Assistant Professor of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics.

Areas of Research: Genotypic variation in co-regulated networks and how it gives rise to phenotypic variation.
  • Ecology and Evolutionary Biology and Lewis-Sigler for Integrative Genomics
Research Lab
150 Carl C. Icahn Laboratory

Faculty Assistant:
Dawn Capizzi

Research Focus

Enabled by powerful genomic technologies, quantitative genetics has focused on identifying functional variants in order to build the genotype-phenotype map. The goal is to formulate models, that describe the population genetic dynamics of these variants, and to connect their evolutionary trajectory to proximal molecular mechanisms and ultimately ecological factors. This is clearly a tall order, but the field is making great progress in this direction. I am interested in understanding the emergence of variation in co-regulated gene networks and how such variation gives rise to phenotypic variation. Allelic effects are clearly context dependent, influenced both by genetic background and by the environment. This realization has far reaching implications ranging from our understanding of response to selection to our understanding of the genetic basis of human disease and the ability to predict phenotype from genotype. The challenge now is to embrace this complexity and develop an experimental and analytical framework that will inform how the genotype-phenotype map influences and is influenced by evolution. Ultimately, I want to understand how natural selection shapes genetic variation and reshapes genomic architecture to produce adaptive phenotypes.

Selected Publications

  • Ayroles JF, Buchanan SM, O'Leary C, Skutt-Kakaria K, Grenier JK, Clark AG, Hartl DL, de Bivort BL. Behavioral idiosyncrasy reveals genetic control of phenotypic variability. Proc Natl Acad Sci U S A. 2015 May 26;112(21):6706-11. doi: 10.1073/pnas.1503830112. Epub 2015 May 7.
  • Corbett-Detig RB, Zhou J, Clark AG, Hartl DL, Ayroles JF †. (2013). Genetic Incompatibilities Within Species are Widespread. Nature. 2013 Dec 5;504(7478):135-7. doi: 10.1038/nature12678. Epub 2013 Nov 6.
  • Ayroles JF, Buchanan S, Clark AG, Hartl DL, De Bivort B. (2013). From Individual Variation to Genetic Control of Variance.
  • Huang W, Richards S, Carbone MA, Zhu D, Anholt RRH, Ayroles JF, et al. (2012) Epistasis Dominates The Genetic Architecture Of Drosophila Quantitative Traits. PNAS, 109:15553-15559.
  • Massouras A, Waszak SM, Albarca M, Hens K, Holcombe K, Ayroles JF, Dermitzakis ET, Eric A Stone EA, Jensen J D, Mackay T.F.C, Deplancke B. (2012) Genomic Variation And Its Impact On Gene Expression In Drosophila Melanogaster. Plos Genetics, in press.
  • Mackay TFC*, Richards S*, Barbadilla A *, Stone EA*, Ayroles JF, Zhu D, Sònia Casillas. et. al. (2012) The Drosophila Genetics Reference Panel:A Community Resource for Analysis of Population Genomics and Quantitative Traits. Nature, 482(7384):173-8.(* Contributed equally).
  • Ober U, Ayroles JF, Stone EA, Richards S, Zhu D,Gibbs RA, Stricker C, Gianola D, Schlather M, Mackay TFC, Simianer H. (2011) Using Whole Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster. PLoS Genetics, 8(5): e1002685. Faculty of 1000.
  • Rowe K, Singhal S, MacManes M, Ayroles JF, Morelli TL, Rubidge E, Bi K, Moritz C. (2011) Museum genomics: Low cost and high accuracy genetic data from historical specimens. Molecular Ecology Ressources, 11(6): 1082–1092.
  • Ayroles JF, Laflamme B, Wolfner MA, Mackay TFC. (2010) Sifting through the data: Identifying top candidates for novelseminal protein genes from Drosophila whole genome expression data.
  • Jumbo-Lucioni P*, Ayroles JF*, Chambers MM, Jordan KW, Leips J, Mackay TF, De Luca M. (2010) Systems genetics analysis of body weight and energy metabolism traits in Drosophila melanogaster. BMC Genomics 11(11): 297. (* Contributed equally).
  • Edwards, A, Ayroles JF, Stone EA, Mackay TFC. (2009) A transcriptional network associated with natural variation in Drosophila aggressive behavior. Genome Biology 10(7): R76.
  • Mackay TFC, Stone EA, Ayroles JF. (2009) Quantitative genetics: Prospects and challenges. Nature Review Genetics 10(8): 565-577.
  • Ayroles JF, Morozova TV, Jordan KW, Duncan LH, Carbone MA, Lyman RF, Stone EA, Govindaraju DR, Ellison RC, Mackay TF, Anholt RR. (2009) Alcohol sensitivity in Drosophila: Translational potential of systems genetics. Genetics 183(2): 733-745.
  • Harbison ST, Carbone MA, Ayroles JF, Stone EA, Lyman RF, Mackay TFC (2009) Co-Regulated Transcriptional Networks Contribute to Natural Genetic Variation in Drosophila Sleep. Nature Genetics 41(3): 371-375.
  • Ayroles JF, Carbone MA, Stone EA, Jordan KW, Lyman RF, Magwire MM, Rollman SM, Duncan LH, Lawrence F, Anholt RH, Mackay TFC (2009) Systems genetics of complex taits in Drosophila melanogaster. Nature Genetics 41(3): 299-307. Faculty of 1000.