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The advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many nonmodel species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of FST for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Finally, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased FST estimator may question the interpretation of population structure inferred from previous analyses.

Non-native species can cause the loss of biological diversity (i.e., genetic, species, and ecosystem diversity) and threaten the well-being of humans when they become invasive. In some cases, however, they can also provide conservation benefits. We examined the ways in which non-native species currently contribute to conservation objectives. These include, for example, providing habitat or food resources to rare species, serving as functional substitutes for extinct taxa, and providing desirable ecosystem functions. We speculate that non-native species might contribute to achieving conservation goals in the future because they may be more likely than native species to persist and provide ecosystem services in areas where climate and land use are changing rapidly and because they may evolve into new and endemic taxa. The management of non-native species and their potential integration into conservation plans depends on how conservation goals are set in the future. A fraction of non-native species will continue to cause biological and economic damage, and substantial uncertainty surrounds the potential future effects of all non-native species. Nevertheless, we predict the proportion of non-native species that are viewed as benign or even desirable will slowly increase over time as their potential contributions to society and to achieving conservation objectives become well recognized and realized. Las especies exóticas pueden causar la pérdida de diversidad biológica (i. e., diversidad genética, de especies y ecosistemas) y amenazar el bienestar de humanos cuando se vuelven invasoras. Sin embargo, en algunos casos también pueden proporcionar beneficios de conservación. Examinamos las formas en que las especies exóticas contribuyen actualmente a objetivos de conservación. Estos incluyen, por ejemplo, proporcionar hábitat o recursos alimenticios para especies raras, fungir como sustitutos funcionales de taxa extintos y proporcionar funciones ecosistémicas deseables. Especulamos que las especies exóticas pueden contribuir a lograr metas de conservación en el futuro porque su probabilidad de persistir y proporcionar servicios ecosistémicos es mayor que la de especies nativas en áreas donde el clima y el uso de suelos están cambiando rápidamente y porque pueden evolucionar hacia taxa nuevos y endémicos. El manejo de especies exóticas y su potencial integración en planes de conservación depende de cómo se definen las metas de conservación en el futuro. Una fracción de especies exóticas continuará causando daños biológicos y económicos, y una considerable incertidumbre rodea a los futuros efectos potenciales de todas las especies exóticas. Sin embargo, pronosticamos que la proporción de especies exóticas que son vistas como benignas o aun deseables incrementará lentamente con el tiempo a medida que sus contribuciones potenciales a la sociedad y al logro de objetivos de conservación sean bien reconocidas y entendidas.

There is a growing literature on the detection of species-specific DNA fragments in water to reveal animals' presence in aquatic environments. Analysis of Rees etal. (Journal of Applied Ecology, 2014, 51, 1450) and additional publications highlight the downside of the method and suggest that some conclusions have to be toned down. Non-detection of species-specific DNA fragments in a water sample does not automatically imply the absence of the target species. A positive signal does not necessarily mean the species is present because the environmental DNA (eDNA) could have been transported or preserved after an animal's death. Detection of aquatic invertebrates is weakly documented. The effect of species abundance on detection efficiency is not always established.Synthesis and applications. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration.

Understanding the mechanisms underlying biological invasions and rapid adaptation to global change remains a fundamental challenge, particularly in small populations lacking in genetic variation. Two under‐studied mechanisms that could facilitate adaptive evolution and adaptive plasticity are the increased genetic variation due to transposable elements, and associated or independent modification of gene expression through epigenetic changes.2.Here we focus on the potential role of these genetic and non‐genetic mechanisms for facilitating invasion success. Because novel or stressful environments are known to induce both epigenetic changes and transposable element activity, these mechanisms may play an underappreciated role in generating phenotypic and genetic variation for selection to act on. We review how these mechanisms operate, the evidence for how they respond to novel or stressful environments, and how these mechanisms can contribute to the success of biological invasions by facilitating adaptive evolution and phenotypic plasticity.3.Because genetic and phenotypic variations due to transposable elements and epigenetic changes are often well regulated or “hidden” in the native environment, the independent and combined contribution of these mechanisms may only become important when populations colonize novel environments. A focus on the mechanisms that generate and control the expression of this variation in new environments may provide insights into biological invasions that would otherwise not be obvious.4.Global changes and human activities impact on ecosystems and allow new opportunities for biological invasions. Invasive species succeed by adapting rapidly to new environments. The degree to which rapid responses to environmental change could be mediated by the epigenome – the regulatory system that integrates how environmental and genomic variation jointly shape phenotypic variation ‐ requires greater attention if we want to understand the mechanisms by which populations successfully colonize and adapt to new environments.

The term \"hormesis\" is used to describe dose-response relationships where the response is reversed between low and high doses of a stressor (generally, stimulation at low doses and inhibition at high ones). A mechanistic explanation is needed to interpret the relevance of such responses, but there does not appear to be a single universal mechanism underlying hormesis. When the endpoint is a life-history trait such as growth or reproduction, a stimulation of the response comes with costs in terms of resources. Organisms have to obey the conservation laws for mass and energy; there is no such thing as a free lunch. Based on the principles of Dynamic Energy Budget theory, we introduce three categories of explanations for hormesis that obey the conservation laws: acquisition (i.e., increasing the input of energy into the individual), allocation (i.e., rearranging the energy flows over various traits) and medication (e.g., the stressor is an essential element or acts as a cure for a disease or infection). In this discussion paper, we illustrate these explanations with cases where they might apply, and elaborate on the potential consequences for field populations.

As the global climate warms, the fate of lacustrine fish is of huge concern, especially given their sensitivity as ectotherms to changes in water temperature. The Arctic charr (Salvelinus alpinus L.) is a salmonid with a Holarctic distribution, with peripheral populations persisting at temperate latitudes, where it is found only in sufficiently cold, deep lakes. Thus, warmer temperatures in these habitats particularly during early life stages could have catastrophic consequences on population dynamics. Here, we combined lake temperature observations, a 1-D hydrodynamic model, and a multi-decadal climate reanalysis to show coherence in warming winter water temperatures in four European charr lakes near the southernmost limit of the species’ distribution. Current maximum and mean winter temperatures are on average ~ 1 °C warmer compared to early the 1980s, and temperatures of 8.5 °C, adverse for high charr egg survival, have frequently been exceeded in recent winters. Simulations of winter lake temperatures toward century-end showed that these warming trends will continue, with further increases of 3–4 °C projected. An additional 324 total accumulated degree-days during winter is projected on average across lakes, which could impair egg quality and viability. We suggest that the perpetuating winter warming trends shown here will imperil the future status of these lakes as charr refugia and generally do not augur well for the fate of coldwater-adapted lake fish in a warming climate.

Population dynamics can be regulated through intra- and interspecific density dependence. In species with close ecological requirements, interspecific competition for resources may add to intraspecific density, or even exceed its effect; it may impact single or multiple traits. However, the relative impact of intra- and interspecific densities on demographic parameters has been rarely empirically assessed. We analyzed 18 years of capture-mark-recapture data from brown trout (Salmo trutta) coexisting with Atlantic salmon (Salmo salar) during the juvenile freshwater phase in the Oir River (France) to estimate the relative effects of intra- and interspecific density on trout early life. In trout, a species with optional migration, we estimated the migration probability of young-of-the-year trout out of their natal site, survival probability during the first winter, as well as body size, in relation to both intra- and interspecific density. Trout density correlated negatively with body size and with winter survival in resident trout but not with trout migration. Salmon density correlated positively with trout migration, but no impact was detected on trout body size or survival. Our study highlighted contrasting effects of intra- and interspecific density on trout early life, and the need to account for both factors when studying population dynamics in coexisting species. In particular, by affecting trout migration decision, salmon density may drive trout life history.

The greatest known global response of lakes to climate change has been an increase in water temperatures. The responses of many lake fishes to warming water temperatures are projected to be inadequate to counter the speed and magnitude of climate change. We experimentally evaluated the responses of embryos from a group of cold, stenothermic fishes (Salmonidae Coregoninae) to increased incubation temperatures. Study groups included cisco (Coregonus artedi) from lakes Superior and Ontario (USA), and vendace (C. albula) and European whitefish (C. lavaretus) from Lake Southern Konnevesi (Finland). Embryos from artificial crossings were incubated at water temperatures of 2.0, 4.5, 7.0, and 9.0°C, and their responses were quantified for developmental and morphological traits. Embryo survival, incubation period, and length-at-hatch were inversely related to incubation temperature whereas yolk-sac volume increased with incubation temperature within study groups. However, varying magnitudes of responses among study groups suggested differential levels of developmental plasticity to climate change. Differential levels of parental effects indicate genetic diversity may enable all study groups to adapt to cope with some degree of changing environmental conditions. Our results suggest that the coregonines sampled within and among systems may have a wide range of embryo responses to warming incubation conditions.

Both the increase in human mobility and climate change contribute to the globalization of vector-borne diseases. Some mosquito species are efficient disease vectors in Europe, thus increasing the risk of epidemic (re)emergence.Bacillus thuringiensis var. israelensis (Bti) is considered as the most efficient larvicide to control mosquito populations with negligible environmental impacts. However, repeated field applications of Bti over many years raise the question of possible long-term effects on non-target invertebrates with putative subsequent alterations of food webs. Environmental effects of Bti have mainly been studied in continental freshwater wetlands. Much less is known for brackish water coastal wetlands. We investigated whether repeated treatments with Bti, applied as VectoBac((R)) WG over seven consecutive years, may affect non-target invertebrate communities in wetlands of the French Atlantic coast. Particular attention was devoted to invertebrates potentially used as food sources by shorebirds and wading birds. Invertebrates were sampled in the water and sediment of control and VectoBac((R))-treated saltmarsh pools between 2006 and 2012. Taxa abundance data were used to calculate community descriptors and to analyse the potential structural changes due to VectoBac((R)) using the principal response curve method and similarity analysis. Physicochemical parameters were measured in the same pools so that homogeneity of the environmental conditions between the control and treated areas could be tested. We demonstrated that long-term use of VectoBac((R)) WG in French Atlantic coastal wetlands had no influence on the temporal evolution of the taxonomic structure and taxa abundance of non-target aquatic invertebrate communities, which is highly driven by abiotic factors. In addition, over the long term, the amount of invertebrates that could be used as food resources by birds is maintained in VectoBac((R))-treated areas.Synthesis and applications. Reduced application rate and targeted spraying of VectoBac((R)) WG in mosquito breeding sites minimize potential environmental impacts of Bacillus thuringiensis var. israelensis (Bti). Even so, surveillance of its possible primary side effects is needed, which requires comparable control and treated areas. Indeed, systematic temporal trends and subtle differences in the range of variation of abiotic factors result in discrepancies between control and treated area in terms of invertebrate abundance, which could be wrongly attributed to VectoBac((R)). Management decisions and mitigation measures may therefore benefit from (i) extending surveillance to a time frame that allows for coverage of the immense temporal variation in taxa abundance and diversity and (ii) the inclusion of environmental variables in the monitoring of non-target animal communities potentially exposed to Bti. Reduced application rate and targeted spraying of VectoBac((R)) WG in mosquito breeding sites minimize potential environmental impacts of Bacillus thuringiensis var. israelensis (Bti). Even so, surveillance of its possible primary side effects is needed, which requires comparable control and treated areas. Indeed, systematic temporal trends and subtle differences in the range of variation of abiotic factors result in discrepancies between control and treated area in terms of invertebrate abundance, which could be wrongly attributed to VectoBac((R)). Management decisions and mitigation measures may therefore benefit from (i) extending surveillance to a time frame that allows for coverage of the immense temporal variation in taxa abundance and diversity and (ii) the inclusion of environmental variables in the monitoring of non-target animal communities potentially exposed to Bti.

Trophic level (TL)-based indicators have been widely used to examine fishing impacts in aquatic ecosystems and the induced biodiversity changes. However, much debate has ensued regarding discrepancies and challenges arising from the use of landings data from commercial fisheries to calculate TL indicators. Subsequent studies have started to examine survey-based and model-based indicators. In this paper, we undertake an extensive evaluation of a variety of TL indicators across 9 well-studied marine ecosystems by making use of model-as well as surveyand catch-based TL indicators. Using detailed regional information and data on fishing history, fishing intensity, and environmental conditions, we evaluate how well TL indicators are capturing fishing effects at the community level of marine ecosystems. Our results highlight that the differences observed between TL indicator values and trends is dependent on the data source and the TL cut-off point used in the calculations and is not attributable to an intrinsic problem with TL-based indicators. All 3 data sources provide useful information about the structural changes in the ecosystem as a result of fishing, but our results indicate that only model-based indicators represent fishing impacts at the whole ecosystem level.