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Horizon scanning is a systematic approach increasingly used to explore emerging trends, issues, opportunities, and threats in conservation. We present the results from one such exercise aimed at identifying emerging issues that could have important scientific, social, technological, and managerial implications for the conservation of inland waters in Canada in the proximate future. We recognized six opportunities and nine challenges, for which we provide research implications and policy options, such that scientists, policy makers, and the Canadian society as a whole can prepare for a potential growth in each of the topic areas we identified. The issues spanned a broad range of topics, from recognizing the opportunities and challenges of community-enabled science and the need to consider the legal rights of nature, to the likely increase of pharmaceuticals in wastewater due to an aging population. These issues represent a first baseline that could help decision makers identify and prioritize efforts while simultaneously stimulate new research avenues. We hope our horizon scan will pave the way for similar exercises related to the conservation of biodiversity in Canada. L'analyse prospective est une approche systematique de plus en plus utilisee pour explorer les nouvelles tendances, questions, occasions et menaces dans le domaine de la conservation. Nous presentons les resultats d'un de ces exercices visant a cerner les questions emergentes qui pourraient etre importantes des points de vue scientifique, social, technologique et de la gestion relativement a la conservation des eaux interieures au Canada, pour l'avenir rapproche. Nous relevons six occasions a saisir et neuf defis, dont nous abordons les repercussions sur la recherche et les possibilites d'action qu'ils presentent, afin que les scientifiques, les decideurs et l'ensemble de la societe canadienne puissent se preparer en vue d'une croissance potentielle dans chacun des domaines cernes. Ces questions couvrent un vaste eventail de sujets allant de la reconnaissance des occasions et defis de la science facilitee par la collectivite et la necessite de prendre en compte les droits de la nature en vertu de la loi, a l'augmentation probable des produits pharmaceutiques dans les eaux usees en raison du vieillissement de la population. Ces questions representent un premier etat de reference qui pourrait aider les decideurs a cerner et prioriser les efforts tout en stimulant de nouvelles avenues de recherche. Nous esperons que cette analyse prospective ouvrira la voie a des exercices semblables concernant la conservation de la biodiversite au Canada. [Traduit par la Redaction], Introduction Rivers, lakes, springs, and other inland waters (i.e., all surface waters contained within lands; FAO 2008) are often classified among the most threatened ecosystems on the planet (Dudgeon et [...]

Ecosystems are connected by flows of nutrients and organisms. Changes to connectivity and nutrient enrichment may destabilise ecosystem dynamics far from the nutrient source.We used gradostats to examine the effects of trophic connectivity (movement of consumers and producers) versus nutrient‐only connectivity on the dynamics of Daphnia pulex (consumers) and algae (resources) in two metaecosystem configurations (linear vs. dendritic).We found that Daphnia peak population size and instability (coefficient of variation; CV) increased as distance from the nutrient input increased, but these effects were lower in metaecosystems connected by all trophic levels compared with nutrient‐only connected systems and/or in dendritic compared with linear systems.We examined the effects of trophic connectivity (i.e. both trophic levels move rather than one or the other) using a generic model to qualitatively assess whether the expectations align with the ecosystem dynamics we observed.Analysis of our model shows that increased Daphnia population sizes and fluctuations in consumer‐resource dynamics are expected with nutrient connectivity, with this pattern being more pronounced in linear rather than dendritic systems.These results confirm that connectivity may propagate and even amplify instability over a metaecosystem to communities distant from the source disturbance, and suggest a direction for future experiments, that recreate conditions closer to those found in natural systems. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The analyses of environmental DNA (eDNA) and environmental RNA (eRNA) released by organisms into their surrounding environment (water, soil and air) have emerged as powerful tools for monitoring biodiversity. While eDNA has been widely adopted for the non‐invasive detection of species and characterization of community composition, the utilization of eRNA is still in its infancy. Due to its functional nature, eRNA holds intriguing potential for biodiversity monitoring offering new avenues of research beyond species detection. For example, conspecifics that are almost genetically identical can exhibit distinct transcriptomic differences depending on their life stage. In this issue of Molecular Ecology Resources, Parsley and Goldberg (2024) demonstrate, through a lab‐validated field study, that eRNA can be used to detect distinct life stages of amphibians. This study elegantly demonstrates that eRNA can be used not only to detect invasive or endangered species but also to reveal population demographic information important for guiding effective conservation strategies. [ABSTRACT FROM AUTHOR]

The term genome was introduced in 1920 by the German botanist Hans Winkler (1877-1945) to describe 'the haploid chromosome set, which, together with the pertinent protoplasm, specifies the material foundations [...]

Aquatic ecosystems offer a continuum of water flow from headwater streams to inland lakes and coastal marine systems. This spatial connectivity influences the structure, function and dynamics of aquatic communities, which are among the most threatened and degraded on the Earth. Here, we determine the spatial resolution of environmental DNA (eDNA) in dendritic freshwater networks, which we use as a model for connected metacommunities. Our intensive sampling campaign comprised over 420 eDNA samples across 21 connected lakes, allowing us to analyse detections at a variety of scales, from different habitats within a lake to entire lake networks. We found strong signals of within-lake variation in eDNA distribution reflective of typical habitat use by both fish and zooplankton. Most importantly, we also found that connecting channels between lakes resulted in an accumulation of downstream eDNA detections in lakes with a higher number of inflows, and as networks increased in length. Environmental DNA achieves biodiversity surveys in these habitats in a high-throughput, spatially integrated way. These findings have profound implications for the interpretation of eDNA detections in aquatic ecosystems in global-scale biodiversity monitoring observations. [ABSTRACT FROM AUTHOR]

Abstract: The combination of DNA barcoding and high-throughput (next-generation) sequencing (metabarcoding) provides many promises but also serious challenges. Generating a reliable comparable estimate of biodiversity remains a central challenge to [...]

Early this year, the Romanian Academy commemorated the centennial birthday of the evolutionary biologist Nicolae Botnariuc (1915-03-13-2011-03-01; Fig. 1). The scientific contribution of Botnariuc has been well recognized within the [...]

Understanding the response of organisms to multiple stressors is critical for predicting if populations can adapt to rapid environmental change. Natural and anthropogenic stressors often interact, complicating general predictions. In this study, we examined the interactive and cumulative effects of two common environmental stressors, lowered calcium concentration, an anthropogenic stressor, and predator presence, a natural stressor, on the water flea DaphniapuJex. We analyzed expression changes of five genes involved in calcium homeostasis--cuticle proteins (Cutie, Icp2), calbindin (Cab), and calcium pump and channel (Serca and Ip3R)--using real-time quantitative PCR (RT-qPCR) in a full factorial experiment. We observed strong synergistic interactions between low calcium concentration and predator presence. While the Ip3R gene was not affected by the stressors, the other four genes were affected in their transcriptional levels by the combination of the stressors. Transcriptional patterns of genes that code for cuticle proteins (Cutie and lcp2) and a sarcoplasmic calcium pump (Serca) only responded to the combination of stressors, changing their relative expression levels in a synergistic response, while a calcium-binding protein (Calb) responded to low calcium stress and the combination of both stressors. The expression pattern of these genes (Cutie, lcp2, and Serca) were nonlinear, yet they were dose dependent across the calcium gradient. Multiple stressors can have complex, often unexpected effects on ecosystems. This study demonstrates that the dominant interaction for the set of tested genes appears to be synergism. We argue that gene expression patterns can be used to understand and predict the type of interaction expected when organisms are exposed simultaneously to natural and anthropogenic stressors. Keywords: gene expression, Daphniapulex, calcium level, predator kairomones, anthropogenic stressors, biotic stressors. Il est critique de comprendre la reponse des organismes a de multiples stress afin de predire si des populations peuvent s'adapter a des changements environnementaux rapides. Les stress naturels et anthropogeniques interagissent souvent, ce qui peut compliquer les predictions generales. Dans ce travail, les auteurs ont examine les effets interactifs et cumulatifs de deux stress environnementaux communs, soit une faible concentration en calcium (un stress anthropogenique) et la presence d'un predateur (stress naturel), sur la puce d'eau Daphniapulex. Les auteurs ont analyse l'expression de cinq genes impliques dans l'homeostasie du calcium, soit les genes codant pour des proteines de la cuticule (Cutie, Icp2), la calbindine (Calb) et une pompe et un canal calciques (Serca et Ip3R), au moyen de la PCR quantitative en temps reel (RT-qPCR) lors d'une experience factorielle complete. Les auteurs ont observe de fortes interactions synergiques entre la faible concentration en calcium et la presence du predateur. Tandis que le gene Ip3R n'etait pas affecte par les stress, la transcription des quatre autres genes a ete affectee par la combinaison des stress. La transcription des genes codant pour les proteines de la cuticule (Cutie et lcp2) ainsi que la pompe calcique sarcoplasmique (Serca) n'a change qu'en reponse a une combinaison des stress, et ceci de maniere synergique, tandis que celle du gene codant pour la proteine de liaison du calcium (Calb) a ete affectee tant par le stress calcique que par la combinaison des deux stress. L'expression de ces genes (Cutie, Icp2 et Serca) etait non-lineaire, mais dose-dependante tout au long du gradient calcique. De multiples stress peuvent entrainer des effets complexes et parfois inattendus sur des ecosystemes. Cette etude demontre que l'interaction dominante au sein de ces genes semble etre la synergie. Les auteurs avancent que l'expression genique permet de comprendre et de predire le type d'interaction attendue lorsque des organismessont exposes simultanement a des stress naturels et anthropogeniques. [Traduit par la Redaction] Mots-cles : expression genique, Daphnia pulex, niveau de calcium, kairomones de predateurs, stress anthropogeniques, stress biotiques., Introduction In nature, organisms are exposed to a plethora of natural and anthropogenic stressors, the combination of which can alter individual survival, growth, and reproduction. A huge challenge in studying [...]

Nucleic acids released by organisms and isolated from environmental substrates are increasingly being used for molecular biomonitoring. While environmental DNA (eDNA) has received much attention, the potential of environmental RNA as a biomonitoring tool remains under‐explored. Several recent studies using paired DNA and RNA metabarcoding of bulk samples suggest that RNA might better reflect "metabolically active" parts of the community. However, such studies mainly capture organismal eDNA and eRNA. For larger eukaryotes, isolation of extra‐organismal RNA will be important, but viability needs to be examined in a field‐based setting. In this study we evaluate (a) whether extra‐organismal eRNA release from macroeukaryotes can be detected given its supposedly rapid degradation, and (b) if the same field collection methods for eDNA can be applied to eRNA. We collected eDNA and eRNA from water in lakes where fish community composition is well documented, enabling a comparison between the two nucleic acids in two different seasons with monitoring using conventional methods. We found that eRNA is released from macroeukaryotes and can be filtered from water and metabarcoded in a similar manner as eDNA to reliably provide species composition information. eRNA had a small but significantly greater true positive rate than eDNA, indicating that it correctly detects more species known to exist in the lakes. Given relatively small differences between the two molecules in describing fish community composition, we conclude that if eRNA provides significant advantages in terms of lability, it is a strong candidate to add to the suite of molecular monitoring tools. [ABSTRACT FROM AUTHOR]

Although the use and development of molecular biomonitoring tools based on environmental nucleic acids (eDNA and eRNA; collectively known as eNAs) have gained broad interest for the quantification of biodiversity in natural ecosystems, studies investigating the impact of site‐specific physicochemical parameters on eNA‐based detection methods (particularly eRNA) remain scarce. Here, we used a controlled laboratory microcosm experiment to comparatively assess the environmental degradation of eDNA and eRNA across an acid–base gradient following complete removal of the progenitor organism (Daphnia pulex). Using water samples collected over a 30‐day period, eDNA and eRNA copy numbers were quantified using a droplet digital PCR (ddPCR) assay targeting the mitochondrial cytochrome c oxidase subunit I (COI) gene of D. pulex. We found that eRNA decayed more rapidly than eDNA at all pH conditions tested, with detectability—predicted by an exponential decay model—for up to 57 h (eRNA; neutral pH) and 143 days (eDNA; acidic pH) post organismal removal. Decay rates for eDNA were significantly higher in neutral and alkaline conditions than in acidic conditions, while decay rates for eRNA did not differ significantly among pH levels. Collectively, our findings provide the basis for a predictive framework assessing the persistence and degradation dynamics of eRNA and eDNA across a range of ecologically relevant pH conditions, establish the potential for eRNA to be used in spatially and temporally sensitive biomonitoring studies (as it is detectable across a range of pH levels), and may be used to inform future sampling strategies in aquatic habitats. [ABSTRACT FROM AUTHOR]

The journal Genome, formally known as the Canadian Journal of Genetics and Cytology, was launched 60 years ago by the Genetics Society of Canada, soon after Francis Crick published the [...]

We live in the age of Big Data, and the current data boom is changing the way we do science. Data can be reanalyzed in new ways contributing to scientific [...]

When environmental stressors of high intensity are sustained for long periods of time, populations face high probabilities of being extirpated. However, depending on the intensity of the stressor, large populations with sufficient genetic diversity may persist. We report the results of an experiment that tracked the persistence of Daphnia populations exposed to copper contamination. We assessed whether genotypic diversity reduced the risk of extinction. We created monoclonal and multiclonal populations and monitored their population sizes during a 32‐week experiment. Cu was applied at a sub‐lethal concentration and then increased every week until the population sizes dropped to about 10% of the carrying capacity (Cu at 180 μg/L). The concentration was then increased up to 186 μg/L and held stable until the end of the experiment. A survival analysis showed that clonal diversity extended the persistence of Daphnia populations, but copper contamination caused a substantial genetic erosion followed by population extirpation. However, some Cu‐treated populations, mostly multiclonal, showed U‐shaped patterns of growth consistent with evolutionary rescue but these did not lead to lasting population recovery. These results highlight the importance of genetic variation for population persistence, but they also show how quickly it can be lost in contaminated environments. [ABSTRACT FROM AUTHOR]

Advances in high‐throughput sequencing (HTS) are revolutionizing monitoring in marine environments by enabling rapid, accurate and holistic detection of species within complex biological samples. Research institutions worldwide increasingly employ HTS methods for biodiversity assessments. However, variance in laboratory procedures, analytical workflows and bioinformatic pipelines impede the transferability and comparability of results across research groups. An international experiment was conducted to assess the consistency of metabarcoding results derived from identical samples and primer sets using varying laboratory procedures. Homogenized biofouling samples collected from four coastal locations (Australia, Canada, New Zealand and the USA) were distributed to 12 independent laboratories. Participants were asked to follow one of two HTS library preparation workflows. While DNA extraction, primers and bioinformatic analyses were purposefully standardized to allow comparison, many other technical variables were allowed to vary among laboratories (amplification protocols, type of instrument used, etc.). Despite substantial variation observed in raw results, the primary signal in the data was consistent, with the samples grouping strongly by geographical origin for all data sets. Simple post hoc data clean‐up by removing low‐quality samples gave the best improvement in sample classification for nuclear 18S rRNA gene data, with an overall 92.81% correct group attribution. For mitochondrial COI gene data, the best classification result (95.58%) was achieved after correction for contamination errors. The identified critical methodological factors that introduced the greatest variability (preservation buffer, sample defrosting, template concentration, DNA polymerase, PCR enhancer) should be of great assistance in standardizing future biodiversity studies using metabarcoding. [ABSTRACT FROM AUTHOR]

Research has demonstrated consistent positive correlations between organism abundance and absolute environmental DNA (eDNA) concentrations. Robust correlations in laboratory experiments indicate strong functional links, suggesting the potential for eDNA to monitor organism abundance in nature. However, correlations between absolute eDNA concentrations and organism abundance in nature tend to be weaker because myriad biotic and abiotic factors influence steady‐state eDNA concentrations, decoupling its direct functional link with abundance. Additional technical challenges can also weaken correlations between relative organism abundance and relative eDNA data derived from metabarcoding. Future research must account for these factors to improve the inference of organism abundance from eDNA, including integrating the effects of organism physiology on eDNA production, eDNA dynamics in lentic/lotic systems, and key environmental parameters that impact estimated steady‐state concentrations. Additionally, it is critical to manage expectations surrounding the accuracy and precision that eDNA can provide – eDNA, for example, cannot provide abundance estimates comparable to intensively managed freshwater fisheries that enumerate every individual fish. Recent developments, however, are encouraging. Current methods could provide meaningful information regarding qualitative conservation thresholds and emergent research has demonstrated that eDNA concentrations in natural ecosystems can provide rough quantitative estimates of abundance, particularly when models integrate physiology and/or eDNA dynamics. Operationalizing eDNA to infer abundance will probably require more than simple correlations with organism biomass/density. Nevertheless, the future is promising – models that integrate eDNA dynamics in nature could represent an effective means to infer abundance, particularly when traditional methods are considered too "costly" or difficult to obtain. [ABSTRACT FROM AUTHOR]

The effective use of metabarcoding in biodiversity science has brought important analytical challenges due to the need to generate accurate taxonomic assignments. The assignment of sequences to genus or species level is critical for biodiversity surveys and biomonitoring, but it is particularly challenging as researchers must select the approach that best recovers information on species composition. This study evaluates the performance and accuracy of seven methods in recovering the species composition of mock communities by using COI barcode fragments. The mock communities varied in species number and specimen abundance, while upstream molecular and bioinformatic variables were held constant, and using a set of COI fragments. We evaluated the impact of parameter optimization on the quality of the predictions. Our results indicate that BLAST top hit competes well with more complex approaches if optimized for the mock community under study. For example, the two machine learning methods that were benchmarked proved more sensitive to reference database heterogeneity and completeness than methods based on sequence similarity. The accuracy of assignments was impacted by both species and specimen counts (query compositional heterogeneity) which ultimately influence the selection of appropriate software. We urge researchers to: (i) use realistic mock communities to allow optimization of parameters, regardless of the taxonomic assignment method employed; (ii) carefully choose and curate the reference databases including completeness; and (iii) use QIIME, BLAST or LCA methods, in conjunction with parameter tuning to better assign taxonomy to diverse communities, especially when information on species diversity is lacking for the area under study. see also the Perspective by Holly M. Bik. [ABSTRACT FROM AUTHOR]

Significant advances have been made towards surveying animal and plant communities using DNA isolated from environmental samples. Despite rapid progress, we lack a comprehensive understanding of the "ecology" of environmental DNA (eDNA), particularly its temporal and spatial distribution and how this is shaped by abiotic and biotic processes. Here, we tested how seasonal variation in thermal stratification and animal habitat preferences influences the distribution of eDNA in lakes. We sampled eDNA depth profiles of five dimictic lakes during both summer stratification and autumn turnover, each containing warm‐ and cool‐water fishes as well as the cold‐water stenotherm, lake trout (Salvelinus namaycush). Habitat use by S. namaycush was validated by acoustic telemetry and was significantly related to eDNA distribution during stratification. Fish eDNA became "stratified" into layers during summer months, reflecting lake stratification and the thermal niches of the species. During summer months, S. namaycush, which rarely ventured into shallow waters, could only be detected at the deepest layers of the lakes, whereas the eDNA of warm‐water fishes was much more abundant above the thermocline. By contrast, during autumn lake turnover, the fish species assemblage as detected by eDNA was homogenous throughout the water column. These findings contribute to our overall understanding of the "ecology" of eDNA within lake ecosystems, illustrating how the strong interaction between seasonal thermal structure in lakes and thermal niches of species on very localized spatial scales influences our ability to detect species. [ABSTRACT FROM AUTHOR]

Abstract Background Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh). Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. Results We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S) for Glutamic acid (F) at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. Conclusions Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive.

The microcrustacean Daphnia is arguably one of the most studied zooplankton species, having a well understood ecology, life history, and a relatively well studied evolutionary history. Despite this wealth of knowledge, species boundaries within closely related species in this genus often remain elusive and the major evolutionary forces driving the diversity of daphniids remain controversial. This genus contains more than 80 species with multiple cryptic species complexes, with many closely related species able to hybridize. Here, we review speciation research in Daphnia within the framework of current speciation theory. We evaluate the role of geography, ecology, and biology in restricting gene flow and promoting diversification. Of the 253 speciation studies on Daphnia, the majority of studies examine geographic barriers (55%). While evidence shows that geographic barriers play a role in species divergence, ecological barriers are also probably prominent in Daphnia speciation. We assess the contribution of ecological and nonecological reproductive isolating barriers between closely related species of Daphnia and found that none of the reproductive isolating barriers are restricting gene flow completely. Research on reproductive isolating barriers has disproportionally focused on two species complexes, the Daphnia pulex and Daphnia longispina species complexes. Finally, we identify areas of research that remain relatively unexplored and discuss future research directions that build our understanding of speciation in daphniids. [ABSTRACT FROM AUTHOR]

Abstract Background The L-lactate and D-lactate dehydrogenases, which are involved in the reduction of pyruvate to L(-)-lactate and D(+)-lactate, belong to evolutionarily unrelated enzyme families. The genes encoding L-LDH have been used as a model for gene duplication due to the multiple paralogs found in eubacteria, archaebacteria, and eukaryotes. Phylogenetic studies have suggested that several gene duplication events led to the main isozymes of this gene family in chordates, but little is known about the evolution of L-Ldh in invertebrates. While most invertebrates preferentially oxidize L-lactic acid, several species of mollusks, a few arthropods and polychaetes were found to have exclusively D-LDH enzymatic activity. Therefore, it has been suggested that L-LDH and D-LDH are mutually exclusive. However, recent characterization of putative mammalian D-LDH with significant similarity to yeast proteins showing D-LDH activity suggests that at least mammals have the two naturally occurring forms of LDH specific to L- and D-lactate. This study describes the phylogenetic relationships of invertebrate L-LDH and D-LDH with special emphasis on crustaceans, and discusses gene duplication events during the evolution of L-Ldh. Results Our phylogenetic analyses of L-LDH in vertebrates are consistent with the general view that the main isozymes (LDH-A, LDH-B and LDH-C) evolved through a series of gene duplications after the vertebrates diverged from tunicates. We report several gene duplication events in the crustacean, Daphnia pulex, and the leech, Helobdella robusta. Several amino acid sequences with strong similarity to putative mammalian D-LDH and to yeast DLD1 with D-LDH activity were found in both vertebrates and invertebrates. Conclusion The presence of both L-Ldh and D-Ldh genes in several chordates and invertebrates suggests that the two enzymatic forms are not necessarily mutually exclusive. Although, the evolution of L-Ldh has been punctuated by multiple events of gene duplication in both vertebrates and invertebrates, a shared evolutionary history of this gene in the two groups is apparent. Moreover, the high degree of sequence similarity among D-LDH amino acid sequences suggests that they share a common evolutionary history.