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Conservation of the Atlantic salmon Salmo salar requires to monitor the spatial distribution and abundance of juveniles at a local scale in tributaries. However, tributaries are rarely accounted for in monitoring programs despite their importance for juvenile life stages. This is mainly because inventories of young salmon populations in tributaries can be technically challenging with traditional methods, as the number of tributaries in a watershed can be important and their access limited compared to the main stem. In this study, we tested the use of environmental DNA (eDNA) to quantify the abundance of juvenile Atlantic salmon in tributaries. We successfully detected eDNA of juvenile Atlantic salmon in 19 tributaries of three main rivers of the Gaspé Peninsula (Québec, Canada) using quantitative real‐time PCR analyses. By comparing the eDNA approach with electrofishing surveys conducted in parallel to water sampling, we found that eDNA concentrations positively correlated with juvenile abundance, total biomass, and body surface area. The use of the allometrically scaled mass (ASM) instead of abundance improved the correlation. Furthermore, we demonstrated that the levels of eDNA molecules detected for juvenile Atlantic salmon were also correlated with water temperature and canopy cover measured in each tributary. Finally, we tested if eDNA concentrations measured in a tributary could be used as a reliable indicator of juvenile abundance or biomass in that tributary. We found that our models slightly better predicted juvenile biomass than juvenile abundance. The use of ASM did not improve model prediction, suggesting that further refinement would be required in the future. Our method will facilitate the implementation of conservation practices appropriate to the ecology of juvenile Atlantic salmon in tributaries. We used quantitative real‐time PCR environmental DNA (eDNA) to track juvenile Atlantic salmon in 19 tributaries of the Gaspe area, Quebec (Canada). We found that eDNA concentrations positively correlated with juvenile abundance, total biomass and body surface area. Furthermore, we demonstrated that the levels of eDNA molecules detected for juvenile Atlantic salmon were mostly influenced by water temperature and vegetation cover measured in each tributary. Finally, we tested if eDNA concentrations measured in one tributary could be used as a reliable indicator of juvenile abundance or biomass, and we highlighted that our models slightly better predicted juvenile biomass, then juvenile abundance.

All life forms across the globe are experiencing drastic changes in environmental conditions as a result of global climate change. These environmental changes are happening rapidly, incur substantial socioeconomic costs, pose threats to biodiversity and diminish a species’ potential to adapt to future environments. Understanding and monitoring how organisms respond to human-driven climate change is therefore a major priority for the conservation of biodiversity in a rapidly changing environment. Recent developments in genomic, transcriptomic and epigenomic technologies are enabling unprecedented insights into the evolutionary processes and molecular bases of adaptation. This Review summarizes methods that apply and integrate omics tools to experimentally investigate, monitor and predict how species and communities in the wild cope with global climate change, which is by genetically adapting to new environmental conditions, through range shifts or through phenotypic plasticity. We identify advantages and limitations of each method and discuss future research avenues that would improve our understanding of species’ evolutionary responses to global climate change, highlighting the need for holistic, multi-omics approaches to ecosystem monitoring during global climate change.Species and communities can respond to global climate change by genetically adapting to new environmental conditions, by shifting their range or through phenotypic plasticity. This Review summarizes approaches that apply and integrate omics tools to experimentally investigate, monitor and predict these species responses.

Background Manipulative parasites are thought to liberate molecules in their external environment, acting as manipulation factors with biological functions implicated in their host’s physiological and behavioural alterations. These manipulation factors are part of a complex mixture called the secretome. While the secretomes of various parasites have been described, there is very little data for a putative manipulative parasite. It is necessary to study the molecular interaction between a manipulative parasite and its host to better understand how such alterations evolve. Methods Here, we used proteomics to characterize the secretome of a model cestode with a complex life cycle based on trophic transmission. We studied Schistocephalus solidus during the life stage in which behavioural changes take place in its obligatory intermediate fish host, the threespine stickleback ( Gasterosteus aculeatus ). We produced a novel genome sequence and assembly of S. solidus to improve protein coding gene prediction and annotation for this parasite. We then described the whole worm’s proteome and its secretome during fish host infection using LC–MS/MS. Results A total of 2290 proteins were detected in the proteome of S. solidus , and 30 additional proteins were detected specifically in the secretome. We found that the secretome contains proteases, proteins with neural and immune functions, as well as proteins involved in cell communication. We detected receptor-type tyrosine-protein phosphatases, which were reported in other parasitic systems to be manipulation factors. We also detected 12 S. solidus -specific proteins in the secretome that may play important roles in host–parasite interactions. Conclusions Our results suggest that S. solidus liberates molecules with putative host manipulation functions in the host and that many of them are species-specific. Graphical abstract

Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group’s diversity and success.

Parasites with complex life cycles have been proposed to manipulate the behaviour of their intermediate hosts to increase the probability of reaching their final host. The cause of these drastic behavioural changes could be manipulation factors released by the parasite in its environment (the secretome), but this has rarely been assessed. We studied a non-cerebral parasite, the cestode Schistocephalus solidus , and its intermediate host, the threespine stickleback ( Gasterosteus aculeatus ), whose response to danger becomes significantly diminished when infected. These altered behaviours appear only during late infection, when the worm is ready to reproduce in its final avian host. Sympatric host–parasite pairs show higher infection success for parasites, suggesting that the secretome effects could differ for allopatric host–parasite pairs with independent evolutionary histories. We tested the effects of secretome exposure on behaviour by using secretions from the early and late infection of S. solidus and by injecting them in healthy sticklebacks from a sympatric and allopatric population. Contrary to our prediction, secretome from late infection worms did not result in more risky behaviours, but secretome from early infection resulted in more cautious hosts, only in fish from the allopatric population. Our results suggest that the secretome of S. solidus contains molecules that can affect host behaviour, that the causes underlying the behavioural changes in infected sticklebacks are multifactorial and that local adaptation between host–parasite pairs may extend to the response to the parasite's secretome content.

America is the world leader in innovation, but many of the innovative ideas that are hatched in American start-ups, labs, and companies end up going abroad to reach commercial scale. Apple, the superstar of innovation, locates its production in China (yet still reaps most of its profits in the United States). When innovation does not find the capital, skills, and expertise it needs to come to market in the United States, what does it mean for economic growth and job creation? Inspired by the MIT Made in America project of the 1980s,Making in Americabrings experts from across MIT to focus on a critical problem for the country.MIT scientists, engineers, social scientists, and management experts visited more than 250 firms in the United States, Germany, and China. In companies across America--from big defense contractors to small machine shops and new technology startups--these experts tried to learn how we can rebuild the industrial landscape to sustain an innovative economy. At each stop, they asked this basic question: \"When you have a new idea, how do you get it into the market?\" They found gaping holes and missing pieces in the industrial ecosystem. Critical strengths and capabilities that once helped bring new enterprises to life have disappeared: production capacity; small and medium-size suppliers; spillovers of research, training, and new technology from big corporations. (Production in the Innovation Economy, also published by the MIT Press in 2013, describes this research.)Even in an Internet-connected world, proximity to innovation and users matters for industry.Making in Americadescribes ways to strengthen this connection, including public-private collaborations, new government-initiated manufacturing innovation institutes, and industry-community college projects. If we can learn from these ongoing experiments in linking innovation to production, American manufacturing could have a renaissance.

Conservation of freshwater biodiversity requires being able to track the presence and abundance of entire fish communities. However, studying fish community composition within rivers remains a technical challenge because of high spatial and temporal physico‐chemical variability, anthropic activities and connections with other river catchments, which may all contribute to important variations in local ecology and communities. Here, we used environmental DNA metabarcoding to document spatial variation in fish communities at a small geographic scale in a large river system. The study was conducted in the Contrecoeur sector (5.5 km long and approximately 1–1.5 km wide) of the St. Lawrence River (Québec, Canada), where two water masses with different physico‐chemical properties, known as \"brown waters\" and \"green waters,\" flow in parallel with limited admixing. Water samples were collected during two consecutive days at 53 stations located in both water masses. Using universal PCR MiFish 12S primers, Illumina MiSeq sequencing, and the Barque (www.github.com/enormandeau/barque) eDNA analysis software developed by our group, a total of 67 fish species were detected. PERMANOVA and redundancy analyses (RDA) performed on relative read abundance revealed that each water mass comprised distinct communities that depended on turbidity, depth, and to a lesser extent on the upstream versus downstream position along the study area. eDNA metabarcoding results were compared with those of traditional surveys conducted previously in the sector and up to 40 km upstream of it. As previously reported, higher species diversity was detected by eDNA and with substantially lower sampling effort. Our results represent one of the few studies documenting the potential of eDNA metabarcoding to investigate small‐scale variation in 2D spatial patterns of distribution of whole fish communities associated with habitat characteristics within a lotic system. We conducted a eDNA metabarcoding study in the Contrecoeur sector of the St. Lawrence River (Québec, Canada), which is only 5.5 km long and is characterized by two water masses with very different physico‐chemical properties that flow in parallel with limited admixing. We collected water samples during two consecutive days at 53 stations localized in both water masses. Using universal PCR MiFish 12S primers and Illumina MiSeq sequencing, we found variation in fish community composition within each water mass that was significantly associated with turbidity, depth, and to a lesser extent with the upstream‐downstream position along the study area. Our results demonstrate that it is possible to detect lateral (from shore toward center) variation in eDNA, and consequently in fish community composition at a small geographic scale in rivers, and that eDNA metabarcoding can efficiently complement traditional capture methods in order to more accurately document the role of physico‐chemical factors in shaping local fish community composition in large fluvial systems.

Conservation of whales, considered as umbrella species in marine environments, requires to be able to understand their relationships with ecosystem components such as prey species, including pelagic fish. However, studying such relationships in nature is a technical challenge. In this study, we used two noninvasive methods in combination, namely hydroacoustics and environmental DNA (eDNA), to detect five pelagic or semipelagic fish species in the Saguenay–St. Lawrence Marine Park (Québec, Canada): the sandlance Ammodytes sp., the Atlantic herring Clupea harengus, the capelin Mallotus villosus, the rainbow smelt Osmerus mordax, and the redfish Sebastes sp. The Marine Park is a major summer feeding ground for a wide diversity of marine wildlife species, including the endangered St. Lawrence beluga whale population. Up to now, scarce research efforts have been dedicated to the estimation of pelagic fish abundance and diversity in this area. Hydroacoustics allowed to easily discriminate the classification of echoes from fish, and with certain limitations to distinguish swim bladder fish from fish without swim bladder. We used eDNA to groundtruth acoustics data and to improve species identification. eDNA analyses especially demonstrated that the capelin was the most predominant species, while the abundance of the redfish and the sandlance was strongly variable over the 2 years of the study. Our results also suggest that there are annual fluctuations in prey availability that marine mammals encounter in this area. Although the approach we used is not without constraints that should be addressed in future studies, we hope that this study will contribute to science‐based conservation and fisheries management policies. We used hydroacoustics and environmental DNA (eDNA) in combination to detect five pelagic or semipelagic fish species in the Saguenay–St. Lawrence Marine Park (Québec, Canada). The Marine Park is a major summer feeding ground for a wide diversity of marine wildlife species, including the endangered St. Lawrence beluga whale population that feeds on fish. Our study, which was conducted over a 2‐year period, highlights the annual fluctuations in prey availability that marine mammals encounter in the Marine Park.

Being able to systematically detect parasitic infection, even when no visual signs of infection are present, is crucial to the establishment of accurate conservation policies. The nematode Anguillicola crassus infects the swimbladder of anguillid species and is a potential threat for eel populations. In North America, naïve hosts such as the American eel Anguilla rostrata are affected by this infection. The accidental introduction of A. crassus following restocking programs may contribute to the actual decline of the American eel in Canada. We present a quantitative real time PCR-based method to detect A. crassus infection in final and intermediate hosts. We tested two protocols on samples from different geographical origins in Canada: 1) a general detection of A. crassus DNA in pools of young final hosts (glass eels) or crustacean intermediate hosts 2) a detection at the individual scale by analyzing swim bladders from elvers, or from adult yellow and silver eels. The DNA of A. crassus was detected in one pool of zooplankton (intermediate host) from the Richelieu River (Montérégie-Québec), as well as in individual swim bladders of 13 elvers from Grande and Petite Trinité rivers (Côte-Nord-Québec). We suggest that our qPCR approach could be used in a quantitative way to estimate the parasitic burden in individual swim bladders of elvers. Our method, which goes beyond most of previous developed protocols that restricted the diagnosis of A. crassus to the moment when it was fully established in its final host, should help to detect early A. crassus infection in nature.

Looking back at extreme-right politics in France in the 1940s and 1950s provides new perspectives on contemporary populism. Stanley Hoffmann’s analyses of support for the Vichy regime and for the Poujade movement emphasized how populist politics flourished in times when major segments of the population felt thwarted in efforts to have their interests and views represented in government. Attempts to explain populism by the economic or cultural characteristics of individuals are insufficient. As Hoffmann suggested, it is the political failure of parties and interest groups to channel the grievances and demands of the “losers” of globalization into policy arenas that fuels the rise of populism today.