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.
To better understand the effect of pollutions on natural population we studied populations of the salt marsh minnow (Fundulus heteroclitus or killifish) that inhabit highly polluted sites along the East coast of the United States. We examined four different populations that can survive these highly polluted waters unlike populations of the same fish species a few miles away. To determine the genes that make fish resistant to the pollutants and different from fish sensitive to the pollutants, we sequence the genomes of many different individuals. Specifically, we used high-throughput sequencing approaches to sequence the genomes of 48 individuals from each of four pairs of populations in MA, CT, NY, and VA. Each pair of populations had fish from polluted and sensitive populations. Thus, a total of eight populations and 384 individual genomes total were produced to gain an understanding of how individuals can be resistant to high levels of pollution. The results from this research produced a well-described genome for the killifish Fundulus heteroclitus. We found strong evidence for approximately 35,000 genes. When comparing the genomes of paired resistant and sensitive populations, many genes appear to have evolved by natural selection. The two most important findings are both that many different solutions exist and that one large shared gene complex is common to all polluted populations. These data suggest that many genes help resist pollution, and a few genes may be essential for this resistance. This research also was leveraged to enhance education and professional development. Specifically, four graduate students and two undergraduate students were trained in the computational skills necessary to analyze large data sets. These bioinformatic skills are increasingly important for today's biological research but also can be applied to many of fields of research. In addition, two undergraduate courses were developed to provide bioinformatic training to a greater number of students.
