What can genetic variation tell us about the evolution of senescence?

Multi-locus homozygosity promotes actuarial senescence in a wild mammal

Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value. Here we infer associations between multi-locus homozygosity (MLH), sex, disease and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers Meles meles in a population naturally infected with Mycobacterium bovis (the causative agent of bovine tuberculosis [bTB]). We find important effects of MLH on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later life. Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bTB. These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.

Pace and shape of senescence in three species of duckweed

Senescence is progressive bodily deterioration associated with declines in survival and fecundity in older age classes. There is great diversity in patterns of senescence across species, but these patterns can be difficult to compare formally due to variation in the absolute time scales in which species live and die: members of some species live for a matter of days, others for millennia. To address this issue, the "pace-shape" approach was developed to decouple absolute time from analyses and instead standardize life history traits in terms of average life expectancy, facilitating intra- and interspecific comparisons. Here, we use this approach to distinguish the generic form of demographic trajectories (shape) from the time scale on which the trajectories occurred (pace) in three species of tiny, free-floating aquatic plants known as duckweeds (Lemna gibba L., L. minor L., and L. turionifera Landolt), which have mean lifespans of less than a month under typical lab conditions, and exhibit age-related declines in survivorship and reproduction. Using a randomized block design in which we tracked a final total of 430 individuals, we report differences in pace and shape among the three species. Specifically, the largest, least-fecund, and typically longest-lived species, L. gibba, tended to exhibit more rapid decreases in time-standardized survivorship and fecundity compared with the other two species. This study emphasizes variation in aging patterns that can be found among plant species, including those in the same genus, and provides further validation for the utility of applying the pace and shape approach in interspecific comparisons.

Life-History Evolution and the Genetics of Fitness Components in Drosophila melanogaster

Life-history traits or "fitness components"-such as age and size at maturity, fecundity and fertility, age-specific rates of survival, and life span-are the major phenotypic determinants of Darwinian fitness. Analyzing the evolution and genetics of these phenotypic targets of selection is central to our understanding of adaptation. Due to its simple and rapid life cycle, cosmopolitan distribution, ease of maintenance in the laboratory, well-understood evolutionary genetics, and its versatile genetic toolbox, the "vinegar fly" Drosophila melanogaster is one of the most powerful, experimentally tractable model systems for studying "life-history evolution." Here, I review what has been learned about the evolution and genetics of life-history variation in D. melanogaster by drawing on numerous sources spanning population and quantitative genetics, genomics, experimental evolution, evolutionary ecology, and physiology. This body of work has contributed greatly to our knowledge of several fundamental problems in evolutionary biology, including the amount and maintenance of genetic variation, the evolution of body size, clines and climate adaptation, the evolution of senescence, phenotypic plasticity, the nature of life-history trade-offs, and so forth. While major progress has been made, important facets of these and other questions remain open, and the D. melanogaster system will undoubtedly continue to deliver key insights into central issues of life-history evolution and the genetics of adaptation.

Ageing Throughout History: The Evolution of Human Lifespan

It is not surprising that one of the most complex phenomena in nature is that of ageing. It does not only bear biological interest, but it is also associated with cultural, psychological, social and even philosophical issues. It is therefore to be expected that a great deal of research is being performed in order to study the evolution of ageing and, more specifically, the evolution of human ageing. Historical aspects of this evolution will be discussed. Evidence from a variety of sources shows that the human lifespan is increasing, and may well continue to increase to levels that are difficult to predict. In addition, the most important theories about ageing based on evolutionary principles will be examined. Examples are mutation accumulation, antagonistic pleiotropy and the disposable soma theory. Finally, a section about future evolution of human ageing, based upon newly emerging research, will shed some light and provide speculative-provocative ideas about the future of ageing in humans.

Running out of developmental program and selfish anti-aging: a new hypothesis explaining the aging process in primates

Of the three complementary theories of aging, two (mutation accumulation and antagonistic pleiotropy) were formulated over fifty years ago before the introduction of molecular biology, and the third (disposable soma) is over thirty years old. Despite rigorous research in the past fifty years, none have gained substantial experimental support. Here, I review these theories and introduce a new hypothesis called the selfish anti-aging (SAA). Aging happens because natural selection is indifferent to the organism's life beyond reproduction; however, many mammalian species acquired anti-aging genes, which are providing instructions following completion of developmental, ontogeny, program. Such instructor-genes might be responsible for the elongation of lifespans of primates as a byproduct of parental care program. According to the SAA hypothesis, the animal models used in aging research could be divided into three groups, based on the degree of perceived presence and action of instructor-genes in each group. This new hypothesis is grounded in evolutionary theory and describes the unique primate aging process.

Alleles of a gene differ in pleiotropy, often mediated through currency metabolite production, in E. coli and yeast metabolic simulations

A major obstacle to the mapping of genotype-phenotype relationships is pleiotropy, the tendency of mutations to affect seemingly unrelated traits. Pleiotropy has major implications for evolution, development, ageing, and disease. Except for disease data, pleiotropy is almost exclusively estimated from full gene knockouts. However, most deleterious alleles segregating in natural populations do not fully abolish gene function, and the degree to which a polymorphism reduces protein function may influence the number of traits it affects. Utilizing genome-scale metabolic models for Escherichia coli and Saccharomyces cerevisiae, we show that most fitness-reducing full gene knockouts of metabolic genes in these fast-growing microbes have pleiotropic effects, i.e., they compromise the production of multiple biomass components. Alleles of the same metabolic enzyme-encoding gene with increasingly reduced enzymatic function typically affect an increasing number of biomass components. This increasing pleiotropy is often mediated through effects on the generation of currency metabolites such as ATP or NADPH. We conclude that the physiological effects observed in full gene knockouts of metabolic genes will in most cases not be representative for alleles with only partially reduced enzyme capacity or expression level.

Horizons in the evolution of aging

Between the 1930s and 50s, evolutionary biologists developed a successful theory of why organisms age, firmly rooted in population genetic principles. By the 1980s the evolution of aging had a secure experimental basis. Since the force of selection declines with age, aging evolves due to mutation accumulation or a benefit to fitness early in life. Here we review major insights and challenges that have emerged over the last 35 years: selection does not always necessarily decline with age; higher extrinsic (i.e., environmentally caused) mortality does not always accelerate aging; conserved pathways control aging rate; senescence patterns are more diverse than previously thought; aging is not universal; trade-offs involving lifespan can be 'broken'; aging might be 'druggable'; and human life expectancy continues to rise but compressing late-life morbidity remains a pressing challenge.

Sex-specific effects of inbreeding on reproductive senescence

Inbreeding depression plays a significant role in evolutionary biology and ecology. However, we lack a clear understanding of the fitness consequences of inbreeding depression. Studies often focus on short-term effects of inbreeding in juvenile offspring, whereas inbreeding depression in adult traits and the interplay between inbreeding depression and age are rarely addressed. Inbreeding depression may increase with age and accelerate the decline in reproductive output in ageing individuals (reproductive senescence), which could be subject to sex-specific dynamics. We test this hypothesis with a longitudinal experimental study in a short-lived songbird. Adult inbred and outbred male and female canaries were paired in a 2 × 2 factorial design, and survival and annual reproductive performance were studied for 3 years. We found inbreeding depression in female egg-laying ability, male fertilization success and survival of both sexes. Annual reproductive success of both males and females declined when paired with an inbred partner independent of their own inbreeding status. This shows that inbreeding can have fitness costs in outbred individuals when they mate with an inbred individual. Further, inbred females showed faster reproductive senescence than outbred females, confirming that inbreeding depression and age can interact to affect fitness. By contrast, there was no evidence for an interaction between inbreeding depression and reproductive senescence in male fertilization success. Our findings highlight the importance of considering sex-specific effects and age to determine the full range of fitness consequences of inbreeding and demonstrate that inbreeding depression can accelerate reproductive senescence.

Antagonistic pleiotropy in species with separate sexes, and the maintenance of genetic variation in life-history traits and fitness

Antagonistic pleiotropy (AP)-where alleles of a gene increase some components of fitness at a cost to others-can generate balancing selection, and contribute to the maintenance of genetic variation in fitness traits, such as survival, fecundity, fertility, and mate competition. Previous theory suggests that AP is unlikely to maintain variation unless antagonistic selection is strong, or AP alleles exhibit pronounced differences in genetic dominance between the affected traits. We show that conditions for balancing selection under AP expand under the likely scenario that the strength of selection on each fitness component differs between the sexes. Our model also predicts that the vast majority of balanced polymorphisms have sexually antagonistic effects on total fitness, despite the absence of sexual antagonism for individual fitness components. We conclude that AP polymorphisms are less difficult to maintain than predicted by prior theory, even under our conservative assumption that selection on components of fitness is universally sexually concordant. We discuss implications for the maintenance of genetic variation, and for inferences of sexual antagonism that are based on sex-specific phenotypic selection estimates-many of which are based on single fitness components.

Testing Two Evolutionary Theories of Human Aging with DNA Methylation Data

The evolutionary theories of mutation accumulation (MA) and disposable soma (DS) provide possible explanations for the existence of human aging. To better understand the relative importance of these theories, we devised a test to identify MA- and DS-consistent sites across the genome using familial DNA methylation data. Two key characteristics of DNA methylation allowed us to do so. First, DNA methylation exhibits distinct and widespread changes with age, with numerous age-differentially-methylated sites observed across the genome. Second, many sites show heritable DNA methylation patterns within families. We extended heritability predictions of MA and DS to DNA methylation, predicting that MA-consistent age-differentially-methylated sites will show increasing heritability with age, while DS-consistent sites will show the opposite. Variance components models were used to test for changing heritability of methylation with age at 48,601 age-differentially-methylated sites across the genome in 610 individuals from 176 families. Of these, 102 sites showed significant MA-consistent increases in heritability with age, while 2266 showed significant DS-consistent decreases in heritability. These results suggest that both MA and DS play a role in explaining aging and aging-related changes, and that while the majority of DNA methylation changes observed in aging are consistent with epigenetic drift, targeted changes exist and may mediate effects of aging-related genes.

Evolution of maternal effect senescence

Increased maternal age at reproduction is often associated with decreased offspring performance in numerous species of plants and animals (including humans). Current evolutionary theory considers such maternal effect senescence as part of a unified process of reproductive senescence, which is under identical age-specific selective pressures to fertility. We offer a novel theoretical perspective by combining William Hamilton's evolutionary model for aging with a quantitative genetic model of indirect genetic effects. We demonstrate that fertility and maternal effect senescence are likely to experience different patterns of age-specific selection and thus can evolve to take divergent forms. Applied to neonatal survival, we find that selection for maternal effects is the product of age-specific fertility and Hamilton's age-specific force of selection for fertility. Population genetic models show that senescence for these maternal effects can evolve in the absence of reproductive or actuarial senescence; this implies that maternal effect aging is a fundamentally distinct demographic manifestation of the evolution of aging. However, brief periods of increasingly beneficial maternal effects can evolve when fertility increases with age faster than cumulative survival declines. This is most likely to occur early in life. Our integration of theory provides a general framework with which to model, measure, and compare the evolutionary determinants of the social manifestations of aging. Extension of our maternal effects model to other ecological and social contexts could provide important insights into the drivers of the astonishing diversity of lifespans and aging patterns observed among species.

Quantitative Genetics of the Aging of Reproductive Traits in the Houbara Bustard

Do all traits within an organism age for the same reason? Evolutionary theories of aging share a common assumption: the strength of natural selection declines with age. A corollary is that additive genetic variance should increase with age. However, not all senescent traits display such increases suggesting that other mechanisms may be at play. Using longitudinal data collected from more than 5400 houbara bustards (Chlamydotis undulata) with an exhaustive recorded pedigree, we investigated the genetics of aging in one female reproductive trait (egg production) and three male reproductive traits (courtship display rate, ejaculate size and sperm viability), that display senescence at the phenotypic level. Animal models revealed an increase in additive genetic variance with age for courtship display rate and egg production but an unexpected absence of increased additive genetic variance for ejaculate size and no additive genetic variance for sperm viability. Our results suggest that the mechanisms behind the senescence of some traits are linked with a change in genetic expression, whereas for some other traits, aging may result from the constraints associated with physiological wear and tear on the organism throughout the life of the individual.

Heterosis in age-specific selected populations of a seed beetle: sex differences in longevity and reproductive behavior

We tested mutation accumulation hypothesis for the evolution of senescence using short-lived and long-lived populations of the seed-feeding beetle, Acanthoscelides obtectus (Say), obtained by selection on early- and late-life for many generations. The expected consequence of the mutation accumulation hypothesis is that in short-lived populations, where the force of natural selection is the strongest early in life, the late-life fitness traits should decline due to genetic drift which increases the frequency of mutations with deleterious effects in later adult stages. Since it is unlikely that identical deleterious mutations will increase in several independent populations, hybrid vigor for late-life fitness is expected in offspring obtained in crosses among populations selected for early-life fitness traits. We tested longevity of both sexes, female fecundity and male reproductive behavior for hybrid vigor by comparing hybrid and nonhybrid short-lived populations. Hybrid vigor was confirmed for male virility, mating speed and copulation duration, and longevity of both sexes at late ages. In contrast to males, the results on female fecundity in short-lived populations did not support mutation accumulation as a genetic mechanism for the evolution of this trait. Contrary to the prediction of this hypothesis, male mating ability indices and female fecundity in long-lived populations exhibited hybrid vigor at all assayed age classes. We demonstrate that nonhybrid long-lived populations diverged randomly regarding female and male reproductive fitness, indicating that sexually antagonistic selection, when accompanied with genetic drift for female fecundity and male virility, might be responsible for overriding natural selection in the independently evolving long-lived populations.

Heredity and self-organization: partners in the generation and evolution of phenotypes

In this review we examine the role of self-organization in the context of the evolution of morphogenesis. We provide examples to show that self-organized behavior is ubiquitous, and suggest it is a mechanism that can permit high levels of biodiversity without the invention of ever-increasing numbers of genes. We also examine the implications of self-organization for understanding the "internal descriptions" of organisms and the concept of a genotype-phenotype map.

Reduced lifespan and increased ageing driven by genetic drift in small populations

Explaining the strong variation in lifespan among organisms remains a major challenge in evolutionary biology. Whereas previous work has concentrated mainly on differences in selection regimes and selection pressures, we hypothesize that differences in genetic drift may explain some of this variation. We develop a model to formalize this idea and show that the strong positive relationship between lifespan and genetic diversity predicted by this model indeed exists among populations of Daphnia magna, and that ageing is accelerated in small populations. Additional results suggest that this is due to increased drift in small populations rather than adaptation to environments favoring faster life histories. First, the correlation between genetic diversity and lifespan remains significant after statistical correction for potential environmental covariates. Second, no trade-offs are observed; rather, all investigated traits show clear signs of increased genetic load in the small populations. Third, hybrid vigor with respect to lifespan is observed in crosses between small but not between large populations. Together, these results suggest that the evolution of lifespan and ageing can be strongly affected by genetic drift, especially in small populations, and that variation in lifespan and ageing may often be nonadaptive, due to a strong contribution from mutation accumulation.

Genome-wide analysis in Drosophila reveals age-specific effects of SNPs on fitness traits

Most organisms exhibit senescence; a decline in physiological function with age. In nature, rates of senescence vary extensively among individuals and this variation has a significant genetic component; however, we know little about the genes underlying senescence. Here we show the first evidence that individual alleles influence fecundity in an age-specific manner and so the genetic basis of natural variation in fecundity changes dramatically with age. We complete a genome-wide association to identify single-nucleotide polymorphisms (SNPs) affecting lifespan and age-specific fecundity using the Drosophila melanogaster Genetic Reference Panel. We identify 1,031 SNPs affecting fecundity and 52 influencing lifespan. Only one SNP is associated with both early- and late-age fecundity. The age-specific effect of candidate genes on fecundity is validated using RNA interference. In addition, there is a dramatic increase in the number of SNPs influencing fecundity with age. This result provides support for the mutation accumulation theory of aging.

Mutation accumulation may only be a minor force in shaping life-history traits, even when reproduction is sexual

In a previous theoretical study we investigated whether adaptive or non-adaptive processes are more important in the evolution of senescence. We built a model that combined both processes and found that mutation accumulation is important only at those ages where mortality has a negligible impact on fitness. This model, however, was limited to haploid organisms. Here we extend our model by introducing diploidy and sexual reproduction. We assume that only recessive (mutated) homozygotes experience detrimental effects. Our results corroborate our previous conclusions, confirming that life histories are largely determined by adaptive processes. We also found that the equilibrium frequencies of mutated alleles are at higher values than in haploid model, because mutations in heterozygotes are hidden for directional selection. Nevertheless, the equilibrium frequencies of recessive homozygotes that make mutations visible to selection are very similar to the equilibrium frequencies of these alleles in our haploid model. Diploidy and sexual reproduction with recombination slows down approaching selection-mutation balance.

Is cellular senescence an example of antagonistic pleiotropy?

It is generally accepted that the permanent arrest of cell division known as cellular senescence contributes to aging by an antagonistic pleiotropy mechanism: cellular senescence would act beneficially early in life by suppressing cancer, but detrimentally later on by causing frailty and, paradoxically, cancer. In this review, we show that there is room to rethink this common view. We propose a critical appraisal of the arguments commonly brought in support of it, and we qualitatively analyse published results that are of relevance to understand whether or not cellular senescence-associated genes really act in an antagonistic-pleiotropic manner in humans.

Mutation accumulation may be a minor force in shaping life history traits

Is senescence the adaptive result of tradeoffs between younger and older ages or the nonadaptive burden of deleterious mutations that act at older ages? To shed new light on this unresolved question we combine adaptive and nonadaptive processes in a single model. Our model uses Penna's bit-strings to capture different age-specific mutational patterns. Each pattern represents a genotype and for each genotype we find the life history strategy that maximizes fitness. Genotypes compete with each other and are subject to selection and to new mutations over generations until equilibrium in gene-frequencies is reached. The mutation-selection equilibrium provides information about mutational load and the differential effects of mutations on a life history trait--the optimal age at maturity. We find that mutations accumulate only at ages with negligible impact on fitness and that mutation accumulation has very little effect on the optimal age at maturity. These results suggest that life histories are largely determined by adaptive processes. The non-adaptive process of mutation accumulation seems to be unimportant at evolutionarily relevant ages.

Inbreeding depression in red deer calves

BACKGROUND

Understanding the fitness consequences of inbreeding is of major importance for evolutionary and conservation biology. However, there are few studies using pedigree-based estimates of inbreeding or investigating the influence of environment and age variation on inbreeding depression in natural populations. Here we investigated the consequences of variation in inbreeding coefficient for three juvenile traits, birth date, birth weight and first year survival, in a wild population of red deer, considering both calf and mother's inbreeding coefficient. We also tested whether inbreeding depression varied with environmental conditions and maternal age.

RESULTS

We detected non-zero inbreeding coefficients for 22% of individuals with both parents and at least one grandparent known (increasing to 42% if the dataset was restricted to those with four known grandparents). Inbreeding depression was evident for birth weight and first year survival but not for birth date: the first year survival of offspring with an inbreeding coefficient of 0.25 was reduced by 77% compared to offspring with an inbreeding coefficient of zero. However, it was independent of measures of environmental variation and maternal age. The effect of inbreeding on birth weight appeared to be driven by highly inbred individuals (F = 0.25). On the other hand first year survival showed strong inbreeding depression that was not solely driven by individuals with the highest inbreeding coefficients, corresponding to an estimate of 4.35 lethal equivalents.

CONCLUSIONS

These results represent a rare demonstration of inbreeding depression using pedigree-based estimates in a wild mammal population and highlight the potential strength of effects on key components of fitness.

Before senescence: the evolutionary demography of ontogenesis

The age-specific mortality curve for many species, including humans, is U-shaped: mortality declines with age in the developing cohort (ontogenescence) before increasing with age (senescence). The field of evolutionary demography has long focused on understanding the evolution of senescence while largely failing to address the evolution of ontogenescence. The current review is the first to gather the few available hypotheses addressing the evolution of ontogenescence, examine the basis and assumptions of each and ask what the phylogenetic extent of ontogenescence may be. Ontogenescence is among the most widespread of life-history traits, occurring in every population for which I have found sufficiently detailed data, in major groups throughout the eukaryotes, across many causes of death and many life-history types. Hypotheses seeking to explain ontogenescence include those based on kin selection, the acquisition of robustness, heterogeneous frailties and life-history optimization. I propose a further hypothesis, arguing that mortality drops with age because most transitions that could trigger the risks caused by genetic and developmental malfunctions are concentrated in early life. Of these hypotheses, only those that frame ontogenescence as an evolutionary by-product rather than an adaptation can explain the tremendous diversity of organisms and environments in which it occurs.

One hundred years of pleiotropy: a retrospective

Pleiotropy is defined as the phenomenon in which a single locus affects two or more distinct phenotypic traits. The term was formally introduced into the literature by the German geneticist Ludwig Plate in 1910, 100 years ago. Pleiotropy has had an important influence on the fields of physiological and medical genetics as well as on evolutionary biology. Different approaches to the study of pleiotropy have led to incongruence in the way that it is perceived and discussed among researchers in these fields. Furthermore, our understanding of the term has changed quite a bit since 1910, particularly in light of modern molecular data. This review traces the history of the term "pleiotropy" and reevaluates its current place in the field of genetics.

Evolutionary demography and quantitative genetics: age-specific survival as a threshold trait

Researchers must understand how mutations affect survival at various ages to understand how ageing evolves. Many models linking mutation to age-specific survival have been proposed but there is little evidence to indicate which model is most appropriate. This is a serious problem because the predicted evolutionary endpoints of ageing depend upon the details of the specific model. We apply an explicitly quantitative genetic perspective to the problem. To determine the inheritance of dichotomous traits (such as survival), quantitative genetics has long employed a threshold model. Beginning from first principles, we show how this is the most defensible mutational model for age-specific survival and how this, relative to the standard model, predicts delayed senescence and mortality deceleration at late age. These are commonly observed patterns of ageing that heretofore have required more complicated survival models. We also show how this model can be developed further to unify quantitative genetics and evolutionary demography into a more complete conceptual framework for understanding the evolution of ageing.

Mutation and the evolution of ageing: from biometrics to system genetics

A notable success for evolutionary genetics during the past century was to generate a coherent, quantitative explanation for an apparent evolutionary paradox: the tendency for multicellular organisms to show declining fitness with age (senescence, often referred to simply as 'ageing'). This general theory is now widely accepted and explains most of the features of senescence that are observed in natural and laboratory populations, but specific instantiations of that theory have been more controversial. To date, most of the empirical tests of these models have relied on data generated from biometric experiments. Modern population genetics and genomics provide new, and probably more powerful, ways to test ideas that are still controversial more than half a century after the original theory was developed. System-genetic experiments have the potential to address both evolutionary and mechanistic questions about ageing by identifying causal loci and the genetic networks with which they interact. Both the biometrical approaches and the newer approaches are reviewed here, with an emphasis on the challenges and limitations that each method faces.