Comparing treatments in the presence of crossing survival curves: an application to bone marrow transplantation

Summary .   In some clinical studies comparing treatments in terms of their survival curves, researchers may anticipate that the survival curves will cross at some point, leading to interest in a long-term survival comparison. However, simple comparison of the survival curves at a fixed point may be inefficient, and use of a weighted log-rank test may be overly sensitive to early differences in survival. We formulate the problem as one of testing for differences in survival curves after a prespecified time point, and propose a variety of techniques for testing this hypothesis. We study these methods using simulation and illustrate them on a study comparing survival for autologous and allogeneic bone marrow transplants.     

Seasonal variation in pre‐fledging survival of lesser scaup Aythya affinis: hatch date effects depend on maternal body mass

Among temperate‐breeding birds, offspring survival and reproductive success are often inversely related to timing of breeding. The mechanisms that produce seasonal declines in offspring survival are not fully understood but may be related to temporal changes in parental quality, environmental quality, or both. We analyzed data for lesser scaup Aythya affinis to evaluate hypothesized effects of parental quality and date on pre‐fledging survival. Maternal quality, as indexed by body mass, did not have an independent effect on offspring survival in this species. Maternal body mass did not decline seasonally and did not have an independent effect on duckling survival. Although we did not detect an independent effect of hatch date on duckling survival, duckling survival declined seasonally for broods raised by lightweight females, indicating an interactive effect of maternal mass and date. We hypothesize that this interaction may be driven by seasonally declining food resources coupled with the influence of female condition on the ability to monopolize food resources or remain attentive to the brood. We also tested morphological predictions of the date hypothesis by examining physical characteristics of ducklings. When corrected for age and size, late‐hatched ducklings tended to have marginally larger digestive systems and smaller leg muscles than did early‐hatched birds. Abundances of intestinal parasites acquired through diet decreased marginally in late‐hatched ducklings. Results for digestive system and parasite infection patterns suggested that later‐hatched broods may shift diets, consistent with a contribution of environmental factors to seasonal variation in offspring survival. Taken together, our results suggest that both female attributes and environmental conditions may influence seasonal patterns of offspring survival in this species.     

Survival of Gunnison sage‐grouse Centrocercus minimus in Colorado,USA

Gunnison sage‐grouse Centrocercus minimus has declined from their historic range and recent monitoring has provided evidence that some populations are continuing to decline. The evaluation of long‐term, population‐specific survival rates is important to assess population stability, and is necessary for conservation of this species of concern. We evaluated adult and yearling survival in two dynamically different populations of Gunnison sage‐grouse (a relatively large, more stable population and a small, declining population). Our goal was to examine the relationship between annual survival and population, and test hypotheses with regards to temporal effects (across years and within year) and individual effects (sex and age). We also evaluated the effects of snow depth on sage‐grouse survival. We tracked 214 radiomarked birds in the large population from 2005–2010 and 25 birds in the small population from 2007–2010. We found no evidence for a difference in survival between yearlings and adults nor did we find an influence of snow depth on survival. Males had the lowest survival during the lekking season (March–April); females had lower survival during the nesting and chick rearing season (May–July) and late‐summer and fall (August–October). The annual survival rate was 0.61 (SE 0.06) for females and 0.39 (SE 0.08) for males. Survival was constant across years and between the populations suggesting observed population changes during this time period are not a result of changes in adult survival.     

Patterns of spatio-temporal variation in the survival rates of a viviparous lizard: the interacting effects of sex,reproductive trade-offs,aridity, and human-induced disturbance

Examination of the spatial and temporal variation in survival rates provides insight on how the action of natural selection varies among populations of single species. In this study, we used mark-recapture data from seven populations of the viviparous lizard Sceloporus grammicus in Central Mexico and a multi-model inference framework to examine interpopulation variation in the survival of adult males and females. We aimed to analyze the potential effects of aridity, human-induced disturbance, and reproductive costs on the survival rates of these lizards. For females in particular, we also searched for a negative relationship between litter size (adjusted for female size) and female survival. Our results demonstrate seasonal changes in survival for males and females. In three out of our seven study sites female survival decreased during the birthing season. In contrast, male survival did not appear to decrease during the mating season. We found an interaction between site-specific aridity and reproductive season affecting female survival. A decrease in female survival during the birthing season was observed in relatively arid sites. In one of these arid sites we found a negative effect of size-adjusted litter size on female survival: females producing more offspring than those expected for their size were more likely to die. This result represents evidence of a physiological trade-off for gravid females occurring in at least one of the studied populations. Interpopulation variation in the degree of human-induced disturbance could not explain the observed patterns of spatial variation in survival rates. Our results demonstrate wide variation in sex-specific survival patterns of this viviparous lizard and provide evidence that negative associations between reproduction and survival are highly dependent on the local environmental conditions.     

Ecological Factors Influencing Nest Survival of Greater Sage-Grouse in Mono County,California

ABSTRACT We studied nest survival of greater sage-grouse (Centrocercus urophasianus) in 5 subareas of Mono County, California, USA, from 2003 to 2005 to 1) evaluate the importance of key vegetation variables for nest success, and 2) to compare nest success in this population with other greater sage-grouse populations. We captured and radiotracked females (n = 72) to identify nest sites and monitor nest survival. We measured vegetation at nest sites and within a 10-m radius around each nest to evaluate possible vegetation factors influencing nest survival. We estimated daily nest survival and the effect of explanatory variables on daily nest survival using nest-survival models in Program MARK. We assessed effects on daily nest survival of total, sagebrush (Artemisia spp.), and nonsagebrush live shrub-cover, Robel visual obstruction, the mean of grass residual height and grass residual cover measurements within 10 m of the nest shrub, and area of the shrub, shrub height, and shrub type at the nest site itself. Assuming a 38-day exposure period, we estimated nest survival at 43.4%, with percent cover of shrubs other than sagebrush as the variable most related to nest survival. Nest survival increased with increasing cover of shrubs other than sagebrush. Also, daily nest survival decreased with nest age, and there was considerable variation in nest survival among the 5 subareas. Our results indicate that greater shrub cover and a diversity of shrub species within sagebrush habitats may be more important to sage-grouse nest success in Mono County than has been reported elsewhere.     

A hierarchical nest survival model integrating incomplete temporally varying covariates

Nest success is a critical determinant of the dynamics of avian populations, and nest survival modeling has played a key role in advancing avian ecology and management. Beginning with the development of daily nest survival models, and proceeding through subsequent extensions, the capacity for modeling the effects of hypothesized factors on nest survival has expanded greatly. We extend nest survival models further by introducing an approach to deal with incompletely observed, temporally varying covariates using a hierarchical model. Hierarchical modeling offers a way to separate process and observational components of demographic models to obtain estimates of the parameters of primary interest, and to evaluate structural effects of ecological and management interest. We built a hierarchical model for daily nest survival to analyze nest data from reintroduced whooping cranes (Grus americana) in the Eastern Migratory Population. This reintroduction effort has been beset by poor reproduction, apparently due primarily to nest abandonment by breeding birds. We used the model to assess support for the hypothesis that nest abandonment is caused by harassment from biting insects. We obtained indices of blood‐feeding insect populations based on the spatially interpolated counts of insects captured in carbon dioxide traps. However, insect trapping was not conducted daily, and so we had incomplete information on a temporally variable covariate of interest. We therefore supplemented our nest survival model with a parallel model for estimating the values of the missing insect covariates. We used Bayesian model selection to identify the best predictors of daily nest survival. Our results suggest that the black fly Simulium annulus may be negatively affecting nest survival of reintroduced whooping cranes, with decreasing nest survival as abundance of S. annulus increases. The modeling framework we have developed will be applied in the future to a larger data set to evaluate the biting‐insect hypothesis and other hypotheses for nesting failure in this reintroduced population; resulting inferences will support ongoing efforts to manage this population via an adaptive management approach. Wider application of our approach offers promise for modeling the effects of other temporally varying, but imperfectly observed covariates on nest survival, including the possibility of modeling temporally varying covariates collected from incubating adults.     

Personality‐Dependent Survival in the Marine Isopod Idotea balthica

We studied the fitness effects of animal personality by measuring activity and its relation to survival in the marine isopod Idotea balthica. We asked (1) whether activity could be considered to be a personality trait, (2) whether this trait is connected to survival, and (3) whether personality and survival exhibit sex differences. We found that activity fulfilled the criteria of personality as individuals had consistent between‐individual differences over time and across situations. Consistent individual differences in activity were associated with fitness as the survival probability of active individuals was lower, but this did not depend on sex. Our results demonstrate that personality exists in I. balthica and support recent suggestions that the association between personality and life‐history traits is a central component in mediating animal personality.     

Endangered Cape Sable Seaside Sparrow Survival

ABSTRACT We investigated survival for male, female, and first-year Cape Sable seaside sparrows (Ammodramus maritimus mirabilis, hereafter sparrows), a federally endangered bird restricted to the Florida Everglades, USA. Accurate estimates of survival are critical to improve management decisions and population estimates for this and other threatened species. We used Program MARK to evaluate effects of age, sex, population membership, temporal variation, and ground-water levels on annual survival from mark-recapture data collected across 3 sparrow populations from 1997 to 2007. We found little evidence that annual survival rates differed between the populations or across ground-water levels, but we found high variability between years for both adult and juvenile survival. Our results revealed female sparrows experienced 14–19% lower survival than males. Sparrows experienced much lower survival during their first year of life and were short-lived (2–3 yr). Our results highlight sparrows' susceptibility to population declines and suggest that management actions aimed at increasing survival may be effective for this species' management.     

Causes and consequences of variation in offspring body mass: meta‐analyses in birds and mammals

Early survival is highly variable and strongly influences observed population growth rates in most vertebrate populations. One of the major potential drivers of survival variation among juveniles is body mass. Heavy juveniles are better fed and have greater body reserves, and are thus assumed to survive better than light individuals. In spite of this, some studies have failed to detect an influence of body mass on offspring survival, questioning whether offspring body mass does indeed consistently influence juvenile survival, or whether this occurs in particular species/environments. Furthermore, the causes for variation in offspring mass are poorly understood, although maternal mass has often been reported to play a crucial role. To understand why offspring differ in body mass, and how this influences juvenile survival, we performed phylogenetically corrected meta‐analyses of both the relationship between offspring body mass and offspring survival in birds and mammals and the relationship between maternal mass and offspring mass in mammals. We found strong support for an overall positive effect of offspring body mass on survival, with a more pronounced influence in mammals than in birds. An increase of one standard deviation of body mass increased the odds of offspring survival by 71% in mammals and by 44% in birds. A cost of being too fat in birds in terms of flight performance might explain why body mass is a less reliable predictor of offspring survival in birds. We then looked for moderators explaining the among‐study differences reported in the intensity of this relationship. Surprisingly, sex did not influence the intensity of the offspring mass–survival relationship and phylogeny only accounted for a small proportion of observed variation in the intensity of that relationship. Among the potential factors that might affect the relationship between mass and survival in juveniles, only environmental conditions was influential in mammals. Offspring survival was most strongly influenced by body mass in captive populations and wild populations in the absence of predation. We also found support for the expected positive effect of maternal mass on offspring mass in mammals (r_pearson = 0.387). As body mass is a strong predictor of early survival, we expected heavier mothers to allocate more to their offspring, leading them to be heavier and so to have a higher survival. However, none of the potential factors we tested for variation in the maternal mass–offspring mass relationship had a detectable influence. Further studies should focus on linking these two relationships to determine whether a strong effect of offspring size on early survival is associated with a high correlation coefficient between maternal mass and offspring mass.     

Survival in king penguins Aptenodytes patagonicus: temporal and sex-specific effects of environmental variability

We investigated annual adult survival rates of king penguins Aptenodytes patagonicus breeding at South Georgia during 6 years in relation to age/breeding experience, sex, and food availability. During the first 3 years of the study, when food availability was good, survival was 97.7% for experienced breeders, which confirmed the very high survival rates observed in penguins in general. In these years survival did not differ between the sexes, presumably because parental investment is shared equally between the sexes, and the sexual dimorphism is small in king penguins. Survival was lower for young, first-time breeders (83.0%). In experienced birds the annual survival rate decreased to 68-82% following a catastrophic year when food availability was extremely low. We address the question how parents balance their current investment in offspring against their chances to reproduce in the future. We argue that the high mortality rate among breeding individuals after the year of food stress provides support for previous suggestions that the response to increased costs in seabirds might be complex to predict and does not always follow intuitive expectations according to general life-history theory. We also found that females survived significantly less well than males following the bad year. We explain this result as follows: the male-biased sex ratio (56:44) that we observed in our study colony clearly does not result from lower female survival during normal conditions. An already existing skewed sex ratio forces males to delay the onset of breeding because of a lack of breeding partners. This in turn causes breeding females to be, on average, younger and less experienced than males and to have lower survival following a year of food shortage. In this study survival was linked with food availability and we suggest that this was connected to climatic/oceanographic features, such as the position of the Antarctic Polar Front Zone. We could, however, not verify this by anomalies in sea surface temperature data.     

One-step targeted maximum likelihood estimation for time-to-event outcomes

Researchers in observational survival analysis are interested in not only estimating survival curve nonparametrically but also having statistical inference for the parameter. We consider right-censored failure time data where we observe n independent and identically distributed observations of a vector random variable consisting of baseline covariates, a binary treatment at baseline, a survival time subject to right censoring, and the censoring indicator. We assume the baseline covariates are allowed to affect the treatment and censoring so that an estimator that ignores covariate information would be inconsistent. The goal is to use these data to estimate the counterfactual average survival curve of the population if all subjects are assigned the same treatment at baseline. Existing observational survival analysis methods do not result in monotone survival curve estimators, which is undesirable and may lose efficiency by not constraining the shape of the estimator using the prior knowledge of the estimand. In this paper, we present a one-step Targeted Maximum Likelihood Estimator (TMLE) for estimating the counterfactual average survival curve. We show that this new TMLE can be executed via recursion in small local updates. We demonstrate the finite sample performance of this one-step TMLE in simulations and an application to a monoclonal gammopathy data.     

Experimental evidence of long‐term reproductive costs in a colonial nesting seabird

Trade‐offs between current and future reproduction are central to the evolution of life histories. Experiments that manipulate brood size provide an effective approach to investigating future costs of current reproduction. Most manipulative studies to date, however, have addressed only the short‐term effects of brood size manipulation. Our goal was to determine whether survival or breeding costs of reproduction in a long‐lived species manifest beyond the subsequent breeding season. To this end, we investigated long‐term survival and breeding effects of a multi‐year reproductive cost experiment conducted on black‐legged kittiwakes Rissa tridactyla, a long‐lived colonial nesting seabird. We used multi‐state capture–recapture modeling to assess hypotheses regarding the role of experimentally reduced breeding effort and other factors, including climate phase and colony size and productivity, on future survival and breeding probabilities during the 16‐yr period following the experiment. We found that forced nest failures had a positive effect on breeding probability over time, but had no effect on long‐term survival. This apparent canalization of survival suggests that adult survival is the most important parameter influencing fitness in this long‐lived species, and that adults should pay reproductive costs in ways that do not compromise this critical life history parameter. When declines in adult survival rate are observed, they may indicate populations of conservation concern.     

Survival Rates of Female Greater Sage-Grouse in Autumn and Winter in Southeastern Oregon

ABSTRACT We estimated survival rates of 135 female greater sage-grouse (Centrocercus urophasianus) on 3 study areas in southeastern Oregon, USA during autumn and winter for 3 years. We used known-fate models in Program MARK to test for differences among study areas and years, investigate the potential influence of weather, and compute estimates of overwinter survival. We found no evidence for differences in survival rates among study areas, which was contrary to our original hypothesis. There also were no declines in survival rates during fall-winter, but survival rates varied among years and time within years. Average survival rate from October through February was 0.456 (SE = 0.062). The coefficient of variation for this estimate was 13.6% indicating good precision in our estimates of survival. We found strong evidence for an effect of weather (i.e., mean daily min. temp, extreme min. temp, snow depth) on bi-weekly survival rates of sage-grouse for 2 of the study areas in one year. Extremely low (<-15°C) temperatures over an 8-week period and accumulation of snow had a negative effect on survival rates during the winter of 1990–1991 on the 2 study areas at the higher (>1,500 m) elevations. In contrast, we found no evidence for an influence of weather on the low-elevation study area or during the winters of 1989–1990 and 1991–1992. Extreme weather during winter can cause lower survival of adult female sage-grouse, so managers should be aware of these potential effects and reduce harvest rates accordingly.     

House sparrow Passer domesticus survival is not associated with MHC‐I diversity,but possibly with specific MHC‐I alleles

The MHC (Major Histocompatibility Complex) plays an important role in the immune system of vertebrates. MHC genes are extremely polymorphic and this variation is considered to be maintained by selection from pathogens. We investigate whether MHC diversity (number of different alleles per individual) affects the survival and recruitment of nestling house sparrows. We hypothesize that individuals with higher MHC diversity can recognize and combat a wider range of pathogens, and therefore are more likely to survive and recruit into the breeding population. Additionally, we hypothesize that specific MHC class I alleles (MHC‐I) could be associated with survival and recruitment. We screened MHC‐I genotypes in 518 house sparrow chicks hatched on Lundy Island but we found no evidence for a relationship between nestling survival, post‐fledging survival or recruitment success with MHC diversity. Then we investigated effects of specific MHC‐I alleles in 195 individuals from a single cohort. Twenty‐one MHC‐I alleles were tested for relationships with nestling survival, post‐fledging survival and recruitment, and we detected associations with survival for three different alleles. This pattern was, however, not different to what would be expected from random, so we could not conclude that particular MHC‐I alleles are associated with survival in house sparrows on Lundy Island. Nonetheless, one of these alleles (1105) showed both a tendency for a higher probability of surviving in nestlings, and a significant association with survival in fledglings. We envision that allele 1105 could be an interesting candidate gene for testing associations with survival in house sparrows in the future.     

Temporal variation of juvenile survival in a long-lived species: the role of parasites and body condition

Studies of population dynamics of long-lived species have generally focused on adult survival because population growth should be most sensitive to this parameter. However, actual variations in population size can often be driven by other demographic parameters, such as juvenile survival, when they show high temporal variability. We used capture–recapture data from a long-term study of a hunted, migratory species, the greater snow goose (Chen caerulescens atlantica), to assess temporal variability in first-year survival and the relative importance of natural and hunting mortality. We also conducted a parasite-removal experiment to determine the effect of internal parasites and body condition on temporal variation in juvenile survival. We found that juvenile survival showed a higher temporal variability than adult survival and that natural mortality was more important than hunting mortality, unlike in adults. Parasite removal increased first-year survival and reduced its annual variability in females only. Body condition at fledging was also positively correlated with first-year survival in treated females. With reduced parasite load, females, which are thought to invest more in their immune system than males according to Bateman’s principle, could probably reallocate more energy to growth than males, leading to a higher survival. Treated birds also had a higher survival than control ones during their second year, suggesting a developmental effect that manifested later in life. Our study shows that natural factors such as internal parasites may be a major source of variation in juvenile survival of a long-lived, migratory bird, which has implications for its population dynamics.     

Regulation of anoikis by Cdc42 and Rac1

Ras family small GTPases play a critical role in malignant transformation, and Rho subfamily members contribute significantly to this process. Anchorage-independent growth and the ability to avoid detachment-induced apoptosis (anoikis) are hallmarks of transformed epithelial cells. In this study, we have demonstrated that constitutive activation of Cdc42 inhibits anoikis in Madin-Darby canine kidney (MDCK) epithelial cells. We showed that activated Cdc42 stimulates the ERK, JNK, and p38 MAPK pathways in suspension condition; however, inhibition of these signaling does not affect Cdc42-stimulated cell survival. However, we demonstrated that inhibition of phosphatidylinositol 3-kinase (PI3K) pathway abolishes the protective effect of Cdc42 on anoikis. Taking advantage of a double regulatory expression system, we also showed that Cdc42-stimulated cell survival in suspension condition is, at least in part, mediated by Rac1. We also provide evidence for a positive feedback loop involving Rac1 and PI3K. In addition, we show that the survival functions of both constitutively active Cdc42 and Rac1 GTPases are abrogated by Latrunculin B, an actin filament-depolymerizing agent, implying an important role for the actin cytoskeleton in mediating survival signaling activated by Cdc42 and Rac1. Together, our results indicate a role for Cdc42 in anchorage-independent survival of epithelial cells. We also propose that this survival function depends on a positive feedback loop involving Rac1 and PI3K.     

Larval Tolerance to Salinity in Three Species of Australian Anuran: An Indication of Saline Specialisation in Litoria aurea

Recent anthropogenic influences on freshwater habitats are forcing anuran populations to rapidly adapt to high magnitude changes in environmental conditions or face local extinction. We examined the effects of ecologically relevant elevated salinity levels on larval growth, metamorphosis and survival of three species of Australian anuran; the spotted marsh frog (Limnodynastes tasmaniensis), the painted burrowing frog (Neobatrachus sudelli) and the green and golden bell frog (Litoria aurea), in order to better understand the responses of these animals to environmental change. Elevated salinity (16% seawater) negatively impacted on the survival of L. tasmaniensis (35% survival) and N sudelli (0% survival), while reduced salinity had a negative impact on L. aurea. (16% seawater: 85% survival; 0.4% seawater: 35% survival). L. aurea tadpoles survived in salinities much higher than previously reported for this species, indicating the potential for inter-populations differences in salinity tolerance. In L. tasmaniensis and L. aurea, development to metamorphosis was fastest in low and high salinity treatments suggesting it is advantageous for tadpoles to invest energy in development in both highly favourable and developmentally challenging environments. We propose that this response might either maximise potential lifetime fecundity when tadpoles experience favourable environments, or, facilitate a more rapid escape from pond environments where there is a reduced probability of survival.     

The effect of maternal care on child survival: a demographic, genetic, and evolutionary perspective

Models of population dynamics generally assume that child survival is independent of maternal survival. However, in humans, the death of a mother compromises her immature children's survival because children require postnatal care. A child's survival therefore depends on her mother's survival in years following her birth. Here, we provide a model incorporating this relationship and providing the number of children surviving until maturity achieved by females at each age. Using estimates of the effect that a mother's death has on her child's survival until maturity, we explore the effect of the model on population dynamics. Compared to a model that includes a uniform child survival probability, our model slightly raises the finite rate of increase lambda and modifies generation time and the stable age structure. We also provide estimates of selection on alleles that change the survival of females. Selection is higher at all adult ages in our model and remains significant after menopause (at ages for which the usual models predict neutrality of such alleles). Finally, the effect of secondary caregivers who compensate maternal care after the death of a mother is also emphasized. We show that allocare (as an alternative to maternal care) can have a major effect on population dynamics and is likely to have played an important role during human evolution.     

Handling Stress as a Measurement of Personality in Great Tit Nestlings (Parus major)

Interest in personality is growing in a wide range of disciplines, but only in a few systems it is possible to assess the survival value of personality. Field studies looking at the relationship between personality and survival value early in life are greatly hampered by the fact that personality can at present only be assessed after individuals become independent from their parents. In passerines, for example, this is often after a period of intensive selection for the survival on fledglings. The main aim of this study is therefore to develop a method to measure personality before this period of selection. For this purpose, we developed the handling stress (HS) test. We measured HS in 14-d-old great tit nestlings by counting the number of breast movements (breath rate) in four subsequent 15-s bouts for 1 min; before and after they were socially isolated from their siblings for 15 min. To calculate the repeatability of HS, we repeated the test 6 mo later. To assess the relationship between HS and exploratory behaviour, we correlated the outcome of both tests. We ran tests both on birds of lines selected for extreme personality and on wild birds from a natural population. We found that birds selected for fast exploration reacted more to HS compared with birds selected for slow exploration and that HS was repeatable in different life phases. We confirmed this by finding an increase in the HS with increasing exploratory scores in wild birds. These results show that we can use the HS test as a measurement of personality, making it a potential tool for studying the relationship between personality and survival value early in life.