Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present in the environment. In this study, we tested whether an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in ecology and conservation. Two key aquatic vertebrate groups were targeted: amphibians and bony fish. The reliability of this method was cautiously validated in silico, in vitro and in situ. When compared with traditional surveys or historical data, eDNA metabarcoding showed a much better detection probability overall. For amphibians, the detection probability with eDNA metabarcoding was 0.97 (CI = 0.90-0.99) vs. 0.58 (CI = 0.50-0.63) for traditional surveys. For fish, in 89% of the studied sites, the number of taxa detected using the eDNA metabarcoding approach was higher or identical to the number detected using traditional methods. We argue that the proposed DNA-based approach has the potential to become the next-generation tool for ecological studies and standardized biodiversity monitoring in a wide range of aquatic ecosystems.

Summary 1. Although the influence of water availability and precipitation regimes on amphibians has been studied at large scales, whether and how interannual rainfall and hydrological variations affect amphibians dynamics at a local scale have rarely been addressed. In this respect, accounting for variations in species detectability in space and time has also been overlooked. 2. We assessed the effects of rainfall and hydrological variations on the breeding dynamics of three amphibian taxa: Pelodytes punctatus, Hyla meridionalis and Pelophylax spp. in 20 ponds of the Camargue region (southern France) over a 7‐year study period. 3. We used multiple season occupancy models to test the effect of winter–spring rainfall and interannual variations in hydroperiod, mean water depth and drought events on tadpole presence in spring (March–June), a proxy for breeding dynamics. 4. We used an independent survey with spatial replicates (dipnet sweeps) to disentangle the relative contributions of phenology and detectability to the absence of records in a given month. For the three taxa considered, the probability of missing a species when that species was actually present in a pond was most often negligible. Hence, we could consider that multiseason models properly tracked changes in species phenology. 5. Pelodytes punctatus was first detected in March, while the two other taxa appeared later in April. Hyla meridionalis appeared as a mid‐season species with much more synchronous pond occupancy than Pelodytes punctatus. The detection peak of Pelophylax spp. was short and unexpectedly early for this taxon. 6. Seasonal winter–spring rainfall was associated with a decrease in extinction rates and even more strongly with an increase in colonisation rates at individual ponds. 7. Colonisation rate increased following an annual drought and was best modelled as a negative quadratic effect of the variance of pond hydroperiod. Extinction probability was best modelled by a negative quadratic effect of mean water level. Hence, breeding was more stochastic (i) in unpredictable and shallow ponds because of yearly drying up and (ii) in highly predictable and deep ponds, possibly due to the presence of predators such as fish and crayfish. 8. Overall, we show that ponds with intermediate rather than extreme variations in environmental conditions currently correspond to optimal breeding sites. Our study demonstrates that amphibian monitoring coupled with fine‐scale analysis of environmental conditions is necessary to understand species dynamics in the long run and to inform conservation efforts for these species.

Comparative studies of mortality in the wild are necessary to understand the evolution of aging; yet, ectothermic tetrapods are underrepresented in this comparative landscape, despite their suitability for testing evolutionary hypotheses. We present a study of aging rates and longevity across wild tetrapod ectotherms, using data from 107 populations (77 species) of nonavian reptiles and amphibians. We test hypotheses of how thermoregulatory mode, environmental temperature, protective phenotypes, and pace of life history contribute to demographic aging. Controlling for phylogeny and body size, ectotherms display a higher diversity of aging rates compared with endotherms and include phylogenetically widespread evidence of negligible aging. Protective phenotypes and life-history strategies further explain macroevolutionary patterns of aging. Analyzing ectothermic tetrapods in a comparative context enhances our understanding of the evolution of aging.

Delayed maturity and high survival rates of immatures and adults characterize long‐lived species’ life histories. Understanding how these traits interact in stochastic environments is essential to understand early life in long‐lived species and to assist conservation planning. Unfortunately, available information of demographic traits in immatures are often fragmentary and the logistical difficulties of capturing and recapturing this cohort leave little room for improvement. Published immature chelonian survival estimates vary broadly, are often not age‐specific, and lack precision. In an attempt to overcome this issue, we developed a novel modelling approach based on Capture‐Recapture data to obtain robust age‐specific survival probabilities in two chelonian species (the freshwater European pond turtle, Emys orbicularis, and the terrestrial Hermann's tortoise, Testudo hermanni). More specifically, we show that implementing a linear relationship between survival probabilities and age does not distort survival estimates and improves precision. Both species display a progressive increase in survival with age, reaching a plateau at the ages of four to five. As maturity occurs later in both species (8–12 years‐old), the survival plateau might be governed by the final hardening of the carapace, which brings obvious survival benefits. Taking advantage of the flexibility of multievent models we encourage a systematic field approach even when very large samples from immatures cannot be amassed. Only so can demographic traits in chelonians, and more generally in long‐lived species, be properly explored.

Within the current context of biodiversity loss a number of biodiversity indicators have been developed to help measure the state of nature and how it is changing. However, most indicators are derived from bird populations. Reptiles and amphibians could be useful ecosystem indicators, but this requires obtaining precise and unbiased population parameters. This is a particularly challenging task for these two groups of species, because individuals are extremely difficult to detect for various reasons. We illustrate the use of a sampling and analytical method that explicitly takes into account imperfect detection to assess the population dynamics of a reptile species and its temporal and spatial variation. European pond turtles (Emys orbicularis) were sampled at two different locations during a 10-year study. The two sites differed by their water management regimes and number of livestock. At each site and for each sex, the data were modeled using a robust design capture-mark-recapture framework to obtain and compare estimates of survival, temporary emigration, time-specific abundance, density, and population growth rate, while taking into account effects of individual heterogeneity, trap-response, and time on capture probabilities. Temporary emigration was higher in males (0.344 +/- 0.046) (mean +/- SE) than in females (0.228 +/- 0.071), did not differ between sites for each sex, and was mainly Markovian. Apparent adult survival was higher in females (0.966 +/- 0.031) than in males (0.864 +/- 0.024), and was negatively related to the proportion of individuals with repaired shell fractures in the population. Average density was 63.7 +/- 6.6 turtles/km2 but was higher for females (39.2 +/- 14.0 females/km2) than for males (23.5 +/- 5.7 males/km2). The population sizes of males and females decreased where long periods of artificial drought and the highest density of livestock occurred. This research highlights differences in demographic parameters according to sex and site in a turtle species, and it provides evidence that significant human-induced disturbance represents a potential risk to European pond turtle populations. The sampling and analytical approaches illustrated in this study are applicable to many other species of reptiles and amphibians, and estimated population parameters could be combined to produce population indicators useful for conservation and management.

The effects of Hg contamination are presumably widespread across the components of aquatic ecosystems, but investigations have been mainly focused on freshwater fish, because this biota represents a major source of Hg for human populations. Yet, the possible bioaccumulation of Hg on other freshwater meso- and apex-predators (e.g., amphibians, reptiles) has been largely overlooked, especially in Western Europe. In this study, the determinants of Hg concentrations were assessed for the viperine snake (Natrix maura) across 6 populations (>130 individuals sampled in 2016 and 2017) in France and Spain. Specifically, body size, sex, and diet were compared with Hg concentrations measured in ventral scales. Overall, N. maura accumulated Hg in their scales. Sex did not seem to influence Hg concentrations in this species. Significant differences in Hg concentrations were observed between study sites, and these differences were likely to be mediated by site-specific diet. Frog-eating individuals were characterized not only by lower mean values of Hg (0.194±0.018μg·g versus 0.386±0.032μg·g for piscivorous individuals), but also by weaker slopes of the body size-Hg relationship as compared to fish-eating snakes, suggesting strong differences in accumulation rates due to food resources. Importantly, the highest slope of the body size-Hg relationship and the highest values of Hg were found in individuals foraging on trout raised by a fish farm, suggesting that fish farming may contribute to Hg contamination in inland freshwater systems. Finally, our results are compared with data on Hg concentrations in other species of aquatic snakes, in order to provide a comparative point for future studies.

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Reserves that are closed to hunting are important to wintering wildfowl Anatidae. Reserves can also benefit local hunters, because they are often used as day-roosts by birds prior to nocturnal feeding in surrounding wetlands. In this study, we used annual hunting bags from 45 hunting estates in the Camargue, southern France, to study the relationship between hunting success and distance to the nearest duck day-roost, which are generally located in protected areas. Five dabbling duck species Anas spp. and a diving duck species (pochard Aythya ferina) were studied. The relationship between hunting bag and distance from roost was negative in all cases except mallard Anas platyrhynchos, which is subject to specific hunting management practices (i.e. raise and release). However, a significant trend was not found for wigeon A. penelope and shoveler A. clypeata. This supports the hypothesis that hunting estates closer to protected areas are more successful. However, the decrease in hunting bags with increasing distance from the nearest roost could be seen in as little as a few thousands of metres in all species. This suggests that only hunting grounds with a distance of < 2-3 kilometres from the nearest roost may actually have increased hunting accessibility for certain duck species.