Protein analysis and gene expression indicate differential vulnerability of Iberian fish species under a climate change scenario

Comparative Transcriptome Analyses Provide New Insights into the Evolution of Divergent Thermal Resistance in Two Eel Gobies

Adaptation to thermal conditions in tidal mudflats always involves tolerating frequent fluctuations and often extreme environmental temperatures. Regulation of gene expression plays a fundamental role in the evolution of these thermal adaptations. To identify the key gene regulatory networks associated with the thermal adaptation, we investigated the capability of cold tolerance, as well as the transcriptomic changes under cold stress in two mudflat inhabitants (Odontamblyopus lacepedii and O. rebecca) with contrasting latitude affinity. Our results revealed a remarkable divergent capacity of cold tolerance (CTmin: 0.61 °C vs. 9.57 °C) between the two gobies. Analysis of transcriptomic changes under cold stress unveiled 193 differentially expressed genes exhibiting similar expression profiles across all tissues and species, including several classic metabolic and circadian rhythm molecules such as ACOD and CIART that may represent the core cold response machinery in eel gobies. Meanwhile, some genes show a unique expression spectrum in the more cold-tolerant O. lacepedii suggesting their roles in the enhanced cold tolerance and hence the extreme thermal adaptations. In addition, a weighted gene co-expression network analysis (WGCNA) revealed a subset of metabolic hub genes including MYH11 and LIPT2 showing distinct down-regulation in O. lacepedii when exposed to cold stress which highlights the role of reduced energy consumption in the enhanced cold tolerance of eel gobies. These findings not only provide new insights into how mudflat teleosts could cope with cold stress and their potential evolutionary strategies for adapting to their thermal environment, but also have important implications for sound management and conservation of their fishery resources in a scenario of global climate warming in the marine realm.

Rhythms and Clocks in Marine Organisms

The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.

Comparative Study of the Molecular Characterization, Evolution, and Structure Modeling of Digestive Lipase Genes Reveals the Different Evolutionary Selection Between Mammals and Fishes

Vertebrates need suitable lipases to digest lipids for the requirement of energy and essential nutrients; however, the main digestive lipase genes of fishes have certain controversies. In this study, two types of digestive lipase genes (pancreatic lipase (pl) and bile salt-activated lipase (bsal)) were identified in mammals and fishes. The neighborhood genes and key active sites of the two lipase genes were conserved in mammals and fishes. Three copies of PL genes were found in mammals, but only one copy of the pl gene was found in most of the fish species, and the pl gene was even completely absent in some fish species (e.g., zebrafish, medaka, and common carp). Additionally, the hydrophobic amino acid residues (Ile and Leu) which are important to pancreatic lipase activity were also absent in most of the fish species. The PL was the main digestive lipase gene in mammals, but the pl gene seemed not to be the main digestive lipase gene in fish due to the absence of the pl gene sequence and the important amino acid residues. In contrast, the bsal gene existed in all fish species, even two to five copies of bsal genes were found in most of the fishes, but only one copy of the BSAL gene was found in mammals. The amino acid residues of bile salt-binding sites and the three-dimensional (3D) structure modeling of Bsal proteins were conserved in most of the fish species, so bsal might be the main digestive lipase gene in fish. The phylogenetic analysis also indicated that pl or bsal showed an independent evolution between mammals and fishes. Therefore, we inferred that the evolutionary selection of the main digestive lipase genes diverged into two types between mammals and fishes. These findings will provide valuable evidence for the study of lipid digestion in fish.

Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species

Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers-Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis-using a population genomics dataset of 23,562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well-differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage, we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.

Adaptation and convergence in circadian-related genes in Iberian freshwater fish

BACKGROUND

The circadian clock is a biological timing system that improves the ability of organisms to deal with environmental fluctuations. At the molecular level it consists of a network of transcription-translation feedback loops, involving genes that activate (bmal and clock - positive loop) and repress expression (cryptochrome (cry) and period (per) - negative loop). This is regulated by daily alternations of light but can also be affected by temperature. Fish, as ectothermic, depend on the environmental temperature and thus are good models to study its integration within the circadian system. Here, we studied the molecular evolution of circadian genes in four Squalius freshwater fish species, distributed across Western Iberian rivers affected by two climatic types with different environmental conditions (e.g., light and temperature). S. carolitertii and S. pyrenaicus inhabit the colder northern region under Atlantic climate type, while S. torgalensis, S. aradensis and some populations of S. pyrenaicus inhabit the warmer southern region affected by summer droughts, under Mediterranean climate type.

RESULTS

We identified 16 circadian-core genes in the Squalius species using a comparative transcriptomics approach. We detected evidence of positive selection in 12 of these genes using methods based on dN/dS. Positive selection was mainly found in cry and per genes of the negative loop, with 55 putatively adaptive substitutions, 16 located on protein domains. Evidence for positive selection is predominant in southern populations affected by the Mediterranean climate type. By predicting protein features we found that changes at sites under positive selection can impact protein thermostability by changing their aliphatic index and isoelectric point. Additionally, in nine genes, the phylogenetic clustering of species that belong to different clades but inhabit southern basins with similar environmental conditions indicated evolutionary convergence. We found evidence for increased nonsynonymous substitution rate in convergent lineages, likely due to positive selection at 27 sites, mostly in cry genes.

CONCLUSIONS

Our results support that temperature may be a selective pressure driving the evolution of genes involved in the circadian system. By integrating sequence-based functional protein prediction with dN/dS-based methods to detect selection we uncovered adaptive convergence in the southern populations, probably related to their similar thermal conditions.

How will farmed populations of freshwater fish deal with the extreme climate scenario in 2100? Transcriptional responses of Colossoma macropomum from two Brazilian climate regions

Tambaqui (Colossoma macropomum Cuvier, 1818) is an endemic fish of the Amazon and Orinoco basins, and it is the most economically important native species in Brazil being raised in five climatically distinct regions. In the face of current global warming, environmental variations in farm ponds represent additional challenges that may drive new adaptive regional genetic variations among broodstocks of tambaqui. In an experimental context based on the high-emission scenario of the 5th Intergovernmental Panel on Climate Change (IPCC) report, we used two farmed tambaqui populations to test this hypothesis. RNA-seq transcriptome analysis was performed in the liver of juvenile tambaqui from northern (Balbina Experimental Station, Balbina, AM) and southeastern (Brumado Fish Farming, Mogi Mirim, SP) Brazilian regions kept for 30 days in artificial environmental rooms mimicking the current and extreme climate scenarios. Three Illumina MiSeq runs produced close to 120 million 500 bp paired-end reads; 191,139 contigs were assembled with N50 = 1595. 355 genes were differentially expressed for both populations in response to the extreme scenario. After enrichment analysis, each population presented a core set of genes to cope with climate change. Northern fish induced genes related to the cellular response to stress, activation of MAPK activity, response to unfolded protein, protein metabolism and cellular response to DNA damage stimuli. Genes biologically involved in regulating cell proliferation, protein stabilisation and protein ubiquitination for degradation through the ubiquitin-proteasome system were downregulated. Genes associated with biological processes, including the cellular response to stress, MAPK cascade activation, homeostatic processes and positive regulation of immune responses were upregulated in southeastern fish. The downregulated genes were related to cytoskeleton organisation, energy metabolism, and the regulation of transcription and biological rhythms. Our findings reveal the signatures of promising candidate genes involved in the regional plasticity of each population of tambaqui in dealing with upcoming climate changes.

Floods, Hurricanes, and Other Catastrophes: A Challenge for the Immune System of Livestock and Other Animals

Climate change involves different dramatic phenomena including desertification and wildfires, severe storms such as hurricanes and blizzards, increased sea levels resulting in flooding coastal cities and rise of atmospheric CO₂ concentration. The alteration of the climate in a specific region affects the life of indigenous animals and humans. The climate changes influence living beings both directly and indirectly. The immune system of animals dramatically suffers the climate instability, making animals more susceptible to infectious and not infectious diseases. Different species of livestock animals respond with similar mechanisms to global warming, but some of them are more susceptible depending on their age, metabolism, and genetic conditions. The selection and study of autochthonous species and breeds, more easily adapted to specific environmental conditions could be an interesting strategy to face livestock rearing in the future.

Microplastics have a more profound impact than elevated temperatures on the predatory performance, digestion and energy metabolism of an Amazonian cichlid

Knowledge on the impacts of microplastics (MPs) pollution on freshwater environments and biota remains limited. Meanwhile, freshwater ecosystems have been threatened by elevated temperatures caused by climate change. To date, no information exists on how MPs-especially under elevated temperature conditions-affect predatory performance, digestive processes and metabolic pathways in freshwater organisms. Here, we examined MPs, elevated temperature and their combined effects on juveniles (0+ group) of an Amazonian cichlid, the discus fish (Symphysodon aequifasciatus). For 30 days, fish were exposed to ambient or elevated temperatures (i.e., 28 or 31 °C) in the absence or presence of MPs (i.e., 0 or 200 μg/L). The following metrics were quantified: MPs accumulation; predatory performance; and biomarkers involved in neurotransmission, digestion and energy production. The results showed that survival rate and body length were not affected by MPs, elevated temperatures or their combination. Elevated temperatures resulted in an increase in MP concentrations in fish bodies. Exposure to MPs decreased the post-exposure predatory performance (PEPP) at ambient temperatures but not at elevated temperatures. Elevated temperatures, however, had no effect on the PEPP but antagonistically interacted with MPs, leading to similar predatory performances under present and future conditions. Acetylcholinesterase (AChE) activity was only affected by MPs and decreased in the presence of MPs, indicating adverse effects in nervous and neuromuscular function and, thus, potentially in predatory performance. Trypsin activity was only influenced by MPs and decreased during exposure to MPs. Elevated temperatures or MPs alone increased the amylase activity but interacted antagonistically. Lipase activity was not influenced by either of the two stressors. In contrast, alkaline phosphatase (ALP) activity was affected by MPs or elevated temperatures alone and decreased with both stressors. Such results indicate deficits in the digestive capabilities of early-stage S. aequifasciatus under elevated temperature conditions and especially during exposure to MPs. Electron transport system (ETS) activity was not influenced by either of the two stressors. Both elevated temperatures and MPs alone increased LDH activity; however, the interaction between the two stressors cancelled activity but was still higher than activity in present conditions. Citrate synthase (CS) activity decreased with elevated temperature but increased during exposure to MPs. Cytochrome c oxidase (COX) activity was only influenced by MPs and increased in the presence of MPs. Thus, S. aequifasciatus juveniles exposed to elevated temperatures and MPs not only relied on anaerobic glycolysis for energy production but also depended on aerobic metabolism in the presence of MPs. Overall, these findings suggested that MPs showed a greater impact than elevated temperatures on the predatory performance, digestion and energy production of S. aequifasciatus. Nevertheless, juvenile survival and growth were minimally impacted, and thus, S. aequifasciatus could cope with near-future temperature increases and MP exposure.