Evolutionary toxicology in an omics world

Evolutionary approach for pollution study: The case of ionizing radiation

Estimating the consequences of environmental changes, specifically in a global change context, is essential for conservation issues. In the case of pollutants, the interest in using an evolutionary approach to investigate their consequences has been emphasized since the 2000s, but these studies remain rare compared to the characterization of direct effects on individual features. We focused on the study case of anthropogenic ionizing radiation because, despite its potential strong impact on evolution, the scarcity of evolutionary approaches to study the biological consequences of this stressor is particularly true. In this study, by investigating some particular features of the biological effects of this stressor, and by reviewing existing studies on evolution under ionizing radiation, we suggest that evolutionary approach may help provide an integrative view on the biological consequences of ionizing radiation. We focused on three topics: (i) the mutagenic properties of ionizing radiation and its disruption of evolutionary processes, (ii) exposures at different time scales, leading to an interaction between past and contemporary evolution, and (iii) the special features of contaminated areas called exclusion zones and how evolution could match field and laboratory observed effects. This approach can contribute to answering several key issues in radioecology: to explain species differences in the sensitivity to ionizing radiation, to improve our estimation of the impacts of ionizing radiation on populations, and to help identify the environmental features impacting organisms (e.g., interaction with other pollution, migration of populations, anthropogenic environmental changes). Evolutionary approach would benefit from being integrated to the ecological risk assessment process.

Contamination acts as a genotype-dependent barrier to gene flow, causing genetic erosion and fine-grained population subdivision in Mussels from the Strait of Istanbul

This study provides evidence of fine-grained genetic structuring in Mediterranean mussels (Mytilus galloprovincialis) from the Strait of Istanbul, caused by barriers to gene flow via contaminant-mediated selection. In this study, mitochondrial D-loop sequences were analyzed in mussels from 8 localities, all less than 30 kilometers apart, with differing contaminant loads. The results were: 1) Intra-population genetic differentiation (ΦST) between sites with high and low contaminant loads was high (up to 0.459), even at distances of only a few kilometers. 2) Genetic diversity was negatively correlated with the contaminant load ("genetic erosion"). 3) There was evidence of selection, based on haplotype frequencies and neutrality tests (Tajima's D), with purifying selection at the most contaminated site and balancing selection at the least contaminated. 4) Genetic distance was not correlated with geographic distance (no isolation-by-distance), but was correlated with contaminant load at each site. 5) Population dendrograms and Bayesian estimators of migration indicated that gene flow between sites was affected by contamination. For the dendrograms of the sampling sites, the clades clustered according to contaminant load more than geographic distance. Overall, these results suggest that 1) contamination may serve as a genotype-dependent dispersal barrier (i.e., contamination may not affect total number of migrants, just the relative proportions of the haplotypes in the established immigrants), leading strong population differentiation over short distances, and 2) genetic erosion may occur by a combination of selection and altered patterns of haplotype-specific gene flow. These effects may be more pronounced in the Strait of Istanbul than in other locations because of the riverine nature and strong, uni-directional current of the strait.

Intraspecific genetic variation is critical to robust toxicological predictions of aquatic contaminants

Environmental risk assessment is a critical tool for protecting aquatic life and its effectiveness is predicated on predicting how natural populations respond to contaminants. Yet, routine toxicity testing typically examines only one genotype, which may render risk assessments inaccurate as populations are most often composed of genetically distinct individuals. To determine the importance of intraspecific variation in the translation of toxicity testing to populations, we quantified the magnitude of genetic variation within 20 Daphnia magna clones derived from one lake using whole genome sequencing and phenotypic assays. We repeated these assays across two exposure levels of microcystins, a cosmopolitan and lethal aquatic contaminant produced by harmful algal blooms. We found considerable intraspecific genetic variation in survival, growth, and reproduction, which was amplified by microcystins exposure. Finally, using simulations we demonstrate that the common practice of employing a single genotype to calculate toxicity tolerance failed to produce an estimate within the 95% confidence interval over half of the time. These results illuminate the importance of incorporating intraspecific genetic variation into toxicity testing to reliably predict how natural populations will respond to aquatic contaminants.

Adaptive plastic responses to metal contamination in a multistress context: a field experiment in fish

Wild populations often differ in their tolerance to environmental stressors, but intraspecific variability is rarely taken into account in ecotoxicology. In addition, plastic responses to multiple stressors have rarely been investigated in realistic field conditions. In this study, we compared the responses to metal contamination of gudgeon populations (Gobio occitaniae) differing in their past chronic exposure to metal contamination, using a reciprocal transplant experiment and an immune challenge mimicking a parasite attack to test for potential effects of multiple stressors across biological levels. We measured fish survival and traits involved in metal bioaccumulation, oxidative stress, immunity, cell apoptosis, and energy management to decipher underpinning physiological mechanisms across biological levels (i.e., gene expression, cell, organism). Fish from the two replicate High Contamination sites had higher survival when transferred into contaminated sites, suggesting a local adaptation to the contaminated site, possibly explained by higher levels of detoxification and antioxidant capacity but with potential higher apoptosis costs compared to their naïve counterparts. We found no evidence of co- or maladaptation to the immune stressor, suggesting no specific costs to face pathogens. In the emerging field of evolutionary ecotoxicology, this study underlines the need to consider intraspecific variability to better understand the effects of pollution in heterogeneous populations.

Evolution and developmental expression of the sodium-iodide symporter (NIS, slc5a5) gene family: Implications for perchlorate toxicology

The vertebrate sodium-iodide symporter (NIS or SLC5A5) transports iodide into the thyroid follicular cells that synthesize thyroid hormone. The SLC5A protein family includes transporters of vitamins, minerals, and nutrients. Disruption of SLC5A5 function by perchlorate, a pervasive environmental contaminant, leads to human pathologies, especially hypothyroidism. Perchlorate also disrupts the sexual development of model animals, including threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), but the mechanism of action is unknown. To test the hypothesis that SLC5A5 paralogs are expressed in tissues necessary for the development of reproductive organs, and therefore are plausible candidates to mediate the effects of perchlorate on sexual development, we first investigated the evolutionary history of Slc5a paralogs to better understand potential functional trajectories of the gene family. We identified two clades of slc5a paralogs with respect to an outgroup of sodium/choline cotransporters (slc5a7); these clades are the NIS clade of sodium/iodide and lactate cotransporters (slc5a5, slc5a6, slc5a8, slc5a8, and slc5a12) and the SGLT clade of sodium/glucose cotransporters (slc5a1, slc5a2, slc5a3, slc5a4, slc5a10, and slc5a11). We also characterized expression patterns of slc5a genes during development. Stickleback embryos and early larvae expressed NIS clade genes in connective tissue, cartilage, teeth, and thyroid. Stickleback males and females expressed slc5a5 and its paralogs in gonads. Single-cell transcriptomics (scRNA-seq) on zebrafish sex-genotyped gonads revealed that NIS clade-expressing cells included germ cells (slc5a5, slc5a6a, and slc5a6b) and gonadal soma cells (slc5a8l). These results are consistent with the hypothesis that perchlorate exerts its effects on sexual development by interacting with slc5a5 or its paralogs in reproductive tissues. These findings show novel expression domains of slc5 genes in stickleback and zebrafish, which suggest similar functions across vertebrates including humans, and provide candidates to mediate the effects of perchlorate on sexual development.

Association between Chromosome 4 and mercury accumulation in muscle of the three-spined stickleback (Gasterosteus aculeatus)

Anthropogenic stressors, such as pollutants, act as selective factors that can leave measurable changes in allele frequencies in the genome. Metals are of particular concern among pollutants, because of interference with vital biological pathways. We use the three-spined stickleback as a model for adaptation to mercury pollution in natural populations. We collected sticklebacks from 21 locations in Flanders (Belgium), measured the accumulated levels of mercury in the skeletal muscle tissue, and genotyped the fish by sequencing (GBS). The spread of muscle mercury content across locations was considerable, ranging from 21.5 to 327 ng/g dry weight (DW). We then conducted a genome-wide association study (GWAS) between 28,450 single nucleotide polymorphisms (SNPs) and the accumulated levels of mercury, using different approaches. Based on a linear mixed model analysis, the GWAS yielded multiple hits with a single top hit on Chromosome 4, with eight more SNPs suggestive of association. A second approach, a latent factor mixed model analysis, highlighted one single SNP on Chromosome 11. Finally, an outlier test identified one additional SNP on Chromosome 4 that appeared under selection. Out of all ten SNPs we identified as associated with mercury in muscle, three SNPs all located on Chromosome 4 and positioned within a 2.5 kb distance of an annotated gene. Based on these results and the genome coverage of our SNPs, we conclude that the selective effect of mercury pollution in Flanders causes a significant association with at least one locus on Chromosome 4 in three-spined stickleback.

Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology

Our ability to predict and assess how environmental changes such as pollution and climate change affect components of the Earth's biome is of paramount importance. This need positioned the fields of ecotoxicology and stress ecology at the center of environmental monitoring efforts. Advances in these interdisciplinary fields depend not only on conceptual leaps but also on technological advances and data integration. High-throughput "omics" technologies enabled the measurement of molecular changes at virtually all levels of an organism's biological organization and thus continue to influence how the impacts of stressors are understood. This bibliometric review describes literature trends (2000-2020) that indicate that more different stressors than species are studied each year but that only a few stressors have been studied in more than two phyla. At the same time, the molecular responses of a diverse set of non-model species have been investigated, but cross-species comparisons are still rare. While transcriptomics studies dominated until 2016, a shift towards proteomics and multiomics studies is apparent. There is now a wealth of data at functional omics levels from many phylogenetically diverse species. This review, therefore, addresses the question of how to integrate omics information across species.

Predator- and competitor-induced responses in amphibian populations that evolved different levels of pesticide tolerance

Exposure to agrochemicals can drive rapid phenotypic and genetic changes in exposed populations. For instance, amphibian populations living far from agriculture (a proxy for agrochemical exposure) exhibit low pesticide tolerance, but they can be induced to possess high tolerance following a sublethal pesticide exposure. In contrast, amphibian populations close to agriculture exhibit high, constitutive tolerance to pesticides. A recent study has demonstrated that induced pesticide tolerance appears to have arisen from plastic responses to predator cues. As a result, we might expect that selection for constitutive pesticide tolerance in populations near agriculture (i.e., genetic assimilation) will lead to the evolution of constitutive responses to natural stressors. Using 15 wood frog (Rana sylvatica) populations from across an agricultural gradient, we conducted an outdoor mesocosm experiment to examine morphological (mass, body length, and tail depth) and behavioral responses (number of tadpoles observed and overall activity) of tadpoles exposed to three stressor environments (no-stressor, competitors, or predator cues). We discovered widespread differences in tadpole traits among populations and stressor environments, but no population-by-environment interaction. Subsequent linear models revealed that population distance to agriculture (DTA) was occasionally correlated with tadpole traits in a given environment and with magnitudes of plasticity, but none of the correlations were significant after Bonferroni adjustment. The magnitudes of predator and competitor plasticity were never correlated with the magnitude of pesticide-induced plasticity that we documented in a companion study. These results suggest that while predator-induced plasticity appears to have laid the foundation for the evolution of pesticide-induced plasticity and its subsequent genetic assimilation, inspection of population-level differences in plastic responses show that the evolution of pesticide-induced plasticity has not had a reciprocal effect on the evolved plastic responses to natural stressors.

Artificial Intelligence and Machine Learning in Computational Nanotoxicology: Unlocking and Empowering Nanomedicine

Advances in nanomedicine, coupled with novel methods of creating advanced materials at the nanoscale, have opened new perspectives for the development of healthcare and medical products. Special attention must be paid toward safe design approaches for nanomaterial-based products. Recently, artificial intelligence (AI) and machine learning (ML) gifted the computational tool for enhancing and improving the simulation and modeling process for nanotoxicology and nanotherapeutics. In particular, the correlation of in vitro generated pharmacokinetics and pharmacodynamics to in vivo application scenarios is an important step toward the development of safe nanomedicinal products. This review portrays how in vitro and in vivo datasets are used in in silico models to unlock and empower nanomedicine. Physiologically based pharmacokinetic (PBPK) modeling and absorption, distribution, metabolism, and excretion (ADME)-based in silico methods along with dosimetry models as a focus area for nanomedicine are mainly described. The computational OMICS, colloidal particle determination, and algorithms to establish dosimetry for inhalation toxicology, and quantitative structure-activity relationships at nanoscale (nano-QSAR) are revisited. The challenges and opportunities facing the blind spots in nanotoxicology in this computationally dominated era are highlighted as the future to accelerate nanomedicine clinical translation.

Cross-Taxa Distinctions in Mechanisms of Developmental Effects for Aquatic Species Exposed to Trifluralin

Standard ecological risk assessment practices often rely on larval and juvenile fish toxicity data as representative of the amphibian aquatic phase. Empirical evidence suggests that endpoints measured in fish early life stage tests are often sufficient to protect larval amphibians. However, the process of amphibian metamorphosis relies on endocrine cues that affect development and morphological restructuring and are not represented by these test endpoints. The present study compares developmental endpoints for zebrafish (Danio rerio) and the African clawed frog (Xenopus laevis), 2 standard test species, exposed to the herbicide trifluralin throughout the larval period. Danio rerio were more sensitive and demonstrated a reduction in growth measurements with increasing trifluralin exposure. Size of X. laevis at metamorphosis was not correlated with exposure concentration; however, time to metamorphosis was delayed relative to trifluralin concentration. Gene expression patterns indicate discrepancies in response by D. rerio and X. laevis, and dose-dependent metabolic activity suggests that trifluralin exposure perturbed biological pathways differently within the 2 species. Although many metabolites were correlated with exposure concentration in D. rerio, nontargeted hepatic metabolomics identified a subset of metabolites that exhibited a nonmonotonic response to trifluralin exposure in X. laevis. Linking taxonomic distinctions in cellular-level response with ecologically relevant endpoints will refine assumptions used in interspecies extrapolation of standard test effects and improve assessment of sublethal impacts on amphibian populations. Environ Toxicol Chem 2020;39:1797-1812. Published 2020. This article is a US government work and is in the public domain in the USA.

On biological evolution and environmental solutions

Drawing insights from multiple disciplines is essential for finding integrative solutions that are required to tackle complex environmental problems. Human activities are causing unprecedented influence on global ecosystems, culminating in the loss of species and fundamental changes in the selective environments of organisms across the tree of life. Our collective understanding about biological evolution can help identify and mitigate many of the environmental problems in the Anthropocene. To this end, we propose a stronger integration of environmental sciences with evolutionary biology.

Pesticide contamination drives adaptive genetic variation in the endemic mayfly Andesiops torrens within a semi-arid agricultural watershed of Chile

Agrichemical contamination can provoke evolutionary responses in freshwater populations. It is a particularly relevant issue in semi-arid regions due to the sensitivity of endemic species to pollutants and to interactions with temperature stress. This paper investigates the presence of pesticides in rivers within a semi-arid agricultural watershed of Chile, testing for their effects on population genetic characteristics of the endemic mayfly Andesiops torrens (Insecta, Ephemeroptera). Pesticides were detected in sediment samples in ten out of the 30 sites analyzed throughout the upper part of the Limarí watershed. To study the evolutionary impact of such contamination on A. torrens, we used a genome-wide approach and analyzed 2056 single nucleotide polymorphisms (SNPs) loci in 551 individuals from all sites. Genetic differentiation was weak between populations, suggesting high gene flow across the study area. While we did not find evidence of pesticide effects on genetic diversity nor on population differentiation, the allele frequency of three outlier SNP loci correlated significantly with pesticide occurrence. Interrogation of genomic resources indicates that two of these SNPs are located within functional genes that encode for the low-density lipoprotein receptor-related protein 2 and Dumpy, both potentially involved in insect cuticle resistance processes. Such genomic signatures of local adaptation are indicative of past adverse effects of pesticide exposure on the locally adapted populations. Our results reveal that A. torrens is sensitive to pesticide exposure, but that a high gene flow may confer resilience to contamination. This research supports the contention that A. torrens is an ideal model organism to study evolutionary responses induced by pesticides on non-target, endemic species.

The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of "Omics" Approaches Directed to Toxicant Mixtures

The last decade witnessed extraordinary advances in “omics” methods, particularly transcriptomics, proteomics and metabolomics, enabling toxicologists to integrate toxicokinetics and toxicodynamics with mechanistic insights on the mode-of-action of noxious chemicals, single or combined. The toxicology of mixtures is, nonetheless, a most challenging enterprise, especially for environmental toxicologists and ecotoxicologists, who invariably deal with chemical mixtures, many of which contain unknowns. Despite costs and demanding computations, the systems toxicology framework, of which “omics” is a major component, endeavors extracting adverse outcome pathways for complex mixtures. Still, the interplay between the multiple components of gene expression and cell metabolism tends to be overlooked. As an example, the proteome allocates DNA methyltransferases whose altered transcription or loss of function by action of chemicals can have a global impact on gene expression in the cell. On the other hand, chemical insult can produce reactive metabolites and radicals that can intercalate or bind to DNA as well as to enzymes and structural proteins, compromising their activity. These examples illustrate the importance of exploring multiple “omes” and the purpose of “omics” and multi-“omics” for building truly predictive models of hazard and risk. Here we will review the state-of-the-art of toxicogenomics highlighting successes, shortcomings and perspectives for next-generation environmental toxicologists.

Stress responses in fish: From molecular to evolutionary processes

In the context of global changes, fish are increasingly exposed to multiple stressors that have cascading effects from molecules to the whole individual, thereby affecting wild fish populations through selective processes. In this review, we synthetize recent advances in molecular biology and evolutionary biology to outline some potentially important effects of stressors on fish across biological levels. Given the burgeoning literature, we highlight four promising avenues of research. First, (1) the exposure to multiple stressors can lead to unexpected synergistic or antagonistic effects, which should be better taken into account to improve our predictions of the effects of actual and future human activities on aquatic organisms. Second, (2) we argue that such interactive effects might be due to switches in energy metabolism leading to threshold effects. Under multiple stress exposure, fish could switch from a "compensation" strategy, i.e. a reallocation of energy to defenses and repair to a "conservation" strategy, i.e. blocking of stress responses leading to strong deleterious effects and high mortality. Third, (3) this could have cascading effects on fish survival and population persistence but multiscale studies are still rare. We propose emerging tools merging different levels of biological organization to better predict population resilience under multiple stressors. Fourth (4), there are strong variations in sensitivity among populations, which might arise from transgenerational effects of stressors through plastic, genetic, and epigenetic mechanisms. This can lead to local adaptation or maladaptation, with strong impacts on the evolutionary trajectories of wild fish populations. With this review, we hope to encourage future research to bridge the gap between molecular ecology, ecotoxicology and evolutionary biology to better understand the evolution of responses of fishes to current and future multiple stressors in the context of global changes.

Using time-lapse omics correlations to integrate toxicological pathways of a formulated fungicide in a soil invertebrate

The use of an integrative molecular approach can actively improve the evaluation of environmental health status and impact of chemicals, providing the knowledge to develop sentinel tools that can be integrated in risk assessment studies, since gene and protein expressions represent the first response barriers to anthropogenic stress. This work aimed to determine the mechanisms of toxic action of a widely applied fungicide formulation (chlorothalonil), following a time series approach and using a soil model arthropod, Folsomia candida. To link effects at different levels of biological organization, data were collected on reproduction, gene expression and protein levels, in a time series during exposure to a natural soil. Results showed a mechanistic mode of action for chlorothalonil, affecting pathways of detoxification and excretion, immune response, cellular respiration, protein metabolism and oxidative stress defense, causing irregular cell signaling (JNK and NOD ½ pathways), DNA damage and abnormal cell proliferation, leading to impairment in developmental features such as molting cycle and reproduction. The omics datasets presented highly significant positive correlations between the gene expression levels at a certain time-point and the corresponding protein products 2-3 days later. The integrated omics in this study has provided useful insights into pesticide mechanisms of toxicity, evidencing the relevance of such analyses in toxicological studies, and highlighting the importance of considering a time-series when integrating these datasets.

What is the relationship between the bioaccumulation of chemical contaminants in the variegated scallop Mimachlamys varia and its health status? A study carried out on the French Atlantic coast using the Path ComDim model

Increasing activity along the French Atlantic coast has led to chronic pollution with, in particular, mixtures of contaminants such as hydrocarbons, phytosanitary products, PCBs and heavy metals. Based on previous research, pollution biomarkers were used in this study as they can indicate health status when monitoring the impact of pollutants on coastal species such as the marine bivalve Mimachlamys varia. Mollusc bivalves were sampled in March 2016, in open and semi-open areas (a harbour zone), from thirteen sites which differed in terms of their level of pollution, and were located along the Atlantic coast from Brittany down to the Nouvelle-Aquitaine region. First, analyses of heavy metals and organic contaminants (e.g. pesticides, polycyclic aromatic hydrocarbons, polychlorobiphenyl) in the digestive gland of bivalves were performed. Second, biochemical assays were used to study defence biomarkers: oxidative stress with Superoxide Dismutase (SOD), detoxification of organic compounds with Glutathione-S Transferase (GST), lipid peroxidation with Malondialdehyde (MDA), and immune processes with Laccase. In addition to the biochemical assays, a genetic approach was used to measure genetic diversity (haplotype and nucleotide diversity) at each site. Biomarker assays and genetic diversity were correlated with the chemical contaminants in bivalves using the Path-ComDim statistical model. Our results showed specific correlations between biochemical assays in the digestive glands with heavy metal contaminants, and between genetic diversity and organic pollution. Blocks of responses were analysed for correlations in order to develop standardized tools and guidelines that could improve our understanding of the short-term and long-term impact of contaminants on physiological parameters.

'Omic' technologies as a helpful tool in radioecological research

This article presents a brief review of the modern 'omic' technologies, namely genomics, epigenomics, transcriptomics, proteomics, and metabolomics, as well as the examples of their possible use in radioecology. For each technology, a short description of advances, limitations, and instrumental applications is given. In addition, the review contains examples of successful use of 'omic' technologies in the assessment of biological effects of pollutants in the field conditions.

Turning natural adaptations to oncogenic factors into an ally in the war against cancer

Both field and experimental evolution studies have demonstrated that organisms naturally or artificially exposed to environmental oncogenic factors can, sometimes rapidly, evolve specific adaptations to cope with pollutants and their adverse effects on fitness. Although numerous pollutants are mutagenic and carcinogenic, little attention has been given to exploring the extent to which adaptations displayed by organisms living in oncogenic environments could inspire novel cancer treatments, through mimicking the processes allowing these organisms to prevent or limit malignant progression. Building on a substantial knowledge base from the literature, we here present and discuss this progressive and promising research direction, advocating closer collaboration between the fields of medicine, ecology, and evolution in the war against cancer.

Evolutionary toxicology in an omics world

Evolutionary toxicology is a young field that has grown rapidly in the past two decades. The potential of this field comes from the ability to link chemical contamination to multigenerational and population-wide effects in various species. The advancements and rapidly decreasing costs of -omic tools are improving the power and resolution of evolutionary toxicology studies. In this manuscript, we aim to address the trajectories and perspectives for conducting evolutionary toxicology studies with -omic approaches. We discuss the complementarity of using multiple -omic tools (genomics, eDNA, transcriptomics, proteomics, and metabolomics) for utility in understanding the toxicological relevance of adaptive responses in populations. In addition, we discuss phenotypic plasticity and its relevance to transcriptomic studies in toxicology. As evolutionary toxicology grows and expands its capacity to link toxicology with population-wide end points, we emphasize the applications of such studies in answering questions about ecological and population health, as well as future applicability to regulation. Thus, we aim to emphasize the enormous potential for evolutionary toxicology in an -omics world and give perspectives on the directions of future investigations.