Slicing:A sustainable approach to structuring samples for analysis in long-term studies

The longitudinal study of populations is a core tool for understanding ecological and evolutionary processes. Long‐term studies typically collect samples repeatedly over individual lifetimes and across generations. These samples are then analysed in batches (e.g. qPCR plates) and clusters (i.e. group of batches) over time in the laboratory. However, these analyses are constrained by cross‐classified data structures introduced biologically or through experimental design. The separation of biological variation from the confounding among‐batch and among‐cluster variation is crucial, yet often ignored. The commonly used approaches to structuring samples for analysis, sequential and randomization, generate bias due to the non‐independence between time of collection and the batch and cluster they are analysed in. We propose a new sample structuring strategy, called slicing, designed to separate confounding among‐batch and among‐cluster variation from biological variation. Through simulations, we tested the statistical power and precision to detect within‐individual, between‐individual, year and cohort effects of this novel approach. Our slicing approach, whereby recently and previously collected samples are sequentially analysed in clusters together, enables the statistical separation of collection time and cluster effects by bridging clusters together, for which we provide a case study. Our simulations show, with reasonable slicing width and angle, similar precision and similar or greater statistical power to detect year, cohort, within‐ and between‐individual effects when samples are sliced across batches, compared with strategies that aggregate longitudinal samples or use randomized allocation. While the best approach to analysing long‐term datasets depends on the structure of the data and questions of interest, it is vital to account for confounding among‐cluster and batch variation. Our slicing approach is simple to apply and creates the necessary statistical independence of batch and cluster from environmental or biological variables of interest. Crucially, it allows sequential analysis of samples and flexible inclusion of current data in later analyses without completely confounding the analysis. Our approach maximizes the scientific value of every sample, as each will optimally contribute to unbiased statistical inference from the data. Slicing thereby maximizes the power of growing biobanks to address important ecological, epidemiological and evolutionary questions

Senescence in natural populations of animals:Widespread evidence and its implications for bio-gerontology

That senescence is rarely, if ever, observed in natural populations is an oft-quoted fallacy within bio-gerontology. We identify the roots of this fallacy in the otherwise seminal works of Medawar and Comfort, and explain that under antagonistic pleiotropy or disposable soma explanations for the evolution of senescence there is no reason why senescence cannot evolve to be manifest within the life expectancies of wild organisms. The recent emergence of long-term field studies presents irrefutable evidence that senescence is commonly detected in nature. We found such evidence in 175 different animal species from 340 separate studies. Although the bulk of this evidence comes from birds and mammals, we also found evidence for senescence in other vertebrates and insects. We describe how high-quality longitudinal field data allow us to test evolutionary explanations for differences in senescence between the sexes and among traits and individuals. Recent studies indicate that genes, prior environment and investment in growth and reproduction influence aging rates in the wild. We argue that – with the fallacy that wild animals do not senesce finally dead and buried – collaborations between bio-gerontologists and field biologists can begin to test the ecological generality of purportedly ‘public’ mechanisms regulating aging in laboratory models

Relative costs of offspring sex and offspring survival in a polygynous mammal.

Costs of reproduction are expected to be ubiquitous in wild animal populations and understanding the drivers of variation in these costs is an important aspect of life-history evolution theory. We use a 43 year dataset from a wild population of red deer to examine the relative importance of two factors that influence the costs of reproduction to mothers, and to test whether these costs vary with changing ecological conditions. Like previous studies, our analyses indicate fitness costs of lactation: mothers whose calves survived the summer subsequently showed lower survival and fecundity than those whose calves died soon after birth, accounting for 5% and 14% of the variation in mothers' survival and fecundity, respectively. The production of a male calf depressed maternal survival and fecundity more than production of a female, but accounted for less than 1% of the variation in either fitness component. There was no evidence for any change in the effect of calf survival or sex with increasing population density

Trait–demography relationships underlying small mammal population fluctuations

1.Large-scale fluctuations in abundance are a common feature of small mammal populations and have been the subject of extensive research. These demographic fluctuations are often associated with concurrent changes in the average body mass of individuals, sometimes referred to as the “Chitty effect”. Despite the long-standing recognition of this phenomenon, an empirical investigation of the underlying coupled dynamics of body mass and population growth has been lacking. 2.Using long-term life-history data combined with a trait-based demographic approach, we examined the relationship between body mass and demography in a small mammal population that exhibits non-cyclic, large-scale fluctuations in abundance. We used data from the male segment of a 25-year study of the monogamous prairie vole, Microtus ochrogaster, in Illinois, USA. Specifically, we investigated how trait–demography relationships and trait distributions changed between different phases of population fluctuations, and the consequences of these changes for both trait and population dynamics. 3.We observed phase-specific changes in male adult body mass distribution in this population of prairie voles. Our analyses revealed that these changes were driven by variation in ontogenetic growth, rather than selection acting on the trait. The resulting changes in body mass influenced most life-history processes, and these effects varied among phases of population fluctuation. However, these changes did not propagate to affect the population growth rate due to the small effect of body mass on vital rates, compared to the overall differences in vital rates between phases. The increase phase of the fluctuations was initiated by enhanced survival, particularly of juveniles, and fecundity whereas the decline phase was driven by an overall reduction in fecundity, survival and maturation rates. 4.Our study provides empirical support, as well as a potential mechanism, underlying the observed trait changes accompanying population fluctuations. Body size dynamics and population fluctuations resulted from different life-history processes. Therefore, we conclude that body size dynamics in our population do not drive the observed population dynamics. This more in-depth understanding of different components of small mammal population fluctuations will help us to better identify the mechanistic drivers of this interesting phenomenon

Decline in telomere length with increasing age across non‐human vertebrates:A meta‐analysis

International audienc

Consequences of measurement error in qPCR telomere data:A simulation study

The qPCR method provides an inexpensive, rapid method for estimating relative telomere length across a set of biological samples. Like all laboratory methods, it involves some degree of measurement error. The estimation of relative telomere length is done subjecting the actual measurements made (the Cq values for telomere and a control gene) to non-linear transformations and combining them into a ratio (the TS ratio). Here, we use computer simulations, supported by mathematical analysis, to explore how errors in measurement affect qPCR estimates of relative telomere length, both in cross-sectional and longitudinal data. We show that errors introduced at the level of Cq values are magnified when the TS ratio is calculated. If the errors at the Cq level are normally distributed and independent of true telomere length, those in the TS ratio are positively skewed and proportional to true telomere length. The repeatability of the TS ratio declines sharply with increasing error in measurement of the Cq values for telomere and/or control gene. In simulated longitudinal data, measurement error alone can produce a pattern of low correlation between successive measures of relative telomere length, coupled with a strong negative dependency of the rate of change on initial relative telomere length. Our results illustrate the importance of reducing measurement error: a small increase in error in Cq values can have large consequences for the power and interpretability of qPCR estimates of relative telomere length. The findings also illustrate the importance of characterising the measurement error in each dataset-coefficients of variation are generally unhelpful, and researchers should report standard deviations of Cq values and/or repeatabilities of TS ratios-and allowing for the known effects of measurement error when interpreting patterns of TS ratio change over time

No sex differences in adult telomere length across vertebrates:a meta-analysis

International audienc

Contrasting drivers of reproductive ageing in albatrosses

1. Age-related variation in reproductive performance is ubiquitous in wild vertebrate populations and has important consequences for population and evolutionary dynamics.2. The ageing trajectory is shaped by both within-individual processes, such as improvement and senescence, and the among-individual effects of selective appearance and disappearance. To date, few studies have compared the role of these different drivers among species or populations.3. In this study, we use nearly 40 years of longitudinal monitoring data to contrast the within-and among-individual processes contributing to the reproductive ageing patterns in three albatross species (two biennial and one annual breeder) and test whether these can be explained by differences in life histories.4. Early-life performance in all species increased with age and was predominantly influenced by within-individual improvements. However, reproductive senescence was detected in only two of the species. In the species exhibiting senescent declines, we also detected a terminal improvement in breeding success. This is suggestive of a trade-off between reproduction and survival, which was supported by evidence of selective disappearance of good breeders.5. We demonstrate that comparisons of closely related species which differ in specific aspects of their life history can shed light on the ecological and evolutionary forces shaping variation in ageing patterns

Heritable variation in telomere length predicts mortality in soay sheep

Telomere length (TL) is considered an important biomarker of whole-organism health and aging. Across humans and other vertebrates, short telomeres are associated with increased subsequent mortality risk, but the processes responsible for this correlation remain uncertain. A key unanswered question is whether TL–mortality associations arise due to positive effects of genes or early-life environment on both an individual’s average lifetime TL and their longevity, or due to more immediate effects of environmental stressors on within-individual TL loss and increased mortality risk. Addressing this question requires longitudinal TL and life history data across the entire lifetimes of many individuals, which are difficult to obtain for long-lived species like humans. Using longitudinal data and samples collected over nearly two decades, as part of a long-term study of wild Soay sheep, we dissected an observed positive association between TL and subsequent survival using multivariate quantitative genetic models. We found no evidence that telomere attrition was associated with increased mortality risk, suggesting that TL is not an important marker of biological aging or exposure to environmental stress in our study system. Instead, we find that among-individual differences in average TL are associated with increased lifespan. Our analyses suggest that this correlation between an individual’s average TL and lifespan has a genetic basis. This demonstrates that TL has the potential to evolve under natural conditions, and suggests an important role of genetics underlying the widespread observation that short telomeres predict mortality

Consistent within-individual plasticity is sufficient to explain temperature responses in red deer reproductive traits

Warming global temperatures are affecting a range of aspects of wild populations, but the exact mechanisms driving associations between temperature and phenotypic traits may be difficult to identify. Here, we use a 36-year data-set on a wild population of red deer to investigate the causes of associations between temperature and two important components of female reproduction: timing of breeding and offspring size. By separating within- versus between-individual associations with temperature for each trait, we show that within-individual phenotypic plasticity (changes within a female’s lifetime) was entirely sufficient to generate the observed population-level association with temperature at key times of year. However, despite apparently adequate statistical power, we found no evidence of any variation between females in their responses (i.e. no ‘IxE’ interactions). Our results suggest that female deer show plasticity in reproductive traits in response to temperatures in the year leading up to calving, and that this response is consistent across individuals, implying no potential for either selection or heritability of plasticity. We estimate that the plastic response to rising temperatures explained 24% of the observed advance in mean calving date over the study period. We highlight the need for comparable analyses of other systems to determine the contribution of within-individual plasticity to population-level responses to climate change