When evolution is the solution to pollution: Key principles, and lessons from rapid repeated adaptation of killifish (Fundulus heteroclitus) populations

Phylogeny predicts sensitivity in aquatic animals for only a minority of chemicals

There are substantial gaps in our empirical knowledge of the effects of chemical exposure on aquatic life that are unlikely to be filled by traditional laboratory toxicity testing alone. One possible alternative of generating new toxicity data is cross-species extrapolation (CSE), a statistical approach in which existing data are used to predict the effect of a chemical on untested species. Some CSE models use relatedness as a predictor of chemical sensitivity, but relatively little is known about how strongly shared evolutionary history influences sensitivity across all chemicals. To address this question, we conducted a survey of phylogenetic signal in the toxicity data from aquatic animal species for a large set of chemicals using a phylogeny inferred from taxonomy. Strong phylogenetic signal was present in just nine of thirty-six toxicity datasets, and there were no clear shared properties among those datasets with strong signal. Strong signal was rare even among chemicals specifically developed to target insects, meaning that these chemicals may be equally lethal to non-target taxa, including chordates. When signal was strong, distinct patterns of sensitivity were evident in the data, which may be informative when assembling toxicity datasets for regulatory use. Although strong signal does not appear to manifest in aquatic toxicity data for most chemicals, we encourage additional phylogenetic evaluations of toxicity data in order to guide the selection of CSE tools and as a means to explore the patterns of chemical sensitivity across the broad diversity of life.

Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria

Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.

Passive accumulation of alkaloids in non-toxic frogs challenges paradigms of the origins of acquired chemical defenses

Understanding the origins of novel, complex phenotypes is a major goal in evolutionary biology. Poison frogs of the family Dendrobatidae have evolved the novel ability to acquire alkaloids from their diet for chemical defense at least three times. However, taxon sampling for alkaloids has been biased towards colorful species, without similar attention paid to inconspicuous ones that are often assumed to be undefended. As a result, our understanding of how chemical defense evolved in this group is incomplete. Here we provide new data showing that, in contrast to previous studies, species from each undefended poison frog clade have measurable yet low amounts of alkaloids. We confirm that undefended dendrobatids regularly consume mites and ants, which are known sources of alkaloids. Further, we confirm the presence of alkaloids in two putatively non-toxic frogs from other families. Our data suggest the existence of a phenotypic intermediate between toxin consumption and sequestration-passive accumulation-that differs from active sequestration in that it involves no derived forms of transport and storage mechanisms yet results in low levels of toxin accumulation. We discuss the concept of passive accumulation and its potential role in the origin of chemical defenses in poison frogs and other toxin-sequestering organisms.

Population-specific responses to pollution exposure suggest local adaptation of invasive red swamp crayfish Procambarus clarkii along the Mediterranean French coastline

Anthropogenic stressors can have an impact in a broad range of physiological processes and can be a major selective force leading to rapid evolution and local population adaptation. In this study, three populations of the invasive crayfish Procambarus clarkii were investigated. They are geographically separated for at least 20 years, and live in different abiotic environments: a freshwater inland lake (Salagou lake) with no major anthropogenic influence and two other coastal wetlands regularly polluted by pesticides along the Mediterranean coast (Camargue region and Bages-Sigean lagoon). Collected adults were genetically characterized using the mitochondrial COI gene and haplotype frequencies were analyzed for genetic variability within and between populations. Results revealed a higher genetic diversity for these invasive populations than any previous report in France, with more than seven different haplotypes in a single population. The contrasting genetic diversity between the Camargue and the other two populations suggest different times and sources of introduction. To identify differences in key physiological responses between these populations, individuals from each population were maintained in controlled conditions. Data on oxygen consumption rates indicate that the Salagou and Bages-Sigean populations possess a high inter-individual variability compared to the Camargue population. The low individual variability of oxygen consumption and low genetic diversity suggest a specific local adaptation for the Camargue population. Population-specific responses were identified when individuals were exposed to a pesticide cocktail containing azoxystrobin and oxadiazon at sublethal concentrations. The Salagou population was the only one with altered hydro-osmotic balance due to pollutant exposure and a change in protease activity in the hepatopancreas. These results revealed different phenotypic responses suggesting local adaptations at the population level.

Urban socioeconomic variation influences the ecology and evolution of trophic interactions

As urbanization expands, it is becoming increasingly important to understand how anthropogenic activity is affecting ecological and evolutionary processes. Few studies have examined how human social patterns within cities can modify eco-evolutionary dynamics. We tested how socioeconomic variation corresponds with changes in trophic interactions and natural selection on prey phenotypes using the classic interaction between goldenrod gall flies (Eurosta solidaginis) and their natural enemies: birds, beetles, and parasitoid wasps. We sampled galls from 84 sites across neighbourhoods with varying socioeconomic levels, and quantified the frequency of predation/parasitism on flies and natural selection by each enemy. We found that bird predation was higher in the highest income neighbourhoods, increasing the strength of selection for smaller galls. Wasp and beetle attack, but not their strength of selection, increased in lower income neighbourhoods. We show that socioeconomic variation in cities can have strong unintended consequences for the ecology and evolution of trophic interactions.

Biomarker selection depends on gene function and organ: the case of the cytochrome P450 family genes in freshwater fish exposed to chronic pollution

Pollution and its effects have been of major concern in recent decades. Many strategies and markers have been developed to assess their effects on biota. Cytochrome P450 (CYP) genes have received significant attention in this context because of their relationship with detoxification and activation of exogenous compounds. While their expression has been identified as a pollution exposure biomarker, in most cases, it has been tested only after acute exposures and for CYP genes associated with exogenous compounds. To elucidate CYP gene expression patterns under chronic pollution exposure, we have used the silverside Basilichthys microlepidotus as a model, which inhabits the Maipo River Basin, a freshwater system with different pollution levels. We performed next-generation RNA sequencing of liver and gill tissues from polluted and non-polluted populations. We found most CYP genes were not dysregulated by pollution, and the seven genes that were present and differentially expressed in liver and gill were mainly downregulated. Three CYP genes associated with exogenous compounds showed differential expression in the gill, while four CYP genes associated with endogenous compounds showed differential expression in the liver. The findings presented here highlight the importance of CYP genes, his family, tissues and his interaction in the context of pollution biomarkers use.

Genomic footprints of (pre) colonialism: Population declines in urban and forest túngara frogs coincident with historical human activity

Urbanisation is rapidly altering ecosystems, leading to profound biodiversity loss. To mitigate these effects, we need a better understanding of how urbanisation impacts dispersal and reproduction. Two contrasting population demographic models have been proposed that predict that urbanisation either promotes (facilitation model) or constrains (fragmentation model) gene flow and genetic diversity. Which of these models prevails likely depends on the strength of selection on specific phenotypic traits that influence dispersal, survival, or reproduction. Here, we a priori examined the genomic impact of urbanisation on the Neotropical túngara frog (Engystomops pustulosus), a species known to adapt its reproductive traits to urban selective pressures. Using whole-genome resequencing for multiple urban and forest populations we examined genomic diversity, population connectivity and demographic history. Contrary to both the fragmentation and facilitation models, urban populations did not exhibit substantial changes in genomic diversity or differentiation compared with forest populations, and genomic variation was best explained by geographic distance rather than environmental factors. Adopting an a posteriori approach, we additionally found both urban and forest populations to have undergone population declines. The timing of these declines appears to coincide with extensive human activity around the Panama Canal during the last few centuries rather than recent urbanisation. Our study highlights the long-lasting legacy of past anthropogenic disturbances in the genome and the importance of considering the historical context in urban evolution studies as anthropogenic effects may be extensive and impact nonurban areas on both recent and older timescales.

Ivermectin Toxicokinetics in Rainbow Trout (Oncorhynchus mykiss) following P-glycoprotein Induction

Alterations in ivermectin (IVM, 22,23-dihydro avermectin B1a+22,23-dihydro avermectin B1b) toxicokinetics following P-glycoprotein (P-gp) induction by clotrimazole (CTZ) were examined in rainbow trout (Oncorhynchus mykiss) to assess the potential importance of P-gp activity levels in xenobiotic distribution and kinetics in fish. Control and fish pretreated with CTZ (30 µmol/kg) were administered 175 µg/kg 3H-IVM into the caudal vasculature. At various time points (0.25, 0.5, 1, 3, 24, 48, 96, and 168 h) following injection, tissues (blood, liver, kidney, gill, intestines, brain [5 regions], eye, gonad and fat) were removed analyzed for IVM-derived radioactivity. IVM concentration declined in blood, liver, kidney and gill, and concentrations in other tissues remained constant over the sampling period. The highest measured concentrations were found in kidney, followed by liver, with the lowest values found in brain, eye and gonad. The highest % of the administered dose was found in the liver and kidney in the immediate hours post-administration, and in the intestines and fat at 24 h post-administration. P-gp induction by CTZ did not alter IVM distribution or any calculated toxicokinetic parameter (AUC, mean residence time, T1/2, clearance rate, volume of distribution), suggesting that P-gp induction may be limited or that P-gp plays a lesser role in xenobiotic kinetics in fish compared to mammals.

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.

Two duckweed species exhibit variable tolerance to microcystin-LR exposure across genotypic lineages

Cyanotoxins produced by harmful cyanobacteria blooms can damage freshwater ecosystems and threaten human health. Floating macrophytes may be used as a means of biocontrol by limiting light and resources available to cyanobacteria. However, genetic variation in macrophyte sensitivity to cyanotoxins could influence their suitability as biocontrol agents. We investigated the influence of such intraspecific variation on the response of two rapidly growing duckweed species, Lemna minor and Spirodela polyrhiza, often used in nutrient and metal bioremediation. We assessed two biomarkers related to productivity (biomass and chlorophyll A production) and two related to fitness measures (population size and growth rate). Fifteen genetic lineages of each species were grown in media containing common cyanotoxin microcystin-LR at ecologically relevant concentrations or control media for a period of twelve days. Genotype identity had a strong impact on all biomarker responses. Microcystin concentration slightly increased the final population sizes of both macrophyte species with a marginal effect on growth rate of L. minor and the chlorophyll A production of S. polyrhiza, but overall these species were very tolerant of microcystin. The strong tolerance supports the potential use of these plants as bioremediators of cyanobacterial blooms. However, differential impact of microcystin exposure discovered in single lineage models among genotypes indicates a potential for cyanotoxins to act as selective forces, necessitating attention to genotype selection for bioremediation.

Differential DNA methylation and metabolite profiling of Atlantic killifish (Fundulus heteroclitus) from the New Bedford Harbor Superfund site

Atlantic killifish (Fundulus heteroclitus) is a valuable model in evolutionary toxicology to study how the interactions between genetic and environmental factors serve the adaptive ability of organisms to resist chemical pollution. Killifish populations inhabiting environmental toxicant-contaminated New Bedford Harbor (NBH) show phenotypes tolerant to polychlorinated biphenyls (PCBs) and differences at the transcriptional and genomic levels. However, limited research has explored epigenetic alterations and metabolic effects in NBH killifish. To identify the involvement of epigenetic and metabolic regulation in the adaptive response of killifish, we investigated tissue- and sex-specific differences in global DNA methylation and metabolomic profiles of NBH killifish populations, compared to sensitive populations from a non-polluted site, Scorton Creek (SC). The results revealed that liver-specific global DNA hypomethylation and differential metabolites were evident in fish from NBH compared with those from SC. The sex-specific differences were not greater than the tissue-specific differences. We demonstrated liver-specific enriched metabolic pathways (e.g., amino acid metabolic pathways converged into the urea cycle and glutathione metabolism), suggesting possible crosstalk between differential metabolites and DNA hypomethylation in the livers of NBH killifish. Additional investigation of methylated gene regions is necessary to understand the functional role of DNA hypomethylation in the regulation of enzyme-encoding genes associated with metabolic processes and physiological changes in NBH populations.

Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect

The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts that adaptation is due to a few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and using RAD-seq genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that one to two large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling. One QTL locus was shared across all populations and another was shared across three populations. One QTL locus showed strong signatures of recent natural selection in the corresponding wild population but another QTL locus did not. Some candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.

Bioenergetic Effects of Polycyclic Aromatic Hydrocarbon Resistance Manifest Later in Life in Offspring of Fundulus heteroclitus from the Elizabeth River

Shifts in key physiological processes can confer resistance to chemical pollutants. However, these adaptations may come with certain trade-offs, such as altered energy metabolic processes, as evident in Atlantic killifish (Fundulus heteroclitus) in Virginia's Elizabeth River (ER) that have evolved resistance to polycyclic aromatic hydrocarbons (PAHs). We seek to understand the bioenergetic costs of PAH resistance among subpopulations of Atlantic killifish with differing contamination levels in order to examine how these changes manifest across multiple life stages and how these costs might be exacerbated by additional stressors. Bioenergetics data revealed differences in metabolic rates between offspring of PAH-resistant fish and reference fish were absent or minimal in both the embryo and larval stages but pronounced at the juvenile life stage, suggesting that bioenergetic changes in pollution-adapted killifish manifest later in life. We also provide evidence that killifish from remediated sites are more sensitive to PAH exposure than killifish from nonremediated sites, suggesting loss of PAH tolerance following relaxed selection. Collectively, our data suggest that the fitness consequences associated with evolved resistance to anthropogenic stressors may manifest differently over time and depend on the magnitude of the selection pressure. This information can be valuable in effective risk and remediation assessments as well as in broadening our understanding of species responses to environmental change.

Insights from a chum salmon (Oncorhynchus keta) genome assembly regarding whole-genome duplication and nucleotide variation influencing gene function

Chum salmon are ecologically important to Pacific Ocean ecosystems and commercially important to fisheries. To improve the genetic resources available for this species, we sequenced and assembled the genome of a male chum salmon using Oxford Nanopore read technology and the Flye genome assembly software (contig N50: ∼2 Mbp, complete BUSCOs: ∼98.1%). We also resequenced the genomes of 59 chum salmon from hatchery sources to better characterize the genome assembly and the diversity of nucleotide variants impacting phenotype variation. With genomic sequences from a doubled haploid individual, we were able to identify regions of the genome assembly that have been collapsed due to high sequence similarity between homeologous (duplicated) chromosomes. The homeologous chromosomes are relics of an ancient salmonid-specific genome duplication. These regions were enriched with genes whose functions are related to the immune system and responses to toxins. From analyzing nucleotide variant annotations of the resequenced genomes, we were also able to identify genes that have increased levels of variants thought to moderately impact gene function. Genes related to the immune system and the detection of chemical stimuli (olfaction) had increased levels of these variants based on a gene ontology enrichment analysis. The tandem organization of many of the enriched genes raises the question of why they have this organization.

Improving hydrocarbon toxicity tolerance in poultry: role of genes and antioxidants

Sustenance of smallholder poultry production as an alternative source of food security and income is imperative in communities exposed to hydrocarbon pollution. Exposure to hydrocarbon pollutants causes disruption of homeostasis, thereby compromising the genetic potential of the birds. Oxidative stress-mediated dysfunction of the cellular membrane is a contributing factor in the mechanism of hydrocarbon toxicity. Epidemiological studies show that tolerance to hydrocarbon exposure may be caused by the activation of genes that control disease defense pathways like aryl hydrocarbon receptor (AhR) and nuclear factor erythroid 2p45-related factor 2 (Nrf2). Disparity in the mechanism and level of tolerance to hydrocarbon fragments among species may exist and may result in variations in gene expression within individuals of the same species upon exposure. Genomic variability is critical for adaptation and serves as a survival mechanism in response to environmental pollutants. Understanding the interplay of diverse genetic mechanisms in relation to environmental influences is important for exploiting the differences in various genetic variants. Protection against pollutant-induced physiological responses using dietary antioxidants can mitigate homeostasis disruptions. Such intervention may initiate epigenetic modulation relevant to gene expression of hydrocarbon tolerance, enhancing productivity, and possibly future development of hydrocarbon-tolerant breeds.

Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect

The genetic architecture of phenotypic traits can affect the mode and tempo of trait evolution. Human-altered environments can impose strong natural selection, where successful evolutionary adaptation requires swift and large phenotypic shifts. In these scenarios, theory predicts the influence of few adaptive variants of large effect, but empirical studies that have revealed the genetic architecture of rapidly evolved phenotypes are rare, especially for populations inhabiting polluted environments. Fundulus killifish have repeatedly evolved adaptive resistance to extreme pollution in urban estuaries. Prior studies, including genome scans for signatures of natural selection, have revealed some of the genes and pathways important for evolved pollution resistance, and provide context for the genotype-phenotype association studies reported here. We created multiple quantitative trait locus (QTL) mapping families using progenitors from four different resistant populations, and genetically mapped variation in sensitivity (developmental perturbations) following embryonic exposure to a model toxicant PCB-126. We found that a few large-effect QTL loci accounted for resistance to PCB-mediated developmental toxicity. QTLs harbored candidate genes that govern the regulation of aryl hydrocarbon receptor (AHR) signaling, where some (but not all) of these QTL loci were shared across all populations, and some (but not all) of these loci showed signatures of recent natural selection in the corresponding wild population. Some strong candidate genes for PCB resistance inferred from genome scans in wild populations were identified as QTL, but some key candidate genes were not. We conclude that rapidly evolved resistance to the developmental defects normally caused by PCB-126 is governed by few genes of large effect. However, other aspects of resistance beyond developmental phenotypes may be governed by additional loci, such that comprehensive resistance to PCB-126, and to the mixtures of chemicals that distinguish urban estuaries more broadly, may be more genetically complex.

Effects of Hudson River Stressors on Atlantic Tomcod: Contaminants and a Warming Environment

The Hudson River (HR) Estuary has a long history of pollution with a variety of contaminants including PCBs, and dioxins. In fact, 200 miles of the mainstem HR is designated a U.S. federal Superfund site, the largest in the nation, because of PCB contamination. The tidal HR hosts the southernmost spawning population of Atlantic tomcod, and studies revealed a correlation between exposure of juveniles to warm water temperature during summer to abundance of spawning adults of the same cohort in the following winter. Further, a battery of mechanistically linked biomarkers, ranging from the molecular to the population levels, were significantly impacted from contaminant exposures of the HR tomcod population. In response to xenobiotic insult, the HR tomcod population developed resistance to PCB sand TCDD toxicity resulting from a deletion in the aryl hydrocarbon receptor2 (AHR2) gene. Furthermore, RNA-Seq analysis of global gene expression demonstrated that effects of the AHR2 polymorphism were far more pervasive than anticipated. The most highly PCB-contaminated sediments in the upper HR were dredged between 2009 and 2015 with the objective of lowering PCB concentrations in fishes in the lower HR. Success of the remediation project has been controversial. These observations suggest that tomcod provides an informative model to evaluate the efficacy of HR PCB remediation efforts on downriver fish populations and possible interactive effects between contaminant exposure and a warming environment.

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.

Environmental stress promotes the persistence of facultative bacterial symbionts in amoebae

Amoebae are one major group of protists that are widely found in natural and engineered environments. They are a significant threat to human health not only because many of them are pathogenic but also due to their unique role as an environmental shelter for pathogens. However, one unsolved issue in the amoeba-bacteria relationship is why so many bacteria live within amoeba hosts while they can also live independently in the environments. By using a facultative amoeba- Paraburkholderia bacteria system, this study shows that facultative bacteria have higher survival rates within amoebae under various environmental stressors. In addition, bacteria survive longer within the amoeba spore than in free living. This study demonstrates that environmental stress can promote the persistence of facultative bacterial symbionts in amoebae. Furthermore, environmental stress may potentially select and produce more amoeba-resisting bacteria, which may increase the biosafety risk related to amoebae and their intracellular bacteria.

The role of structural variants in pest adaptation and genome evolution of the Colorado potato beetle, Leptinotarsa decemlineata (Say)

Structural variation has been associated with genetic diversity and adaptation. Despite these observations, it is not clear what their relative importance is for evolution, especially in rapidly adapting species. Here, we examine the significance of structural polymorphisms in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a parent offspring trio sequencing procedure, we develop highly contiguous reference genomes to characterize structural variation. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral nonpest individuals. We identify >200,000 structural variations, which appear to be nonrandomly distributed across the genome as they co-occur with transposable elements and genes. Structural variations intersect with exons in a large proportion of gene annotations (~20%) that are associated with insecticide resistance (including cytochrome P450s), development, and transcription. To understand the role structural variations play in adaptation, we measure their allele frequencies among an additional 57 individuals using whole genome resequencing data, which represents pest and nonpest populations of North America. Incorporating multiple independent tests to detect the signature of natural selection using SNP data, we identify 14 genes that are probably under positive selection, include structural variations, and SNPs of elevated frequency within the pest lineages. Among these, three are associated with insecticide resistance based on previous research. One of these genes, CYP4g15, is coinduced during insecticide exposure with glycosyltransferase-13, which is a duplicated gene enclosed within a structural variant adjacent to the CYP4g15 genic region. These results demonstrate the significance of structural variations as a genomic feature to describe species history, genetic diversity, and adaptation.

Rapid evolution of insecticide resistance in the Colorado potato beetle, Leptinotarsa decemlineata

Despite considerable research, efforts to manage insecticide resistance continue to fail. The Colorado potato beetle (CPB), Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae), epitomizes this problem, as it has repeatedly and rapidly evolved resistance to>50 insecticides. The patterns of resistance evolution are intriguing, as they defy models where resistance evolves from rare mutations. Here, we synthesize recent research on insecticide resistance in CPB showing that polygenic resistance drawn from standing genetic diversity explains genomic patterns of insecticide resistance evolution. However, rapid gene regulatory evolution suggests that other mechanisms might also facilitate adaptive change. We explore the hypothesis that sublethal stress from insecticide exposure could alter heritable epigenetic modifications, and discuss the range of experimental approaches needed to fully understand insecticide resistance evolution in this super pest.

Response of soil protists to antimony and arsenic contamination

Microorganisms can mediate antimony (Sb) and arsenic (As) transformation and thus change their mobility and toxicity. Having similar geochemical behavior, Sb and As are generally considered to exert similar environmental pressure on microbiome. However, it needs further validation, especially for protists. In this study, the responses of protistan communities to Sb and As were investigated by collecting soils from Xikuangshan Sb mine and Shimen As mine in China. Antimony and As contamination taxonomically and functionally (consumer and phototroph) changed the alpha and beta diversities of protistan communities, but exerted different impacts on the parasitic community. Based on multiple statistical tools, As contamination had a greater impact on protistan communities than Sb. The ecological networks of highly contaminated sites were less complex but highly positively connected compared to less contaminated sites. High As contamination raised the ratio of consumers and decreased the ratio of phototrophs in ecological networks, while the opposite tendency was observed in Sb contaminated soils. High Sb and As contamination enriched different keystone taxa resistant to Sb and As. These results demonstrate that protistan community respond differently to Sb and As.

Telomeres and anthropogenic disturbances in wildlife: A systematic review and meta-analysis

Human-driven environmental changes are affecting wildlife across the globe. These challenges do not influence species or populations to the same extent and therefore a comprehensive evaluation of organismal health is needed to determine their ultimate impact. Evidence suggests that telomeres (the terminal chromosomal regions) are sensitive to environmental conditions and have been posited as a surrogate for animal health and fitness. Evaluation of their use in an applied ecological context is still scarce. Here, using information from molecular and occupational biomedical studies, we aim to provide ecologists and evolutionary biologists with an accessible synthesis of the links between human disturbances and telomere length. In addition, we perform a systematic review and meta-analysis on studies measuring telomere length in wild/wild-derived animals facing anthropogenic disturbances. Despite the relatively small number of studies to date, our meta-analysis revealed a significant small negative association between disturbances and telomere length (-0.092 [-0.153, -0.031]; n = 28; k = 159). Yet, our systematic review suggests that the use of telomeres as a biomarker to understand the anthropogenic impact on wildlife is limited. We propose some research avenues that will help to broadly evaluate their suitability: (i) further causal studies on the link between human disturbances and telomeres; (ii) investigating the organismal implications, in terms of fitness and performance, of a given telomere length in anthropogenically disturbed scenarios; and (iii) better understanding of the underlying mechanisms of telomere dynamics. Future studies in these facets will help to ultimately determine their role as markers of health and fitness in wildlife facing anthropogenic disturbances.

Proper modulation of AHR signaling is necessary for establishing neural connectivity and oligodendrocyte precursor cell development in the embryonic zebrafish brain

2,3,7,8-tetrachlorodibenzo-[p]-dioxin (TCDD) is a persistent global pollutant that exhibits a high affinity for the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor. Epidemiological studies have associated AHR agonist exposure with multiple human neuropathologies. Consistent with the human data, research studies using laboratory models have linked pollutant-induced AHR activation to disruptions in learning and memory as well as motor impairments. Our understanding of endogenous AHR functions in brain development is limited and, correspondingly, scientists are still determining which cell types and brain regions are sensitive to AHR modulation. To identify novel phenotypes resulting from pollutant-induced AHR activation and ahr2 loss of function, we utilized the optically transparent zebrafish model. Early embryonic TCDD exposure impaired embryonic brain morphogenesis, resulted in ventriculomegaly, and disrupted neural connectivity in the optic tectum, habenula, cerebellum, and olfactory bulb. Altered neural network formation was accompanied by reduced expression of synaptic vesicle 2. Loss of ahr2 function also impaired nascent network development, but did not affect gross brain or ventricular morphology. To determine whether neural AHR activation was sufficient to disrupt connectivity, we used the Gal4/UAS system to express a constitutively active AHR specifically in differentiated neurons and observed disruptions only in the cerebellum; thus, suggesting that the phenotypes resulting from global AHR activation likely involve multiple cell types. Consistent with this hypothesis, we found that TCDD exposure reduced the number of oligodendrocyte precursor cells and their derivatives. Together, our findings indicate that proper modulation of AHR signaling is necessary for the growth and maturation of the embryonic zebrafish brain.

Sodium arsenite but not aluminum chloride stimulates ABC transporter activity in renal proximal tubules of killifish (Fundulus heteroclitus)

ABC export proteins including Multidrug resistance-related protein 2 (Mrp2) serve as detoxification mechanism in renal proximal tubules due to active transport of xenobiotics and metabolic waste products into primary urine. The environmental pollutants aluminum and arsenic interfere with a multitude of regulatory mechanisms in the body and here their impact on ABC transporter function was studied. NaAsO₂ but not AlCl₃ rapidly stimulated Mrp2-mediated Texas Red (TR) transport in isolated renal proximal tubules from killifish, a well-established laboratory model for the determination of efflux transporter activity by utilizing fluorescent substrates for the ABC transporters of interest and confocal microscopy followed by image analysis. This observed stimulation remained unaffected by the translation inhibitor cycloheximide (CHX), but it was abrogated by antagonists and inhibitors of the endothelin receptor type B (ET_B)/nitric oxide synthase (NOS)/protein kinase C (PKC) signaling pathway. NaAsO₂-triggered effects were abolished as a consequence of PKCα inhibition through Gö6976 and PKCα inhibitor peptide C2-4. Phosphatidylinositol 3-kinase (PI3K) inhibitor LY 294,002 as well as the mammalian target of rapamycin (mTOR) inhibitor rapamycin suppressed NaAsO₂-triggered stimulation of luminal TR transport. In addition, the stimulatory effect of NaAsO₂ was abolished by GSK650394, an inhibitor of serum- and glucocorticoid-inducible kinase 1 (SGK1), which is an important downstream target. Environmentally relevant concentrations of NaAsO₂ further stimulated transport function of P-glycoprotein (P-gp), Multidrug resistance-related protein 4 (Mrp4) and Breast cancer resistance protein (Bcrp) while AlCl₃ was ineffective. To our knowledge, this is the first report engaging in the impact of NaAsO₂ on efflux transporter signaling and it may contribute to the understanding of defense mechanisms versus this worrying pollutant.

Did decades of glyphosate use have selected for resistant amphibians in agricultural habitats?

Glyphosate-based herbicides are used worldwide, and glyphosate's primary metabolite (aminomethylphosphonic acid: AMPA), is globally retrieved in surface waters. AMPA induces various adverse effects on aquatic wildlife, including selective mortality, which suggests that glyphosate exposure may have selected for AMPA-resistant individuals. We tested this hypothesis using spined toads (Bufo spinosus), an amphibian found in a variety of habitats, from AMPA-exposed agricultural lands to AMPA-free forested areas. We predicted that the offspring of individuals originating from agricultural habitats would develop AMPA-resistance - and be less prone to develop adverse effects from- AMPA exposure. To investigate this question, we performed a common garden brood-rearing experiment. The embryos and larvae of 40 spined toad pairs captured in agricultural and forest ponds were exposed either to an environmental relevant concentration of AMPA (0.4 μg L^-1) or to control conditions (n = 8160 embryos, n = 240 tadpoles). We monitored development durations, developmental abnormalities and morphology, measured across key developmental stages. Although we observed significant effects of AMPA on fitness parameters in each group, these effects were not exacerbated in individuals from AMPA-free habitats. We suggest that temporal and/or spatial dynamics of contamination, as well as gene flow between exposed and preserved populations, may hinder adaptive divergence between populations. Yet, we show strong adverse effects of AMPA exposure at early developmental stages. AMPA could therefore be one of the numerous causes of declining wild amphibian populations.

Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas

Background

The fathead minnow (Pimephales promelas) is a model species for toxicological research. A high-quality genome reference sequence is available, and genomic methods are increasingly used in toxicological studies of the species. However, phylogenetic relationships within the genus remain incompletely known and little population-genomic data are available for fathead minnow despite the potential effects of genetic background on toxicological responses. On the other hand, a wealth of extant samples is stored in museum collections that in principle allow fine-scale analysis of contemporary and historical genetic variation.

Methods

Here we use short-read shotgun resequencing to investigate sequence variation among and within Pimephales species. At the genus level, our objectives were to resolve phylogenetic relationships and identify genes with signatures of positive diversifying selection. At the species level, our objective was to evaluate the utility of archived-sample resequencing for detecting selective sweeps within fathead minnow, applied to a population introduced to the San Juan River of the southwestern United States sometime prior to 1950.

Results

We recovered well-supported but discordant phylogenetic topologies for nuclear and mitochondrial sequences that we hypothesize arose from mitochondrial transfer among species. The nuclear tree supported bluntnose minnow (P. notatus) as sister to fathead minnow, with the slim minnow (P. tenellus) and bullhead minnow (P. vigilax) more closely related to each other. Using multiple methods, we identified 11 genes that have diversified under positive selection within the genus. Within the San Juan River population, we identified selective-sweep regions overlapping several sets of related genes, including both genes that encode the giant sarcomere protein titin and the two genes encoding the MTORC1 complex, a key metabolic regulator. We also observed elevated polymorphism and reduced differentation among populations (F_ST) in genomic regions containing certain immune-gene clusters, similar to what has been reported in other taxa. Collectively, our data clarify evolutionary relationships and selective pressures within the genus and establish museum archives as a fruitful resource for characterizing genomic variation. We anticipate that large-scale resequencing will enable the detection of genetic variants associated with environmental toxicants such as heavy metals, high salinity, estrogens, and agrichemicals, which could be exploited as efficient biomarkers of exposure in natural populations.

Interactions between soil protists and pollutants: An unsolved puzzle

Soil protists are essential but often overlooked in soils, although they play crucial functional roles in the terrestrial ecosystem. While soil protists have drawn increased attention to their functional role in soils, their interaction with soil pollutants remains unresolved. This review provides a first overview of the current understanding of interactions between soil protists and major pollutants (heavy metals, organic pollutants, nanoparticles, and soil pathogens). We summarize how soil pollutants affect protists and vice versa, showing that we are just beginning to understand their complex interactions. In addition, we identify five research gaps, including hidden diversity, adaptive mechanisms, species interactions, soil bioindicators and environmental applications, and we hope that our review will help promote and build research guidelines for the future. In conclusion, a better understanding of soil pollutant-protist interactions will significantly increase our knowledge of the pollution ecology in the soil and how soil organisms respond and adapt to environmental pollution, which will contribute to the bioremediation and environmental applications of protists in soil.

Reduced genetic diversity of freshwater amphipods in rivers with increased levels of anthropogenic organic micropollutants

Anthropogenic chemicals in freshwater environments contribute majorly to ecosystem degradation and biodiversity decline. In particular anthropogenic organic micropollutants (AOM), a diverse group of compounds, including pesticides, pharmaceuticals, and industrial chemicals, can significantly impact freshwater organisms. AOM were found to impact genetic diversity of freshwater species; however, to which degree AOM cause changes in population genetic structure and allelic richness of freshwater macroinvertebrates remains poorly understood. Here, the impact of AOM on genetic diversity of the common amphipod Gammarus pulex (Linnaeus, 1758) (clade E) was investigated on a regional scale. The site‐specific AOM levels and their toxic potentials were determined in water and G. pulex tissue sample extracts for 34 sites along six rivers in central Germany impacted by wastewater effluents and agricultural run‐off. Population genetic parameters were determined for G. pulex from the sampling sites by genotyping 16 microsatellite loci. Genetic differentiation among G. pulex from the studied rivers was found to be associated with geographic distance between sites and to differences in site‐specific concentrations of AOM. The genetic diversity parameters of G. pulex were found to be related to the site‐specific AOM levels. Allelic richness was significantly negatively correlated with levels of AOM in G. pulex tissue (p < 0.003) and was reduced by up to 22% at sites with increased levels of AOM, despite a positive relationship of allelic richness and the presence of waste‐water effluent. In addition, the inbreeding coefficient of G. pulex from sites with toxic AOM levels was up to 2.5 times higher than that of G. pulex from more pristine sites. These results indicate that AOM levels commonly found in European rivers significantly contribute to changes in the genetic diversity of an ecologically relevant indicator species.

Multi- and Trans-Generational Effects on Daphnia Magna of Chlorpyrifos Exposures

Chlorpyrifos, a broad-spectrum neurotoxic organophosphate insecticide, is subject to atmospheric and hydrolytic transport from application sites to aquatic ecosystems. Across the landscape, concentrations in surface water can vary spatially and temporally according to seasonal use practices. Standardized bioassays can provide a screening-level understanding of aquatic receptor acute and chronic toxicity. However, these bioassays do not address ecologically relevant exposure patterns that may impact fitness and survival within and across generations. The aim of the present study was to evaluate the utility of a second-tier, screening-level methodology employing Daphnia magna multi- and transgenerational bioassays spanning four generations to investigate the effect of variable chronic chlorpyrifos exposure. The multigenerational assay consisted of continuous chlorpyrifos exposure across four consecutive 21-day bioassays using progeny from the previous assay for each successive generation. In the transgenerational assay, only the parent (F0) generation was exposed. For both assays, survival and reproduction were assessed across treatments and generations. Results indicated that (1) following continuous chlorpyrifos exposure at ecologically relevant concentrations to four generations of D. magna, the highest treatment showed an apparent tolerance response for both survival and reproductive success in the F3 generation, and (2) chlorpyrifos exposure to the F0 generation did not result in treatment effects in the unexposed F1, F2, and F3 generations in the apical endpoints of survival and reproduction. Employing a suite of acute and chronic bioassays, including chronic exposures spanning multiple generations, allows for a more robust screening-level evaluation of the potential impact of chlorpyrifos on aquatic receptors for variable periods of exposure. Environ Toxicol Chem 2022;41:1054-1065. © 2021 SETAC.

On the genetic architecture of rapidly adapting and convergent life history traits in guppies

The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use four independent F2 QTL crosses to examine the genetic basis of seven (five female, two male) guppy life history phenotypes and discuss how these genetic architectures may facilitate or constrain rapid adaptation and convergence. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many loci of small-effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid, repeatable phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but subsequent genetic redundancy may limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent analyses of wild guppies.

Potential differences in chitin synthesis ability cause different sensitivities to diflubenzuron among three strains of Daphnia magna

Ecotoxicity testing of crustaceans using Daphnia magna has been implemented in the chemical management systems of various countries. While the chemical sensitivity of D. magna varies depending on genetically different clonal lineages, the strain used in ecotoxicity tests, including the acute immobilization test (OECD TG202), has not been specified. We hypothesized that comprehensive gene expression profiles could provide useful information on phenotypic differences among strains, including chemical sensitivity. To test this hypothesis, we performed mRNA sequencing on three different strains (NIES, England, and Clone 5) of D. magna under culture conditions. The resulting expression profile of the NIES strain was clearly different compared to the profiles of the other two strains. Gene ontology (GO) enrichment analysis suggested that chitin metabolism was significantly enriched in the NIES strain compared to that in the England strain. Consistent with the GO analysis, evidence of high levels of chitin metabolism in the NIES strain were observed across multiple levels of biological organization, such as expression of chitin synthase genes, chitin content, and chitinase activity, which suggested that the different strains would exhibit different sensitivities to chemicals used to inhibit chitin synthesis. We found that among all strains, the NIES strain was more tolerant to diflubenzuron, a chitin synthesis inhibitor, with a 14-fold difference in the 48 h-EC₅₀ value for the acute immobilization test compared to the England strain. The present study demonstrates that the differences among strains in chitin metabolism may lead to sensitivity difference to diflubenzuron, and serves as a case study of the usefulness of comprehensive gene expression profiles in finding sensitivity differences.

Swimming behaviour in two ecologically similar three-spined (Gasterosteus aculeatus L.) and nine-spined sticklebacks (Pungitius pungitius L.): a comparative approach for modelling the toxicity of metal mixtures

Sticklebacks (Gasterosteiformes) are increasingly used in ecological and evolutionary research and have become well established as role model species for biologists. However, ecotoxicology studies concerning behavioural effects in sticklebacks regarding stress responses, mainly induced by chemical mixtures, have hardly been addressed. For this purpose, we investigated the swimming behaviour (including mortality rate based on 96-h LC₅₀ values) of two ecologically similar three-spined (Gasterosteus aculeatus) and nine-spined sticklebacks (Pungitius pungitius) to short-term (up to 24 h) metal mixture (MIX) exposure. We evaluated the relevance and efficacy of behavioural responses of test species in the early toxicity assessment of chemical mixtures. Fish exposed to six (Zn, Pb, Cd, Cu, Ni, and Cr) metals in the mixture were either singled out by the Water Framework Directive as priority or as relevant substances in surface water, which was prepared according to the environmental quality standards (EQSs) of these metals set for inland waters in the European Union (EU) (Directive 2013/39/EU). The performed behavioural analysis showed the main effect on the interaction between time, species, and treatment variables. Although both species exposed to MIX revealed a decreasing tendency in swimming activity, these species' responsiveness to MIX was somewhat different. Substantial changes in the activity of G. aculeatus were established after a 3-h exposure to MIX solutions, which was 1.43-fold lower, while in the case of P. pungitius, 1.96-fold higher than established 96-h LC₅₀ values for each species. This study demonstrated species-specific differences in response sensitivity to metal-based water pollution, indicating behavioural insensitivity of P. pungitius as model species for aquatic biomonitoring and environmental risk assessments.

Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle

Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to non-pest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.

Impacts of heavy metal pollution on the ionomes and transcriptomes of Western mosquitofish (Gambusia affinis)

Our understanding of the mechanisms mediating the resilience of organisms to environmental change remains lacking. Heavy metals negatively affect processes at all biological scales, yet organisms inhabiting contaminated environments must maintain homeostasis to survive. Tar Creek in Oklahoma, USA, contains high concentrations of heavy metals and an abundance of Western mosquitofish (Gambusia affinis), though several fish species persist at lower frequency. To test hypotheses about the mechanisms mediating the persistence and abundance of mosquitofish in Tar Creek, we integrated ionomic data from seven resident fish species and transcriptomic data from mosquitofish to test hypotheses about the mechanisms mediating the persistence of mosquitofish in Tar Creek. We predicted that mosquitofish minimize uptake of heavy metals more than other Tar Creek fish inhabitants and induce transcriptional responses to detoxify metals that enter the body, allowing them to persist in Tar Creek at higher density than species that may lack these responses. Tar Creek populations of all seven fish species accumulated heavy metals, suggesting mosquitofish cannot block uptake more efficiently than other species. We found population-level gene expression changes between mosquitofish in Tar Creek and nearby unpolluted sites. Gene expression differences primarily occurred in the gill, where we found upregulation of genes involved with lowering transfer of metal ions from the blood into cells and mitigating free radicals. However, many differentially expressed genes were not in known metal response pathways, suggesting multifarious selective regimes and/or previously undocumented pathways could impact tolerance in mosquitofish. Our systems-level study identified well characterized and putatively new mechanisms that enable mosquitofish to inhabit heavy metal-contaminated environments.

Cardiac physiology and metabolic gene expression during late organogenesis among F. heteroclitus embryo families from crosses between pollution-sensitive and -resistant parents

BACKGROUND

The teleost fish Fundulus heteroclitus inhabit estuaries heavily polluted with persistent and bioaccumulative chemicals. While embryos of parents from polluted sites are remarkably resistant to toxic sediment and develop normally, embryos of parents from relatively clean estuaries, when treated with polluted sediment extracts, are developmentally delayed, displaying deformities characteristic of pollution-induced embryotoxicity. To gain insight into parental effects on sensitive and resistant phenotypes during late organogenesis, we established sensitive, resistant, and crossed embryo families using five female and five male parents from relatively clean and predominantly PAH-polluted estuaries each, measured heart rates, and quantified individual embryo expression of 179 metabolic genes.

RESULTS

Pollution-induced embryotoxicity manifested as morphological deformities, significant developmental delays, and altered cardiac physiology was evident among sensitive embryos resulting from crosses between females and males from relatively clean estuaries. Significantly different heart rates among several geographically unrelated populations of sensitive, resistant, and crossed embryo families during late organogenesis and pre-hatching suggest site-specific adaptive cardiac physiology phenotypes relative to pollution exposure. Metabolic gene expression patterns (32 genes, 17.9%, at p < 0.05; 11 genes, 6.1%, at p < 0.01) among the embryo families indicate maternal pollutant deposition in the eggs and parental effects on gene expression and metabolic alterations.

CONCLUSION

Heart rate differences among sensitive, resistant, and crossed embryos is a reliable phenotype for further explorations of adaptive mechanisms. While metabolic gene expression patterns among embryo families are suggestive of parental effects on several differentially expressed genes, a definitive adaptive signature and metabolic cost of resistant phenotypes is unclear and shows unexpected sensitive-resistant crossed embryo expression profiles. Our study highlights physiological and metabolic gene expression differences during a critical embryonic stage among pollution sensitive, resistant, and crossed embryo families, which may contribute to underlying resistance mechanisms observed in natural F. heteroclitus populations living in heavily contaminated estuaries.

Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam

Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.

Cryptic eco-evolutionary feedback in the city: Urban evolution of prey dampens the effect of urban evolution of the predator

Most research on eco-evolutionary feedbacks focuses on ecological consequences of evolution in a single species. This ignores the fact that evolution in response to a shared environmental factor in multiple species involved in interactions could alter the net cumulative effect of evolution on ecology. We empirically tested whether urbanization-driven evolution in a predator (nymphs of the damselfly Ischnura elegans) and its prey (the water flea Daphnia magna) jointly shape the outcome of predation under simulated heatwaves. Both interactors show genetic trait adaptation to urbanization, particularly to higher temperatures. We cross-exposed common-garden reared damselflies and Daphnia from replicated urban and rural populations, and quantified predation rates and functional response traits. Urban damselfly nymphs showed higher encounter and predation rates than rural damselflies when exposed to rural prey, but this difference disappeared when they preyed on urban Daphnia. This represents a case of a cryptic evo-to-eco feedback, where the evolution of one species dampens the effects of the evolution of another species on their interaction strength. The effects of evolution of each single species were strong: the scenario in which only the predator or prey was adapted to urbanization resulted in a c. 250% increase in encounter rate and a c. 25% increase in predation rate, compared to the rural predator-rural prey combination. Our results provide unique evidence for eco-evolutionary feedbacks in cities, and underscore the importance of a multi-species approach in eco-evolutionary dynamics research.

Immunotoxicity of Xenobiotics in Fish: A Role for the Aryl Hydrocarbon Receptor (AhR)?

The impact of anthropogenic contaminants on the immune system of fishes is an issue of growing concern. An important xenobiotic receptor that mediates effects of chemicals, such as halogenated aromatic hydrocarbons (HAHs) and polyaromatic hydrocarbons (PAHs), is the aryl hydrocarbon receptor (AhR). Fish toxicological research has focused on the role of this receptor in xenobiotic biotransformation as well as in causing developmental, cardiac, and reproductive toxicity. However, biomedical research has unraveled an important physiological role of the AhR in the immune system, what suggests that this receptor could be involved in immunotoxic effects of environmental contaminants. The aims of the present review are to critically discuss the available knowledge on (i) the expression and possible function of the AhR in the immune systems of teleost fishes; and (ii) the impact of AhR-activating xenobiotics on the immune systems of fish at the levels of immune gene expression, immune cell proliferation and immune cell function, immune pathology, and resistance to infectious disease. The existing information indicates that the AhR is expressed in the fish immune system, but currently, we have little understanding of its physiological role. Exposure to AhR-activating contaminants results in the modulation of numerous immune structural and functional parameters of fish. Despite the diversity of fish species studied and the experimental conditions investigated, the published findings rather uniformly point to immunosuppressive actions of xenobiotic AhR ligands in fish. These effects are often associated with increased disease susceptibility. The fact that fish populations from HAH- and PAH-contaminated environments suffer immune disturbances and elevated disease susceptibility highlights that the immunotoxic effects of AhR-activating xenobiotics bear environmental relevance.

CRISPR/Cas9 mutagenesis reveals a role for ABCB1 in gut immune responses to Vibrio diazotrophicus in sea urchin larvae

The ABC transporter ABCB1 plays an important role in the disposition of xenobiotics. Embryos of most species express high levels of this transporter in early development as a protective mechanism, but its native substrates are not known. Here, we used larvae of the sea urchin Strongylocentrotus purpuratus to characterize the early life expression and role of Sp-ABCB1a, a homolog of ABCB1. The results indicate that while Sp-ABCB1a is initially expressed ubiquitously, it becomes enriched in the developing gut. Using optimized CRISPR/Cas9 gene editing methods to achieve high editing efficiency in the F0 generation, we generated ABCB1a crispant embryos with significantly reduced transporter efflux activity. When infected with the opportunistic pathogen Vibrio diazotrophicus, Sp-ABCB1a crispant larvae demonstrated significantly stronger gut inflammation, immunocyte migration and cytokine Sp-IL-17 induction, as compared with infected control larvae. The results suggest an ancestral function of ABCB1 in host-microbial interactions, with implications for the survival of invertebrate larvae in the marine microbial environment.

P-glycoprotein induction and its energetic costs in rainbow trout (Oncorhynchus mykiss)

Biological organisms are constantly challenged by xenobiotics and have evolved mechanisms to reduce, neutralize, or repair toxic outcomes. The various chemical defenses all utilize energy, but their specific costs and impacts on energy budgets are currently unknown. In this study, the energetic costs associated with the induction and substrate transport of the efflux transporter P-glycoprotein (P-gp [ABCB1, MDR1]) were examined in rainbow trout. An intraperitoneal injection of the P-gp inducer clotrimazole (0, 0.1, 1.0, and 10 mg/kg) increased P-gp activity (as measured by a competitive rhodamine 123 transport assay in hepatocytes) in a dose-dependent manner reaching a maximum induction of 2.8-fold. Maximum P-gp induction occurred at 50 h post-administration with the highest dose; significant induction of P-gp activity remained elevated over constitutive values until the last sampling time point (168 h). In vitro measurements of hepatocyte respiration indicated that basal P-gp activity transporting R123 as a substrate did not significantly increase respiration rates (range 18.0 to 23.2 ng O₂/min/10⁶ cells); however, following the induction of P-gp by clotrimazole and exposure to the P-gp substrate R123, respiration rates increased significantly (3.52-fold) over baseline values. Using whole animal respirometry, it was shown that respiration rates in fish exposed to R123 only or induced with clotrimazole were not different from controls (range 1.2 to 2.1 mg O₂/kg/min); however, respiration rates were significantly increased in fish with induced P-gp levels and also exposed to R123. This work indicates that basal and induced levels of P-gp activity do not incur significant energetic costs to fish; however, upon induction of P-gp and concomitant substrate exposures, energetic costs can increase and could pose challenges to organisms facing limited energy resources.

Incipient resistance to an effective pesticide results from genetic adaptation and the canalization of gene expression

The resistance of pest species to chemical controls has vast ecological, economic, and societal costs. In most cases, resistance is only detected after spreading throughout an entire population. Detecting resistance in its incipient stages, by comparison, provides time to implement preventative strategies. Incipient resistance can be detected by coupling standard toxicology assays with large-scale gene expression experiments. We apply this approach to a system where an invasive parasite, sea lamprey (Petromyzon marinus), has been treated with the highly effective pesticide 3-trifluoromethyl-4-nitrophenol (TFM) for 60 years. Toxicological experiments revealed that lamprey from treated populations did not have higher survival to TFM exposure than lamprey from untreated populations, demonstrating that full-fledged resistance has not yet evolved. In contrast, we find hundreds of genes differentially expressed in response to TFM in the population with the longest history of exposure, many of which relate to TFM's primary mode of action, the uncoupling of oxidative phosphorylation, and subsequent depletion of ATP. Three genes critical to oxidative phosphorylation, ATP5PB, PLCB1, and NDUFA9, were nearly fixed for alternative alleles in comparisons of SNPs between treated and untreated populations (FST  > 5 SD from the mean). ATP5PB encodes subunit b of ATP synthase and an additional subunit, ATP5F1B, was canalized for high expression in treated populations, but remained plastic in response to TFM treatment in individuals from the untreated population. These combined genomic and transcriptomic results demonstrate that an adaptive, genetic response to TFM is likely driving incipient resistance in a damaging pest species.

Expression of DNA repair genes in arctic char (Salvelinus alpinus) from Bjørnøya in the Norwegian Arctic

High levels of organochlorines (OCs) have been measured in arctic char (Salvelinus alpinus) from Lake Ellasjøen on Bjørnøya, Norway (74.30°N, 19.0°E). In a nearby lake, Laksvatn, the OC-levels in arctic char were low. A previous study has shown that char from Ellasjøen had significantly higher levels of DNA double strand breaks (DSBs) than char from Lake Laksvatn. Even though there is increasing evidence of the genotoxic effects of OCs, little is known about the effects of OCs on the DNA repair system. The aim of the present study was to determine if the two main DNA DSB repair mechanisms, homologous recombination (HR) and non-homologous end-joining (NHEJ), are affected by the higher OC and DSB level in char from Ellasjøen. This was analysed by comparing the transcript level of 11 genes involved in DNA DSB repair in char liver samples from Ellasjøen (n = 9) with char from Laksvatn (n = 12). Six of the investigated genes were significantly upregulated in char from Ellasjøen. As the expression of DNA DSB repair genes was increased in the contaminant-exposed char, it is likely that the DNA DSB repair capacity is induced in these individuals. This induction was positively correlated with the DNA DSB and negatively correlated with one or several OCs for four of these genes. However, the strongest predictor variable for DNA repair genes was habitat, indicating genetic differences in repair capacity between populations. As char from Ellasjøen still had significantly higher levels of DSBs compared to char from Laksvatn, it is possible that chronic exposure to OCs and continued production of DSB has caused selective pressure within the population for fixation of adaptive alleles. It is also possible that DSB production was exceeding the repair capacity given the prevailing conditions, or that the OC or DSB level was above the threshold value of inhibition of the DNA repair system resulting in the rate of DNA damage exceeding the rate of repair.

Intraspecific variability of responses to combined metal contamination and immune challenge among wild fish populations

Wild organisms are increasingly exposed to multiple anthropogenic and natural stressors that can interact in complex ways and lead to unexpected effects. In aquatic ecosystems, contamination by trace metals has deleterious effects on fish health and commonly co-occurs with pathogens, which affect similar physiological and behavioral traits. However, the combined effects of metal contamination and parasitism are still poorly known. In addition, the sensitivity to multiple stressors could be highly variable among different fish populations depending on their evolutionary history, but this intraspecific variability is rarely taken into account in existing ecotoxicological studies. Here, we investigated i) the interactive effects of metal contamination (i.e., realistic mixture of Cd, Cu and Zn) and immune challenge mimicking a parasite attack on fish health across biological levels. In addition, we compared ii) the physiological and behavioral responses among five populations of gudgeon fish (Gobio occitaniae) having evolved along a gradient of metal contamination. Results show that single stressors exposure resulted in an increase of immune defenses and oxidative stress at the expense of body mass (contamination) or fish swimming activity (immune challenge). Multiple stressors had fewer interactive effects than expected, especially on physiological traits, but mainly resulted in antagonistic effects on fish swimming activity. Indeed, the immune challenge modified or inhibited the effects of contamination on fish behavior in most populations, suggesting that multiple stressors could reduce behavioral plasticity. Interestingly, the effects of stressors were highly variable among populations, with lower deleterious effects of metal contamination in populations from highly contaminated environments, although the underlying evolutionary mechanisms remain to be investigated. This study highlights the importance of considering multiple stressors effects and intraspecific variability of sensitivity to refine our ability to predict the effects of environmental contaminants on aquatic wildlife.

Testing for population differences in evolutionary responses to pesticide pollution in brown trout (Salmo trutta)

Pesticides are often toxic to nontarget organisms, especially to those living in rivers that drain agricultural land. The brown trout (Salmo trutta) is a keystone species in many such rivers, and natural populations have hence been chronically exposed to pesticides over multiple generations. The introduction of pesticides decades ago could have induced evolutionary responses within these populations. Such a response would be predicted to reduce the toxicity over time but also deplete any additive genetic variance for the tolerance to the pesticides. If so, populations are now expected to differ in their susceptibility and in the variance for the tolerance depending on the pesticides they have been exposed to. We sampled breeders from seven natural populations that differ in their habitats and that show significant genetic differentiation. We stripped them for their gametes and produced 118 families by in vitro fertilization. We then raised 20 embryos per family singly in experimentally controlled conditions and exposed them to one of two ecologically relevant concentrations of either the herbicide S-metolachlor or the insecticide diazinon. Both pesticides affected embryo and larval development at all concentrations. We found no statistically significant additive genetic variance for tolerance to these stressors within or between populations. Tolerance to the pesticides could also not be linked to variation in carotenoid content of the eggs. However, pesticide tolerance was linked to egg size, with smaller eggs being more tolerant to the pesticides than larger eggs. We conclude that an evolutionary response to these pesticides is currently unlikely and that (a) continuous selection in the past has either depleted genetic variance in all the populations we studied or (b) that exposure to the pesticides never induced an evolutionary response. The observed toxicity selects against large eggs that are typically spawned by larger and older females.

Socio-eco-evolutionary dynamics in cities

Cities are uniquely complex systems regulated by interactions and feedbacks between nature and human society. Characteristics of human society-including culture, economics, technology and politics-underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing research on urban ecology and evolutionary biology has coincided with growing interest in eco-evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco-evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological-and even social-significance. Still, little work fully integrates urban evolutionary biology and eco-evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban "socio-eco-evolutionary dynamics." Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions and their contributions to people within and outside cities.

Hepatobiliary PAHs and prevalence of pathological changes in Red Snapper

Red Snapper (Lutjanus campechanus) were collected throughout the Gulf of Mexico (GoM) from 2011 to 2017 and analyzed for biliary (n = 496) fluorescent aromatic compounds (FACs), hepatic (n = 297) polycyclic aromatic hydrocarbons (PAHs) and microscopic hepatobiliary changes (MHC, n = 152). Gross and histological evaluations were conducted with liver tissues to identify and characterize pathological changes. This is the first report to interrelate hepatobiliary PAH concentrations and MHCs in Red Snapper. Hepatic PAHs measured in GoM Red Snapper ranged from 192 to 8530 ng g^-1 w.w. and biliary FACs ranged from 480 to 1,100,000 ng FAC g^-1 bile. Biliary FACs in Red Snapper collected along the west Florida Shelf and north central region declined after 2011 and were relatively stable until a sharp increase was noted in 2017. Increases in the PAH exposures are likely due to a number of sources including leaking infrastructure, annual spills, riverine input and the resuspension of contaminated sediments. In contrast, hepatic PAH concentrations were relatively stable indicating Red Snapper are able to maintain metabolic clearance however this energetic cost may be manifesting as microscopic hepatic changes (MHCs). Virtually all (99 %) of the evaluated Red Snapper had one to nine MHCs with an average of five coinciding changes in an individual fish. The observed changes were broadly classified as inflammatory responses, metabolic responses, degenerative lesions, nonneoplastic proliferation and neoplastic lesions. Biliary FACs were associated with parasitic infection and intracellular breakdown product accumulation such as intra-macrophage hemosiderin, lipofuscin and ceroid laden prevalence. Whereas, hepatic PAHs were associated with increased myxozoan plasmodia prevalence. This study evaluates relationships between hepatobiliary PAH concentrations and biometrics, somatic indices, condition factors and microscopic hepatic changes in Red Snapper located in the north central GoM. Together, these results may be signaling increased disease progression in Gulf of Mexico Red Snapper more than likely resulting from chronic environmental stressors including elevated PAH exposures and concentrations.

Natural history collections are critical resources for contemporary and future studies of urban evolution

Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.

Evolutionary responses of marine organisms to urbanized seascapes

Many of the world's major cities are located in coastal zones, resulting in urban and industrial impacts on adjacent marine ecosystems. These pressures, which include pollutants, sewage, runoff and debris, temperature increases, hardened shorelines/structures, and light and acoustic pollution, have resulted in new evolutionary landscapes for coastal marine organisms. Marine environmental changes influenced by urbanization may create new selective regimes or may influence neutral evolution via impacts on gene flow or partitioning of genetic diversity across seascapes. While some urban selective pressures, such as hardened surfaces, are similar to those experienced by terrestrial species, others, such as oxidative stress, are specific to aquatic environments. Moreover, spatial and temporal scales of evolutionary responses may differ in the ocean due to the spatial extent of selective pressures and greater capacity for dispersal/gene flow. Here, we present a conceptual framework and synthesis of current research on evolutionary responses of marine organisms to urban pressures. We review urban impacts on genetic diversity and gene flow and examine evidence that marine species are adapting, or are predicted to adapt, to urbanization over rapid evolutionary time frames. Our findings indicate that in the majority of studies, urban stressors are correlated with reduced genetic diversity. Genetic structure is often increased in urbanized settings, but artificial structures can also act as stepping stones for some hard-surface specialists, promoting range expansion. Most evidence for rapid adaptation to urban stressors comes from studies of heritable tolerance to pollutants in a relatively small number of species; however, the majority of marine ecotoxicology studies do not test directly for heritability. Finally, we highlight current gaps in our understanding of evolutionary processes in marine urban environments and present a framework for future research to address these gaps.