Fun with Fundulus: The Evolution of Pollution Resistance in Killifish

(credit to Evan D'Alessandro, Rosenstiel School of Marine and Atmospheric Science)

In honor of Mr. Charlie Darwin’s birthday I thought I would read an evolution paper. Put that together with the turn my career has taken into ecotoxicology (and the associated steep learning curve), I was steered towards a study about adapting to pollution.

Let me start by introducing you to today’s study organism: The mummichog (Fundulus heteroclitus) is a species of non-migratory killifish found along the Atlantic coast of North America. They can be found in the brackish waters of tidal creeks, saltwater marshes, and estuaries. These fish are remarkably hardy, adaptable, and easy to study. Throughout the decades, a great deal of knowledge has been gathered about their life history, genetics, behavior, and endocrinology. They have also been used to study embryological processes and responses to chemicals and toxins. The mummichog’s adaptability to varying temperature, salinity, and oxygen along with their ability to survive in highly polluted areas has made them a popular subject in toxicology.

We know that animal populations adapt to environmental stressors through genetic and epigenetic (heritable changes in gene activity that are not caused by changes in the DNA sequence) changes. Changes that, in turn, affect gene expression and/or protein function. In this way, toxic chemicals can drive selection. A big part of the field of toxicology is understanding the molecular basis of these changes as natural populations adapt to altered environments. The mummichog’s ability to live in grossly contaminated waters has been used to better test and understand the molecular mechanisms by which natural populations adapt to long-term, multi-generational exposure to pollution.

Toxicologists, like geneticists, seem to love acronyms. And once you start reading chemical names, you know why. So let’s get some chemical terminology out of the way first. There are several chemicals that are under the umbrella of “dioxin-like compounds” (DLCs) which are by-products of various industrial processes and are all highly toxic. Aromatic hydrocarbons such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs), and polycyclic aromatic hydrocarbons (PAHs) all cause toxicity similar to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and DLCs. This toxicity manifests as interference in embryonic development, reproductive problems, immune impairment, and other not-so-pretty consequences.

A new study in BMC Evolutionary Biology takes a look at the Fundulus of New Bedford Harbor, Massachusetts. This 18,000 acre estuary and seaport is one of the EPA’s Superfund sites. It is highly contaminated with PCBs and heavy metals. Through their various stages of development and into adulthood, the killifish of these waters are less sensitive and/or resistant to the effects of the toxins. The researchers took a candidate gene approach to investigate the molecular basis of this adaptation to DLCs. To do this, they went to New Bedford Harbor and other polluted sites to collect fish. They also collected from reference sites where the PCB sensitivities of the killifish have been characterized and measured. Their methods included a lot of genetic work that, for the sake of space and sanity, I’m not going to detail. Let’s just skip along to the results shall we?

The researchers found a repeated evolution of resistance to DLCs in widely separated populations of Fundulus along the east coast of the U.S. There is strong evidence that this adaptation involves altered sensitivity of the aryl hydrocarbon receptor (AHR). Genes encoding proteins in the (AHR)-dependent signaling pathway are a master regulator of responses to many of the most toxic DLCs. The AHR is a ligand-activated transcription factor that exhibits high affinity for DLCs, regulates the expression of a large set of genes in response to DLC exposure, and is required for TCDD or PCB toxicity in fish (and mammals too). Two paralogs (or clades) of the AHR pathway have been identified in mummichog, AHR1 and AHR2, as well as an AHR repressor (AHRR). The loci (gene locations) for these three genes were found to contain a large number of polymorphisms, many of which encoded changes in amino acids. Perhaps most interesting was AHR2, the predominant form expressed in many fishes which has 951 amino acids whose variants lead to 26 different forms of the protein. The genetic diversity at these the three loci was not significantly different between contaminated and reference sites except in the case of AHR2. This paralog had significant FST values (the fixation index that measures population differentiation due to genetic structure) and showed very low nucleotide variability (0.1%).

So what's happening here? When polluted sites are compared to reference sites there is similar genetic diversity. However, when you look at specific nucleotides you see a story start to emerge. AHR1, AHR2, and AHRR are resistance genes that mediate toxic effects, and populations of killifish exhibit strong genetic structure at all three of these loci. The selection observed at AHR1 and AHR2, specifically the latter, at the highly polluted New Bedford Harbor site suggests an adaptation to the PCBs present there. AHR2 seems to be one of the genes, possibly the major one, involved in this resistance and may be one of the recurring targets for selection during local adaptation to DLCs. This adaptation allows the mummichog to survive in a really polluted environment. These results are consistent with several lines of evidence from similar studies both in the field and the lab.

Witnessing, quantifying, and mapping these mechanisms greatly advances our understanding of the consequences of environmental toxins. Overall, this is a very interesting example of adaptation in an ever changing environment.


Adam M. Reitzel, Sibel I. Karchner, Diana G. Franks, Brad R. Evans, Diane Nacci, Denise Champlin, Verónica M. Vieira, & Mark E. Hahn (2014). Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats BMC Evolutionary Biology, 14 (1) DOI: 10.1186/1471-2148-14-6


Read more about this study in the Woods Hole Oceanographic Institute's New Release "Solving An Evolutionary Puzzle New Bedford Harbor Pollution Prompts PCB-Resistance in Atlantic Killifish"
(also the source of the above image)

EPA's New Bedford Harbor Superfund Site page

And you can learn more about how the mummichog became a model organism here:
Atz, J. W. 1986. Fundulus heteroclitus in the Laboratory: A History. Amer. Zool. 26(1): 111-120. DOI: 10.1093/icb/26.1.111 (LINK)