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Killifish Adaptation in Response to Complex Pollution

killifish

What's the research project?

Human activity is rapidly altering Earth’s ecosystems – in many cases, too rapidly for species to adapt. In "The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish," Reid et al. compare the genomes and transcribed gene products of eight populations of Atlantic killifish (Fundulus heteroclitus) in salt marsh estuaries along the Eastern US coast, some of which have been recently doused in once-thought lethal levels of industrial pollution. They examined four geographically distinct pairs of pollution-tolerant and pollution-susceptible populations. The researchers sought to discern the genetic adaptations that conferred tolerance to the tolerant group, and the effect of adaptation on the tolerant groups’ genetic variation.


fish_1

Figure 1. A. The geographic locations of their Tolerant and Susceptible killifish populations. C. A phylogenetic tree created by examining SNP frequencies, showing that geographic location remains the greatest determinant of genetic similarity between killifish populations. B. Larval survival of susceptible and tolerant subpopulations when introduced to increasing concentrations of PCB 126, a toxic pollutant impacting the AHR pathway. Killifish were kept in identical conditions for two generations preceding hatching these larvae, showing that genes, not environment, determines larval resistance to PCB 126. (Replicated Reid et al. 2016) 


Is this hypothesis testing or discovery science?

Reid et al. used a combination of hypothesis testing and discovery science: while they set out with the intention of determining if tolerant populations share adaptations, they analyzed mass amounts of killifish genetic and transcriptomic data to find candidate genes.

What genomic technology was used in the project?

The researchers fully sequences 43 to 50 individuals from each of the eight sample populations, though the intensity varied: T1 and S1 genomes were sequenced an average of 7x/individual, and the others were only 0.6x/individual. Reid et al. split the sequenced genome into 5-kb chunks, and searched for regions that showed less than 0.1% chance of having evolved randomly. They found strong signals of recent convergent evolution in the pollution-tolerant populations, particularly in genes involved in the aryl hydrocarbon receptor signaling pathway (AHR).
fish_4
Fig 2A. The difference between allele frequencies (top) and nucleotide diversity (bottom) between tolerant and susceptible population pairs. Areas outside the red dashed lines indicate outliers, including the five AHR-implicated genes indicated at the top of the figure. (Replicated Reid et al. 2016)


They also RNA-seq data to determine which gene products differed between the tolerant and susceptible populations. Reid et al. found that 70 genes regulated by the AHR pathway were up-regulated in susceptible fish populations introduced to polychlorinated biphenyl , but not in tolerant populations. This is also indicative of convergent natural selection to survive human pollution as two AHR-interfering pollutants (halogenated aromatic hydrocarbons (HAHs), and polycyclic aromatic hydrocarbons (PAHs)) dominated at tolerant sites.

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Fig 3A. Reid et al.'s gene model of AHR pathway-related genes, with black bars indicating regions deleted from indicated tolerant populations. 3B. The number of individuals found to have homozygous deletions (black), heterozygous deletions (striped), and no deletions (grey). Notice that S3 is the only susceptible population to display a deletion genotype, and T2 is the only tolerant population to display no deletion genotype. (Replicated Reid et al. 2016)

The researchers found that tolerant fish had common and population-specific adaptations. For example, in sites 1, 2, and 3 a transcriptional target of AHR, the gene CYP1A showed consistent duplication. However, site 4 was mainly contaminated with PAHs and lacked this duplication. This indicates that the tolerant fish are not only evolving tolerance to complex chemical pollutants, but compensatory measures to survive evolving that tolerance.


  fish_6
Fig 3E. T1, T2, and T3 show duplication of the CPY1A gene. (Replicated Reid et al. 2016) 

Take Home Message

The main takeaway from this paper was that while natural selection targeted the aryl hydrocarbon receptor signaling pathway (AHR) in all populations, the mechanism varied between populations. Additionally, mechanisms varied based on the chemical makeup of the pollutants affecting the region, suggesting that killifish populations evolving “complex adaptations” in response to unique and “complex chemical mixtures.” (Reid et al. 2016) Additionally, AHR interacts with a variety of signaling pathways, from immune signaling to cell cycle regulation. A signaling pathway so integral to so many physiological functions can't be tamped down without side effects, and killifish may be evolving compensatory adaptations to mitigate the effects of interfering with AHR while evolving the pollution tolerance that's knocking it down.

Evaluation

On one hand, this research is encouraging as it suggests species are capable of evolving and therefore surviving human-caused environmental degradation. While geographic T-S pairs remained more genetically similar than any other pairing, tolerant populations showed analogous patterns of adaptation facing complex mixtures of pollution. However, strong selection pressure, wherein unfit individuals are incapable of survival and or reproduction, decreases genetic variation in a population. In fact, all tolerant populations showed a smaller effective population size, meaning that there is less variation per fish – a worrying development in terms of long-term species survival in a quickly changing world. Reid et al end their paper by reminding the reader that killifish started out as a widespread and genetically diverse species, and so were an ideal candidate for studying adaptation in a variety of polluted habitats. Being widespread and abundant puts killifish at little risk of extinction regardless of their capacity to evolve. 

Nevertheless, it's important to keep in mind the fact that most species are rare. In my opinion choosing killifish makes this paper a good precursor for genomic studies of evolution in endemic species rather than a conclusive answer to the question of if threatened organisms will be capable of adapting to humanity's destructive effect on their habitats.




Bibliography

Reid, Noah M. et al. 2016. The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish. Science [Internet]. [cited 5 Feb 2017];354(6317) : 1305. Available from http://science.sciencemag.org/content/354/6317/1305
SA Biosciences, Qiagen. 2012. AHR Pathway [Internet]. [Cited 5 Feb 2017.] Available from http://www.sabiosciences.com/pathway.php?sn=AHR_Pathway
Killifish image: Wikipedia. 2017. Mummuchog [Internet]. [Cited 5 Feb 2017]. Available from  https://en.wikipedia.org/wiki/Mummichog

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