A proteomics approach reveals divergent molecular responses to salinity in populations of European whitefish (Coregonus lavaretus)

Genomic evidence for demographic fluctuations, genetic burdens and adaptive divergence in fourfinger threadfin Eleutheronema rhadinum

Declining populations and bottlenecks lead to the accumulation of deleterious mutations in fish populations. These processes also trigger genetic purging, which is a key genetic factor in reducing the deleterious burdens and increasing population viability. However, there is a lack of empirical evidence on the interaction between demographic history and the genome-wide pattern of deleterious variations. Here, we generated genome resequencing data of Eleutheronema rhadinum from China and Thailand, representing the major distribution of the species' southern regions. E. rhadinum had exceptionally low genome-wide variability and experienced dramatic population expansions followed by continuous declines. The geographical divergence, which occurred ~ 23,000 years ago, shaped different demographic trajectories and generated different regional patterns of deleterious mutations in China and Thailand populations. Several lines of evidence revealed that this geographical pattern of deleterious mutation was driven by the purging of highly deleterious mutations. We showed that purifying selection had inbreeding-associated fitness costs and was more efficient against missense mutations in the Thailand population, which had the lowest genetic burden of homozygous deleterious mutations. Multiple evolutionarily conserved protein domains were disrupted by the loss-of-function mutations, posing a high probability of gene functionality elimination. Moreover, thermal and salinity genes (Trpm3, Nek4, Gtf2f2, Cldn14) were identified in genomic divergence regions of E. rhadinum among China and Thailand populations. Our findings highlight the importance of demographic history factors shaping the geographical patterns of deleterious mutations. The results serve to deepen our understanding of the adaptive evolution and divergence of E. rhadinum with implications for other marine fish.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00276-4.

Gene expression signatures between Limia perugiae (Poeciliidae) populations from freshwater and hypersaline habitats, with comparisons to other teleosts

Salinity gradients act as strong environmental barriers that limit the distribution of aquatic organisms. Changes in gene expression associated with transitions between freshwater and saltwater environments can provide insights into organismal responses to variation in salinity. We used RNA-sequencing (RNA-seq) to investigate genome-wide variation in gene expression between a hypersaline population and a freshwater population of the livebearing fish species Limia perugiae (Poeciliidae). Our analyses of gill gene expression revealed potential molecular mechanisms underlying salinity tolerance in this species, including the enrichment of genes involved in ion transport, maintenance of chemical homeostasis, and cell signaling in the hypersaline population. We also found differences in gene expression patterns associated with cell-cycle and protein-folding processes between the hypersaline and freshwater L. perugiae. Bidirectional freshwater-saltwater transitions have occurred repeatedly during the diversification of fishes, allowing for broad-scale examination of repeatable patterns in evolution. Therefore, we compared transcriptomic variation in L. perugiae with other teleosts that have made freshwater-saltwater transitions to test for convergence in gene expression. Among the four distantly related population pairs from high- and low-salinity environments that we included in our analysis, we found only ten shared differentially expressed genes, indicating little evidence for convergence. However, we found that differentially expressed genes shared among three or more lineages were functionally enriched for ion transport and immune functioning. Overall, our results-in conjunction with other recent studies-suggest that different genes are involved in salinity transitions across disparate lineages of teleost fishes.

Understanding and applying biological resilience, from genes to ecosystems

The natural world is under unprecedented and accelerating pressure. Much work on understanding resilience to local and global environmental change has, so far, focussed on ecosystems. However, understanding a system's behaviour requires knowledge of its component parts and their interactions. Here we call for increased efforts to understand 'biological resilience', or the processes that enable components across biological levels, from genes to communities, to resist or recover from perturbations. Although ecologists and evolutionary biologists have the tool-boxes to examine form and function, efforts to integrate this knowledge across biological levels and take advantage of big data (e.g. ecological and genomic) are only just beginning. We argue that combining eco-evolutionary knowledge with ecosystem-level concepts of resilience will provide the mechanistic basis necessary to improve management of human, natural and agricultural ecosystems, and outline some of the challenges in achieving an understanding of biological resilience.

An environmental gradient dominates ecological and genetic differentiation of marine invertebrates between the North and Baltic Sea

Environmental gradients have emerged as important barriers to structuring populations and species distributions. We set out to test whether the strong salinity gradient from the marine North Sea to the brackish Baltic Sea in northern Europe represents an ecological and genetic break, and to identify life history traits that correlate with the strength of this break. We accumulated mitochondrial cytochrome oxidase subunit 1 sequence data, and data on the distribution, salinity tolerance, and life history for 28 species belonging to the Cnidaria, Crustacea, Echinodermata, Mollusca, Polychaeta, and Gastrotricha. We included seven non‐native species covering a broad range of times since introduction, in order to gain insight into the pace of adaptation and differentiation. We calculated measures of genetic diversity and differentiation across the environmental gradient, coalescent times, and migration rates between North and Baltic Sea populations, and analyzed correlations between genetic and life history data. The majority of investigated species is either genetically differentiated and/or adapted to the lower salinity conditions of the Baltic Sea. Species exhibiting population structure have a range of patterns of genetic diversity in comparison with the North Sea, from lower in the Baltic Sea to higher in the Baltic Sea, or equally diverse in North and Baltic Sea. Two of the non‐native species showed signs of genetic differentiation, their times since introduction to the Baltic Sea being about 80 and >700 years, respectively. Our results indicate that the transition from North Sea to Baltic Sea represents a genetic and ecological break: The diversity of genetic patterns points toward independent trajectories in the Baltic compared with the North Sea, and ecological differences with regard to salinity tolerance are common. The North Sea–Baltic Sea region provides a unique setting to study evolutionary adaptation during colonization processes at different stages by jointly considering native and non‐native species.

Effects of environmental salinity on the immune response of the coastal fish Scatophagus argus during bacterial infection

The coastal aquaculture is characterized with environmental salinity fluctuation, and the effects of salinity stress on the immunity of cultured fish are needed to be further explored. Scatophagus argus is an important species in the wild fisheries and aquaculture industry, it would be of great value to reveal the impact of salinity change on the immune response in this species. Understanding the effects of salinity stress on immune response can provide valuable insights into salinity management in the aquacultural process. The head kidney, which is an organ unique for teleost fish, functions not only as a central immune organ but also as a crucial role in the stress response during which the secretion of immunoregulatory molecules i.e. cytokines is facilitated. In the present study, Individuals of S. argus acclimated to 3 different salinities [0‰ (FW), 10‰ (BW), and 25‰ (SW)] were injected intraperitoneally with A. hydrophila, and then monitored throughout one week. The effects of environmental salinity on the immune response in S. argus stimulated by A. hydrophila infection were investigated. mRNA expression profiles of cytokine genes IL-1β, IL-6, IL-10 and TNF-α in different salinity groups was quite different. mRNA expression of cytokine genes in BW group and SW group rose more quickly and significantly higher than FW group (p < 0.05) at early stages (6-24 hpi) after bacterial injection, and before 96 hpi, the highest value of cytokine expression at each time point was recorded in SW group. Immune parameters such as lysozyme level, complement C3 activity and IgM content in BW and FW groups were lower than SW group at each time point from 24 to 144 hpi after bacterial injection. In addition, leukocyte profiles in the head kidney and blood were also investigated. Although hypoosmotic acclimation could temporarily stimulate monocyte and neutrophil proliferation, it was observed that the number of monocytes, neutrophils and lymphocytes of the head kidney and blood in SW group increased more quickly than BW and FW groups after bacterial infection. Our results indicate that hypoosmotic stress due to the decrease of environmental salinity has suppressive immunoregulatory effects on the immune response of S. argus.

Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms

Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Investigating Diadromy in Fishes and Its Loss in an -Omics Era

Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.

Genomic basis of the loss of diadromy in Galaxias maculatus: Insights from reciprocal transplant experiments

Diadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species. Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.

Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata

Deducing impacts of environmental change on species and the populations they form in nature is an important goal in contemporary ecology. Achieving this goal is hampered by our limited understanding of the influence of naturally occurring environmental variation on the molecular systems of ecologically relevant species, as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms and under controlled laboratory conditions. Here, to test the hypothesis that proteome variation systematically relates to variation in abiotic conditions, we establish such relationships by profiling the proteomes of 24 natural populations of the spring-dwelling caddisfly Crunoecia irrorata. We identified protein networks whose abundances correlated with environmental (abiotic) gradients such as in situ pH, oxygen- and nitrate concentrations but also climatic data such as past thermal minima and temperature seasonality. Our analyses suggest that variations in abiotic conditions induce discrete proteome responses such as the differential abundance of proteins associated with cytoskeletal function, heat-shock proteins and proteins related to post-translational modification. Identifying these drivers of proteome divergence characterizes molecular "noise", and positions it as a background against which molecular signatures of species' adaptive responses to stressful conditions can be identified.

Identifying Neuropeptide and G Protein-Coupled Receptors of Juvenile Oriental River Prawn (Macrobrachium nipponense) in Response to Salinity Acclimation

Neuropeptides and their G protein-coupled receptors (GPCRs) from the central nervous system regulate the physiological responses of crustaceans. However, in crustaceans, our knowledge regarding GPCR expression patterns and phylogeny is limited. Thus, the present study aimed to analyze the eyestalk transcriptome of the oriental river prawn Macrobrachium nipponense in response to salinity acclimation. We obtained 162,250 unigenes after de novo assembly, and 1,392 and 1,409 differentially expressed genes were identified in the eyestalk of prawns in response to low and high salinity, respectively. We used combinatorial bioinformatic analyses to identify M. nipponense genes encoding GPCRs and neuropeptides. The mRNA levels of seven neuropeptides and one GPCR were validated in prawns in response to salinity acclimation using quantitative real-time reverse transcription polymerase chain reaction. A total of 148 GPCR-encoding transcripts belonging to three classes were identified, including 77 encoding GPCR-A proteins, 52 encoding GPCR-B proteins, and 19 encoding other GPCRs. The results increase our understanding of molecular basis of neural signaling in M. nipponense, which will promote further research into salinity acclimation of this crustacean.

Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout

A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.

Divergent transcriptomic signatures in response to salinity exposure in two populations of an estuarine fish

In estuary and coastal systems, human demand for freshwater, climate change-driven precipitation variability, and extreme weather impact salinity levels, reducing connectivity between mesohaline coastal fish populations and potentially contributing to genomic divergence. We examined gill transcriptome responses to salinity in wild-caught juveniles from two populations of Sacramento splittail (Pogonichthys macrolepidotus), a species of conservation concern that is endemic to the San Francisco Estuary, USA, and the lower reaches of its tributaries. Recent extreme droughts have led to salinities above the tolerance limits for this species, creating a migration barrier between these populations, which potentially contributed to population divergence. We identified transcripts involved in a conserved response to salinity; however, the more salinity-tolerant San Pablo population had greater transcriptome plasticity (3.6-fold more transcripts responded than the Central Valley population) and a response consistent with gill remodeling after 168 hr of exposure to elevated salinity. The reorganization of the gill in response to changing osmotic gradients is a process critical for acclimation and would facilitate enhanced salinity tolerance. We detected an upregulation of receptors that control the Wnt (wingless-type) cell signaling pathway that may be required for an adaptive response to increases in salinity, patterns not observed in the relatively salinity-sensitive Central Valley population. We detected 62 single nucleotide polymorphisms (SNPs) in coding regions of 26 transcripts that differed between the populations. Eight transcripts that contained SNPs were associated with immune responses, highlighting the importance of diversity in immune gene sequences as a defining characteristic of genomic divergence between these populations. Our data demonstrate that these populations have divergent transcriptomic responses to salinity, which is consistent with observed physiological differences in salinity tolerance.

Evolution of heat-shock protein expression underlying adaptive responses to environmental stress

Heat-shock proteins (Hsps) and their cognates are primary mitigators of cell stress. With increasingly severe impacts of climate change and other human modifications of the biosphere, the ability of the heat-shock system to affect evolutionary fitness in environments outside the laboratory and to evolve in response is topic of growing importance. Since the last major reviews, several advances have occurred. First, demonstrations of the heat-shock response outside the laboratory now include many additional taxa and environments. Many of these demonstrations are only correlative, however. More importantly, technical advances in "omic" quantification of nucleic acids and proteins, genomewide association analysis, and manipulation of genes and their expression have enabled the field to move beyond correlation. Several consequent advances are already evident: The pathway from heat-shock gene expression to stress tolerance in nature can be extremely complex, mediated through multiple biological processes and systems, and even multiple species. The underlying genes are more numerous, diverse and variable than previously appreciated, especially with respect to their regulatory variation and epigenetic changes. The impacts and limitations (e.g., due to trade-offs) of natural selection on these genes have become more obvious and better established. At last, as evolutionary capacitors, Hsps may have distinctive impacts on the evolution of other genes and ecological consequences.

Tolerance of whitefish (Coregonus lavaretus) early life stages to manganese sulfate is affected by the parents

European whitefish (Coregonus lavaretus) embryos and larvae were exposed to 6 different manganese sulfate (MnSO₄ ) concentrations from fertilization to the 3-d-old larvae. The fertilization success, offspring survival, larval growth, yolk consumption, embryonic and larval Mn tissue concentrations, and transcript levels of detoxification-related genes were measured in the long-term incubation. A full factorial breeding design (4 females × 2 males) allowed examination of the significance of both female and male effects, as well as female-male interactions in conjunction with the MnSO₄ exposure in terms of the observed endpoints. The MnSO₄ exposure reduced the survival of the whitefish early life stages. The offspring MnSO₄ tolerance also was affected by the female parent, and the female-specific mean lethal concentrations (LC50s) varied from 42.0 mg MnSO₄ /L to 84.6 mg MnSO₄ /L. The larval yolk consumption seemed slightly inhibited at the exposure concentration of 41.8 mg MnSO₄ /L. The MnSO₄ exposure caused a significant induction of metallothionein-A (mt-a) and metallothionein-B (mt-b) in the 3-d-old larvae, and at the exposure concentration of 41.8 mg MnSO₄ /L the mean larval mt-a and mt-b expressions were 47.5% and 56.6% higher, respectively, than at the control treatment. These results illustrate that whitefish reproduction can be impaired in waterbodies that receive Mn and SO₄ in concentrations substantially above the typical levels in boreal freshwaters, but the offspring tolerance can be significantly affected by the parents and in particular the female parent. Environ Toxicol Chem 2017;36:1343-1353. © 2016 SETAC.

Sublethal salinity stress contributes to habitat limitation in an endangered estuarine fish

As global change alters multiple environmental conditions, predicting species' responses can be challenging without understanding how each environmental factor influences organismal performance. Approaches quantifying mechanistic relationships can greatly complement correlative field data, strengthening our abilities to forecast global change impacts. Substantial salinity increases are projected in the San Francisco Estuary, California, due to anthropogenic water diversion and climatic changes, where the critically endangered delta smelt (Hypomesus transpacificus) largely occurs in a low-salinity zone (LSZ), despite their ability to tolerate a much broader salinity range. In this study, we combined molecular and organismal measures to quantify the physiological mechanisms and sublethal responses involved in coping with salinity changes. Delta smelt utilize a suite of conserved molecular mechanisms to rapidly adjust their osmoregulatory physiology in response to salinity changes in estuarine environments. However, these responses can be energetically expensive, and delta smelt body condition was reduced at high salinities. Thus, acclimating to salinities outside the LSZ could impose energetic costs that constrain delta smelt's ability to exploit these habitats. By integrating data across biological levels, we provide key insight into the mechanistic relationships contributing to phenotypic plasticity and distribution limitations and advance the understanding of the molecular osmoregulatory responses in nonmodel estuarine fishes.

Transcriptomic analysis reveals specific osmoregulatory adaptive responses in gill mitochondria-rich cells and pavement cells of the Japanese eel

BACKGROUND

Homeostasis of ions and water is important for the maintenance of cellular functions. The regulation of the homeostasis is particularly important in euryhaline fish that migrate between freshwater (FW) and seawater (SW) environments. The fish gill, the major tissue that forms an interface separating the extracellular fluids and external water environment, has an effective transport system to maintain and regulate a constant body osmolality. In fish gills, the two major epithelial cells, pavement cells (PVCs) and mitochondria-rich cells (MRCs), are known to play key and complementary roles in ion transport at the interface. Discovering the robust mechanisms underlying the two cell types' response to osmotic stress would benefit our understanding of the fundamental mechanism allowing PVCs and MRCs to handle osmotic stress. Owing to the limited genomic data available on estuarine species, existing knowledge in this area is slim. In this study, transcriptome analyses were conducted using PVCs and MRCs isolated from Japanese eels adapted to FW or SW environments to provide a genome-wide molecular study to unravel the fundamental processes at work.

RESULTS

The study identified more than 12,000 transcripts in the gill cells. Interestingly, remarkable differential expressed genes (DEGs) were identified in PVCs (970 transcripts) instead of MRCs (400 transcripts) in gills of fish adapted to FW or SW. Since PVCs cover more than 90 % of the gill epithelial surface, the greater change in gene expression patterns in PVCs in response to external osmolality is anticipated. In the integrity pathway analysis, 19 common biological functions were identified in PVCs and MRCs. In the enriched signaling pathways analysis, most pathways differed between PVCs and MRCs; 14 enriched pathways were identified in PVCs and 12 in MRCs. The results suggest that the osmoregulatory responses in PVCs and MRCs are cell-type specific, which supports the complementary functions of the cells in osmoregulation.

CONCLUSIONS

This is the first study to provide transcriptomic analysis of PVCs and MRCs in gills of eels adapted to FW or SW environments. It describes the cell-type specific transcriptomic network in different tonicity. The findings consolidate the known osmoregulatory pathways and provide molecular insight in osmoregulation. The presented data will be useful for researchers to select their targets for further studies.

Transcriptome and proteome dynamics in larvae of the barnacle Balanus Amphitrite from the Red Sea

Background

The barnacle Balanus amphitrite is widely distributed in marine shallow and tidal waters, and has significant economic and ecological importance. Nauplii, the first larval stage of most crustaceans, are extremely abundant in the marine zooplankton. However, a lack of genome information has hindered elucidation of the molecular mechanisms of development, settlement and survival strategies in extreme marine environments. We sequenced and constructed the genome dataset for nauplii to obtain comprehensive larval genetic information. We also investigated iTRAQ-based protein expression patterns to reveal the molecular basis of nauplii development, and to gain information on larval survival strategies in the Red Sea marine environment.

Results

A nauplii larval transcript dataset, containing 92,117 predicted open reading frames (ORFs), was constructed and used as a reference for the proteome analysis. Genes related to translation, oxidative phosphorylation and cytoskeletal development were highly abundant. We observed remarkable plasticity in the proteome of Red Sea larvae. The proteins associated with development, stress responses and osmoregulation showed the most significant differences between the two larval populations studied. The synergistic overexpression of heat shock and osmoregulatory proteins may facilitate larval survival in intertidal habitats or in extreme environments.

Conclusions

We presented, for the first time, comprehensive transcriptome and proteome datasets for Red Sea nauplii. The datasets provide a foundation for future investigations focused on the survival mechanisms of other crustaceans in extreme marine environments.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2262-1) contains supplementary material, which is available to authorized users.

Statistical analysis of the individual variability of 1D protein profiles as a tool in ecology: an application to parasitoid venom

Understanding the forces that shape eco-evolutionary patterns often requires linking phenotypes to genotypes, allowing characterization of these patterns at the molecular level. DNA-based markers are less informative in this aim compared to markers associated with gene expression and, more specifically, with protein quantities. The characterization of eco-evolutionary patterns also usually requires the analysis of large sample sizes to accurately estimate interindividual variability. However, the methods used to characterize and compare protein samples are generally expensive and time-consuming, which constrains the size of the produced data sets to few individuals. We present here a method that estimates the interindividual variability of protein quantities based on a global, semi-automatic analysis of 1D electrophoretic profiles, opening the way to rapid analysis and comparison of hundreds of individuals. The main original features of the method are the in silico normalization of sample protein quantities using pictures of electrophoresis gels at different staining levels, as well as a new method of analysis of electrophoretic profiles based on a median profile. We demonstrate that this method can accurately discriminate between species and between geographically distant or close populations, based on interindividual variation in venom protein profiles from three endoparasitoid wasps of two different genera (Psyttalia concolor, Psyttalia lounsburyi and Leptopilina boulardi). Finally, we discuss the experimental designs that would benefit from the use of this method.

Spatial variation in transcript and protein abundance of Atlantic salmon during feeding migration in the Baltic Sea

The fitness and reproductive output of fishes can be affected by environmental disturbances. In this study, transcriptomics and label-free proteomics were combined to investigate Atlantic salmon (Salmo salar) sampled from three different field locations within the Baltic Sea (Baltic Main Basin (BMB), Gulf of Finland (GoF), and Bothnian Sea (BS)) during marine migration. The expression of several stress related mRNAs and proteins of xenobiotic metabolism, oxidative stress, DNA damage, and cell death were increased in salmon from GoF compared to salmon from BMB or BS. Respiratory electron chain and ATP synthesis related gene ontology-categories were upregulated in GoF salmon, whereas those associated with RNA processing and synthesis, translation, and protein folding decreased. Differences were seen also in metabolism and immune function related gene expression. Comparisons of the transcriptomic and proteomic profiles between salmon from GoF and salmon from BMB or BS suggest environmental stressors, especially exposure to contaminants, as a main explanation for differences. Salmon feeding in GoF are thus “disturbed by hazardous substances”. The results may also be applied in evaluating the conditions of pelagic ecosystems in the different parts of Baltic Sea.

Anthropogenic hybridization between endangered migratory and commercially harvested stationary whitefish taxa (Coregonus spp.)

Natural hybridization plays a key role in the process of speciation. However, anthropogenic (human induced) hybridization of historically isolated taxa raises conservation issues. Due to weak barriers to gene flow and the presence of endangered taxa, the whitefish species complex is an excellent study system to investigate the consequences of hybridization in conservation. We focused on three naturally reproductively isolated whitefish taxa in Germany: the endangered, anadromous North Sea houting (NSH) and Baltic houting (BH), which were reintroduced after local extinction, and the commercially stocked European whitefish (EW). To evaluate the genetic integrity of each taxon, source and reintroduced populations of NSH and BH, and EW populations were characterized based on two mitochondrial and 17 microsatellite loci. Additionally, we investigated gill raker counts as an adaptive phenotypic trait. Even though clear genetic and phenotypic differentiation confirmed the houtings as separate evolutionarily significant units, admixture analyses revealed an extensive hybrid zone. Hybridizations were introgressive, positively correlated with genetic diversity, and were reflected in the gill raker counts. The BH distribution range showed higher heterogeneity and stronger admixture than the NSH range. Erroneous stocking with non-native genotypes best explained these patterns, which pose challenges for the conservation of the endangered NSH and BH.

Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions

Understanding the factors that shape the evolution of gene expression is a central goal in biology, but the molecular mechanisms behind this remain controversial. A related major goal is ascertaining how such factors may affect the adaptive potential of a species or population. Here we demonstrate that temperature-driven gene expression changes in fish adapted to differing thermal environments are constrained by the level of gene pleiotropy estimated by either the number of protein interactions or gene biological processes. Genes with low pleiotropy levels were the main drivers of both plastic and evolutionary global expression profile changes, while highly pleiotropic genes had limited expression response to temperature treatment. Our study provides critical insights into the molecular mechanisms by which natural populations can adapt to changing environments. In addition to having important implications for climate change adaptation, these results suggest that gene pleiotropy should be considered more carefully when interpreting expression profiling data.

The factors that shape the evolution of gene expression and their role in adaptation are poorly understood. Here, Papakostas et al. show that gene pleiotropy constrains protein expression evolution in freshwater salmonids adapted to different temperatures.

Proteomics to study adaptations in marine organisms to environmental stress

Comparisons of proteomic responses of closely related congeners and populations have shown which cellular processes are critical to adapt to environmental stress. For example, several proteomic species comparisons showed that increasing abundances of oxidative stress proteins indicate that reactive oxygen species (ROS) represent a ubiquitous signal and possible co-stressor of warm and cold temperature, acute hyposaline and low pH stress, possibly causing a shift from pro-oxidant NADH-producing to anti-oxidant NADPH-producing and -consuming metabolic pathways. Changes in cytoskeletal and actin-binding proteins in response to several stressors, including ROS, suggest that both are important structural and functional elements in responding to stress. Disruption of protein homeostasis, e.g., increased abundance of molecular chaperones, was severe in response to acute heat stress, inducing proteolysis, but was also observed in response to chronic heat and cold stress and was concentrated to the endoplasmic reticulum during hyposaline stress. Small GTPases affecting vesicle formation and transport, Ca(2+)-signaling and ion transport responded to salinity stress in species- and population-specific ways. Aerobic energy metabolism was in general down-regulated in response to temperature, hypoxia, hyposalinity and low pH stress, but other metabolic pathways were activated to respond to increased oxidative stress or to switch metabolic fuels. Thus, comparative proteomics is a powerful approach to identify functionally adaptive variation. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Footprints of directional selection in wild Atlantic salmon populations: evidence for parasite-driven evolution?

Mechanisms of host-parasite co-adaptation have long been of interest in evolutionary biology; however, determining the genetic basis of parasite resistance has been challenging. Current advances in genome technologies provide new opportunities for obtaining a genome-scale view of the action of parasite-driven natural selection in wild populations and thus facilitate the search for specific genomic regions underlying inter-population differences in pathogen response. European populations of Atlantic salmon (Salmo salar L.) exhibit natural variance in susceptibility levels to the ectoparasite Gyrodactylus salaris Malmberg 1957, ranging from resistance to extreme susceptibility, and are therefore a good model for studying the evolution of virulence and resistance. However, distinguishing the molecular signatures of genetic drift and environment-associated selection in small populations such as land-locked Atlantic salmon populations presents a challenge, specifically in the search for pathogen-driven selection. We used a novel genome-scan analysis approach that enabled us to i) identify signals of selection in salmon populations affected by varying levels of genetic drift and ii) separate potentially selected loci into the categories of pathogen (G. salaris)-driven selection and selection acting upon other environmental characteristics. A total of 4631 single nucleotide polymorphisms (SNPs) were screened in Atlantic salmon from 12 different northern European populations. We identified three genomic regions potentially affected by parasite-driven selection, as well as three regions presumably affected by salinity-driven directional selection. Functional annotation of candidate SNPs is consistent with the role of the detected genomic regions in immune defence and, implicitly, in osmoregulation. These results provide new insights into the genetic basis of pathogen susceptibility in Atlantic salmon and will enable future searches for the specific genes involved.

Proteome variance differences within populations of European whitefish (Coregonus lavaretus) originating from contrasting salinity environments

Variation in gene expression is an important component of the phenotypic differences observed in nature. Gene expression variance across biological groups and environmental conditions has been studied extensively and has revealed specific genes and molecular mechanisms of interest. However, little is known regarding the importance of within-population gene expression variation to environmental adaptation. To address this issue, we quantified the proteomes of individuals of European whitefish (Coregonus lavaretus) from populations that have previously been shown to have adapted during early development to freshwater and brackishwater salinity environments. Using MS-based label-free proteomics, we studied 955 proteins in eight hatch-stage fish embryos from each population that had been reared in either freshwater or brackishwater salinity conditions. By comparing the levels of within-population protein expression variance over individuals and per protein between populations, we found that fish embryos from the population less affected by salinity level had also markedly higher levels of expression variance. Gene Ontologies and molecular pathways associated with osmoregulation showed the most significant difference of within-population proteome variance between populations. Several new candidate genes for salinity adaptation were identified, emphasising the added value of combining assessments of within-population gene expression variation with standard gene expression analysis practices for better understanding the mechanisms of environmental adaptation.

BIOLOGICAL SIGNIFICANCE

We demonstrate the benefits of studying within-population gene expression variance together with more typical methods of gene expression profiling. Proteome variance differences within European whitefish populations originating from different salinity environments allowed us to identify several new candidate genes for salinity adaptation in teleost fish and generate many further hypotheses to be tested. This article is part of a Special Issue entitled: Proteomics of non-model organisms.

Transcriptomic and iTRAQ proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the Japanese eel (Anguilla japonica)

Osmoregulation is critical for the survival of fishes that migrate between freshwater (FW) and seawater (SW). The eel, as a catadromous fish, has been studied for decades to reveal the mechanisms of osmoregulation. These studies, however, have been limited by the lack of a genomic database to decipher the mechanism of osmoregulation at a molecular level. In this study, using high-throughput transcriptomic and proteomic technologies, we have provided the first genome-wide study to identify hyperosmotic responsive proteins in the gills of the Japanese eel. Deep sequencing using the 454 platform produced over 660,000 reads with a mean length of 385 bp. For the proteomic study, we collected gill samples from three different treatment groups of fish that had fully adapted to FW/SW or were transferred from FW to SW for 6h. The respective group of gill proteins were extracted and labeled using an isobaric tag for relative and absolute quantitation (iTRAQ) using LTQ-Orbitrap, a high resolution mass spectrometer. Among the 1519 proteins identified from the gill samples, 96 proteins were differentially expressed between FW and SW adapted fish. Nineteen hyperosmotic responsive proteins were detected (10 up-regulated and 9 down-regulated proteins) after 6h post FW to SW transfer.

BIOLOGICAL SIGNIFICANCE

The study has provided the most comprehensive, targeted investigation of eel gill proteins to date, and shown the powerfulness of combining transcriptomic and proteomic approaches to provide molecular insights of osmoregulation mechanisms in a non-model organism, eel.

Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster

Shotgun proteomics offers an efficient means to characterize proteins in a complex mixture, particularly when sufficient genomic resources are available. In order to assess the practical application of shotgun proteomics in the Pacific oyster (Crassostrea gigas), liquid chromatography coupled with tandem mass spectrometry was used to characterize the gill proteome. Using information from the recently published Pacific oyster genome, 1043 proteins were identified. Biological samples (n = 4) and corresponding technical replicates (three) were similar in both specific proteins identified and expression, as determined by normalized spectral abundance factor. A majority of the proteins identified (703) were present in all biological samples. Functional analysis of the protein repertoire illustrates that these proteins represent a wide range of biological processes, supporting the dynamic function of the gill. These insights are important for understanding environmental influences on the oyster, because the gill tissue acts as the interface between the oyster and its environment. In silico analysis indicated that this sequencing effort identified a large proportion of the complete gill proteome. Together, these data demonstrate that shotgun sequencing is a viable approach for biological discovery and will play an important role in future studies of oyster physiology.

Ecological proteomics: finding molecular markers that matter

It is becoming increasingly clear that local adaptation can occur even in the face of high gene flow and limited overall genomic differentiation among populations (reviewed by Nosil et al. 2009). Thus, one important task for molecular ecologists is to sift through genomic data to identify the genes that matter for local adaptation (Hoffmann & Willi 2008; Stapley et al. 2010). Recent advances in high-throughput molecular technologies have facilitated this search, and a variety of approaches can be applied, including those grounded in population genetics [e.g. outlier analysis (Pavlidis et al. 2008)], classical and quantitative genetics [e.g. quantitative trait locus analysis (MacKay et al. 2009)], and cellular and molecular biology [e.g. transcriptomics (Larsen et al. 2011)]. However, applying these approaches in nonmodel organisms that lack extensive genetic and genomic resources has been a formidable challenge. In this issue, Papakostas et al. (2012). demonstrate how one such approach – high-throughput label-free proteomics (reviewed by Gstaiger & Aebersold 2009; Domon & Aebersold 2010) – can be applied to detect genes that may be involved in local adaptation in a species with limited genomic resources. Using this approach, they identified genes that may be implicated in local adaptation to salinity in European whitefish (Coregonus lavaretus L.) and provide insight into the mechanisms by which fish cope with changes in this critically important environmental parameter.

Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

In recent years, the explosion of affordable next generation sequencing technology has provided an unprecedented opportunity to conduct genome-wide studies of adaptive evolution in organisms previously lacking extensive genomic resources. Here, we characterize genome-wide patterns of variability and differentiation using pooled DNA from eight populations of the nine-spined stickleback (Pungitius pungitius L.) from marine, lake and pond environments. We developed a novel genome complexity reduction protocol, defined as paired-end double restriction-site-associated DNA (PE dRAD), to maximize read coverage at sequenced locations. This allowed us to identify over 114,000 short consensus sequences and 15,000 SNPs throughout the genome. A total of 6834 SNPs mapped to a single position on the related three-spined stickleback genome, allowing the detection of genomic regions affected by divergent and balancing selection, both between species and between freshwater and marine populations of the nine-spined stickleback. Gene ontology analysis revealed 15 genomic regions with elevated diversity, enriched for genes involved in functions including immunity, chemical stimulus response, lipid metabolism and signalling pathways. Comparisons of marine and freshwater populations identified nine regions with elevated differentiation related to kidney development, immunity and MAP kinase pathways. In addition, our analysis revealed that a large proportion of the identified SNPs mapping to LG XII is likely to represent alternative alleles from divergent X and Y chromosomes, rather than true autosomal markers following Mendelian segregation. Our work demonstrates how population-wide sequencing and combining inter- and intra-specific RAD analysis can uncover genome-wide patterns of differentiation and adaptations in a non-model species.