Populations of the Atlantic killifish (Fundulus heteroclitus) inhabiting urban estuaries have rapidly and repeatedly evolved tolerance to extreme pollution stress, yet the genetic changes that enabled this adaptive tolerance are unknown. This grant will facilitate sequencing the full killifish genome, and re-sequencing of genomes from many sensitive and tolerant populations, to enable discovery of the genetic changes that facilitated tolerance to human pollutants, and address whether there are a few or many genetic variants that confer tolerance or sensitivity to pollution among the many different populations inhabiting polluted sites.

A major ambition of both evolutionary biology and medical genetics is to identify the genetic variants within and among populations that contribute to an individual's tolerance to stress or disease. For example, human individuals vary in their sensitivity to disease and environmental pollutants, and a portion of this variation has a genetic basis. Studies of the genomic changes in killifish exposed to pollutants provide an excellent opportunity to discover the genetic basis of individual sensitivity to common environmental pollutants in a vertebrate animal that shares many traits with humans. This research could identify genetic variants that contribute to human sensitivity to environmental pollutant exposures and also offer detailed insight into fundamental mechanisms of the evolutionary process.

Project Report

The Atlantic killifish, Fundulus heteroclitus, is a powerful established model in the study of genetic adaptation to varied environmental conditions, a type of aquatic sentinel to warn us of deleterious changes in our lakes, rivers, and salt water estuaries. Multiple populations of this species have independently derived locally adaptive tolerance to diverse but mechanistically-related pollutants. The major goal of this collaborative research project is to identify the genomic basis of this dramatic, rapid, convergent evolutionary adaptation to extreme environmental stress. We have deployed state of the art sequencing and assembly strategies to build a high quality genome reference for this consortium of scientists to discover the molecular signatures in response to these aquatic pollutants. Our genome reference was completed and the assembly spans 932Mb with 262 scaffolds >1Mb in length. This genome model serves as another proof of principle for groups seeking to sequence and assemble reference genomes from non-traditional model species at low cost. We have already seen the benefits on the use of this genome resource by community that represents several scientific disciplines. Two examples are the production of a near complete set of gene models for interpretation by other disciplines and population genomics analysis that has yielded some very exciting preliminary results. In summary, the assembled genome will serve as a critical foundation for future studies that explore the genomic structural variation that may ultimately underlie the extraordinary phenotypic diversity harbored among individuals and populations in this wild outbred species.

National Science Foundation (NSF)
Division of Environmental Biology (DEB)
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George W. Gilchrist
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Washington University School of Medicine
Saint Louis
United States
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