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Evolutionary Genomics of Environmental Pollution

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Ecological Genomics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 781))

Abstract

Chemical toxins have been a persistent source of evolutionary challenges throughout the history of life, and deep within the genomic storehouse of evolutionary history lay ancient adaptations to diverse chemical poisons. However, the rate of change of contemporary environments mediated by human-introduced pollutants is rapidly screening this storehouse and severely testing the adaptive potential of many species. In this chapter, we briefly review the deep history of evolutionary adaptation to environmental toxins, and then proceed to describe the attributes of stressors and populations that may facilitate contemporary adaptation to pollutants introduced by humans. We highlight that phenotypes derived to enable persistence in polluted habitats may be multi-dimensional, requiring global genome-scale tools and approaches to uncover their mechanistic basis, and include examples of recent progress in the field. The modern tools of genomics offer promise for discovering how pollutants interact with genomes on physiological timescales, and also for discovering what genomic attributes of populations may enable resistance to pollutants over evolutionary timescales. Through integration of these sophisticated genomics tools and approaches with an understanding of the deep historical forces that shaped current populations, a more mature understanding of the mechanistic basis of contemporary ecological-evolutionary dynamics should emerge.

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  1. Department of Environmental Toxicology, University of California, Davis, CA, 95616, USA

    Andrew Whitehead

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  1. Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Quebec, Québec, Canada

    Christian R. Landry

  2. Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Quebec, Québec, Canada

    Nadia Aubin-Horth

Glossary

AHR

The aryl hydrocarbon receptor (AHR) is a cytosolic transcription factor. Pollutants such as dioxins, PCBs, and PAHs, act as ligands for this receptor. Once activated, the receptor-ligand complex migrates to the nucleus, and acts as a transcription factor to activate the transcription of a battery of genes. Some of the activated genes are responsible for metabolism of the ligand and for the emergence of toxicity

Anthropogenic

Anthropogenic refers to effects or objects that are of human origin, or that are influenced by humans

Comparative transcriptomics

Comparative transcriptomics is an experimental design that includes the comparison of transcriptomic responses to some experimental variable (e.g., environmental or pollutant challenge) between strains, populations, or species

Contaminant

A contaminant is a compound that is released into the environment as a result of human activities, but that may or may not be toxic to exposed organisms

Contemporary evolution

Contemporary evolution refers to evolutionary change in response to recent changes in the environment

Copy number variation

Specific regions of the genome may increase in copy number from duplication of chromosome segments, duplication of whole chromosomes, or duplication of entire genomes. Protein family expansion (e.g., globins, HOX genes) is often from duplication of chromosome segments that include an entire protein sequence. The fate of duplicate copies may include pseudogenization, maintenance of function, neofunctionalization, or subfunctionalization

Epistasis

Epistasis is a phenomenon that refers to the non-additive effects of multiple genes, where the effects of different loci are not independent – where the effects of one gene are dependent on other genes

Genome scan

Given genome-scale sequence data for many individuals for two or more populations, genome scans are a suite of exploratory methods that are designed to detect genetic signatures of natural selection in populations. Genetic markers that exhibit signatures of selection could be the causative genetic variants, but are more likely to be physically linked to causative variants

Neofunctionalization

Neofunctionalization is a result of functional divergence of gene paralogs following duplication, where the duplicate copy acquires an entirely new function that is distinct from the original gene’s functions

PAH

Polycyclic aromatic hydrocarbons (PAHs) are a class of chemicals that are common environmental pollutants, where major sources are from spilled crude oil and from fuel combustion. PAHs act as ligands for the AHR, and exert at least part of their toxicity through the activation of the AHR signaling pathway

PCB

Polychlorinated biphenyls (PCBs) are a class of chemicals that are persistent environmental pollutants, where major sources are from wastes from industrial processes where they were used as coolant fluids, hydraulic fluids, and insulation fluids. PCBs act as ligands for the AHR, and exert at least part of their toxicity through the activation of the AHR signaling pathway

Pleiotropy

A gene product is considered pleiotropic if it influences more than one phenotypic trait

Pollutant

A pollutant is a compound that is released into the environment as a result of human activities, and that has negative effects in exposed organisms

QTL mapping

Quantitative trait locus (QTL) mapping involves matching genotype to phenotype from experimental crosses to detect genetic variants that are physically linked to phenotypes of interest. Genetic markers that are associated with the phenotype are not necessarily the causative loci, but are presumed to be physically linked with causative loci

Subfunctionalization

Subfunctionalization is a result of functional divergence of gene paralogs following duplication, where the duplicate copies retain different parts of the original gene’s functions

Toxicant

Toxicants are chemicals that exert toxic effects at sufficiently high doses, and that are not natural products, but rather products of human activity

Toxin

Toxins are chemicals that exert toxic effects at sufficiently high doses, and that are natural products of biosynthesis by organisms.

Xenobiotic

A compound that may be found within organisms, but that is foreign to those organisms, usually in reference to manufactured chemicals

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© 2014 Springer Science+Business Media Dordrecht

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Whitehead, A. (2014). Evolutionary Genomics of Environmental Pollution. In: Landry, C., Aubin-Horth, N. (eds) Ecological Genomics. Advances in Experimental Medicine and Biology, vol 781. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7347-9_16

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