Seasonal weather patterns drive population vital rates and persistence in a stream fish

Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark–recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout (Salvelinus fontinalis) at a broad spatial scale using a novel stage‐structured population model. The data were a 15‐year record of brook trout abundance from 72 sites distributed across a 170‐km‐long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site‐specific conditions. Specifically, young‐of‐year survival was most strongly affected by spring temperature, adult survival by elevation and per‐capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel‐scouring flows on eggs and newly hatched individuals. However, high‐elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density‐dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage‐structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics.     

Survival and migration patterns of naturally and hatchery-reared Atlantic salmon (Salmo salar) smolts in a Lake Ontario tributary using acoustic telemetry

1. Atlantic salmon (Salmo salar) smolts are often stocked into rivers to supplement natural reproduction, yet hatchery-reared fish have lower survival compared to wild conspecifics. However, few studies have assessed riverine migratory performance and survival differences in hatchery and wild smolts, or more specifically naturally reared smolts (hatchery fish released earlier as parr), particularly in rivers with weirs which may further reduce survival.
2. Using acoustic telemetry, including a subset of fish with novel transmitters that identify predation events, we assessed survival and migration patterns of hatchery- (2017: n = 32; 2018: n = 30) and naturally reared Atlantic salmon smolts (2017: n = 8; 2018: n = 30) in a Lake Ontario tributary with two weirs to better understand their ecology and assess the influence of environmental parameters on migration.
3. Naturally reared smolts were 13.9 times more likely to survive than hatchery-reared smolts and mark–recapture models indicated that weirs did not reduce survival for either group. Survival per km was lowest at the release site, indicating pre-migration mortality, and specifically high stocking-related mortality of hatchery-reared smolts. Speed and times of day fish migrated (i.e. migratory performance) did not vary by rearing group, suggesting that the high mortality of hatchery-reared smolts may be due to other factors related to hatchery and stocking operations. Overall mean (± SD) migration speed for smolts was 0.70 ± 0.39 km/hr and movements occurred significantly more frequently at night (18:00–06:00).
4. Smolts were detected in Lake Ontario after they left the river; however, the array in Lake Ontario was not conducive to providing much detail regarding movement patterns. There was no predation of the two predation tags detected in Lake Ontario, indicating that movements were made by smolts and not predators.
5. With ongoing restoration efforts of Atlantic salmon in Lake Ontario, it was important to understand the smolt migration patterns and success of the stocked fish. Our findings of similar migratory performance yet different relative survival of hatchery- and naturally reared smolts help inform management with regards to stocking strategies that could improve Atlantic salmon reintroduction success.

     

Estimability of migration survival rates from integrated breeding and winter capture–recapture data

Long‐distance migration is a common phenomenon across the animal kingdom but the scale of annual migratory movements has made it difficult for researchers to estimate survival rates during these periods of the annual cycle. Estimating migration survival is particularly challenging for small‐bodied species that cannot carry satellite tags, a group that includes the vast majority of migratory species. When capture–recapture data are available for linked breeding and non‐breeding populations, estimation of overall migration survival is possible but current methods do not allow separate estimation of spring and autumn survival rates. Recent development of a Bayesian integrated survival model has provided a method to separately estimate the latent spring and autumn survival rates using capture–recapture data, though the accuracy and precision of these estimates has not been formally tested. Here, I used simulated data to explore the estimability of migration survival rates using this model. Under a variety of biologically realistic scenarios, I demonstrate that spring and autumn migration survival can be estimated from the integrated survival model, though estimates are biased toward the overall migration survival probability. The direction and magnitude of this bias are influenced by the relative difference in spring and autumn survival rates as well as the degree of annual variation in these rates. The inclusion of covariates can improve the model's performance, especially when annual variation in migration survival rates is low. Migration survival rates can be estimated from relatively short time series (4–5 years), but bias and precision of estimates are improved when longer time series (10–12 years) are available. The ability to estimate seasonal survival rates of small, migratory organisms opens the door to advancing our understanding of the ecology and conservation of these species. Application of this method will enable researchers to better understand when mortality occurs across the annual cycle and how the migratory periods contribute to population dynamics. Integrating summer and winter capture data requires knowledge of the migratory connectivity of sampled populations and therefore efforts to simultaneously collect both survival and tracking data should be a high priority, especially for species of conservation concern.     

Density estimation in a wolverine population using spatial capture–recapture models

Classical closed-population capture–recapture models do not accommodate the spatial information inherent in encounter history data obtained from camera-trapping studies. As a result, individual heterogeneity in encounter probability is induced, and it is not possible to estimate density objectively because trap arrays do not have a well-defined sample area. We applied newly-developed, capture–recapture models that accommodate the spatial attribute inherent in capture–recapture data to a population of wolverines (Gulo gulo) in Southeast Alaska in 2008. We used camera-trapping data collected from 37 cameras in a 2,140-km² area of forested and open habitats largely enclosed by ocean and glacial icefields. We detected 21 unique individuals 115 times. Wolverines exhibited a strong positive trap response, with an increased tendency to revisit previously visited traps. Under the trap-response model, we estimated wolverine density at 9.7 individuals/1,000 km² (95% Bayesian CI: 5.9–15.0). Our model provides a formal statistical framework for estimating density from wolverine camera-trapping studies that accounts for a behavioral response due to baited traps. Further, our model-based estimator does not have strict requirements about the spatial configuration of traps or length of trapping sessions, providing considerable operational flexibility in the development of field studies. © 2011 The Wildlife Society.     

Use of posterior predictive checks as an inferential tool for investigating individual heterogeneity in animal population vital rates

The investigation of individual heterogeneity in vital rates has recently received growing attention among population ecologists. Individual heterogeneity in wild animal populations has been accounted for and quantified by including individually varying effects in models for mark–recapture data, but the real need for underlying individual effects to account for observed levels of individual variation has recently been questioned by the work of Tuljapurkar et al. (Ecology Letters, 12, 93, 2009) on dynamic heterogeneity. Model‐selection approaches based on information criteria or Bayes factors have been used to address this question. Here, we suggest that, in addition to model‐selection, model‐checking methods can provide additional important insights to tackle this issue, as they allow one to evaluate a model's misfit in terms of ecologically meaningful measures. Specifically, we propose the use of posterior predictive checks to explicitly assess discrepancies between a model and the data, and we explain how to incorporate model checking into the inferential process used to assess the practical implications of ignoring individual heterogeneity. Posterior predictive checking is a straightforward and flexible approach for performing model checks in a Bayesian framework that is based on comparisons of observed data to model‐generated replications of the data, where parameter uncertainty is incorporated through use of the posterior distribution. If discrepancy measures are chosen carefully and are relevant to the scientific context, posterior predictive checks can provide important information allowing for more efficient model refinement. We illustrate this approach using analyses of vital rates with long‐term mark–recapture data for Weddell seals and emphasize its utility for identifying shortfalls or successes of a model at representing a biological process or pattern of interest.     

Modeling association among demographic parameters in analysis of open population capture-recapture data

We present a hierarchical extension of the Cormack-Jolly-Seber (CJS) model for open population capture-recapture data. In addition to recaptures of marked animals, we model first captures of animals and losses on capture. The parameter set includes capture probabilities, survival rates, and birth rates. The survival rates and birth rates are treated as a random sample from a bivariate distribution, thus the model explicitly incorporates correlation in these demographic rates. A key feature of the model is that the likelihood function, which includes a CJS model factor, is expressed entirely in terms of identifiable parameters; losses on capture can be factored out of the model. Since the computational complexity of classical likelihood methods is prohibitive, we use Markov chain Monte Carlo in a Bayesian analysis. We describe an efficient candidate-generation scheme for Metropolis-Hastings sampling of CJS models and extensions. The procedure is illustrated using mark-recapture data for the moth Gonodontis bidentata.     

Effects of environmental factors on the ecology and survival of a widespread,endemic Cerrado frog

Understanding the mechanisms that affect habitat use by vertebrates is critical for understanding how species are distributed across landscapes and how they cope with habitat change. The Brazilian Savanna (the Cerrado) has vegetation ranging from grassland to woodland savannas and harbors a rich and diverse amphibian fauna impacted by accelerated habitat loss. Here, we test the influence of vegetation type (from grassy scrubland to woodland) and distance from breeding sites (ephemeral water bodies) on body size, abundance, and survival of the frog Physalaemus nattereri in a natural metapopulation system of south-central Brazil. We also test whether body size is a significant predictor of population abundance. We found that the abundance of P. nattereri varies according to the mean snout–vent length of each metapopulation (sampling unit), as well as a higher estimated mortality rate in woodlands compared with typical Cerrado. Furthermore, we found no difference in estimated mortality among sampling units located far or close to ephemeral water bodies. Thus, our results highlight variable responses of P. nattereri metapopulations to environmental factors, despite the observed high heterogeneity among sampled habitats and the importance of ephemeral water bodies for reproduction. These findings highlight that land cover and availability of breeding sites might not always interact to explain population persistence of Cerrado frogs.     

Transience in the humpback whale population of New Caledonia and implications for abundance estimation

A phenomenon of transience in the humpback whale population breeding in New Caledonia has been highlighted in recent analyses. We used these data to illustrate the risk of flawed inference when transience is not properly accounted for in abundance estimation of resident populations. Transients are commonly defined as individuals that pass through the sampling area once, i.e., have a null probability of being caught again, and therefore induce heterogeneity in the detection process. The presence of transients can lead to severe bias in the estimation of abundance and we demonstrate how to correct for this feature when estimating abundance of resident populations. In New Caledonia, very different conclusions about the number of resident whales in the southern lagoon between 1999 and 2005 are obtained when the abundance estimate accounts for the transient whales. Without correction, the estimates of the abundance were up to twice as high across all years compared to the estimates of the resident population when a correction for transients had been incorporated. Having reliable population estimates when assessing the status of endangered species is essential in documenting recovery and monitoring of population trends. Therefore, we encourage researchers to account for transients when reporting abundances of resident populations.     

Heterogeneity and typology of fish habitat in the main stream of a Breton coastal river (Elorn-Finistère,France)

Hydrobiologia - To study the salmonids potential production of a coastal river main stream from simple characterization of the fish habitat, it was necessary to rate the hydrosystem's spatial...     

Modeling stream fish distributions using interval‐censored detection times

Controlling for imperfect detection is important for developing species distribution models (SDMs). Occupancy‐detection models based on the time needed to detect a species can be used to address this problem, but this is hindered when times to detection are not known precisely. Here, we extend the time‐to‐detection model to deal with detections recorded in time intervals and illustrate the method using a case study on stream fish distribution modeling. We collected electrofishing samples of six fish species across a Mediterranean watershed in Northeast Portugal. Based on a Bayesian hierarchical framework, we modeled the probability of water presence in stream channels, and the probability of species occupancy conditional on water presence, in relation to environmental and spatial variables. We also modeled time‐to‐first detection conditional on occupancy in relation to local factors, using modified interval‐censored exponential survival models. Posterior distributions of occupancy probabilities derived from the models were used to produce species distribution maps. Simulations indicated that the modified time‐to‐detection model provided unbiased parameter estimates despite interval‐censoring. There was a tendency for spatial variation in detection rates to be primarily influenced by depth and, to a lesser extent, stream width. Species occupancies were consistently affected by stream order, elevation, and annual precipitation. Bayesian P‐values and AUCs indicated that all models had adequate fit and high discrimination ability, respectively. Mapping of predicted occupancy probabilities showed widespread distribution by most species, but uncertainty was generally higher in tributaries and upper reaches. The interval‐censored time‐to‐detection model provides a practical solution to model occupancy‐detection when detections are recorded in time intervals. This modeling framework is useful for developing SDMs while controlling for variation in detection rates, as it uses simple data that can be readily collected by field ecologists.     

Estimating the proportion of identifiable individuals and group sizes in photographic identification studies

Simple Bayesian statistical models are introduced to estimate the proportion of identifiable individuals and group sizes in photographic identification, or photo‐ID, studies of animals that are found in groups. The models require a simple random photographic sampling of animals, where the photographic captures are treated as sampling with replacement within each group. The total number of images, including those that cannot be identified, and the number of images that contain identifiable individuals are used to make inference about the proportion of identifiable individuals within each group and as the population when a number of groups are sampled. The numbers of images for individuals within each group are used to make inference about the group size. Based on analyses of simulated and real data, the models perform well with respect to accuracy and precision of posterior distributions of the parameters. Widths of posterior intervals were affected by the number of groups sampled, sampling duration, and the proportion of identifiable individuals in each group that was sampled. The structure of the models can accommodate covariates, which may affect photographic efficiency, defined in this study as the probability of photographically capturing individuals.     

Climate change hastens the turnover of stream fish assemblages

Stream fish are expected to be significantly influenced by climate change, as they are ectothermic animals whose dispersal is limited within hydrographic networks. Nonetheless, they are also controlled by other physical factors that may prevent them moving to new thermally suitable sites. Using presence–absence records in 655 sites widespread throughout nine French river units, we predicted the potential future distribution of 30 common stream fish species facing temperature warming and change in precipitation regime. We also assessed the potential impacts on fish assemblages' structure and diversity. Only cold-water species, whose diversity is very low in French streams, were predicted to experience a strong reduction in the number of suitable sites. In contrast, most cool-water and warm-water fish species were projected to colonize many newly suitable sites. Considering that cold headwater streams are the most numerous on the Earth's surface, our results suggested that headwater species would undergo a deleterious effect of climate change, whereas downstream species would expand their range by migrating to sites located in intermediate streams or upstream. As a result, local species richness was forecasted to increase greatly and high turnover rates indicated future fundamental changes in assemblages' structure. Changes in assemblage composition were also positively related to the intensity of warming. Overall, these results (1) stressed the importance of accounting for both climatic and topographic factors when assessing the future distribution of riverine fish species and (2) may be viewed as a first estimation of climate change impacts on European freshwater fish assemblages.     

Estimating abundance of mountain lions from unstructured spatial sampling

Mountain lions (Puma concolor) are often difficult to monitor because of their low capture probabilities, extensive movements, and large territories. Methods for estimating the abundance of this species are needed to assess population status, determine harvest levels, evaluate the impacts of management actions on populations, and derive conservation and management strategies. Traditional mark–recapture methods do not explicitly account for differences in individual capture probabilities due to the spatial distribution of individuals in relation to survey effort (or trap locations). However, recent advances in the analysis of capture–recapture data have produced methods estimating abundance and density of animals from spatially explicit capture–recapture data that account for heterogeneity in capture probabilities due to the spatial organization of individuals and traps. We adapt recently developed spatial capture–recapture models to estimate density and abundance of mountain lions in western Montana. Volunteers and state agency personnel collected mountain lion DNA samples in portions of the Blackfoot drainage (7,908 km²) in west-central Montana using 2 methods: snow back-tracking mountain lion tracks to collect hair samples and biopsy darting treed mountain lions to obtain tissue samples. Overall, we recorded 72 individual capture events, including captures both with and without tissue sample collection and hair samples resulting in the identification of 50 individual mountain lions (30 females, 19 males, and 1 unknown sex individual). We estimated lion densities from 8 models containing effects of distance, sex, and survey effort on detection probability. Our population density estimates ranged from a minimum of 3.7 mountain lions/100 km² (95% CI 2.3–5.7) under the distance only model (including only an effect of distance on detection probability) to 6.7 (95% CI 3.1–11.0) under the full model (including effects of distance, sex, survey effort, and distance × sex on detection probability). These numbers translate to a total estimate of 293 mountain lions (95% CI 182–451) to 529 (95% CI 245–870) within the Blackfoot drainage. Results from the distance model are similar to previous estimates of 3.6 mountain lions/100 km² for the study area; however, results from all other models indicated greater numbers of mountain lions. Our results indicate that unstructured spatial sampling combined with spatial capture–recapture analysis can be an effective method for estimating large carnivore densities. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.     

Rainfall and population dynamics of Grey Pileated Finch <Emphasis Type=Italic>Coryphospingus pileatus</Emphasis> (Aves: Passeriformes) in a Neotropical dry forest

In tropical dry environments rainfall periodicity may affect demographic parameters, resulting in fluctuations in bird abundance. We used capture–recapture data for the Grey Pileated Finch from a Neotropical dry forest to evaluate the hypothesis that intra- and inter-annual survival, individuals entrance and population abundance, are related to local rainfall. Sampling occurred across 3 years, with individuals captured, tagged and evaluated for age and presence of brood patch every 14 days. Using the POPAN formulation, we generated demographic models to evaluate study population temporal dynamics. Best-fit models indicated a low apparent annual survival in the first year (16%) compared to other years (between 47 and 62%), with this low value associated with an extreme drought. The abundance of juveniles at each capture occasion was significantly dependent on the accumulated precipitation in the previous 14 days, and the juvenile covariate was a strong predictor of the intra-annual entrance probability (natality). Individuals entrance during the reproductive period corresponded to 53, 52 and 75% of total ingress for each year, respectively. The trend in sampled population size indicated positive exponential growth (N_initial = 50, N_last = 600), with intra-annual fluctuations becoming progressively more intense. Low survival was relevant during population decline at study onset, while at study end intense Individuals entrance promoted rapid population growth. Thus, the indirect effects of rainfall and the combined effect of two demographic rates operated synergistically on the immediate population abundance of Grey Pileated Finch, an abundant bird in a Neotropical dry forest.     

Relative contributions of fixed and dynamic heterogeneity to variation in lifetime reproductive success in kestrels (Falco tinnunculus)

Many species show large variation in lifetime reproductive success (LRS), with a few individuals producing the majority of offspring. This variation can be explained by factors related to individuals (fixed heterogeneity) and stochastic differences in survival and reproduction (dynamic heterogeneity). In this study, we study the relative effects of these processes on the LRS of a Dutch Kestrel population, using three different methods. First, we extended neutral simulations by simulating LRS distributions of populations consisting of groups with increasingly different population parameters. Decomposition of total LRS variance into contributions from fixed and dynamic heterogeneity revealed that the proportion of fixed heterogeneity is probably lower than 10% of the total variance. Secondly, we used sensitivities of the mean and variance in LRS to each parameter to analytically show that it is impossible to get equal contributions of fixed and dynamic heterogeneity when only one parameter differs between groups. Finally, we computed the LRS probability distribution to show that even when all individuals have identical survival and reproduction rates, the variance in LRS is large (females: 27.52, males: 12.99). Although each method has its limitations, they all lead to the conclusion that the majority of the variation in kestrel LRS is caused by dynamic heterogeneity. This large effect of dynamic heterogeneity on LRS is similar to results for other species and contributes to the evidence that in most species the majority of individual variation in LRS is due to dynamic heterogeneity.     

Spatial and temporal occurrence of invertebrates in a chalk stream,Berkshire, England

The invertebrate assemblages of the River Lambourn and its tributary, the Winterbourne stream, were investigated as part of a broad ecological study prior to water resource development in the catchment. The longitudinal distribution of the invertebrate fauna within the Winterbourne stream was examined in detail and supporting data for the R. Lambourn revealed that the upstream intermittent section of each water course had an invertebrate assemblage which was distinct from the fauna downstream where flow was permanent. Within the perennial zone taxon richness tended to increase downstream.A one-year programme of monthly quantitative sampling on five distinct biotopes (Ranunculus, Berula, Callitriche, gravel and silt) at two contrasted sites (shaded and unshaded) was undertaken in the lower perennial of the R. Lambourn below the confluence with the Winterbourne. On each study site, the taxon richness, numerical abundance and biomass of invertebrates were significantly higher on the three macrophytes than on gravel and silt. There were also statistically significant seasonal changes in the biomass of invertebrates on each site. Estimates of total biomass of invertebrates per site revealed a late spring peak (May/June) and a late autumn (November/December) peak, neither of which coincided with the summer peak biomass of macrophytes. This suggested that, in the lower perennial, the level of food resources (epiphytic algae in late spring and fallen tree leaves plus decaying macrophytes in autumn) rather than available habitat, were a major influence on population levels for most of the year.Quantitative sampling of each biotope on each site continued in June and December only for a period of 8 years (1971–78), during which time the river experienced a minor drought (1973) and a severe drought (1976). The Chironomidae showed a strong positive response to conditions of low flow in June of 1973 and 1976, when exceptionally high densities of larvae were recorded. Although further between-year differences were recorded in several other major components of the invertebrate fauna, which may have been related to conditions of low discharge, they did not have long-term consequences for the fauna in the lower perennial of the R. Lambourn.In contrast, in the upper perennial, the prolonged drought of 1976 resulted in the loss of wetted perimeter and macrophytes, coupled with deposition of silt, all of which had deleterious effects on the invertebrate assemblages. The following year, despite a normal discharge regime and the removal of silt, some submerged macrophytes were slow to return to their pre-drought condition. In the intermittent section, the drought of 1976 resulted in the total loss of flow for a 16 month period instead of a more typical four month period of water loss.Thus, chalk streams encompass within a single system both stable and extreme hydrological regimes which offer unique opportunities for investigating the processes of community formation and maintenance.     

Dispersal and recruitment of fish in an intermittent stream network

Animal movement is an important process connecting habitats in heterogeneous landscapes, and can play a key role in population persistence. Laboratory swim trials were conducted to determine and compare the dispersal capabilities of two native Australian fish, mountain galaxias (Galaxias olidus, Family Galaxiidae) and southern pygmy perch (Nannoperca australis, Family Nannopercidae) that maintain populations in hydrologically variable and intermittently flowing streams in south‐eastern Australia. These experiments showed that G. olidus had significantly greater swimming endurance under a range of flow velocities. Concurrent field surveys were used to establish whether swimming abilities observed in laboratory studies were consistent with patterns of inferred movement from distribution and abundance patterns observed in the field. Data collected at multiple sites from headwater to lowland reaches along multiple streams revealed substantial temporal changes in the distribution of young‐of‐year (0+) G. olidus, with spawning occurring at upland sites in winter, followed by downstream larval migration and subsequent upstream movement in late spring. Observed spatial and temporal patterns in G. olidus abundances were consistent with a source‐sink population structure, which may be disrupted by prolonged cease‐to‐flow periods during drought years. In contrast, results for N. australis suggested limited dispersal, with restricted local populations that persist at sites with permanent surface water. These field and laboratory findings complement our understanding of the spatial population structure of these two species in intermittent streams, and highlight the importance of understanding the role of dispersal in species conservation and habitat restoration.