*Papers selected by Faculty of 1000

Hoekstra Lab publications


  • Kocher D.S., C.Li, W. Yang, H. Tan, V.S. Yi, X. Yang, E.H. Hoekstra, G. Zhang, E.N. Pierce and W.D. Yu. 2013. The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. Genome Biology 14:R142. PDF
  • Kowalko, J., N. Rohner, S.B. Rompani, B.K. Peterson, T.A. Linden, M. Yoshizawa, E.H. Kay, J. Weber, H.E. Hoekstra, W.R. Jeffery, R. Borowsky and C.J. Tabin. 2013. Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms. Current Biology 23:1874-1883. PDF
  • *Linnen, C.R., Y.-P. Poh, B.K. Peterson, R.D.H. Barrett, J.G. Larson, J.D. Jensen and H.E. Hoekstra. 2013. Adaptive evolution of multiple traits through multiple mutations at a single gene. Science 339:1312-1316. PDF
  • *Weber, J.N., B.K. Peterson and H.E. Hoekstra. 2013. Discrete genetic modules are responsible for the evolution of complex burrowing behaviour in deer mice. Nature 493:402-405. PDF (commentaries in Science and Nature News in Focus, Editorial Natural History and News and Views; auditory commentary on Nature Podcast)
  • *Losos, J.B., S.J. Arnold, G. Bejerano, E.D. Brodie III, D. Hibbett, H.E. Hoekstra, D.P. Mindell, A. Monteiro, C. Moritz, H.A. Orr, D.A. Petrov, S.S. Renner, R.E. Ricklefs, P.S. Soltis, and T.L. Turner. 2013. Evolutionary Biology for the 21st Century. PLoS Biology 11(1): e1001466. PDF


  • Tong, W. and H.E. Hoekstra. 2012. Mus spicilegus Current Biology 20:858-859. PDF
  • *Peterson, B.K, J.N. Weber, E.H. Kay, H.S. Fisher and H.E. Hoekstra. 2012. Double Digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7(5):e37135. PDF, protocol and codes
  • Kronforst, M.R., G.S. Barsh, A. Kopp, J. Mallet, A. Monteiro, S.P. Mullen, M. Protas, E.B. Rosenblum, C.J. Schneider and H.E. Hoekstra. 2012. Unraveling the thread of nature's tapestry: the genetics of diversity and convergence in animal pigmentation. Pigment Cell and Melanoma Research 25:411-433. PDF
  • Hoekstra, H.E. 2012. Genomics: Stickleback is the catch of the day. Nature 484:46-7. PDF
  • Domingues, V.S., Y.-P. Poh, B.K. Peterson, P. Pfennigs, J. Jensen and H.E. Hoekstra. Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution 66:3209-3223. PDF


  • Goncalves, G., H.E. Hoekstra and T.R.O. de Freitas. 2011. Striking coat colour variation in tuco-tucos (Rodentia: Ctenomyidae): a role for the melanocortin-1 receptor? Biological Journal of the Linnean Society 105:665-680. PDF
  • Barrett R.D.H. and H.E. Hoekstra. 2011. Molecular spandrels: tests of adaptation at the genetic level Nature Reviews Genetics 12:767-780. PDF
  • Manceau, M., V.S Domingues, R. Mallarino and H.E. Hoekstra. 2011. The developmental role of Agouti in color pattern evolution. Science 331:1062-1065. PDF


  • Metz, H.C., M. Manceau and H.E. Hoekstra. 2010. Turing patterns: how the fish got its spots. Pigment Cell and Melanoma Research 24(1):12-14. PDF
  • Robinson, G.E. et al. 2010 Empowering 21st century biology. BioScience 60:923-930. PDF
  • Manceau, M., V.S Domingues, C.R. Linnen, E.B. Rosenblum and H.E. Hoekstra. 2010. Convergence in pigmentation at multiple levels: mutations, genes and function. Philosophical Transactions of the Royal Society 365:2439-2450. PDF
  • Hoekstra, H.E. 2010. From mice to molecules: the gentic basis of color adaptation. In In the Light of Evolution: Essays from the Laboratory and Field. (Ed. J.B. Losos). Roberts and Co. Publishers, Greenwood Village, CO. PDF
  • Vignieri, S.N., J. Larson and H.E. Hoekstra. 2010. The selective advantage of cryptic coloration in mice. Evolution 64:2153-2158. PDF
  • Hoekstra, H.E. 2010. Evolutionary Biology: the next 150 years. In Evolution Since Darwin: The First 150 Years. (Eds. M.A. Bell, D.A. Futuyma, W.F. Eanes and J.S. Levinton). Sinauer Press, Sunderland, MA.
  • Hull, J.M., D.P. Mindell, S.L. Talbot, E.H. Kay, H.E. Hoekstra and H.B. Ernest. 2010. Population structure and plumage polymorphism: the intraspecific evolutionary relationships of a polymorphic raptor. BMC Evolutionary Biology 10:224. PDF
  • Hoekstra, H.E. 2010. In search of the elusive behavior gene. In Search of the Causes of Evolution: From Field Observations to Mechanisms. (Eds. P. Grant and R. Grant). Princeton University Press, Princeton, NJ.
  • Linnen, C.R. and H.E. Hoekstra. 2010. Measuring natural selection on genotypes and phenotypes in the wild. Cold Spring Harbor Symposia on Quantitative Biology 74:155-168. PDF
  • Chuong, E.B., W. Tong and H.E. Hoekstra. 2010. Maternal-fetal conflict: rapidly evolving proteins in the rodent placenta. Molecular Biology and Evolution 27:1221-1225. PDF
  • Turner, L.M, A. Young, H. Römpler, T. Schöneberg, S. Phelps and H.E. Hoekstra. 2010 Monogamy evolves through multiple mechanisms: evidence from V1aR in deer mice. Molecular Biology and Evolution 27:1269-1278. PDF
  • Hubbard, J.K., J.A.C. Uy, M.E. Hauber, H.E. Hoekstra, and R.J. Safran. 2010. Vertebrate pigmentation: from underlying genes to adaptive function. Trends in Genetics 26:231-239. PDF
  • *Fisher, H.S. and H.E. Hoekstra. 2010. Competition drives cooperation among closely-related sperm of deer mice. Nature 463:801-803. PDF ( NPR talk and Current Biology Dispatch)
  • *Rosenblum, E. B., H. Römpler, T. Schöneberg and H.E. Hoekstra. 2010. The molecular and functional basis of phenotypic convergence in white lizards at White Sands. PNAS 107:2113-2117 PDF (and PNAS Commentary)
  • Weber, J.N., M.B. Peters, O.V. Tsyusko, C.R. Linnen, C.Hagen, N.A. Schable, T.D. Tuberville, A.M. McKee, S.L. Lance, K.L. Jones, H.S. Fisher, M.J. Dewey, H.E. Hoekstra and T.C. Glenn. 2010. Five hundred microsatellite markers for Peromyscus. Conservation Genetics 11:1243-1246. PDF


  • *Aminetzach, Y.T., J.R. Srouji, C.Y. Kong and H.E. Hoekstra. 2009. Convergent evolution of novel protein function in shrew and lizard venom. Current Biology 19:1925-1931. PDF (and Current Biology Dispatch)
  • Mullen, L.M., S.N. Vignieri, J.A. Gore and H.E. Hoekstra. 2009. Adaptive basis of geographic variation: genetic, phenotypic and environmental differentiation among beach mouse populations. Proceedings of the Royal Society B 276:3809-3818. PDF
  • *Linnen, C.R., E.P. Kingsley, J.D. Jensen and H.E. Hoekstra. 2009. On the origin and spread of an adaptive allele in deer mice. Science 325:1095-1098. PDF
  • Hoekstra, H.E. 2009. “The Evolution Ringmaster” review of The Greatest Show on Earth: the Evidence for Evolution by Richard Dawkins. Cell 139:454-455. PDF
  • Kingsley, E.P., M. Manceau, C.D. Wiley and H.E. Hoekstra. 2009. Melanism in Peromyscus is caused by independent mutations in Agouti. PloS One 4:e6435. PDF
  • Berry, A.J. and H.E. Hoekstra. 2009. (Re)Reading The Origin. Current Biology 19(3):R9. PDF
  • Weber, J.N. and H.E. Hoekstra. 2009. The evolution of burrowing behavior in deer mice. Animal Behavior 77:603-609. PDF
  • Steiner, C.C., H. Römpler, L.M. Boettger, T. Schöneberg and H.E. Hoekstra. 2009. The genetics basis of phenotypic convergence in beach mice: similar pigmentation patterns but different genes.  Molecular Biology and Evolution 26(1):35-45. PDF


  • Turner, L.M., E.B. Chuong and H.E. Hoekstra. 2008. Comparative analysis of testis protein evolution in rodents. Genetics 179:2075-2089. PDF
  • Mullen, L.M. and H.E. Hoekstra. 2008. Natural selection along an environmental gradient: a classic cline in mouse pigmentation. Evolution 62(7):1555-1570. PDF
  • Turner, L.M. and H.E. Hoekstra. 2008. The evolution of reproductive proteins: causes and consequences. International Journal of Developmental Biology 52:769-780. PDF
  • Abzhanov, A., C. Extavour, A. Groover, S. Hodges, H.E. Hoekstra, E.M. Kramer and A. Monteiro. 2008.  Are we there yet? Tracking the development of new model systems. Trends in Genetics 24(7):353-360. PDF
  • Turner, L.M. and H.E. Hoekstra. 2008. Reproductive protein evolution within and between species: maintenance of divergent ZP3 alleles in Peromyscus. Molecular Ecology 17:2616-2628. PDF
  • Kay, E.H. and H.E. Hoekstra. 2008. Rodents. Current Biology 18(10):R406-410. PDF


  • *Steiner, C.C., J.N. Weber and H.E. Hoekstra. 2007. Adaptive variation in beach mice caused by two interacting pigmentation genes. PLoS Biology 5(9):1880-1889. PDF (and PLoS Biology Primer)
  • Coyne, J.A. and H.E. Hoekstra. 2007. Evolution of protein expression: new genes for a new diet. Current Biology 17:R1014-1016. PDF
  • *Hoekstra, H.E. and J.A. Coyne. 2007. The locus of evolution: evo devo and the genetics of adaptation.  Evolution 61(5):995-1016. PDF (and Science News Focus)
  • Storz, J.F. and H.E. Hoekstra. 2007. The study of adaptation and speciation in the genomic era. Journal of Mammalogy 88(1):1-4. PDF
  • Stinchcombe, J.R. and H.E. Hoekstra. 2007. Population genomics and quantitative genetics: combined approaches for finding the genes underlying ecologically important traits. Heredity 100:158-170. PDF
  • Hoekstra, H.E. 2006. Genetics, development and evolution of adaptive pigmentation in vertebrates.  Heredity 97:222-234. PDF


  • Turner, L.M. and H.E. Hoekstra. 2006. Adaptive evolution of fertilization proteins within a genus: variation in ZP2 and ZP3 in deer mice (Peromyscus). Molecular Biology and Evolution. 23(9):1656-1669. PDF
  • *Hoekstra, H.E., Hirschmann, R.J., Bundey, R.J., Insel, P. and J.P. Crossland. 2006. A single amino acid mutation contributes to adaptive color pattern in beach mice. Science. 313:101-104. PDF
  • Mullen, L.M., Hirschmann, R.J., Prince, K.L., Glenn, T.C., Dewey, M.J. and H.E. Hoekstra. 2006. Sixty polymorphic microsatellite markers for the oldfield mouse developed in Peromyscus polionotus and P. maniculatus. Molecular Ecology Notes. 6:36-40. PDF
  • *Payseur, B.A. and H.E. Hoekstra. 2005. Signature of reprodutive isolation in patterns of single nucleotide polymorphism across inbred strains of mice. Genetics. 171:1905-1916. PDF

2005 and prior years

  • Hoekstra, H.E., Krenz, J.G.and M.W. Nachman. 2005. Local adaptation in the rock pocket mouse (Chaetodipus intermedius): natural selection and phylogenetic history of populations. Heredity 94:217-228. PDF
  • Hoekstra, H.E. and M.W. Nachman. 2005. Coat-color variation in rock pocket mice (Chaetodipus intermedius): from phenotype to genotype.  In Mammalian Diversification: from Chromosomes to Phylogeography, UC Press, Zoology. Vol. 133, pp.79- 99. PDF (Entire Volume PDF)
  • Rosenblum, E.B, Hoekstra, H.E. and M.W. Nachman. 2004. Adaptive reptile color variation and the evolution of the MC1R gene.  Evolution 58(8):1794-1808. PDF
  • *Hoekstra, H.E., Drumm, K.E. and M.W. Nachman. 2004. Ecological genetics of adaptive color polymorphism in pocket mice: geographic variation in neutral and selected genes. Evolution 58(6):1329-1341. PDF
  • Hoekstra, H.E. and T. Price. 2004. Parallel evolution is in the genes. Science 303:1779-1780. PDF (comment on Mundy et al. 2004 PDF)
  • *Nachman, M.W., Hoekstra, H.E. and S. L. D’Agostino. 2003. The genetic basis of adaptive melanism in pocket mice.  PNAS 100(9):5268-73. PDF (and Trends in Genetics Research Focus PDF)
  • Hoekstra, H.E. and M.W. Nachman. 2003. Different genes underlie adaptive melanism in different populations of pocket mice.  Molecular Ecology 12:1185-94. PDF.
  • Hoekstra, H. E. 2003. Unequal transmission of mitochondrial haplotypes in natural populations of field mice with XY females (genus Akodon).  The American Naturalist 161(1):29-39. PDF
  • Hoekstra, H.E. and J.M. Hoekstra. 2001. An unusual sex-determination system in South American field mice (genus Akodon): the role of mutation, selection and meiotic drive in maintaining XY females. Evolution 55(1):190-197. PDF
  • Hoekstra, H.E., Hoekstra, J.M. Berrigan, D., Vigneri, S.N., Hill, C.E., Hoang, A, Beerli, P. and J.G. Kingsolver. 2001. Strength and tempo of directional selection in the wild. PNAS 98(16):9157-9160. PDF
  • Kingsolver, J.G., Hoekstra, H.E., Hoekstra, J.M. Berrigan, D., Vigneri, S.N., Hill, C.E., Hoang, A, Gibert, P. and P. Beerli. 2001. The strength of phenotypic selection in natural populations. The American Naturalist 157(3):245-261. PDF
  • Lingenfelter, P.A., Delbridge, M.L., Thomas, S., Hoekstra, H.E., Mitchell, M., Graves, J.A.M and C.M. Disteche. 2001. Expression and conservation of processed copies of the RBMX gene. Mammalian Genome 12(7):538-545. PDF
  • Hoekstra, H.E. and S.V. Edwards. 2000. Multiple origins of XY mice (genus Akodon): phylogenetic and chromosomal evidence. Proceedings of the Royal Society of London B. 267(1445):1825-1831. PDF
  • Hess, C.M., Gasper, J., Hoekstra, H.E., Hill, C.E. and S.V. Edwards. 2000. MHC class II pseudogene and genomic signature of a 32-kb cosmid in the house finch (Carpodacus mexicanus). Genome Research 10(5):613-623.
  • Hoekstra, H.E. and W.F. Fagan. 1998. Body size, dispersal ability and compositional disharmony: the carnivore dominated fauna of the Kuril Islands. Diversity and Distributions 4:135-149.
  • Gunther, K.E. and H.E. Hoekstra. 1997. Bear-human interactions in Yellowstone National Park, 1972-1994. Ursus 10:377-384.