Transposable elements (TEs) are major components of vertebrate genomes, with major roles in genome architecture and evolution. In order to characterize both common patterns and lineage-specific differences in TE content and TE evolution, we have compared the mobilomes of 23 vertebrate genomes, including 10 actinopterygian fish, 11 sarcopterygians, and 2 nonbony vertebrates. We found important variations in TE content (from 6% in the pufferfish tetraodon to 55% in zebrafish), with a more important relative contribution of TEs to genome size in fish than in mammals. Some TE superfamilies were found to be widespread in vertebrates, but most elements showed a more patchy distribution, indicative of multiple events of loss or gain. Interestingly, loss of major TE families was observed during the evolution of the sarcopterygian lineage, with a particularly strong reduction in TE diversity in birds and mammals. Phylogenetic trends in TE composition and activity were detected: Teleost fish genomes are dominated by DNA transposons and contain few ancient TE copies, while mammalian genomes have been predominantly shaped by nonlong terminal repeat retrotransposons, along with the persistence of older sequences. Differences were also found within lineages: The medaka fish genome underwent more recent TE amplification than the related platyfish, as observed for LINE retrotransposons in the mouse compared with the human genome. This study allows the identification of putative cases of horizontal transfer of TEs, and to tentatively infer the composition of the ancestral vertebrate mobilome. Taken together, the results obtained highlight the importance of TEs in the structure and evolution of vertebrate genomes, and demonstrate their major impact on genome diversity both between and within lineages.

Empirical evidence for declines in fitness components (survival and reproductive performance) with age has recently accumulated in wild populations, highlighting that the process of senescence is nearly ubiquitous in the living world. Senescence patterns are highly variable among species and current evolutionary theories of ageing propose that such variation can be accounted for by differences in allocation to growth and reproduction during early life. Here, we compiled 26 studies of free-ranging vertebrate populations that explicitly tested for a trade-off between performance in early and late life. Our review brings overall support for the presence of early-late life trade-offs, suggesting that the limitation of available resources leads individuals to trade somatic maintenance later in life for high allocation to reproduction early in life. We discuss our results in the light of two closely related theories of ageing-the disposable soma and the antagonistic pleiotropy theories-and propose that the principle of energy allocation roots the ageing process in the evolution of life-history strategies. Finally, we outline research topics that should be investigated in future studies, including the importance of natal environmental conditions in the study of trade-offs between early-and late-life performance and the evolution of sex-differences in ageing patterns.

This study of a French deer population reveals the demographic costs associated with the failure of a herbivore to modify its life cycle timing to respond to a warming world.

General rightsThis document is made available in accordance with publisher policies. Please cite only the published version using the reference above. abstract: Understanding how the natural world will be impacted by environmental change over the coming decades is one of the most pressing challenges facing humanity. Addressing this challenge is difficult because environmental change can generate both populationlevel plastic and evolutionary responses, with plastic responses being either adaptive or nonadaptive. We develop an approach that links quantitative genetic theory with data-driven structured models to allow prediction of population responses to environmental change via plasticity and adaptive evolution. After introducing general new theory, we construct a number of example models to demonstrate that evolutionary responses to environmental change over the short-term will be considerably slower than plastic responses and that the rate of adaptive evolution to a new environment depends on whether plastic responses are adaptive or nonadaptive. Parameterization of the models we develop requires information on genetic and phenotypic variation and demography that will not always be available, meaning that simpler models will often be required to predict responses to environmental change. We consequently develop a method to examine whether the full machinery of the evolutionarily explicit models we develop will be needed to predict responses to environmental change or whether simpler nonevolutionary models that are now widely constructed may be sufficient.

How populations respond to climate change depends on the interplay between life history, resource availability, and the intensity of the change. Roe deer are income breeders, with high levels of allocation to reproduction, and are hence strongly constrained by the availability of high quality resources during spring. We investigated how recent climate change has influenced demographic processes in two populations of this widespread species. Spring began increasingly earlier over the study, allowing us to identify 2 periods with contrasting onset of spring. Both populations grew more slowly when spring was early. As expected for a long-lived and iteroparous species, adult survival had the greatest potential impact on population growth. Using perturbation analyses, we measured the relative contribution of the demographic parameters to observed variation in population growth, both within and between periods and populations. Within periods, the identity of the critical parameter depended on the variance in growth rate, but variation in recruitment was the main driver of observed demographic change between periods of contrasting spring earliness. Our results indicate that roe deer in forest habitats cannot currently cope with increasingly early springs. We hypothesise that they should shift their distribution to richer, more heterogeneous landscapes to offset energetic requirements during the critical rearing stage.

The predictive adaptive response (PAR) hypothesis proposes that animals adjust their physiology and developmental trajectory during early life in anticipation of their future environments. Accordingly, when environmental conditions in early life match environmental conditions during adulthood, individual fitness should be greater. Here, we test this hypothesis in a longlived mammal, the roe deer, using data from two contrasting populations, intensively monitored for more than 35 years. In the highly productive site, the fitness of female roe deer increased with the quality of environment during adulthood and, contrary to predictions of PAR, individuals born in good conditions always outperformed those born under poor conditions. In the resource-limited site, the fitness of female roe deer born in poor years was better than those born in good conditions in poor years when the animals were adult, but not in good years. Although consistent with predictions of PAR, we showed that this pattern is likely to be a consequence of increased viability selection during the juvenile stage for animals born in poor years. While PARs are often advanced in evolutionary medicine, our findings suggest that detailed biological processes should be investigated before drawing conclusions about the existence of this phenomenon.

Population dynamics models have long assumed that populations are composed of a restricted number of groups, where individuals in each group have identical demographic rates and where all groups are similarly affected by density‐dependent and ‐independent effects. However, individuals usually vary tremendously in performance and in their sensitivity to environmental conditions or resource limitation, such that individual contributions to population growth will be highly variable. Recent efforts to integrate individual processes in population models open up new opportunities for the study of eco‐evolutionary processes, such as the density‐dependent influence of environmental conditions on the evolution of morphological, behavioral, and life‐history traits. We review recent advances that demonstrate how including individual mechanisms in models of population dynamics contributes to a better understanding of the drivers of population dynamics within the framework of integrated population models (IPMs). IPMs allow for the integration in a single inferential framework of different data types as well as variable population structure including sex, social group, or territory, all of which can be formulated to include individual‐level processes. Through a series of examples, we first show how IPMs can be beneficial for getting more accurate estimates of demographic traits than classic matrix population models by including basic population structure and their influence on population dynamics. Second, the integration of individual‐ and population‐level data allows estimating density‐dependent effects along with their inherent uncertainty by directly using the population structure and size to feedback on demography. Third, we show how IPMs can be used to study the influence of the dynamics of continuous individual traits and individual quality on population dynamics. We conclude by discussing the benefits and limitations of IPMs for integrating data at different spatial, temporal, and organismal levels to build more mechanistic models of population dynamics.

The timing of birth has marked impacts on early life and early development of newborns in many species. In seasonal environments, early-born offspring often survive and grow better than late-born offspring, but despite the long-lasting effects of early conditions on life history traits, the influence of birth date on fitness has rarely been investigated for longlived species. In this study, we analyzed both the short-and long-term effects of birth date on individual life history traits and explored its subsequent impact on individual fitness in a population of roe deer. We considered both the direct effects, as well as the indirect effects of birth date mediated through the effects of body mass, on demographic parameters. We found that in addition to short-term effects on early body growth and survival, birth date generates ''silver spoon'' effects on adult life history traits of female roe deer. Birth date had long-lasting effects on female adult body mass such that early-born females were, on average, 3 kg heavier as adults than late-born females, although female adult survival was similar between these categories. Based on the observed relationships between birth date, body mass, and demographic parameters, we built an integral projection model describing the simultaneous distributions of birth date and body mass to quantify the fitness consequences of birth date. We found that the fitness of early-born females was higher than that of late-born females. These long-lasting effects of birth date on fitness were mostly mediated through the influence of birth date on recruitment and adult body mass. By determining development of newborns during the early stages of life, birth date has a critical influence on each step of an individual's subsequent life history trajectory.