2017 Mittermeier, J.C., G. Dutson, R.E. James, T.E. Davies, R. Tako & J.A.C. Uy. The avifauna of Makira (San Cristobal), Solomon Islands. Wilson Journal of Ornithology. In Press.
  Uy, F.M.K., S. Ravichandran, K.S. Patel, J. Aresty, P.P. Aresty, R. Audett, K. Chen* L. Epple, S.F. Jeffries, G. Serein, P. Tullis-Joyce & J.A.C. Uy. Active background choice facilitates crypsis in a tropical crab. Biotropica 49:365-371. PDF
  Cooper, E.A. & J.A.C. Uy. Genomic evidence for convergent evolution of a key trait underlying divergence in island birds. Molecular Ecology. 26: 3760-3774 PDF
2016 Chaves, J.A., E. A. Cooper, A.P. Hendry, J. Podos, L.F. De León , J.A.M. Raeymaekers, O.W. McMillan & J.A.C. Uy. Genomic variation at the tips of the adaptive radiation of Darwin’s finches. Molecular Ecology. 25: 5282-5295. A "From the Cover" article. PDF

Accompanied by a "News & Views Perspective": Population genomics fits the bill: Genetics of adaptive beak variation in Darwin's finches by N.I. Mundy PDF

  Uy, J.A.C., E.A. Cooper, S. Cutie, M.R. Concannon, J. Poelstra, R.G. Moyle & C.E. Filardi.. Mutations in different genes mediate convergent melanism between isolated populations of an island flycatcher. Proceedings of the Royal Society of London, Ser. B. doi: 10.1098/rspb.2016.0731. PDF
  Sardell, J.M. & Uy, J.A.C. Hybridization following recent secondary contact results in asymmetric genotypic and phenotypic introgression between island species of Myzomela honeyeaters. Evolution 70: 257-269. PDF
  Toews, D.P. L., L. Campagna, S.A. Taylor, C.N. Balakrishnan, D.T. Baldassarre, P.E. Deane-Coe, M.G. Harvey, D.M. Hooper, D.E. Irwin, C.D. Judy, N.A. Mason, J.E. McCormack, K.G. McCracken, C.H. Oliveros, R.J. Safran, E.S.C. Scordato, K.F. Stryjewski, A. Tigano, J.A.C. Uy, and B.M. Winger. Genomic approaches to understanding population divergence and speciation in birds. Auk 133:13-30. PDF
2015 Uy, J.A.C.. & L.E. Vargas-Castro. Island size predicts the frequency of melanic birds in the color-polymorphic flycatcher Monarcha castaneiventris of the Solomon Islands. Auk 132: 787-794. PDF.
2014 Hurtado-Gonzales, J.L., E. Loew & J.A.C. Uy. Variation in the visual habitat may mediate the maintenance of color polymorphism in a poeciliid fish. PLoS One 9 (7): e101497. PDF.
  Reynolds, S., J.A.C. Uy, G.L.Patricelli, S. Coleman, M. Braun & G. Borgia. Tests of the kin selection model of mate choice and inbreeding avoidance in satin bowerbirds. Behavioral Ecology. 25: 1005-1014. PDF
2013 Uy, J.A.C. & R.J. Safran. Variation in the temporal and spatial use of signals and its implications for multimodal communication. Behavioral Ecology & Sociobiology. 67: 1499-1511. PDF
  Seddon, N., C.A. Botero, J.A. Tobias, P.O. Dunn, H.E.A. MacGregor, D.R. Rubinstein, J.A.C. Uy, J.T. Weir, L.A. Whittingham & R.J. Safran. 2013. Sexual selection accelerates signal evolution during speciation in birds. Proceedings of the Royal Society of London, Ser B. 280: 20131065. PDF
  Parchman, T.L., Z. Gompert, M.J. Braun, R.T. Brumfeild, D.B. McDonald, J.A.C. Uy, G. Zhang, E.D. Jarvis, B.A. Schlinger & C.A. Buerkle. 2013. The genomic consequences of adaptive divergence and reproductive isolation between species of manakins. Molecular Ecology, 22: 3304-3317. PDF
2012 Concannon, M.R., A.C. Stein & J.A.C. Uy. . Kin selection may contribute to lek evolution and trait introgression across an avian hybrid zone. Molecular Ecology, 21: 1477-1486. PDF
  Safran, R. et al. . A robust new metric of phenotypic distance to estimate and
compare multiple trait differences among populations. Current Zoology, 58: 426-439. PDF
2011 Uy, J.A.C.. Book review: Do we need a textbook in tropical ecology? Ecology. PDF
  Hurtado-Gonzales & J.A.C. Uy. Intrasexual competition facilitates the evolution of alternative mating strategies in a colour polymorphic fish. BMC Evolutionary Biology. 10:391. PDF
  Hurtado-Gonzales, J.L., D.T. Baldassarre & J.A.C. Uy. Interaction between female mating preferences and predation may explain the maintenance of rare males in the pentamorphic fish Poecilia parae. Journal of Evolutionary Biology. 23: 1293-1301. PDF
  Hubbard, J.K., J.A.C. Uy, M.E. Hauber, H.E. Hoekstra & R.J. Safran. Vertebrate pigmentation: from underlying genes to adaptive function. Trends in Genetics. 26: 231-240. PDF
2009 Uy, J.A.C., R.G. Moyle, C.E. Filardi & Z.A. Cheviron. Difference in plumage color used in species recognition between incipient species is linked to a single amino acid substitution in the melanocortin-1 receptor. American Naturalist. 174: 244-254. PDF.
  Faculty 1000
  Pitnick, S., K.R.H. Henn, S.D. Maheux, D.M. Higginson, J.L. Hurtado-Gonzales, M.K. Manier, K.S. Berben, C. Guptill & J.A.C. Uy. Size-dependent alternative mating tactics in the yellow dung fly. Proceedings of the Royal Society of London, Series B. doi:10.1098/rspb.2009.0632. PDF.
  Hurtado-Gonzales, J.L. & J.A.C. Uy. Alternative mating strategies may favor the persistence of a genetically based colour polymorphism in a pentamorphic fish. Animal Behaviour. 77: 1187-1194. PDF
  Uy, J.A.C., R. Moyle & C.E. Filardi. Plumage color & song differences mediate species recognition between incipient flycatcher species of the Solomon Islands, Evolution 63: 153-164. PDF
  Reynolds, S., M.C. Christman, J.A.C. Uy, G.L. Patricelli, M.J. Braun & G. Borgia. Lekking satin bowerbird males aggregate with relatives to mitigate aggression. Behavioral Ecology 20: 410-415. PDF
2008 Tori, W.P., R. Duraes, T.B. Ryder, M. Anciaes, J. Karubian, R. Macedo, J.A.C. Uy, P. Parker, T.B. Smith, A.C. Stein, M. Webster, J.G. Blake & B.A. Loiselle. Advances in sexual selection theory: Insights from tropical avifauna. Ornitologia Neotropical 19: S151-S163 (synthesis from symposium at the Neotropical Ornithological Congress). PDF
2007 Uy, J. A. C. & A.C. Stein. Variable visual habitats may influence the spread of colourful plumage across an avian hybrid zone. Journal of Evolutionary Biology 20: 1847-1858. PDF
  Reynolds, S.M., K. Dryer, J. Bollback, J.A.C. Uy, G.L. Patricelli, T. Robson, G. Borgia & M.J. Braun. Behavioral paternity predicts genetic paternity in satin bowerbirds, a species with a non-resource-based mating system. The Auk 124: 857-867. PDF
2006 Stein, A.C. & J. A. C. Uy. Plumage brightness predicts male mating success in the lekking golden-collared manakin. Behavioral Ecology. 17: 41-47. PDF
  Stein, A.C. & J. A. C. Uy. Unidirectional introgression of a secondary sexual character: A role for female choice? Evolution. 60: 1476-1485. PDF
2004 Uy, J. A. C. & J.A. Endler. Modification of the visual background increases the conspicuousness of golden-collared manakin displays. Behavioral Ecology. 15: 1103-1015. PDF
  Patricelli, G. L., J. A. C. Uy & G. Borgia. Female signals enhance the efficiency of mate assessment in satin bowerbirds (Ptilonorhynchus violaceus). Behavioral Ecology. 15: 297-304. PDF
2003 Patricelli, G. L., J. A. C. Uy & G. Borgia. Multiple male traits interact: attractive bower decorations facilitate attractive behavioural displays in satin bowerbirds. Proc. Roy. Soc. B. 270: 2389-2395. PDF
  Borgia, G., M. Egeth, J. A. C. Uy & G.L. Patricelli. Juvenile infection and male display: Testing the bright male hypothesis across individual life histories. Behavioral Ecology. 15: 722-728. PDF
2002 G. L. Patricelli, J. A. C. Uy & G. Borgia. Male displays adjusted to female’s response. Nature, 415: 279-280. PDF
2001 Uy, J. A. C., G. L. Patricelli & G. Borgia. Complex mate searching in the satin bowerbird Ptilonorhynchus violaceusAm. Naturalist, 158: 530-542. PDF
  Uy, J. A. C., G. L. Patricelli & G. Borgia. Loss of attractive mates forces female satin bowerbirds Ptilonorhynchus violaceus to increase mate searching. Proc. Roy. Soc. B., 268: 633-638. PDF
2000 Uy, J. A. C. & G. Borgia. Sexual selection drives rapid divergence in bowerbird display traits.  Evolution, 54: 273-278. PDF
  Uy, J. A. C., G. L. Patricelli & G. Borgia. Dynamic mate-searching tactic allows female satin bowerbirds Ptilonorhynchus violaceus to reduce searching.  Proc. Roy. Soc. B., 267: 251-256. PDF
1997 Kusmierski, R., G. Borgia, J. A. C. Uy & R. Crozier. Labile evolution of display traits in bowerbirds indicates reduced effects of phylogenetic constraints.Proc. Roy. Soc. B., 264: 307-313. PDF
2002 Uy, J. A. C. Say it with bowers. Natural History, vol. 111, Issue 2, pp. 76-83. PDF