Publications
Hey J., Chung Y., Sethuraman A., Lachance J., Tishkoff S.A., Sousa V.C., and Y. Wang 2018 Phylogeny Estimation by Integration over Isolation with Migration Models. Molecular Biology and Evolution 35:2805–2818.
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Kern, A. D., and J. Hey, 2017 Exact calculation of the joint allele frequency spectrum for generalized isolation with migration models. Genetics 207: 241-253.
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Chung, Y., and J. Hey, 2017 Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models. Molecular Biology and Evolution 34: 1517-1528.
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Knoblauch J, Sethuraman A, and J. Hey 2017. IMGui - a desktop GUI applicatoin for isolation with migration analyses. Molecular Biology and Evolution.34:500-504.
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Sethuraman, A, J Hey. 2016. IMa2p - parallel MCMC and inference of ancient demography under the Isolation with migration (IM) model. Molecular Ecology Resources 16: 206-215 DOI: 10.1111/1755-0998.12437
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Hey, J., Y. Chung, and A. Sethuraman. 2015. On the occurrence of false positives in tests of migration under an isolation-with-migration model. Mol. Ecol. 24:5078-5083.
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Chen, H, J Hey, K Chen. 2015. Inferring Very Recent Population Growth Rate from Population-Scale Sequencing Data: Using a Large-Sample Coalescent Estimator. Molecular Biology and Evolution.32:2996-3011
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Chen, H, J Hey, M Slatkin. 2015. A hidden Markov model for investigating recent positive selection through haplotype structure. Theoretical Population Biology 99:18-30.
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Hey, J. 2014. Species Concepts. Oxford Bibliographies Online: Evolutionary Biology. DOI: 10.1093/obo/9780199941728-0054
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Wang, S., J. Lachance, S. Tishkoff, J. Hey, and J. Xing. 2013. Apparent Variation in Neanderthal Admixture among African Populations is Consistent with Gene Flow from non-African Populations. Genome Biology and Evolution 5:2075-2081.
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Joo, D., Y.-s. Kwan, J. Song, C. Pinho, J. Hey, and Y.-J. Won. 2013. Identification of Cichlid Fishes from Lake Malawi Using Computer Vision. PLoS ONE 8:e77686.
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Sousa, V. C. and J. Hey. 2013. Understanding the origin of species with genome-scale Data: modeling gene flow. Nature Reviews Genetics. 14: 404-414
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Sousa, V. C., M. Carneiro, N. Ferrand, and J. Hey. 2013. Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models. Genetics 194:211-233.
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Loh, Y.-H. E., E. Besault, F. M. Muenzel, R. B. Roberts, M. Barluenga, C. E. Kidd, A. E. Howe, F. Di Palma, K. Lindblad-Toh, J. Hey, O. Seehausen, O. Salzburger, T. D. Kocher, and J. T. Streelman. 2013. Origins of shared genetic variation in African cichlids. Mol. Biol. Evol.30:906-917
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Moser, A., J. Hey, P. Dranchak, M. Karaman, J. Zhao, L. Cox, O. Ryder, and J. Hacia. 2013. Diverse captive non-human primates with phytanic acid-deficient diets rich in plant products have substantial phytanic acid levels in their red blood cells. Lipids in Health and Disease 12:10.
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Hey, J. 2013. What Genetics Can Tell Us about the Origins of the Modern Human Brain. . Pp. 91-104 in G. C. Hatfield, and H. Pittman, eds. Evolution of Mind Brain and Culture. University of Pennsylvania Press. Philadelphia, PA.
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Lukic, S., J. Hey. 2012. Demographic Inference Using Spectral Methods on SNP Data, with an Analysis of the Human Out-of-Africa Expansion. Genetics 192:619-639.
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Hey, J., and C. Pinho. 2012. Population genetics and objectivity in species diagnosis. Evolution 66:1413-1429.
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Runemark, A,. J. Hey, B. Hansson and E. I. Svensson. 2012. Vicariance divergence and gene flow among islet populations of an endemic lizard. Molecular Ecology, 21:117-129.
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Hey, J. 2011. Regarding the confusion between the population concept and Mayr's "population thinking" . Quarterly Review of Biology 86: 253-264
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Choi, S. C. and J. Hey. 2011. Joint inference of population assignment and demographic history. Genetics 189: 561-577
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Sousa, V. C., A. Grelaud, and J. Hey. 2011. On the nonidentifiability of migration time estimates in isolation with migration models. Molecular Ecology, 20: 3956-3962.
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Lukic, S., J. Hey, and K. Chen. 2011. Non-equilibrium allele frequency spectra via spectral methods. Theoretical Population Biology, 79:203-219.
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Jiang, Z.-F., D. A. Croshaw, Y. Wang, J. Hey, and C. A. Machado. 2011. Enrichment of mRNA-like non-coding RNAs in the divergence of Drosophila males. Molecular Biology and Evolution. 28: 1339-1348
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Pinho, C., and J. Hey. 2010. Divergence with Gene Flow: Models and Data. Annual Review of Ecology, Evolution, and Systematics 41:215-230.
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Beaumont, M., R. Nielsen, C. Robert, J. Hey, O. Gaggiotti, L. Knowles, A. Estoup, M. Panchal, J. Corander, M. Hickerson, S. Sisson, N. Fagundes, L. Chikhi, P. Beerli, R. Vitalis, J.-M. Cornuet, J. Huelsenbeck, J. Novembre, M. Foll, Z. Yang, F. Rousset, D. Balding, and L. Excoffier. 2010. In defense of model-based inference in phylogeography. Molecular Ecology 19:436-446.
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Hey, J. 2010. Isolation with Migration Models for more than Two Populations. Molecular Biology and Evolution 27:905-920.
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Hey, J. 2010. The Divergence of Chimpanzee Species and Subspecies as Revealed in Multi-population Isolation-with-Migration Analyses. Molecular Biology and Evolution 27:921-933.
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Wang, Y and J. Hey 2010. Estimating Divergence Parameters with Small Samples from a Large Number of Loci. Genetics 184:363-379.
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Hey, J. 2009. On the arbitrary identification of real species pp. 15-28 in Speciation and Patterns of Diversity. Edited by R. K. Butlin, J. Bridle, and D. Schluter. Cambridge University Press, Cambridge.
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Hey, J. 2008. A model in two acts: a commentary on "The model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a genetic population" by Timoko Ohta and Motoo Kimura. Genetics Research 89:365-366.
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Hoelzel, A. R., J. Hey, M. E. Dahlheim, C. Nicholson, V. Burkanov, and N. Black. 2007. Evolution of population structure in a highly social top predator, the Killer Whale. Molecular Biology and Evolution 6:1407-1415.
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Shimada, M., K. Panchapakesan, S. Tishkoff, A. Nato and J. Hey. 2007. Divergent haplotypes and human history as revealed in a worldwide survey of X-linked DNA sequence variation. Molecular Biology and Evolution 24:687-698
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Hey J, Nielsen R. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. USA 104:2785-2790.
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Hey, J. 2006. Recent advances in assessing gene flow between diverging populations and species. Current Opinions in Genetics and Development 16:592-596
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Hey, J. 2006. On the failure of modern species concepts. Trends in Ecology and Evolution. 21:447-450
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Won, Y.-J., Y. Wang, A. Sivasundar, J. Raincrow and J. Hey. 2006. Nuclear gene variation and molecular dating of the cichlid species flock of Lake Malawi. Molecular Biology and Evolution 23: 828-837.
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Hey, J. 2005. On the number of New World founders: A population genetic portrait of the peopling of the Americas. PLoS Biol 3(6): e193.
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Sivasundar, A. and J. Hey. 2005. Sampling from natural populations with RNAi reveals high outcrossing and population structure in Caenorhabditis elegans. Current Biology 15: 1598-1602.
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Hey, J. 2005. On the number of new world founders: a population genetic portrait of the peopling of the Americas. PLoS Biology 3: 0965-0975.
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Won, Y.-J., A. Sivasundar, Y. Wang and J. Hey. 2005. On the origin of Lake Malawi cichlids: a population genetic analysis of divergence. Proc. Natl. Acad. Sci. USA. 102: 6581-6586.
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Won, Y. J., and J. Hey. 2005. Divergence population genetics of chimpanzees. Molecular Biology and Evolution 22:297-307.
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Hey, J., W. M. Fitch, and F. J. Ayala. 2005. Systematics and the origin of species: an introduction. Proc Natl Acad Sci U S A 102:6515-6519.
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Hey, J., and R. Nielsen. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167: 747-760.
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Hey, J., Y.-J. Won, A. Sivasundar, R. Nielsen and J. A. Markert. 2004. Using nuclear haplotypes with microsatellites to study gene flow between recently separated populations. Molecular Ecology 13: 909-919.
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Hey, J. 2004. What's so hot about recombination hotspots? Public Library of Science Biology 6: 0730-0733.
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Hey, J., R. S. Waples, M. L. Arnold, R. K. Butlin and R. G. Harrison. 2003. Understanding and confronting species uncertainty in biology and conservation. Trends in Ecology and Evolution 18: 597-603
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Hey, J. and C. A. Machado. 2003. The study of structured populations - new hope for a difficult and divided science. Nature Reviews Genetics 4: 535-543
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Machado, C. A. and J. Hey 2003. The causes of phylogenetic conflict in a classic Drosophila species group. Proceedings of the Royal Society, London, Series B 270: 1193-1202
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Sivasundar, A. and J. Hey. 2003. Population genetics of Caenorhabditis elegans: the paradox of low polymorphism in a widespread species. Genetics 163: 147-157
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Yang, Z. H., D. Stephens, K. J. Dawson, A. Drummond, G. Nicholls, R. C. Griffiths, H. M. Wilkinson-Herbots, M. A. Beaumont, S. J. E. Baird, M. Lascoux, R. Leblois, A. Estoup, R. Nielsen, J. Hey, and M. P. H. Stumpf. 2003. Discussion on the paper by Wilson, Weale and Balding Journal of the Royal Statistical Society Series A-Statistics in Society 166:188-201.
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Hacia, J. G. and J. Hey. 2003. Human evolution: select your words carefully. Heredity 90: 343-344.
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OrtĂz-Barrientos, D., J. Reiland, J. Hey, and M.A.F. Noor. 2002. Recombination and divergence of hybridizing species. Genetica 115:167-178.
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Machado, C. A., R. M. Kliman, J. A. Markert and J. Hey 2002. Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and its close relatives. Molecular Biology and Evolution 19: 472-488.
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Hey, J. and R. M. Kliman, 2002. Interactions between natural selection, recombination, and gene density in the genes of Drosophila. Genetics 160:595-608.
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Harris, E. E. and J. Hey 2001. Human populations show reduced DNA sequence variation at the Factor IX locus. Current Biology 11: 774-778.
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Hey, J. 2001. Let us appreciate evolving genes: A review of "Adaptive Evolution of Genes and Genomes" by Austin L. Hughes. Evolution 55: 2369-2370.
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Kliman, R. M., P. Andolfatto, J. A. Coyne, F. Depaulis, M. Kreitman, A. J. Berry, J. McCarter, J. Wakeley and J. Hey. 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156:1913-1931.
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Hey, J. 2000. Anticipating scientific revolutions in evolutionary genetics. Evolutionary Biology 32: 97-111.
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Hey, J. 2000. Migration Mumbles: A review of "Migration and Colonization in Human Microevolution" by A. G. Fix, Trends in Ecology and Evolution. 15: 256
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Hey, J. 2000. Human mitochondrial DNA recombination: can it be true? [News & Comment in] Trends in Ecology and Evolution. 15: 181-182.
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Hey, J. and E. E. Harris. 1999. Population bottlenecks and patterns of human polymorphism. Molecular Biology and Evolution 16: 1423-1426.
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Harris, E. E. and J. Hey. 1999. Human demography in the Pleistocene: do mitochondrial and nuclear genes tell the same story? Evolutionary Anthropology 8: 81-86.
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Wang, R.-L., A. Stec, J. Hey, L. Lukens and J. Doebley. 1999. The limits of selection during maize domestication. Nature 398: 236-239.
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Harris, E. E. and J. Hey. 1999. X chromosome evidence for ancient human histories. Proceedings of the National Academy of Sciences, USA 96: 3320-3324.
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Hey, J. 1999. The neutralist, the fly, and the selectionist. Trends in Ecology and Evolution 14: 35-38
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Hey, J. 1999. Parasite populations: The puzzle of Plasmodium. [Dispatch in] Current Biology 9: R565-R567.
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Hey, J. 1998. Selfish Genes, Pleiotropy and the Origin of Recombination. Genetics 149: 2089-2097
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Hey, J., H. Hilton, N. Leahy and R.-L. Wang. 1998. Testing models of speciation and extinction with phylogenetic trees of extant taxa. pp. 70-90 in Biodiversity Dynamics : Turnover of Populations, Taxa, and Communities. edited by M. L. McKinney. Columbia University Press.
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Wakeley, J. and J. Hey. 1998. Testing speciation models with DNA sequence data. pp 157-175 in Molecular Approaches to Ecology and Evolution. edited by R. DeSalle and B. Schierwater. Birkhäuser-Verlag, Basel.
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Hilton, H. and J. Hey. 1997. A Multilocus View of Speciation in the Drosophila virilis species group reveals complex histories and taxonomic conflicts. Genetical Research 70: 185-194.
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Wang, R-L., J. Wakeley and J. Hey. 1997. Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives. Genetics 147: 1091-1106
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Wakeley, J. and J. Hey. 1997. Estimating Ancestral Population Parameters. Genetics 145: 847-855.
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Hey, J. and J. Wakeley. 1997. A coalescent estimator of the population recombination rate. Genetics 145: 833-846.
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Hey, J. 1997. Mitochondria and nuclear genes present conflicting portraits of human origins. Molecular Biology and Evolution 14: 166-172.
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Hilton, H. and J. Hey. 1996. DNA sequence variation at the period locus reveals the history of species and speciation events in the Drosophila virilis group. Genetics 144: 1015-1025.
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Wang, R.-L. and J. Hey. 1996. The speciation history of Drosophila pseudoobscura and close relatives: inference from DNA sequence variation at the period locus. Genetics 144: 1113-1126.
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Hilton, H., R. M. Kliman and J. Hey. 1994. Using hitchhiking genes to study adaptation and divergence during speciation within the Drosophila melanogaster species complex. Evolution 48: 1900-1913.
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Kliman, R. M. and J. Hey. 1994. The effects of mutation and natural selection on codon bias in the genes of Drosophila. Genetics 137: 1049-1056.
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Hey, J. 1994. Bridging phylogenetics and population genetics with gene tree models. pp. 435-449 in Molecular Approaches to Ecology and Evolution, edited by B. Schierwater, B. Streit, G. Wagner and R. DeSalle. Birkhäuser-Verlag, Basel.
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Hey, J. and R. M. Kliman. 1994. Genealogical portraits of speciation in the Drosophila melanogaster species complex. pp. 208-216 in Non-neutral evolution: Theories and Data, edited by B. Golding. Chapman and Hall, New York.
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Kliman, R. M. and J. Hey. 1993. Reduced natural selection associated with low recombination in Drosophila melanogaster. Molecular Biology and Evolution 10: 1239-1258.
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Hey, J. and R. M. Kliman. 1993. Population genetics and phylogenetics of DNA sequence variation at multiple loci within and among species of the Drosophila melanogaster complex. Molecular Biology and Evolution 10: 804-822.
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Kliman, R. M. and J. Hey. 1993. DNA sequence variation at the period locus within and among species of the Drosophila melanogaster complex. Genetics 133: 375-387.
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Hey, J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution 46: 627-640.
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Hey, J. 1991. The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations. Genetics 128: 831-840.
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Hey, J. 1991. A multi-dimensional coalescent process applied to multi-allelic selection models and migration models. Theoretical Population Biology 39: 30-48.
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Eanes, W. F., J. W. Ajioka, J. Hey and C. Wesley. 1989. Restriction map variation associated with the G6PD polymorphism in natural populations of Drosophila melanogaster. Molecular Biology and Evolution 6: 384 398.
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Hey, J. 1989. Speciation via hybrid dysgenesis: negative evidence from the Drosophila affinis subgroup. Genetica 78: 97 104.
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Hey, J. 1989. The transposable portion of the genome of Drosophila algonquin is very different from that in D. melanogaster. Molecular Biology and Evolution 6: 66 79.
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Eanes, W. F., C. Wesley, J. Hey, D. Houle and J. W. Ajioka. 1987. The fitness consequences of P-element insertion in Drosophila melanogaster. Genetical Research 52: 17 26.
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Hey, J. and D. Houle. 1987. Habitat choice in the Drosophila affinis subgroup. Heredity 58: 463 471.
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Eanes, W. F. and J. Hey. 1986. In vivo function of rare G6PD variants collected from natural populations of Drosophila melanogaster. Genetics 113: 679 693.
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Eanes, W. F., J. Hey and D. Houle. 1985. Homozygous and hemizygous viability variation on the X chromosome of Drosophila melanogaster. Genetics 111: 831 844.
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