., Jin, G., Wallis, R., and F. Breden. 2010. Structural and micro-anatomical changes in vertebrae associated with idiopathic-type spinal curvature in the curveback guppy model. Scoliosis 5:10.

Watson, C. T., Ramagopalan, S. V., Morrison, K. M., Ebers, G. C. and F. Breden. 2010. IGHV4-39 deletion polymorphism does not associate with risk or outcome of multiple sclerosis. Journal of Neuroimmunology 225: 164-166.

Willing, E-M., Bentzen, P., van Oosterhout, C., Hoffmann, M., Cable, J., Breden, F., Weigel, D., and C. Dreyer. 2010. Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies. Molecular Ecology 19:968-984.

Gorman, K. F. and F. Breden. 2010. Disproportionate body lengths correlate with idiopathic-type curvature in the curveback guppy. Spine 35:511-516.

Bowler, M. G. and F. Breden. 2010. Assessing the Potential Threat to Natural Habitats from Insect Resistance Transgenes. In: Temporal Niche Dynamics and Ecological Processes (eds. Colleen Kelly, Michael Bowler, and Gordon Cox) Cambridge University Press.

Gorman, K. F. and F. Breden. 2009. Idiopathic-type scoliosis is not exclusive to bipedalism. Medical Hypotheses 72: 348-352.

Ward, M. N., Churcher, A. M., , Dick, K. J., Laver, C. R. J., Owens, G. L., Polack, M. D., Ward, P. R., Breden, F.*, and J. S. Taylor.* 2008. The molecular basis of color vision in colorful fish: Four Long Wave-Sensitive (LWS) opsins in guppies (Poecilia reticulata) are defined by amino acid substitutions at key functional sites. BMC Evolutionary Biology 8:210-. (*co-corresponding).

Gorman, K. F. and F. Breden. 2007. Teleosts as models for human vertebral stability and deformity. Comparative Biochemistry and Physiology Part C 145: 28-38.

Gorman, K. F., Tredwell, S. and F. Breden. 2007. The guppy curveback syndrome as a model for heritable spinal curvature in humans. Spine 32(7): 735-741.

Hoffmann, M., Tripathi, N., Henz, S. R., Lindholm, A. K., Weigel, D., Breden, F.*, and C. Dreyer*. 2007. Opsin gene duplication and diversification in the guppy, a model for sexual selection. Proceedings of the Royal Society of London Series B, 274:33-42. *F. Breden and C. Dreyer contributed equally to design of guppy opsin project.

Brummell, M., Kazianis, S., Davidson, W. S., and F. Breden. 2006. Conservation of synteny between guppy and Xiphophorus genomes. Zebrafish 3: 347-357 .

Alexander, H., Taylor, J. S., Wu, S. S-T., and F. Breden. 2006. Parallel evolution and vicariance in the guppy (Poecilia reticulata) over multiple temporal and spatial scales. Evolution 60:2352-2369.

Kelly, C. K., Bowler, M. G., and F. Breden. 2006. An analytical model assessing the potential threat to natural habitats from insect resistance transgenes: continuous transgene input. Biology Letters 2:293-297.

Kelly, C. K., Bowler, M. G., Breden, F., Fenner, M., and Poppy, G. M. 2005. An analytical model assessing the potential threat to natural habitats from insect resistance transgenes. Proceedings of the Royal Society of London Series B: Biological Sciences 272:1759-1767.

Lindholm, A. K,, Breden, F., Alexander, H. J., Chan, W-K., Thakurta, S. G., and R. Brooks. 2005. Invasion success and genetic diversity of introduced populations of guppies Poecilia reticulata in Australia. Molecular Ecology 14:3671-3682.

Lindholm, A., Brooks, R., and F. Breden. 2004. Extreme polymorphism in a Y-linked, sexually selected trait. Heredity 92:156-162.

Alexander, H. and F. Breden. 2004. Sexual isolation and extreme morphological divergence in the Cumaná guppy: a possible case of incipient speciation. Journal of Evolutionary Biology 17:1238-1254.

Bourne, G. R., Breden, F., and T. C. Allen. 2003. Females prefer carotenoid males as mates in the pentamorphic livebearing fish, Poecilia parae. Naturwissenschaften 90:402-405.

Taylor, J. S. and F. Breden. 2002. The inheritance of heteroplasmy in guppies. Journal of Fish Biology 60:1346-1350.

Lindholm, A. and F. Breden. 2002. Sex chromosomes and sexual selection in poeciliid fishes. American Naturalist 160:S214-S224.

Boake, C. R. B, Arnold, S. J., Breden, F., Meffert, L. M., Ritchie, M. G., Taylor, B. J., Wolf, J. B., and A. J. Moore. 2002. Genetic tools for studying adaptation and the evolution of behavior. American Naturalist 160:S143-S159.

Taylor, J. S. and F. Breden. 2000. Slipped-strand mispairing at non-contiguous repeats in Poecilia reticulata: A model for minisatellite birth. Genetics 155:1313-1320.

Taylor, J.S., Sanny, S. P., and F. Breden. 1999. Microsatellite allele size homoplasy in the guppy (Poecilia reticulata). Journal of Molecular Evolution 48:245-247.

Taylor, J. S., Durkin, J. M. H., and F. Breden. 1999. The death of a microsatellite: A phylogenetic perspective on microsatellite interruptions. Molecular Biology and Evolution 16:567-572.

Breden, F., Ptacek, M. B., Rashed, M., Taphorn, D., and C. A. Figueiredo. 1999. Molecular phylogeny of a live-bearing fish genus Poecilia (Poeciliidae: Cyprinodontiformes). Molecular Phylogenetics and Evolution 12:95-104.

Breden, F. and M. Bertrand. 1999. A test for female attraction to male orange coloration in Poecilia picta. Environmental Biology of Fishes 55:449-453.

Ptacek, M. B. and F. Breden. 1998. Phylogenetic relationships among the mollies (Poeciliidae: Poecilia: Mollienesia group) based on mitochondrial DNA sequences. Journal of Fish Biology 53 (Supplement 1): 64-81.

Hornaday, K., Alexander, S., and F. Breden. 1995. Distribution of a repeated DNA sequence in natural populations of the Trinidad guppy (Poecilia reticulata). Copeia 1995:809-817.

McCauley, D. E., Schiff, N., Breden, F., and G. M. Chippendale. 1995. Genetic differentiation accompanying a range expansion by the Southwestern Corn Borer (Lepidoptera:Pyralidae). Annals of the Entomological Society of America 88:357-359.

Breden, F., Novinger, D., and A. Schubert. 1995. The effect of experience on mate choice in the Trinidad Guppy. Environmental Biology of Fishes 42:323-328.

Breden, F. and K. Hornaday. 1994. A test of indirect models of selection in the Trinidad guppy. Heredity 73:291-297.

Hornaday, K., Alexander, S., and F. Breden. 1994. Absence of repetitive DNA sequences associated with sex chromosomes in natural populations of the Trinidad guppy (Poecilia reticulata). Journal of Molecular Evolution 39:431-433.

Tarpley, M., Breden, F., and G. M. Chippendale. 1993. Genetic control of geographic variation for cannibalism in the southwestern corn borer, Diatraea grandiosella. Entomologia experimentalis et applicata 66:145-152.

Chippendale, G. M., Breden, F., and D. E. McCauley. 1992. Factors controlling the distribution of a subtropical corn borer, Diatraea grandiosella. Studies on Neotropical Fauna and Environment 27:83-90.

Fajen, A. and F. Breden. 1992. Mitochondrial DNA sequence variation among natural populations of the Trinidad Guppy. Evolution 46:1457-1465.

Breden, F. and M. J. Wade. 1991. Runaway social evolution: reinforcing selection for inbreeding and altruism. Journal of Theoretical Biology 153:323-337.

McCauley, D. M., F. Breden, G. M. Chippendale, and J. A. Mihm. 1990. Genetic differentiation of populations of the southwestern corn borer (Lepidoptera: Pyralidae) from the United States and Mexico. Annals of the Entomological Society of America 83: 586-590.

Breden, F. 1990. Partitioning of covariance as a method for studying kin selection. Trends in Ecology and Evolution 5: 224-228.

Breden, F. and G. Hausfater. 1990. Selection within and between groups for infanticide. American Naturalist 136:673-688.

Shaffer, H. B. and F. Breden. 1989. The relationship between allozyme variation and life history: non-transforming salamanders are less variable. Copeia 1989:1016-1023.

Breden, F. and G. M. Chippendale. 1989. Effect of larval density and cannibalism on growth and development of the southwestern corn borer, Diatraea grandiosella, and the European corn borer, Ostrinia nubilalis (Lepidoptera: Pyralidae). Journal of the Kansas Entomological Society 62:307-315.

Breden, F. and M. J. Wade. 1989. Selection within and between kin groups of the imported willow leaf beetle, Plagiodera versicolora. The American Naturalist 134:35-50.

Breden, F. 1988. 1988. The ecology and natural history of the Fowler's toad, Bufo woodhousei fowleri (Amphibia:Bufonidae) in the Indiana Dunes National Lakeshore. Fieldiana Zoology 49:1-16.

Stoner, G. and F. Breden. 1988. Phenotypic variation in female choice related to geographic variation in male predation risk in the Trinidad guppy, Poecilia reticulata. Behavioral Ecology and Sociobiology 22:285-291.

McCauley, D., Wade, M. J., Breden, F., and M. Wohltman. 1988. Spatial and temporal variation in group relatedness: evidence from the imported willow leaf beetle. Evolution 42:184-192.

Wade, M. J. and F. Breden. 1987. Kin selection in complex groups: Mating structure, migration structure and the evolution of social behavior. In: Mammalian Dispersal Patterns: The Effects of Social Structure on Population Genetics (eds. B.D. Chepko Sade and Z.T. Halpin), pp. 273-283. University of Chicago Press, Chicago.

Breden, F. 1987. The effect of migration on the population genetic structure of the Fowler's toad, Bufo woodhousei fowleri. Copeia 1987:386-395.

Breden, F. and M. J. Wade. 1987. An experimental study of the effect of group size on larval growth and survivorship in the willow leaf beetle, Plagiodera versicolora (Coleoptera: Chrysomelidae). Environmental Entomology 16:1082-1086.

Breden, F., M. Scott, and E. Michel. 1987. Genetic differentiation for anti-predator behavior in the Trinidad guppy, Poecilia reticulata. Animal Behavior 35:618-620.

Breden, F. and G. Stoner. 1987. Male predation risk determines female preference in the Trinidad guppy. Nature 329:831-833.

Wade, M. J. and F. Breden. 1986. Life history of natural populations of the imported willow leaf beetle, Plagiodera versicolora (Coleoptera: Chrysomelidae). Annals of the Entomological Society of America 79:73-79.

Breden, F. and M. J. Wade. 1985. The effect of group size and cannibalism rate on larval growth and survivorship in Plagiodera versicolora. Entomography 3:455-463.

Breden, F., Lum, A., and R. Wassersug. 1982. Body size and orientation in aggregates of toad tadpoles. Copeia 1982:672-680.

Breden, F. and C. Kelly. 1982. The effect of conspecific interactions on metamorphosis in Bufo americanus. Ecology 63:1682-1689.

Wade, M. J. and F. Breden. 1981. The effect of inbreeding on the evolution of altruistic behavior by kin selection. Evolution 35:844-858.

Breden, F. and M. J. Wade. 1981. Inbreeding and evolution by kin selection. Ethology and Sociobiology 2:2-16.

Wade, M. J. and F. Breden. 1980. The evolution of "cheating" and selfish behavior. Behavioral Ecology and Sociobiology 7:167-172.

Breden, F. 1979. Population structure and ecology of the Fowler's toad, Bufo woodhousei fowleri, in the Indiana Dunes National Lakeshore. Proceedings of the Second Conference on Scientific Research in the National Parks, NPS, Washington, D.C.




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