Joshua Akey
Professor of Ecology and Evolutionary Biology and the Lewis-Sigler Institute for Integrative Genomics

Areas of Research: Evolutionary genomics & adaptation
  • The Lewis-Sigler Institute for Integrative Genomics
Research Lab
146 Carl Icahn Laboratory

Faculty Assistant:
Marybeth Fedele

Research Focus

The biology and evolution of genomes

Our work is guided by the principle that answers to complex and important problems should not be confined by rigid disciplinary boundaries. Thus, we are primarily motivated by important biological questions and use both experimental, computational, and theoretical methods in our research. Our favorite "model organisms" are yeast, dogs, and humans, each of which are uniquely poised to answer specific questions about the biology and evolution of genomes. More specific information about current research in each of these organisms is provided below.

Humans. We have a long-standing interest in human population genomics, with a particular emphasis on identifying regions of the genome that have been substrates of recent adaptive evolution. Although not typically viewed as a model organism, humans have become a powerful system to study genome-wide patterns of natural selection, as considerable sequence and polymorphism data exists in geographically diverse populations. We maintain an interest in developing and applying novel statistical and computational approaches for detecting selection, and have more recently been using new large-scale datasets to address questions about selection, demographic history, and archaic introgression.

Yeast. We are currently using yeast as a model system to understand the genetic architecture and evolution of high-dimensional molecular phenotypes such as gene expression, protein expression, and metabolite levels. The rapidly accumulating complete genome sequences of natural yeast isolates combined with these functional genomics phenotypes provides a powerful, and challenging, opportunity to more comprehensively understand how genetic and environmental variation conspire to produce phenotypic variation.

Dogs. Our research in canine genomics is currently focused on two projects. First, we are studying the genetic basis of adverse drug responses observed across breeds. This work is being performed in collaboration with Katrina Mealey at Washington State University. Second, we have characterized the genomic distribution of segmental duplications and copy number variants (CNVs) within and between different breeds. Our CNV projects are done in close collaboration with Evan Eichler, also in the Department of Genome Sciences.

Selected Publications

  • Tucci S, Vohr SH, McCoy RC, Vernot B, Robinson MR, Barbieri C, Nelson BJ, Fu W, Purnomo GA, Sudoyo H, Eichler EE, Barbujani G, Visscher PM, Akey JM, Green RE. 2018. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science. 361:511-516. Pubmed
  • Press MO, McCoy RC, Hall AN, Akey JM, Queitsch C. 2018. Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana. Genome Res. 28(8):1169-1178. Pubmed
  • Wolf AB, Akey JM. 2018. Outstanding questions in the study of archaic hominin admixture. PLoS Genet. 14:e1007349. Pubmed
  • Jin Y, Gittelman RM, Lu Y, Liu X, Li MD, Ling F, Akey JM. 2018. Evolution of DNAase I Hypersensitive Sites in MHC Regulatory Regions of Primates. Genetics. 209:579-589. Pubmed
  • Browning SR, Browning BL, Zhou Y, Tucci S, Akey JM. 2018. Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture. Cell. 173:53-61.e9. Pubmed
  • McCoy RC and Akey JM. 2017. Selection plays the hand it was dealt: evidence that human adaptation commonly targets standing genetic variation. Genome Biol. 18:139. Pubmed
  • McCoy RC, Wakefield J, Akey JM. 2017. Impact of Neandertal introgressed sequence on the landscape of human gene expression variation. Cell. 168:916-927. Pubmed
  • Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E. 2017. Tracing the peopling of the world through genomics. Nature. 541:302-310. Pubmed
  • Fu W, Ligabue A, Rogers KJ, Akey JM, Monnat RJ Jr. 2016. Human RECQ Helicase Pathogenic Variants, Population Variation and "Missing" Diseases. Hum Mutat. 38:193-203. Pubmed 
  • Fu W, Browning S, Browning BL, Akey JM. 2016. Robust inferences of identify by descent from exome sequencing data. American Journal of Human Genetics. 99(5):1106-1116. Pubmed
  • Tucci S, Akey JM. 2016. Population genetics: A map of human wanderlust. Nature. 538:179-180. Pubmed 
  • Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE. 2016. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature. 536:205-209. Pubmed