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.     

The effects of force‐fledging and premature fledging on the survival of nestling songbirds

Despite the broad consensus that force‐fledging of nestling songbirds lowers their probability of survival and therefore should be generally avoided by researchers, that presumption has not been tested. We used radiotelemetry to monitor the survival of fledglings of Ovenbirds Seiurus aurocapilla and Golden‐winged Warblers Vermivora chrysoptera that we unintentionally force‐fledged (i.e. nestlings left the nest in response to our research activities at typical fledging age), that fledged prematurely (i.e. nestlings left the nest earlier than typical fledging age), and that fledged independently of our activities. Force‐fledged Ovenbirds experienced significantly higher survival than those that fledged independent of our activities, and prematurely fledged Ovenbirds had a similarly high survival to those that force‐fledged at typical fledging age. We observed a similar, though not statistically significant, pattern in Golden‐winged Warbler fledgling survival. Our results suggest that investigator‐induced force‐fledging of nestlings, even when deemed premature, does not necessarily result in reduced fledgling survival in these species. Instead, our results suggest that a propensity or ability to fledge in response to disturbance may be a predictor of a higher probability of fledgling survival.     

Estimating age‐dependent survival when juveniles resemble females: Invasive ring‐necked parakeets as an example

Many species only show sexual dimorphism at the age of maturity, such that juveniles typically resemble females. Under these circumstances, estimating accurate age‐specific demographic parameters is challenging. Here, we propose a multievent model parameterization able to estimate age‐dependent survival using capture–recapture data with uncertainty in age and sex assignment of individuals. We illustrate this modeling approach with capture–recapture data from the ring‐necked parakeet Psittacula krameri. We analyzed capture, recapture, and resighting data (439 recaptures/resightings) of 156 ring‐necked parakeets tagged with neck collars in Barcelona city from 2003 to 2016 to estimate the juvenile and adult survival rate. Our models successfully estimated the survival probabilities of the different age classes considered. Survival probability was similar between adults (0.83, 95% CI = 0.77–0.87) and juveniles during their second (0.79, 95% CI = 0.58–0.87) and third winter (0.83, 95% CI = 0.65–0.88). The youngest juveniles (1st winter) showed a slightly lower survival (0.57, 95% CI = 0.37–0.79). Among adults, females showed a slightly higher survival than males (0.87, 95% CI = 0.78–0.93; and 0.80, 95% CI = 0.73–0.86, respectively). These high survival figures predict high population persistence in this species and urge management policies. The analysis also stresses the usefulness of multievent models to estimate juvenile survival when age cannot be fully ascertained.     

Adult dietary protein has age‐ and context‐dependent effects on male post‐copulatory performance

The highly conserved effect of dietary protein restriction on lifespan and ageing is observed in both sexes and across a vast range of taxa. This extension of lifespan is frequently accompanied by a reduction in female fecundity, and it has been hypothesized that individuals may reallocate resources away from reproduction and into somatic maintenance. However, effects of dietary protein restriction on male reproduction are less consistent, suggesting that these effects may depend on other environmental parameters. Using the neriid fly, Telostylinus angusticollis, we examined age‐specific effects of adult dietary protein restriction on male post‐copulatory reproductive performance (fecundity and offspring viability). To explore the context dependence of these effects, we simultaneously manipulated male larval diet and adult mating history. We found that protein‐restricted males sired less viable offspring at young ages, but offspring viability increased with paternal age and eventually exceeded that of fully fed males. The number of eggs laid by females was not affected by male dietary protein, whereas egg hatching success was subject to a complex interaction of male adult diet, age, larval diet and mating history. These findings suggest that effects of protein restriction on male reproduction are highly context dependent and cannot be explained by a simple reallocation of resources from reproduction to somatic maintenance. Rather, these effects appear to involve changes in the scheduling of male reproductive investment with age.     

genecap: a program for analysis of multilocus genotype data for non‐invasive sampling and capture‐recapture population estimation

We created genecap to facilitate analysis of multilocus genotype data for use in non‐invasive DNA sampling and genetic capture‐recapture studies. genecap is a Microsoft excel macro that uses multilocus genetic data to match samples with identical genotypes, calculate frequency of alleles, identify sample genotypes that differ by one and two alleles, calculate probabilities of identity, and match probabilities for matching samples. genecap allows the user to include background data and samples with missing genotypes for multiple loci. Capture histories for each user‐defined sampling period are output in formats consistent with commonly employed population estimation programs.     

MHC‐dependent survival in a wild population: evidence for hidden genetic benefits gained through extra‐pair fertilizations

Females should prefer to be fertilized by males that increase the genetic quality of their offspring. In vertebrates, genes of the major histocompatibility complex (MHC) play a key role in the acquired immune response and have been shown to affect mating preferences. They are therefore important candidates for the link between mate choice and indirect genetic benefits. Higher MHC diversity may be advantageous because this allows a wider range of pathogens to be detected and combated. Furthermore, individuals harbouring rare MHC alleles might better resist pathogen variants that have evolved to evade common MHC alleles. In the Seychelles warbler, females paired with low MHC‐diversity males elevate the MHC diversity of their offspring to levels comparable to the population mean by gaining extra‐pair fertilizations. Here, we investigate whether increased MHC diversity results in higher life expectancy and whether there are any additional benefits of extra‐pair fertilizations. Our 10‐year study found a positive association between MHC diversity and juvenile survival, but no additional survival advantage of extra‐pair fertilizations. In addition, offspring with a specific allele (Ase‐ua4) had a fivefold longer life expectancy than offspring without this allele. Consequently, the interacting effects of sexual selection and pathogen‐mediated viability selection appear to be important for maintaining MHC variation in the Seychelles warbler. Our study supports the prediction that MHC‐dependent extra‐pair fertilizations result in genetic benefits for offspring in natural populations. However, such genetic benefits might be hidden and not necessarily apparent in the widely used fitness comparison of extra‐ and within‐pair offspring.     

Climate change,phenology, and habitat degradation: drivers of gosling body condition and juvenile survival in lesser snow geese

Nesting migratory geese are among the dominant herbivores in (sub) arctic environments, which have undergone unprecedented increases in temperatures and plant growing days over the last three decades. Within these regions, the Hudson Bay Lowlands are home to an overabundant breeding population of lesser snow geese that has dramatically damaged the ecosystem, with cascading effects at multiple trophic levels. In some areas the overabundance of geese has led to a drastic reduction in available forage. In addition, warming of this region has widened the gap between goose migration timing and plant green‐up, and this ‘mismatch’ between goose and plant phenologies could in turn affect gosling development. The dual effects of climate change and habitat quality on gosling body condition and juvenile survival are not known, but are critical for predicting population growth and related degradation of (sub) arctic ecosystems. To address these issues, we used information on female goslings marked and measured between 1978 and 2005 (4125 individuals). Goslings that developed within and near the traditional center of the breeding colony experienced the effects of long‐term habitat degradation: body condition and juvenile survival declined over time. In newly colonized areas, however, we observed the opposite pattern (increase in body condition and juvenile survival). In addition, warmer than average winters and summers resulted in lower gosling body condition and first‐year survival. Too few plant ‘growing days’ in the spring relative to hatch led to similar results. Our assessment indicates that geese are recovering from habitat degradation by moving to newly colonized locales. However, a warmer climate could negatively affect snow goose populations in the long‐run, but it will depend on which seasons warm the fastest. These antagonistic mechanisms will require further study to help predict snow goose population dynamics and manage the trophic cascade they induce.     

New records of angular rough sharks Oxynotus centrina in the coastal waters of Malta,with observations on post‐capture resilience and release behaviour

One male and one female angular rough sharks Oxynotus centrina were caught south‐east of Malta between May and June at a depth of 60–100 m < 5 km from shore. The immature female (total length, L_T 565 mm) was landed dead but the male (535 mm L_T) was found alive. This communication presents important biological observations on post‐capture recovery and release behaviour of this species.     

Toe‐bud clipping of juvenile small marsupials for ecological field research: No detectable negative effects on growth or survival

Toe clipping is widely used to permanently mark many species of small vertebrates including marsupials, particularly didelphids and dasyurids. Small marsupials are marked as juveniles, by removing the tip of developing toe buds. It has recently been shown that survival and/or recapture probability decreases with increasing number of toes clipped in frogs. Because of this and other animal welfare concerns, toe clipping of adult vertebrates is increasingly being discouraged. The short‐ and long‐term effects of toe‐bud clipping have not been evaluated in marsupials. We used an experiment to test if marking more toes results in slower growth or higher mortality in the brown antechinus (Antechinus stuartii, Dasyuridae) in the short or long term. We found no harmful effects of toe‐bud clipping. There were no infections associated with clipping, marking more toes did not reduce growth in young or adults, and did not affect survival of young in captivity, survival of independent animals in the wild, or recapture probability. Toe‐bud clipping is done at an extremely immature stage, when the area cut is tiny and perception and memory of pain is unlikely to be a problem. We suggest that toe‐bud clipping is a humane and benign method of permanently marking antechinuses, and probably also the young of other morphologically similar small marsupials.     

Artificial selection,pre‐release diet,and gut symbiont inoculation effects on sterile male longevity for area‐wide fruit‐fly management

Longevity is an important life‐history trait for successful and cost‐effective application of the sterile insect technique. Furthermore, it has been shown that females of some species – e.g., Anastrepha ludens (Loew) (Diptera: Tephritidae) – preferentially copulate with ‘old’, sexually experienced males, rather than younger and inexperienced males. Long‐lived sterile males may therefore have greater opportunity to find and mate with wild females than short‐lived males, and be more effective in inducing sterility into wild populations. We explored the feasibility of increasing sterile male lifespan through selection of long‐lived strains and provision of pre‐release diets with added protein, and inoculated with bacterial symbionts recovered from cultures of the gut of wild Anastrepha obliqua (Macquart). Artificial selection for long‐lived A. ludens resulted in a sharp drop of fecundity levels for F1 females. Nevertheless, the cross of long‐lived males with laboratory females produced a female F1 progeny with fecundity levels comparable to those of females in the established colony. However, the male progeny of long‐lived males*laboratory females did not survive in higher proportions than laboratory males. Provision of sugar to A. obliqua adults resulted in increased survival in comparison to adults provided only with water, whereas the addition of protein to sugar‐only diets had no additional effect on longevity. Non‐irradiated males lived longer than irradiated males, and supplying a generic probiotic diet produced no noticeable effect in restoring irradiated male longevity of A. obliqua. We discuss the need to evaluate the time to reach sexual maturity and survival under stress for long‐lived strains, and the inclusion of low amounts of protein and specific beneficial bacteria in pre‐release diets to increase sterile male performance and longevity in the field.     

Brood parasitism of Black‐capped Vireos: frontline and post‐laying behavioral responses and effects on productivity

The cost of brood parasitism favors the evolution of host behaviors that reduce the risk or expense of being parasitized. Endangered Black‐capped Vireos (Vireo atricapilla) have likely coexisted with brood‐parasitic Brown‐headed Cowbirds (Molothrus ater) for more than 10,000 yr, so it is likely that they have evolved anti‐parasitic behaviors. We monitored naturally parasitized and non‐parasitized vireo nests to evaluate factors that might explain parasitism risk and nest desertion behavior and also assessed whether behaviors that occurred after being parasitized improved reproductive output. Vireos reduced the risk of parasitism by initiating breeding early and nesting farther from open grasslands and edges of woody thickets. Post‐laying, nest desertion was common (70% of parasitized nests) and increased with both the presence of at least one cowbird egg in nests and clutch reduction by cowbirds. After accounting for these cues, desertion was also more likely at nests located closer to cowbird foraging habitat and below potential cowbird vantage points. Despite its regularity, desertion did not appear to provide reproductive benefits to vireos. Instead, accepting cowbird eggs was a more effective strategy because 42% of cowbird eggs did not hatch. Furthermore, cowbird eggs were somehow ejected from at least three vireo nests. Our results suggest that Black‐capped Vireos can behave in a variety of ways that reduce the impact of brood parasitism, with frontline behaviors appearing to provide the greatest benefit. Our results also suggest that habitat management should focus on providing Black‐capped Vireos with adequate breeding habitat that provides access to safe nesting sites, and with high‐quality wintering habitat that allows vireos to migrate and initiate nesting early.     

Application of multivariate analysis and mass transfer principles for refinement of a 3‐L bioreactor scale‐down model—when shake flasks mimic 15,000‐L bioreactors better

Characterization of manufacturing processes is key to understanding the effects of process parameters on process performance and product quality. These studies are generally conducted using small‐scale model systems. Because of the importance of the results derived from these studies, the small‐scale model should be predictive of large scale. Typically, small‐scale bioreactors, which are considered superior to shake flasks in simulating large‐scale bioreactors, are used as the scale‐down models for characterizing mammalian cell culture processes. In this article, we describe a case study where a cell culture unit operation in bioreactors using one‐sided pH control and their satellites (small‐scale runs conducted using the same post‐inoculation cultures and nutrient feeds) in 3‐L bioreactors and shake flasks indicated that shake flasks mimicked the large‐scale performance better than 3‐L bioreactors. We detail here how multivariate analysis was used to make the pertinent assessment and to generate the hypothesis for refining the existing 3‐L scale‐down model. Relevant statistical techniques such as principal component analysis, partial least square, orthogonal partial least square, and discriminant analysis were used to identify the outliers and to determine the discriminatory variables responsible for performance differences at different scales. The resulting analysis, in combination with mass transfer principles, led to the hypothesis that observed similarities between 15,000‐L and shake flask runs, and differences between 15,000‐L and 3‐L runs, were due to pCO₂ and pH values. This hypothesis was confirmed by changing the aeration strategy at 3‐L scale. By reducing the initial sparge rate in 3‐L bioreactor, process performance and product quality data moved closer to that of large scale. © 2015 American Institute of Chemical Engineers Biotechnol. Prog., 31:1370–1380, 2015     

Weighing the relative potential impacts of climate change and land‐use change on an endangered bird

Climate change and land‐use change are projected to be the two greatest drivers of biodiversity loss over the coming century. Land‐use change has resulted in extensive habitat loss for many species. Likewise, climate change has affected many species resulting in range shifts, changes in phenology, and altered interactions. We used a spatially explicit, individual‐based model to explore the effects of land‐use change and climate change on a population of the endangered Red‐cockaded Woodpecker (RCW; Picoides borealis). We modeled the effects of land‐use change using multiple scenarios representing different spatial arrangements of new training areas for troops across Fort Benning. We used projected climate‐driven changes in habitat and changes in reproductive output to explore the potential effects of climate change. We summarized potential changes in habitat based on the output of the dynamic vegetation model LPJ‐GUESS, run for multiple climate change scenarios through the year 2100. We projected potential changes in reproduction based on an empirical relationship between spring precipitation and the mean number of successful fledglings produced per nest attempt. As modeled in our study, climate change had virtually no effect on the RCW population. Conversely, simulated effects of land‐use change resulted in the loss of up to 28 breeding pairs by 2100. However, the simulated impacts of development depended on where the development occurred and could be completely avoided if the new training areas were placed in poor‐quality habitat. Our results demonstrate the flexibility inherent in many systems that allows seemingly incompatible human land uses, such as development, and conservation actions to exist side by side.     

Effects of river temperature and climate warming on stock‐specific survival of adult migrating Fraser River sockeye salmon (Oncorhynchus nerka)

Mean summer water temperatures in the Fraser River (British Columbia, Canada) have increased by ～1.5 °C since the 1950s. In recent years, record high river temperatures during spawning migrations of Fraser River sockeye salmon (Oncorhynchus nerka) have been associated with high mortality events, raising concerns about long‐term viability of the numerous natal stocks faced with climate warming. In this study, the effect of freshwater thermal experience on spawning migration survival was estimated by fitting capture–recapture models to telemetry data collected for 1474 adults (captured in either the ocean or river between 2002 and 2007) from four Fraser River sockeye salmon stock‐aggregates (Chilko, Quesnel, Stellako‐Late Stuart and Adams). Survival of Adams sockeye salmon was the most impacted by warm temperatures encountered in the lower river, followed by that of Stellako‐Late Stuart and Quesnel. In contrast, survival of Chilko fish was insensitive to the encountered river temperature. In all stocks, in‐river survival of ocean‐captured sockeye salmon was higher than that of river‐captured fish and, generally, the difference was more pronounced under warm temperatures. The survival–temperature relationships for ocean‐captured fish were used to predict historic (1961–1990) and future (2010–2099) survival under simulated lower river thermal experiences for the Quesnel, Stellako‐Late Stuart and Adams stocks. A decrease of 9–16% in survival of all these stocks was predicted by the end of the century if the Fraser River continues to warm as expected. However, the decrease in future survival of Adams sockeye salmon would occur only if fish continue to enter the river abnormally early, towards warmer periods of the summer, as they have done since 1995. The survival estimates and predictions presented here are likely optimistic and emphasize the need to consider stock‐specific responses to temperature and climate warming into fisheries management and conservation strategies.     

Evaluation of effectiveness of enhanced‐efficiency fertilizers as mitigation options for N2O and NO emissions from agricultural soils: meta‐analysis

Agricultural fields are an important anthropogenic source of atmospheric nitrous oxide (N₂O) and nitric oxide (NO). Although many field studies have tested the effectiveness of possible mitigation options on N₂O and NO emissions, the effectiveness of each option varies across sites due to environmental factors and field management. To combine these results and evaluate the overall effectiveness of enhanced‐efficiency fertilizers [i.e., nitrification inhibitors (NIs), polymer‐coated fertilizers (PCFs), and urease inhibitors (UIs)] on N₂O and NO emissions, we performed a meta‐analysis using field experiment data (113 datasets from 35 studies) published in peer‐reviewed journals through 2008. The results indicated that NIs significantly reduced N₂O emissions (mean: ?38%, 95% confidential interval: ?44% to ?31%) compared with those of conventional fertilizers. PCFs also significantly reduced N₂O emissions (?35%, ?58% to ?14%), whereas UIs were not effective in reducing N₂O. NIs and PCFs also significantly reduced NO (?46%, ?65% to ?35%; ?40%, ?76% to ?10%, respectively). The effectiveness of NIs was relatively consistent across the various types of inhibitors and land uses. However, the effect of PCFs showed contrasting results across soil and land‐use type: they were significantly effective for imperfectly drained Gleysol grassland (?77%, ?88% to ?58%), but were ineffective for well‐drained Andosol upland fields. Because available data for PCFs were dominated by certain regions and soil types, additional data are needed to evaluate their effectiveness more reliably. NIs were effective in reducing N₂O emission from both chemical and organic fertilizers. Moreover, the consistent effect of NIs indicates that they are potent mitigation options for N₂O and NO emissions.     

A multi‐criteria based review of models that predict environmental impacts of land use‐change for perennial energy crops on water,carbon and nitrogen cycling

Reduction in energy sector greenhouse gas GHG emissions is a key aim of European Commission plans to expand cultivation of bioenergy crops. Since agriculture makes up 10–12% of anthropogenic GHG emissions, impacts of land‐use change must be considered, which requires detailed understanding of specific changes to agroecosystems. The greenhouse gas (GHG) balance of perennials may differ significantly from the previous ecosystem. Net change in GHG emissions with land‐use change for bioenergy may exceed avoided fossil fuel emissions, meaning that actual GHG mitigation benefits are variable. Carbon (C) and nitrogen (N) cycling are complex interlinked systems, and a change in land management may affect both differently at different sites, depending on other variables. Change in evapotranspiration with land‐use change may also have significant environmental or water resource impacts at some locations. This article derives a multi‐criteria based decision analysis approach to objectively identify the most appropriate assessment method of the environmental impacts of land‐use change for perennial energy crops. Based on a literature review and conceptual model in support of this approach, the potential impacts of land‐use change for perennial energy crops on GHG emissions and evapotranspiration were identified, as well as likely controlling variables. These findings were used to structure the decision problem and to outline model requirements. A process‐based model representing the complete agroecosystem was identified as the best predictive tool, where adequate data are available. Nineteen models were assessed according to suitability criteria, to identify current model capability, based on the conceptual model, and explicit representation of processes at appropriate resolution. FASSET, ECOSSE, ANIMO, DNDC, DayCent, Expert‐N, Ecosys, WNMM and CERES‐NOE were identified as appropriate models, with factors such as crop, location and data availability dictating the final decision for a given project. A database to inform such decisions is included.     

Restorative mowing on an abandoned semi‐natural meadow: short‐term and predicted long‐term effects

Abstract. When management, in the form of cattle grazing and mowing, ceases the abundance of competitively superior plant species tends to increase in abandoned semi‐natural meadows. Litter accumulation elevates the soil nutrient levels and hinders seedling recruitment. We surveyed changes in plant cover and species composition of a formerly grazed meadow in permanent plots for six years. Some plots were unmown, while others were mown and raked annually in August. The cover of grasses decreased and herb cover remained unchanged regardless of the treatment. Mowing and raking significantly reduced litter accumulation and increased the number of ground layer species. The expected long‐term effects of abandonment and restorative mowing were studied by calculating the transition probabilities for unmown and mown plots and simulating the course of succession as projected by the transition matrices. During a simulation period of 30 yr, abandonment led to (1) a decrease in the cover of small herbs, (2) a slight increase in the cover of tall herbs and (3) a slight decrease in the cover of grasses. In contrast, the cover of small herbs on the mown plots remained unchanged or slightly increased during the course of simulation. These results suggest that mowing late in the season is primarily a management tool for the maintenance of the existing species diversity and composition. However, it may not be an effective restorative tool to induce overall changes in the resident vegetation of abandoned grass‐dominated meadows. Grazing or mowing early in the season may be more effective in this respect. Consequently, mowing early or, alternatively, late in the season may provide management strategies for the maintenance and restoration of species diversity, respectively.     

Evidence of maternal effects on temperature preference in side‐blotched lizards: implications for evolutionary response to climate change

Natural populations respond to selection pressures like increasing local temperatures in many ways, including plasticity and adaptation. To predict the response of ectotherms like lizards to local temperature increase, it is essential to estimate phenotypic variation in and determine the heritability of temperature‐related traits like average field body temperature (T_b) and preferred temperature (T_p). We measured T_p of Uta stansburiana in a laboratory thermal gradient and assessed the contribution of sex, reproductive status and throat color genotype to phenotypic variation in T_b of adult lizards. Females had higher T_p than males. However, they temporarily preferred lower temperature when gravid than when nongravid. Using a nested half‐sib design for genetic crosses in the laboratory, we estimated relative contributions of additive genetic variation and maternal effects to T_p of hatchlings. Our results show that maternal effects, but not additive genetic variation, influence T_p of hatchlings in U. stansburiana. Maternal T_p and the presence or absence of blue throat color alleles significantly influenced T_p of hatchlings. We discuss ecological and evolutionary consequences of these maternal effects in the context of rapid climate change and natural selection that we measure on progeny survival to maturity as a function of maternal T_p.