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Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus).

Publication ,  Journal Article
Osterberg, JS; Cammen, KM; Schultz, TF; Clark, BW; Di Giulio, RT
Published in: Aquatic toxicology (Amsterdam, Netherlands)
July 2018

In many human-altered ecosystems, organisms are increasingly faced with more diverse and complex environmental stressors and pollutant mixtures, to which the adaptations necessary to survive exposure are likely to be numerous and varied. Improving our understanding of the molecular mechanisms that underlie complex polygenic adaptations in natural settings requires significant toxicological, biochemical, physiological, and genomic data rarely available for non-model organisms. Here, we build upon two decades of study of adaptation to anthropogenic pollutants in a population of Atlantic killifish (Fundulus heteroclitus) that inhabits the creosote-contaminated Atlantic Wood Industries Superfund (AW) site on the Elizabeth River, Virginia in the United States. To better understand the genotypes that underlie previously characterized resistance to PCBs and PAHs, we performed Restriction site-Associated DNA sequencing (RADseq) on killifish from AW and two relatively clean reference sites (King's Creek-KC, and Mains Creek-MC). Across the genome, we analyzed over 83,000 loci and 12,000 single nucleotide polymorphisms (SNPs). Shared across both comparisons of killifish from polluted (AW) and relatively unpolluted (KC and MC) sites, we found eight genomic regions with smoothed FST values significantly (p < 0.001) elevated above background. Using the recently published F. heteroclitus reference genome, we identified candidate genes in these significant regions involved in the AHR pathway (e.g. AIP, ARNT1c), as well as genes relating to cardiac structure and function. These genes represent both previously characterized and potentially novel molecular adaptations involved with various aspects of resistance to these environmental toxins.

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Published In

Aquatic toxicology (Amsterdam, Netherlands)

DOI

EISSN

1879-1514

ISSN

0166-445X

Publication Date

July 2018

Volume

200

Start / End Page

73 / 82

Related Subject Headings

  • Water Pollutants, Chemical
  • Toxicology
  • Sequence Analysis, DNA
  • Rivers
  • Polymorphism, Single Nucleotide
  • Polycyclic Aromatic Hydrocarbons
  • Polychlorinated Biphenyls
  • Myocardium
  • Heart
  • Genome
 

Citation

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Osterberg, J. S., Cammen, K. M., Schultz, T. F., Clark, B. W., & Di Giulio, R. T. (2018). Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus). Aquatic Toxicology (Amsterdam, Netherlands), 200, 73–82. https://doi.org/10.1016/j.aquatox.2018.04.017
Osterberg, J. S., K. M. Cammen, T. F. Schultz, B. W. Clark, and R. T. Di Giulio. “Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus).Aquatic Toxicology (Amsterdam, Netherlands) 200 (July 2018): 73–82. https://doi.org/10.1016/j.aquatox.2018.04.017.
Osterberg JS, Cammen KM, Schultz TF, Clark BW, Di Giulio RT. Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus). Aquatic toxicology (Amsterdam, Netherlands). 2018 Jul;200:73–82.
Osterberg, J. S., et al. “Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus).Aquatic Toxicology (Amsterdam, Netherlands), vol. 200, July 2018, pp. 73–82. Epmc, doi:10.1016/j.aquatox.2018.04.017.
Osterberg JS, Cammen KM, Schultz TF, Clark BW, Di Giulio RT. Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus). Aquatic toxicology (Amsterdam, Netherlands). 2018 Jul;200:73–82.
Journal cover image

Published In

Aquatic toxicology (Amsterdam, Netherlands)

DOI

EISSN

1879-1514

ISSN

0166-445X

Publication Date

July 2018

Volume

200

Start / End Page

73 / 82

Related Subject Headings

  • Water Pollutants, Chemical
  • Toxicology
  • Sequence Analysis, DNA
  • Rivers
  • Polymorphism, Single Nucleotide
  • Polycyclic Aromatic Hydrocarbons
  • Polychlorinated Biphenyls
  • Myocardium
  • Heart
  • Genome