Integrating detection probabilities in species distribution models of amphibians breeding in Mediterranean temporary ponds

Aim The imperfect detection of species may lead to erroneous conclusions about species–environment relationships. Accuracy in species detection usually requires temporal replication at sampling sites, a time‐consuming and costly monitoring scheme. Here, we applied a lower‐cost alternative based on a double‐sampling approach to incorporate the reliability of species detection into regression‐based species distribution modelling. Location Doñana National Park (south‐western Spain). Methods Using species‐specific monthly detection probabilities, we estimated the detection reliability as the probability of having detected the species given the species‐specific survey time. Such reliability estimates were used to account explicitly for data uncertainty by weighting each absence. We illustrated how this novel framework can be used to evaluate four competing hypotheses as to what constitutes primary environmental control of amphibian distribution: breeding habitat, aestivating habitat, spatial distribution of surrounding habitats and/or major ecosystems zonation. The study was conducted on six pond‐breeding amphibian species during a 4‐year period. Results Non‐detections should not be considered equivalent to real absences, as their reliability varied considerably. The occurrence of Hyla meridionalis and Triturus pygmaeus was related to a particular major ecosystem of the study area, where suitable habitat for these species seemed to be widely available. Characteristics of the breeding habitat (area and hydroperiod) were of high importance for the occurrence of Pelobates cultripes and Pleurodeles waltl. Terrestrial characteristics were the most important predictors of the occurrence of Discoglossus galganoi and Lissotriton boscai, along with spatial distribution of breeding habitats for the last species. Main conclusions We did not find a single best supported hypothesis valid for all species, which stresses the importance of multiscale and multifactor approaches. More importantly, this study shows that estimating the reliability of non‐detection records, an exercise that had been previously seen as a naïve goal in species distribution modelling, is feasible and could be promoted in future studies, at least in comparable systems.     

Reproductive dynamics of three amphibian species in Mediterranean wetlands: the role of local precipitation and hydrological regimes

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.     

Environmental drivers of anuran calling phenology in a seasonal Neotropical ecosystem

Temporal variation represents an important component in understanding the structure of ecological communities and species coexistence. We examined calling phenology of an assemblage of anurans in the Gran Chaco ecoregion of Bolivia by deploying automated recording devices to document nocturnally vocalizing amphibians nightly at seven ponds from 20 January 2011 until 31 October 2011. Using logistic regression, we modelled the relationships between temperature, rainfall and photoperiod with calling activity. There was a distinct seasonal effect with calling activity concentrated in the rainy season with no species detected during the dry season from June until the end of October. Calling activity was positively and significantly correlated with photoperiod in 9 of the 10 species analyzed, but there were distinct species‐specific relationships associated with rainfall and temperature. All of these species utilize ephemeral ponds as breeding sites, which can account for their reliance on rainfall as an important driver in calling activity. Two prolonged breeders exhibited similar seasonal breeding patterns across the rainy season, but differed in their response to daily abiotic factors, which might be attributed to the constraints imposed by their reproductive mode. Explosive breeders needed several days of rain to elicit calling. Two pairs of congeners had distinct species‐specific relationships between their calling activity and abiotic factors, even though the congeners shared the same reproductive mode, suggesting that the reproductive modes vary in the constraints imposed on calling activity. The patterns observed suggest that calling phenology of tropical anurans is determined by the interaction of exogenous factors (i.e. climatic variables) and endogenous factors (i.e. reproductive modes).     

Gap analysis revealed a low efficiency of Natura 2000 network for the conservation of endemic species in Mediterranean temporary freshwater habitats

Listed and rare species are abundant in temporary freshwater habitats. Among them, the endemic contingent represents a crucial conservation target particularly in the areas characterized by abundant endemic flora for which the local administrations have a high level of responsibility. The aim of this research was to test how the endemic plants found in Mediterranean temporary ponds were represented in Natura 2000 network in a biodiversity hotspot of the Mediterranean region. The results of our research at regional scale pointed out that the existing Nature 2000 sites provide a limited degree of protection and that the gap analysis should be taken into account when conservation priorities are set.     

Habitat associations of pool-breeding amphibians in eastern Massachusetts,USA

There is a pressing need to develop a sound conservation strategy for pool-breeding amphibians, which includes gaining a better understanding of the habitat and landscape-scale characteristics associated with populations. To investigate relationships between amphibian species richness and characteristics of breeding pools and surrounding landscapes, we surveyed 85 pools in eastern Massachusetts (USA) in 1996 and 1997. A total of 11 species was detected, with most pools having 2–5 species. Pools were typically small, 77.6% were <0.2 ha, but most pools (72%) had hydroperiods that persisted at least into August in most years. Based on linear regression analyses, species richness was positively associated with three within-pool variables (pool surface area, hydroperiod, and the amount of emergent vegetation), and a landscape-level variable (presence of another breeding pool within 1 km), while one within-pool variable (tree canopy cover) exhibited a significant negative association with species richness. These within-pool habitat variables and connectivity to other breeding pools are important characteristics to consider when attempting to identify breeding sites that could provide core habitat in conservation reserves designed for the conservation of pool-breeding amphibian species richness. Conservation reserves for pool-breeding amphibian populations should include pool complexes functioning as habitat for metapopulations. Core pool habitats within such reserves should be large (0.5–1.0 ha), with seasonal hydroperiods that persist into August or that dry in some years, and with sufficient emergent vegetation to provide diverse microhabitats and refugia.     

Use of seasonally flooded marshes by fish in a Mediterranean wetland: timing and demographic consequences

In the Camargue (southern France), movements of fish between a canal and two seasonally flooded marshes were monitored continuously by fish traps for 3 years for one marsh and for 2 years for the other. The timing of the entry and exit of the main species was determined together with species annual demographic balance, defined as the difference between the number of fish leaving and the number of fish entering. Only some of the species inhabiting the canal colonized the marshes. Except those species that reproduced in salt or brackish waters, all the species colonizing the marshes reproduced in it. The most abundant of these species were small sized (mosquitofish, sand smelt and three-spined stickleback). The unpredictability of water levels in summer was particularly unfavourable for recruitment and survival of species that breed late in the year, e.g. pumpkinseed sunfish, or which prolonged their stay in the marsh and only attempted to leave just before the connection was broken, e.g. carp. Only the three-spined stickleback always had a positive demographic balance as a result of colonizing the marshes. Adults of this species entered in winter and young-of-the-year left in April. By limiting its stay in the seasonally flooded marshes, the stickleback minimized the risks related to environmental unpredictability. These results suggest that hydrology (temporal variations of water depth) may influence the fish community structure through interspecific differences in survival and recruitment, as a result of temporal variations in the use of seasonally flooded marshes.     

Spatial and temporal variability of aquatic habitat use by amphibians in a hydrologically modified landscape

1. Habitat loss is a major driver of biodiversity decline worldwide. Temporary waterbodies are especially vulnerable because they are sensitive both to human impact and to climatic variations. Pond‐breeding amphibians are often dependent on temporary waterbodies for their reproduction, and hence are sensitive to loss of temporary ponds. 2. Here we present the results of a 5‐year study regarding the use of temporary aquatic habitats by amphibians in a hydrologically modified area of Eastern Europe (Romania). The annual number of aquatic habitats varied between 30 and ～120. Each aquatic habitat was characterised by a number of variables such as: ‘type’ (pond, drainage ditch and archaeological ditch), ‘hydroperiod’ (number of weeks the ponds were filled in a given year), ‘depth’ (cm), ‘area’ (m²) and the density of predatory insects (‘predation’). The turnover rate for each amphibian species for each wetland was calculated based on the pond occupancy. 3. Eight amphibian species were recorded from the aquatic habitats. Hydroperiod was the most important variable, positively influencing wetland use by amphibians and their reproductive success. Most species preferred drainage ditches for reproduction, and the reproductive success was highest in this habitat type every year. For most of the species, the local extinction rate was higher than the colonisation rate in the first 4 years, but the situation reversed in the last year of the study when wetland use by amphibians sharply increased because of high rainfall. 4. This study confirms the importance for amphibians of maintaining and managing aquatic habitat diversity at small spatial scales. Man‐made aquatic habitats such as drainage ditches may be important habitats for amphibians, and this should be considered in restoration activities.     

Cross‐scale effects of structural and functional connectivity in pond networks on amphibian distribution in agricultural landscapes

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Early assessment of the impact of alien species: differential consequences of an invasive crayfish on adult and larval amphibians

Aim Early assessment of the impact of invasive alien species is crucial to set up timely management, but often the impact is evident when it is too late for action. We evaluated relationships between the alien crayfish, Procambarus clarkii, the distribution of native amphibians, and the abundance of their larvae. We assessed whether considering measures of reproductive success provide a more prompt measure of impact than considering just species distribution. Location One hundred and twenty‐five wetlands in Northern Italy, in an area recently invaded by P. clarkii. Methods We surveyed wetlands to assess the presence of breeding activity of amphibians and the distribution of P. clarkii. We measured the abundance of amphibian larvae before metamorphosis through pipe sampling. We built models analysing the relationships between amphibian and crayfish distribution, while taking into account spatial autocorrelation and environmental features. Analyses were performed at both the species level (generalized linear models and spatial eigenvector mapping) and community level (constrained redundancy analysis). Results In terms of breeding site distribution, only two amphibians (Lissotriton vulgaris and Hyla intermedia) were negatively associated with P. clarkii, while the relationships between other the species and P. clarkii were positive or not significant. However, larval abundance for all amphibian species was negatively associated with the alien crayfish. Analyses performed at community and single species levels yielded consistent results. Main conclusions Procambarus clarkii impacts amphibians through different processes. Newts probably avoid invaded wetlands for breeding. Other species attempt breeding in wetlands with crayfish, but suffer very low success. Considering distribution data alone would not provide a correct picture of the impact of this alien species; measures of reproductive success may allow a more accurate assessment of the impact.     

The Natural History of a Nearctic Temporary Pond in Ontario with Remarks on Continental Variation in such Habitats

The seasonal succession of members of the invertebrate community of a temporary vernal pond in southern Ontario is described. Although succession was essentially continuous, 5 faunal groups are suggested, based on time of appearance and duration of active forms in the pond. Some species were found during virtually the entire aquatic phase, while others completed their life cycles in only 2-3 weeks. Analysis of growth rates revealed many different patterns between species and groups. Analysis of community structure in terms of trophic status indicated shifts which coincided with the seasonal occurrence of the pond's potential food resources. Comparison of this fauna with that of a similar pond on Vancouver Island, British Columbia (some 2,400 km to the west) showed many similarities in niche occupancy, including 6 species in common. The biological characteristics leading to the success of these cosmopolitan species in temporary aquatic habitats is discussed.     

Demography of a population of Moina micrura kurz (Crustacea: Cladocera) in a temporary pond,peninsula of paraguaná, Venezuela

A population of M. micrura Kurz from a shallow, muddy and temporary pond, located in Peninsula of Paraguaná, western Venezuela, was studied from filling to drying phase. Population density, age structure, fecundity, and length of females, were determined. This population showed a low population density (< 50 ind/1), a low and density-dependent fecundity (mean eggs/adults = 1.3; mean clutch size = 2.1 eggs + embryos), and low juveniles to adults ratio (0.71). No significant correlation was detected between mean clutch size and mean body length of ovigerous females. Our results suggest effects of food limitations, and fish predation on demographic parameters of this population. Still, in unfavourable conditions, some demographics features associated to opportunistic species were evident.     

Seasonal patterns of activity and community structure in an amphibian assemblage at a pond network with variable hydrology

We studied community structure and seasonal activity patterns in a system of four ponds with seasonally-variable hydrology at a Mediterranean area in central Italy. We used a set of field methods to assess species presence and relative frequency of observation. The network of ponds was inhabited by six species of amphibians, two salamanders and four frogs. The breeding phenology of the six species did not vary remarkably among ponds, but there were significant differences among species in use of ponds. Factorial analysis of pond similarity drawn from percentage composition of the amphibian fauna, revealed that each of the four ponds was treatable as independent units, with no influence of relative inter-pond distance. PCA analysis allowed us to spatially arrange the amphibian species into three main groups: two were monospecific groups (i.e., Triturus vulgaris and Bufo bufo) and the third consisted of those species that selected not only the largest-deepest ponds, but also the ephemeral ones (i.e., Triturus carnifex, Hyla intermedia, the green frogs and Rana dalmatina). Our results suggest that the inter-pond differences in riparian vegetation, water depth, aquatic vegetation structure/abundance, and soil composition may produce differences among pond ecological characteristics (i.e., water turbidity and temperature, shelter availability, abundance of oviposition micro-sites), which may in turn influence different patterns of use by amphibians. To our knowledge, this is the first study emphasizing the potential role of heterochrony in the maintenance of a high species richness in Mediterranean amphibian communities. Preservation of freshwater vertebrate biodiversity requires management and protection not only of the main ponds and water bodies but also the temporary and ephemeral shallow ponds.     

Identifying groundwater‐fed climate refugia in remote arid regions with citizen science and isotope hydrology

1. Groundwater and surface water‐fed systems act as biodiversity hotspots and ecological refuges and evolutionary refugia in arid regions. Groundwater‐dominated systems are sustained by underground aquifers that are recharged by rain that has fallen in the distant past, while surface water‐dominated systems are fed by recent local rain or floods. Some waterbodies are fed by a mixture of these sources. Perennial, groundwater‐dominated systems will act as refuges and refugia under future rainfall declines associated with global warming. We sought to identify climate refugia, based on groundwater dominance, by using isotope hydrology to characterise water samples collected by citizen scientists across arid central Australia.
2. There is a linear relationship between hydrogen isotopes (²H/¹H, δ²H) and oxygen isotopes (¹⁸O/¹⁶O, δ¹⁸O) in rainfall. This relationship is known as the meteoric water line (MWL). By comparing our samples with the Australian MWL, and developing a local evaporation line, we were able to test the hypotheses that groundwater‐dominated systems will follow the Australian MWL while temporary systems follow the local evaporation line, and, accordingly, distinguish between groundwater and surface water‐dominated systems. The isotopic composition of samples collected over a 36‐month period was determined using isotope ratio infrared spectrometry. The electrical conductivity of each sample was recorded to determine where freshwater is available for biota within this arid region.
3. Over 240 water samples were collected from 62 waterbodies and seven bores (groundwater wells) spanning an area of more than 250,000 km². Approximately 75% of the samples were collected by citizen scientists and 25% by research scientists.
4. Twenty groundwater‐dominated waterbodies, characterised by a small range of δ²H and δ¹⁸O values (c. ?55 to ?20‰ and c. ?9 to ?3‰, respectively) clustered around the long‐term mean composition of rainfall (δ²H = ?37.5‰, δ¹⁸O = ?6.4‰), were identified as future evolutionary refugia. These sites are likely to contain water through the most severe of droughts and will be critically important for the persistence of water‐dependent species.
5. Based on their isotopic composition, we identified 45 waterbodies (rockholes/waterholes) as temporary or ephemeral (δ²H c. ?40 to ?100‰ and δ¹⁸O c. ?4 to +25‰), that is, with no evidence of groundwater inflow. These, together with waterbodies supported by a mix of groundwater and surface water, can act as stepping stones and form part of the aquatic mosaic that is critical to supporting species in arid regions. Over two‐thirds of the waterholes sampled were very fresh (electrical conductivity <0.8 mS/cm), indicating that they provide the freshwater needed to support much of the regional aquatic and terrestrial fauna.
6. All evolutionary refugia are located within protected areas (i.e. national parks or Indigenous Protected Areas), but some are subject to the impacts of feral animal species and invasive plants. Our findings indicate where control programmes and restoration actions can be prioritised to support biodiversity conservation and climate change adaptation. Our approach, combining citizen science and isotope hydrology, can be used to identify future refugia in other remote and arid regions where water scarcity is likely to increase under global climate change.

     

Habitat stability and the larval mosquito community in treeholes and other containers on a temperate Island

The temporal fluctuation of water levels and the presence of mosquito larvae were investigated for four types of small container habitats (treeholes, bamboo stumps, cemetery stone vases, and cemetery stone vessels) on Kabeshima Island in Kyushu, southwestern Japan. The probability that containers held water was positively correlated with the quantity of the preceding rainfall and with the depth and volume of the containers. It was estimated that dehydration occurred more regularly in autumn and winter than in summer. The probability that mosquito larvae were present in each type of container was positively correlated with habitat stability in terms of the probability of the existence of standing water and the coefficient of variation of the water level. Twelve species of mosquito larvae, including two rare predators, were found. Species composition differed between the different types of container. Although 4 to 10 species used each type of container, the median number of species per container was two for treeholes and bamboo stumps, and one for the others. The dominant species wasTripteroides bambusa in treeholes and bamboo stumps,Aedes albopictus in stone vases, andA. japonicus in stone vessels. The larval mosquito community, which lacked major predators, possessed the following features that may facilitate the coexistence of many species: (1) niche segregation amongst species in terms of their selection of container types; (2) an aggregated distribution of the individual species among containers of the same type; (3) high intraspecific mean crowding (and hence probably intense intraspecific competition) in the dominant species in each type of container; (4) independent species associations within the same type of container; and (5) low interspecific mean crowding (and hence probablynot intense interspecific competition) between species in the same type of container.     

Reproductive strategies of Amazonian stream fishes and their fine‐scale use of habitat are ordered along a hydrological gradient

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A reversal of the shift towards earlier spring phenology in several Mediterranean reptiles and amphibians during the 1998–2013 warming slowdown

Herps, especially amphibians, are particularly susceptible to climate change, as temperature tightly controls many parameters of their biological cycle—above all, their phenology. The timing of herps’ activity or migration period—in particular the dates of their first appearance in spring and first breeding—and the shift to earlier dates in response to warming since the last quarter of the 20^th century has often been described up to now as a nearly monotonic trend towards earlier phenological events. In this study, we used citizen science data opportunistically collected on reptiles and amphibians in the northern Mediterranean basin over a period of 32 years to explore temporal variations in herp phenology. For 17 common species, we measured shifts in the date of the species’ first spring appearance—which may be the result of current changes in climate—and regressed the first appearance date against temperatures and precipitations. Our results confirmed the expected overall trend towards earlier first spring appearances from 1983 to 1997, and show that the first appearance date of both reptiles and amphibians fits well with the temperature in late winter. However, the trend towards earlier dates was stopped or even reversed in most species between 1998 and 2013. We interpret this reversal as a response to cooling related to the North Atlantic Oscillation (NAO) in the late winter and early spring. During the positive NAO episodes, for certain species only (mainly amphibians), the effect of a warm weather, which tends to advance the phenology, seems to be counterbalanced by the adverse effects of the relative dryness.     

Predicting risk of invasion in a Mediterranean island using niche modelling and valuable biota

Invasion by alien species is nowadays considered as one of the major threats to biodiversity. Thus, the identification of the areas exposed to a greater risk of invasion represents a priority for management purpose, especially in presence of habitats worthy of conservation. This paper aims to propose a method to produce a map of risk of invasion, merging together the threat of invasion by invasive plants and the distribution of habitats with high conservation value, on the case study of the Island of Elba (Tuscan Archipelago). We modelled the potential distribution of six particularly harmful invasive plants and merged these distributions into a map of threat of invasion. This map was overlapped to the map of density of Natura2000 habitats, finally obtaining a map of risk of invasion. According to our analyses, the potential distribution of the invasive species resulted highly influenced by human-related factors. The habitats more at risk are those closer to streets and anthropic habitats, which are more likely to be colonized by the invasive species we studied. We identified some rare habitats which are strongly endangered, highlighting that around 20% of the surface of the Island is exposed to some level of risk of invasion.