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Hey Lab                                                                         

Jody Hey and Hey lab researchers

Publications

Journal Articles and Reviews

2015

Hey, J., Y. Chung and A. Sethuraman. 2015. On the occurrence of false positives in tests of migration under an isolation-with-migration model. Molecular Ecology 24:5078-5083.

Chen, H., J. Hey and 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.

Sethuraman, A, J Hey. 2015. IMa2p - Parallel MCMC and inference of ancient demography under the Isolation with Migration (IM) model. Molecular Ecology Resources 16:206-215.

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.

2014

Hey, J. 2014. Species Concepts. Oxford Bibliographies Online: Evolutionary Biology.

2013

Sousa, V., and J. Hey. 2013. Understanding the origin of species with genome-scale data: modelling gene flow. Nat Rev Genet 14:404-414.

Sousa, V. M. C., M. Carneiro, N. Ferrand, and J. Hey. 2013. Identifying Loci Under Selection Against Gene Flow in Isolation with Migration Models. Genetics.

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.

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.

Wang S, Lachance J, Tishkoff SA, Hey J, Xing J. 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.

 

2012

Hey, J. and C. Pinho 2012.  Population Genetics and Objectivity in Species Diagnosis. Evolution 66:1413–1429

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.

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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2011

Hey J. 2011  Regarding the confusion between the population concept and Mayr's "population thinking". Quarterly Review of Biology, 86: 253-264

 Sousa, V. C., A. Grelaud, and J. Hey. 2011. On the nonidentifiability of migration time estimates in isolation with migration models. Mol. Ecol. 20:3956–3962, .

Choi, S. C., and J. Hey. 2011. Joint Inference of Population Assignment and Demographic History. Genetics 189:561-577..

 Lukic, S., J. Hey, and K. Chen. 2011. Non-equilibrium allele frequency spectra via spectral methods. Theoretical Population Biology, 79:203-219.  (Archive)

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.
 

2010 

Pinho, C., and J. Hey. 2010. Divergence with Gene Flow: Models and Data. Annual Review of Ecology, Evolution, and Systematics 41:215-230.

Hey J. 2010. Isolation with Migration Models for More Than Two Populations. Mol Biol Evol 27: 905-20

Hey J. 2010. The Divergence of Chimpanzee Species and Subspecies as Revealed in Multipopulation Isolation-with-Migration Analyses. Mol Biol Evol 27: 921-33

Wang, Y., and J. Hey. 2010. Estimating Divergence Parameters With Small Samples From a Large Number of Loci. Genetics 363-379.

Beaumont, M. A., 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. P. Huelsenbeck, M. Foll, Z. Yang, F. Rousset, D. J. Balding, and L. Excoffier. 2010. In defence of model-based inference in phylogeography. Mol. Ecol. 19:436-446.

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2007

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. Mol. Biol. Evol. 24:1407-1415.  [download PDF]

Hey, J., and R. Nielsen. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. PNAS 104:2785–2790. [download PDF]

Shimada, M. K., K. Panchapakesan, S. A. Tishkoff, A. Q. Nato, Jr, and J. Hey. 2007. Divergent Haplotypes and Human History as Revealed in a Worldwide Survey of X-Linked DNA Sequence Variation. Mol Biol Evol 24:687-698. [download PDF]

  

2006

Hey J. 2006. On the failure of modern species concepts. Trends Ecol Evol 21:447-450. [download PDF] 

Hey J. 2006. Recent advances in assessing gene flow between diverging populations and species. Current Opinion in Genetics & Development 16:592-596. [download PDF] 

Won YJ, Wang Y, Sivasundar A, Raincrow J, Hey J. 2006. Nuclear gene variation and molecular dating of the cichlid species flock of Lake Malawi. Mol Biol Evol 23:828-837. [download PDF]

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2005

Hey, J. 2005. On the Number of New World Founders: A Population Genetic Portrait of the Peopling of the Americas. PLoS Biol 3:0965-0975.  [download PDF]

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. [download PDF]

Won, Y. J., A. Sivasundar, Y. Wang, and J. Hey. 2005. On the origin of Lake Malawi cichlid species: a population genetic analysis of divergence. Proc Natl Acad Sci U S A 102:6581-6586.  [download PDF]

Won, Y. J., and J. Hey. 2005. Divergence population genetics of chimpanzees. Mol Biol Evol 22:297-307.  [download PDF]

2004

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  [download PDF]

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  [download PDF]

Hey, J. 2004. What's so hot about recombination hotspots. Public Library of Science 2:0730-0733.  [download PDF]

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2003

Hey J., Waples R.S., Arnold M.L., Butlin R.K. & Harrison R.G. 2003 Understanding and confronting species uncertainty in biology and conservation. Trends in Ecology and Evolution, 18, 597-603.  [download PDF]

Hey, J., and C. A. Machado. 2003. The study of structured populations--new hope for a difficult and divided science. Nat Rev Genet 4:535-43  [download PDF]

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 [download PDF]

Sivasundar, A., and J. Hey. 2003. Population Genetics of Caenorhabditis elegans. The paradox of low polymorphism in a widespread species. Genetics 163:147-57  [download PDF]

Hey, J. 2003. Speciation and inversions: Chimps and humans. Bioessays 25:825-8 [download PDF]

2002

Ortíz-Barrientos, D., J. Reiland, J. Hey, and M. Noor. 2002. Recombination and divergence of hybridizing species. Genetica 115:167-178 [download PDF]

Machado, C., R. M. Kliman, J. M. Markert and J. Hey, 2002 Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and its close relatives. Mol. Biol. Evol. 19: 472-488 [download PDF]

Hey, J., and R. M. Kliman, 2002 Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160: 595-608  [download PDF]

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2001

Hey, J.  2001 The Mind of the Species Problem. Trends in Ecology and Evolution 16: 326-329  [download PDF]

Harris, E. E. and J. Hey 2001 Human populations show reduced DNA sequence variation at the Factor IX locus. Current Biology 11: 774-778.  [download PDF]

2000

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.  [download PDF]

1999

Hey, J. and E. E. Harris. 1999 Population bottlenecks and patterns of human polymorphism. Molecular Biology and Evolution 16: 1423-1426. [download PDF]

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. [download PDF]

Wang, R.-L., A. Stec, J. Hey, L. Lukens and J. Doebley. 1999 The limits of selection during maize domestication. Nature 398: 236-239. [download PDF]

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.  [download PDF]

Hey, J. 1999. The neutralist, the fly, and the selectionist. Trends in Ecology and Evolution 14: 35-38  [download PDF]

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1998

Hey, J. 1998  Selfish Genes, Pleiotropy and the Origin of Recombination.  Genetics 149: 2089-2097  [download PDF]

1997

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.  [download PDF]

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   [download PDF]

Wakeley, J. and J. Hey. 1997 Estimating Ancestral Population Parameters. Genetics 145: 847-855.  [download PDF]

Hey, J. and J. Wakeley. 1997 A coalescent estimator of the population recombination rate. Genetics 145: 833-846.- [download PDF]

Hey, J. 1997 Mitochondria and nuclear genes present conflicting portraits of human origins. Molecular Biology and Evolution 14: 166-172.   [download PDF]

1994

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.  [download PDF]

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.  [download PDF]

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1993

Kliman, R. M. and J. Hey. 1993. Reduced natural selection associated with low recombination in Drosophila melanogaster.  Molecular Biology and Evolution 10: 1239-1258.  [download PDF]

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.  [download PDF]

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.  [download PDF]

1992

Hey, J. 1992. Using phylogenetic trees to study speciation and extinction. Evolution 46: 627-640. [download PDF]

1991

Hey, J. 1991. The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations.  Genetics 128: 831-840.  [download PDF]

Hey, J. 1991. A multi-dimensional coalescent process applied to multi-allelic selection models and migration models. Theoretical Population Biology 39: 30-48. [download PDF]

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1989

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. [download PDF]

Hey, J. 1989. Speciation via hybrid dysgenesis: negative evidence from the Drosophila affinis subgroup.  Genetica 78: 97-104. [download PDF]

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.  [download PDF]

<= 1988

Eanes, W. F., C. Wesley, J. Hey, D. Houle and J. W. Ajioka. 1988. The fitness consequences of P-element insertion in Drosophila melanogaster.  Genetical Research 52: 17-26. [download PDF]

Hey, J. and D. Houle. 1987. Habitat choice in the Drosophila affinis subgroup. Heredity 58: 463-471. [download PDF]

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.  [download PDF]

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. [download PDF]

Eanes, W. F., B. Bingham, J. Hey and D. Houle. 1985. Targeted selection experiments and enzyme polymorphism: negative evidence for octanoate selection at the G6PD locus in Drosophila melanogaster.  Genetics 109: 379-391. [download PDF]

Hey, J. and M. K. Gargiulo. 1985. Sex ratio changes in Leptopilina heterotoma in response to inbreeding.  Journal of Heredity 76: 209-211. [download PDF]

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Book Chapters

Hey, J. 2009. On the arbitrary identification of real species Pp. 15-28 in R. K. Butlin, J. Bridle, and D. Schluter, eds. Speciation and Patterns of Diversity. Cambridge University Press, Cambridge.

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.

Hey, J. 2000. Anticipating scientific revolutions in evolutionary genetics. Evolutionary Biology 32: 97-111.  [download PDF]

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. [download PDF]

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.  [download PDF]

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.  [download PDF]

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.  [download PDF]

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Books

 

Genes, Categories and Species  Jody Hey (2001) Oxford University Press

 

 

 

 

 Amazon.com link

Systematics and the Origin of Species: On Ernst Mayr's 100th Anniversary  Edited by Jody Hey, Walter Fitch and Francisco Ayala  (2005) National Academies Press

 

 

 

 Amazon.com link

 

 

 

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Invited Commentaries, Book Reviews, Letters, Abstracts and Non-refereed Articles

Hey, J. 2009. Why Should We Care about Species. Scitable by Nature Education. Nature Education.

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.

Hey, J. 2004. What's so hot about recombination hotspots. Public Library of Science 2:0730-0733.

Hey, J. 2003. Speciation and inversions: Chimps and humans. Bioessays 25:825-8. PDF.

Nielsen, R., and J. Hey. 2003. Discussion on the Paper by Wilson, Weale and Balding. Journal of the Royal Statistical Society Series A-Statistics in Society 166:188.

Hacia, J. G. and J. Hey. 2003.  Human evolution: select your words carefully. Heredity 90: 343-344.

Kliman, R. M. and J. Hey. 2003. Hill –Robertson interference in Drosophila melanogaster : reply to Marais, Mouchiroud and Duret. Genetical Research 81: 89-90. PDF

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. - PDF DOWNLOAD

Noor, M. A. F., N. A. Johnson and J. Hey.  2000 Gene flow between Drosophila pseudoobscura  and D. persimilis [Commentary].  Evolution 54: 2174-2175 - PDF DOWNLOAD

Hey, J.  2000. Reply from J. Hey [Correspondence in ] Trends in Ecology and Evolution 15: 471.

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

Hey, J.  2000. Human mitochondrial DNA recombination: can it be true?  [News & Comment  in] Trends in Ecology and Evolution. 15: 181-182.- PDF DOWNLOAD

Hey, J. and E. E. Harris. 2000. The origins of modern humans still look recent [Correspondence in] Current Biology 10: R8-R9. - PDF DOWNLOAD

Hey, J. 1999. Parasite populations: The puzzle of Plasmodium. [Dispatch in] Current Biology 9: R565-R567.- PDF DOWNLOAD

Hey, J. 1998. Population genetics and human origins: Haplotypes are key!. [Correspondence in] Trends in Genetics 14: 303-304.- PDF DOWNLOAD

Hey, J. 1989. Evolution under the scope. A review of  “Principles of Population Genetics” by D. Hartl and A.Clark.  Trends in Genetics 5: 349

Hey, J. 1985. Speciation via hybrid dysgenesis is unlikely.  [Abstract in] Genetics 110: s75.

Hey, J. and D. Houle. 1985. Rearing Drosophila athabasca.  [short article in] Drosophila Information Service 61: 192-193.

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Unpublished

A reduction of "Species" and a Resolution of the Species Problem

This paper represents an early attempt  (well before work began on the book,  Genes, Categories and Species) to address the species problem.  It contains a fairly full, and I still think correct, description of the reasons why some groups of related organisms deserve to be called species.   However it does not broach most of the issues raised in  Genes, Categories and Species and it bears a preoccupation with definitions of the word "species". 

'A Reduction of "Species" and a Resolution of the Species Problem' PDF 

 

 

Words and Distinction

In the midst of thinking about the species problem,  I spent a fair bit of time wondering over the utility of our words, and the ways that we use words to describe things in nature that are not very distinct.  One outcome of all this was an experiment conducted over the internet.  The results of this study are in a short paper entitled "Words and Distinction" 

'Words and Distinction' PDF

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