Publications

 


2013


  1. Prado-Martinez, J.*, Sudmant, P.H.*, Kidd, J.M., Li, H., Kelley, J.L., Lorente-Galdos, B., Veeramah, K., Woerner, A., O'Connor, T.D., Santpere, G., Cagan, A., Theunert, C., Casals, F., Laayouni, H., Munch, K., Hobolth, A., Halager, A.E., Malig, M., Hernandez-Rodriguez, J., Hernando-Herraez, I., Prüfer, K., Pybus, M., Johnstone, L., Lachmann, M., Alkan, C., Twigg, D., Petit, N., Baker, C., Hormozdiari, F., Fernandez-Callejo, M., Dabad, M., Wilson, M.L., Stevison, L., Camprubí, C., Carvalho, T., Ruiz-Herrera, A., Vives, L., Mele, M., Abello, T., Kondova, I., Bontrop, R.E., Pusey, A., Lankester, F., Kiyang, J.A., Bergl, R.A., Lonsdorf, E., Myers, S., Ventura, M., Gagneux, P., Comas, D., Siegismund, H., Blanc, J., Agueda-Calpena, L., Gut, M., Fulton, L., Tishkoff, S.A., Mullikin, J.C., Wilson, R.K., Gut, I.G., Gonder, M.K., Ryder, O.A., Hahn, B.H., Navarro, A., Akey, J.M., Bertranpetit, J., Reich, D., Mailund, T., Schierup M.H., Hvilsom, C., Andrés, A.M., Wall, J., Bustamante, C.D., Hammer, M., Eichler, E.E.+, Marques-Bonet, T+ (2013) Great ape genetic diversity and population history. Nature. doi:10.1038/nature12228


  1. Ma X., Kelley J.L., Gutenkust R.N., Eilerton K., Musharoff S., Degenhardt J.D., Martins A.L., Vinar T., Kosiol C., Siepel A., and C. Bustamante (2013) Population genomic analysis reveals a rich demographic history of orang-utan species. In review.


  1. Ségurel, L., Austerlitz, F., Toupance, B., Gautier, M., Kelley J.L., Pasquet P., Lonjou, C., Georges, M., Voisin, S., Cruaud, C., Couloux, A., Hegay, T., Aldashev, A., Vitalis, R. and E. Heyer (2013) Positive selection of protective variants for type 2 diabetes from the Neolithic onward: a case study in Central Asia. European Journal of Human Genetics. doi:10.1038/ejhg.2012.295

    In the news: http://sciencelife.uchospitals.edu/2013/03/07/how-type-2-diabetes-survived-evolution/


2012


  1. Teets, N.M, Peyton, J.T., Colinet, H., Renault, D., Kelley, J.L., Kawarasaki , Y., Lee Jr., R.E., and D.L. Denlinger (2012) Gene expression changes governing extreme dehydration tolerance in an Antarctic insect. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1218661109 [pubmed] [PNAS]

   Data access: Gene transcripts

   In the news: Miami University news office


  1. Kelley, J.L., Passow, C., Plath, M., Rodrigues, L.A., Yee, M.C., and M. Tobler. (2012) Genomic resources for a model in adaptation and speciation research: characterization of the Poecilia mexicana transcriptome. BMC Genomics. 13:652 [link]. Highly accessed

  2. Data access: http://www.sulfide-life.info/mtobler/databases


  1. Kelley, J.L. (2012) Biased estimates of dating selection pressures in recent human evolution. Frontiers in Evolutionary and Population Genetics. 3:165 [link]


  1. Kelley, J.L., Yee, M.C., Lee, C., Levandowsky, E., Shah, M., Harkins, T., Earley, R.L., and C.D. Bustamante. (2012) The possibility of de novo assembly of a genome and population genomics of the mangrove rivulus Kryptolebias marmoratus. Integrative and Comparative Biology. 52:737-42 [pubmed]



2011


  1. Hernandez, R.D., Kelley, J.L., Elyashiv, E., Melton, S.C., Auton, A., McVean, G., Sella, G., Przeworski, M., and 1000 Genomes Project Consortium. (2011) Classic selective sweeps were rare in recent human evolution. Science 331: 920-24. [pubmed]


  1. Zakai, N., Lange, L., Longstreth, W.T. Jr., O’Meara, E.S., Kelley, J.L., Fornage, M., Nickerson, D., Cushman, M., Reiner, A.P. (2011) Association of Coagulation and Inflammation Related Genes and Factor VIIc Levels with Stroke:  The Cardiovascular Health Study. Journal of Thrombosis and Haemostasis 9(2):267-74. [pubmed]


2010


  1. 1000 Genomes Project Consortium, Abecasis G.R., Altshuler D.L., Auton A., Brooks L.D., Durbin R.M., Gibbs R.A., Hurles M.E., McVean G.A. (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061-73. [pubmed]


  1. Kelley, J.L., Aagaard, J., MacCoss, M. and W. Swanson. (2010) Functional diversification and evolution of antifreeze proteins in the Antarctic fish Lycodichthys dearborni. Journal of Molecular Evolution 71:111-118. [pubmed]


  1. Kosova, G., Pickrell, J.K., Kelley, J.L., McArdle, P.F., Shuldiner, A.R., Abney, M. and C Ober. (2010) The CFTR Met 470 allele is associated with lower birth rates in fertile men from a population isolate. PLoS Genetics. 6(6): e1000947. [pubmed]


2009


  1. Kelley, J.L., Turkheimer, K., Haney, M., and W. Swanson. (2009) Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations. Human Molecular Genetics. 18: 779-84. [pubmed]


2008


  1. Kelley, J.L. and W. Swanson. (2008) Positive selection in the human genome: from genome scans to biological significance. Annual Review of Genomics and Human Genetics. 9:143-60. [pubmed]   


  1. Kelley, J.L. and W. Swanson. (2008) Dietary change and adaptive evolution of enamelin in human and among primates. Genetics. 178(3):1595-603. [pubmed] 


2007 and earlier


  1. Kelley, J.L., Madeoy, J., Calhoun, J., Swanson, W. and J. Akey. (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Research. 16(8):980-9. [pubmed]


  1. Thomas, J., Kelley, J.L., Roberston, H., Ly, K., and W. Swanson. (2005) Adaptive evolution in the SRZ chemoreceptor families of C. elegans and C. briggsae. Proceedings of the National Academy of Sciences. 102(12): 4476 - 4481. [pubmed]


  1. Kelley, J.L.*, Stinchcombe, J.R.*, Weinig, C. and J. Schmitt. (2005) Soft and hard selection on plant defense traits in Arabidopsis thaliana. Evolutionary Ecology Research. 7(2): 287 - 302. *authors contributed jointly