No abstract

Crude oils from distinct geological sources worldwide are toxic to developing fish hearts. When oil spills occur in fish spawning habitats, natural resource injury assessments often rely on conventional morphometric analyses of heart form and function. The extent to which visible indicators correspond to molecular markers for cardiovascular stress is unknown for pelagic predators from the Gulf of Mexico. Here we exposed mahi (Coryphaena hippurus) embryos to field-collected crude oil samples from the 2010 Deepwater Horizon disaster. We compared visible heart defects (edema, abnormal looping, reduced contractility) to changes in expression of cardiac-specific genes that are diagnostic of heart failure in humans or associated with loss-of-function zebrafish cardiac mutants. Mahi exposed to crude oil during embryogenesis displayed typical symptoms of cardiogenic syndrome as larvae. Contractility, looping, and circulatory defects were evident, but larval mahi did not exhibit downstream craniofacial and body axis abnormalities. A gradation of oil exposures yielded concentration-responsive changes in morphometric and molecular responses, with relative sensitivity being influenced by age. Our findings suggest that 1) morphometric analyses of cardiac function are more sensitive to proximal effects of crude oil-derived chemicals on the developing heart, and 2) molecular indicators reveal a longer-term adverse shift in cardiogenesis trajectory.

Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically difficult, ontology-driven information systems can help generate testable hypotheses about developmental processes in experimentally tractable organisms. Here, we tested candidate gene hypotheses suggested by expert use of the Phenoscape Knowledgebase, specifically looking for genes that are candidates responsible for evolutionarily interesting phenotypes in the ostariophysan fishes that bear resemblance to mutant phenotypes in zebrafish. For this, we searched ZFIN for genetic perturbations that result in either loss of basihyal element or loss of scales phenotypes, because these are the ancestral phenotypes observed in catfishes (Siluriformes). We tested the identified candidate genes by examining their endogenous expression patterns in the channel catfish, Ictalurus punctatus. The experimental results were consistent with the hypotheses that these features evolved through disruption in developmental pathways at, or upstream of, brpf1 and eda/edar for the ancestral losses of basihyal element and scales, respectively. These results demonstrate that ontological annotations of the phenotypic effects of genetic alterations in model organisms, when aggregated within a knowledgebase, can be used effectively to generate testable, and useful, hypotheses about evolutionary changes in morphology.

Biodiversity conservation is a worldwide concern and proper management of threatened species or communities depends on reliable and accurate data collection. Despite the broad utility of environmental DNA (eDNA) for conservation management and the necessity for appropriate biodiversity management in the tropics, eDNA-based research conducted in tropical regions so far comprises only a small proportion of the cumulative eDNA literature. To address the growing demand for rapid and reliable species and community level ecological data in tropical regions, we provide an aquatic eDNA-focused review of (1) challenges and considerations for sampling design and inference of eDNA data in the tropics, and (2) eDNA applications relevant to ecological research and biodiversity management in the tropics. We propose that the collaborative incorporation of eDNA sampling with conventional field surveys harbours the potential to revolutionize the effectiveness of biodiversity conservation management in tropical regions.

Normalization of fluorescence-based quantitative real-time PCR (qPCR) data varies across quantitative gene expression studies, despite its integral role in accurate data quantification and interpretation. Identification of suitable reference genes plays an essential role in accurate qPCR normalization, as it ensures that uncorrected gene expression data reflect normalized data. The reference residual normalization (RRN) method presented here is a modified approach to conventional 2(-ΔΔCt)qPCR normalization that increases mathematical transparency and incorporates statistical assessment of reference gene stability. RRN improves mathematical transparency through the use of sample-specific reference residuals (RR i ) that are generated from the mean Ct of one or more reference gene(s) that are unaffected by treatment. To determine stability of putative reference genes, RRN uses ANOVA to assess the effect of treatment on expression and subsequent equivalence-threshold testing to establish the minimum permitted resolution. Step-by-step instructions and comprehensive examples that demonstrate the influence of reference gene stability on target gene normalization and interpretation are provided. Through mathematical transparency and statistical rigor, RRN promotes compliance with Minimum Information for Quantitative Experiments and, in so doing, provides increased confidence in qPCR data analysis and interpretation.

Urban stormwater runoff is a globally significant threat to the ecological integrity of aquatic habitats. Green stormwater infrastructure methods such as bioretention are increasingly used to improve water quality by filtering chemical contaminants that may be harmful to fish and other species. Ubiquitous examples of toxics in runoff from highways and other impervious surfaces include polycyclic aromatic hydrocarbons (PAHs). Certain PAHs are known to cause functional and structural defects in developing fish hearts. Therefore, abnormal heart development in fish can be a sensitive measure of clean water technology effectiveness. Here we use the zebrafish experimental model to assess the effects of untreated runoff on the expression of genes that are classically responsive to contaminant exposures, as well as heart-related genes that may underpin the familiar cardiotoxicity phenotype. Further, we assess the effectiveness of soil bioretention for treating runoff, as measured by prevention of both visible cardiac toxicity and corresponding gene regulation. We find that contaminants in the dissolved phase of runoff (e.g., PAHs) are cardiotoxic and that soil bioretention protects against these harmful effects. Molecular markers were more sensitive than visible toxicity indicators, and several cardiac-related genes show promise as novel tools for evaluating the effectiveness of evolving stormwater mitigation strategies.

We investigated how thermal stress may alter the locomotor phenotype of barramundi, Lates calcarifer , from genetically distinct northern (low latitude) and southern (high latitude) populations in tropical Australia. Following early growth and development under native (25 °C and 30 °C) and non-native (20 °C and 35 °C) temperatures, we observed distinct differences in the swimming performance of northern and southern individuals that were consistent with expectations based on local thermal adaptation. Southern population fish exhibited significantly faster swimming speeds (32.10 ± 0.33 cm·s–1, mass-adjusted mean ± 95% confidence limit) than their northern counterparts (28.58 ± 0.64 cm·s–1) under cold-stress (20 °C) conditions. Conversely, northern population fish performed significantly better (51.63 ± 2.1 cm·s–1) than their southern counterparts (44.18 ± 3.11 cm·s–1) under heat-stress (35 °C) conditions. We conclude that L. calcarifer display locomotor phenotypes thermally adapted to their local environment, with early growth under non-native temperatures leading to significantly reduced phenotypic fitness.

Coal tar sealcoats applied to asphalt surfaces in North America, east of the Continental Divide, are enriched in petroleum-derived compounds, including polycyclic aromatic hydrocarbons (PAHs). The release of PAHs and other chemicals from sealcoat has the potential to contaminate nearby water bodies, reducing the resiliency of aquatic communities. Despite this, relatively little is known about the aquatic toxicology of sealcoat-derived contaminants. We assessed the impacts of stormwater runoff from sealcoated asphalt on juvenile coho salmon (Oncorhynchus kisutch) and embryo-larval zebrafish (Danio rerio). We furthermore evaluated the effectiveness of bioretention as a green stormwater method to remove PAHs and reduce lethal and sublethal toxicity in both species. We applied a coal tar sealcoat to conventional asphalt and collected runoff from simulated rainfall events up to 7 months postapplication. Whereas sealcoat runoff was more acutely lethal to salmon, a spectrum of cardiovascular abnormalities was consistently evident in early life stage zebrafish. Soil bioretention effectively reduced PAH concentrations by an order of magnitude, prevented mortality in juvenile salmon, and significantly reduced cardiotoxicity in zebrafish. Our findings show that inexpensive bioretention methods can markedly improve stormwater quality and protect fish health.