An official website of the United States government
Changes in DNA methylation with age are observed across the tree of life. The stereotypical nature of these changes can be modeled to produce epigenetic clocks capable of predicting chronological age with unprecedented accuracy. Despite the predictive ability of epigenetic clocks and their utility as biomarkers in clinical applications, the underlying processes that produce clock signals are not fully resolved, which limits their interpretability. Here, we develop a computational approach to spatially resolve the within read variability or “disorder” in DNA methylation patterns and test if age-associated changes in DNA methylation disorder underlie signals comprising epigenetic clocks. We find that epigenetic clock loci are enriched in regions that both accumulate and lose disorder with age, suggesting a link between DNA methylation disorder and epigenetic clocks. We then develop epigenetic clocks that are based on regional disorder of DNA methylation patterns and compare their performance to other epigenetic clocks by investigating the influences of development, lifespan interventions, and cellular dedifferentiation. We identify common responses as well as critical differences between canonical epigenetic clocks and those based on regional disorder, demonstrating a fundamental decoupling of epigenetic aging processes. Collectively, we identify key linkages between epigenetic disorder and epigenetic clocks and demonstrate the multifaceted nature of epigenetic aging in which stochastic processes occurring at non-random loci produce predictable outcomes.
more »
« less
The rate of epigenetic drift scales with maximum lifespan across mammals
Abstract Epigenetic drift or “disorder” increases across the mouse lifespan and is suggested to underlie epigenetic clock signals. While the role of epigenetic drift in determining maximum lifespan across species has been debated, robust tests of this hypothesis are lacking. Here, we test if epigenetic disorder at various levels of genomic resolution explains maximum lifespan across four mammal species. We show that epigenetic disorder increases with age in all species and at all levels of genomic resolution tested. The rate of disorder accumulation occurs faster in shorter lived species and corresponds to species adjusted maximum lifespan. While the density of cytosine-phosphate-guanine dinucleotides (“CpGs”) is negatively associated with the rate of age-associated disorder accumulation, it does not fully explain differences across species. Our findings support the hypothesis that the rate of epigenetic drift explains maximum lifespan and provide partial support for the hypothesis that CpG density buffers against epigenetic drift.
more »
« less
- Award ID(s):
- 2026210
- PAR ID:
- 10506566
- Publisher / Repository:
- Nature Communications
- Date Published:
- Journal Name:
- Nature Communications
- Volume:
- 14
- Issue:
- 1
- ISSN:
- 2041-1723
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
null (Ed.)Abstract Is it possible to slow the rate of ageing, or do biological constraints limit its plasticity? We test the ‘invariant rate of ageing’ hypothesis, which posits that the rate of ageing is relatively fixed within species, with a collection of 39 human and nonhuman primate datasets across seven genera. We first recapitulate, in nonhuman primates, the highly regular relationship between life expectancy and lifespan equality seen in humans. We next demonstrate that variation in the rate of ageing within genera is orders of magnitude smaller than variation in pre-adult and age-independent mortality. Finally, we demonstrate that changes in the rate of ageing, but not other mortality parameters, produce striking, species-atypical changes in mortality patterns. Our results support the invariant rate of ageing hypothesis, implying biological constraints on how much the human rate of ageing can be slowed.more » « less
-
Heino, Mikko (Ed.)Abstract: Chance pervades life. In turn, life histories are described by probabilities (e.g. survival and breeding) and averages across individuals (e.g. mean growth rate and age at maturity). In this study, we explored patterns of luck in lifetime outcomes by analysing structured population models for a wide array of plant and animal species. We calculated four response variables: variance and skewness in both lifespan and lifetime reproductive output (LRO), and partitioned them into contributions from different forms of luck. We examined relationships among response variables and a variety of life history traits. We found that variance in lifespan and variance in LRO were positively correlated across taxa, but that variance and skewness were negatively correlated for both lifespan and LRO. The most important life history trait was longevity, which shaped variance and skew in LRO through its effects on variance in lifespan. We found that luck in survival, growth, and fecundity all contributed to variance in LRO, but skew in LRO was overwhelmingly due to survival luck. Rapidly growing populations have larger variances in LRO and lifespan than shrinking populations. Our results indicate that luck‐induced genetic drift may be most severe in recovering populations of species with long mature lifespan and high iteroparity.more » « less
-
Abstract Data from nearly 1000 species reveal the upper bound to rates of biomass production achievable by natural selection across the Tree of Life. For heterotrophs, maximum growth rates scale positively with organism size in bacteria but negatively in eukaryotes, whereas for phototrophs, the scaling is negligible for cyanobacteria and weakly negative for eukaryotes. These results have significant implications for understanding the bioenergetic consequences of the transition from prokaryotes to eukaryotes, and of the expansion of some groups of the latter into multicellularity. The magnitudes of the scaling coefficients for eukaryotes are significantly lower than expected under any proposed physical-constraint model. Supported by genomic, bioenergetic, and population-genetic data and theory, an alternative hypothesis for the observed negative scaling in eukaryotes postulates that growth-diminishing mutations with small effects passively accumulate with increasing organism size as a consequence of associated increases in the power of random genetic drift. In contrast, conditional on the structural and functional features of ribosomes, natural selection has been able to promote bacteria with the fastest possible growth rates, implying minimal conflicts with both bioenergetic constraints and random genetic drift. If this extension of the drift-barrier hypothesis is correct, the interpretations of comparative studies of biological traits that have traditionally ignored differences in population-genetic environments will require revisiting.more » « less
-
Abstract AimThe accumulation of species through time has been proposed to have a hump‐shaped relationship on volcanic islands (highest species richness during intermediate stages of an island's lifespan). Change in topographic complexity (TC) of islands over time is assumed to follow the same relationship. However, TC can be measured in different ways and may not have the same impact across taxonomic groups. Here, we quantify TC across the Galápagos Islands and test the assumption that TC follows a predictable trajectory with island age. Subsequently, we ask whether including TC improves statistical models seeking to explain variation in species richness across islands. LocationGalápagos Archipelago, Ecuador. TaxonNative and endemic terrestrial animals and plants. MethodsFor each island, we generated eight TC indices from a 30‐m resolution digital elevation model. We tested for a relationship between each index and island age, and whether it significantly contributes to observed variation in species richness, using 11 different models for 12 taxonomic groups across the Galápagos Islands. ResultsFour TC indices were significantly negatively correlated with either island age or ontogenetic age and only one index followed the hump‐shaped relationship with age. No index consistently contributed to the variation in species richness for all taxonomic groups. However, for all 12 taxonomic groups, incorporating at least one TC index in modelling species richness improved one or more models. The most common TC index improving models was standard deviation of slope, although each index improved at least five models across all taxa. Different factors predicted taxon‐specific richness, and habitat diversity was significant for all taxa. Main conclusionsTopographic complexity is an important component influencing species richness, but its impact likely differs among taxonomic groups and different scales. Therefore, future studies should incorporate broad, multi‐dimensional measures of TC to understand the biological importance of TC.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1038/s41467-023-43417-6
