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opencc-by-4.0Mar 2020View details →

Quantitative translation of dog-to-human aging by conserved remodeling of the DNA methylome

This repository contains processed data files, custom python scripts and jupyter notebooks containing analyses accompanying the manuscript, Quantitative translation of dog-to-human aging by conserved remodeling of the DNA methylome.

opencc-by-4.0Mar 2020View details →

Benchmark maps of 33 years of secondary forest age for Brazil

Title: Benchmark maps of 33 years of secondary forest age for Brazil Contact: Celso H. L. Silva Junior (celsohlsj@gmail.com)   Data: Increment (Product 1), Extent (Product 2), Loss (Product 3), and Age (Product 4) of Brazilian Secondary Vegetation Coverage: Brazil land Period: 1986 to 2018 (1987 to 2018 for secondary forest loss) Spatial resolution: 30-meters Temporal resolution: Annual Coordinate reference system: Geographic Coordinate System with Datum WGS84 File format: 131 zip files per year (being 33 for increment, 33 for extent, 33 for age and 32 for loss). Each zip file containing eight tiles in compressed TIFF format. Code: <a href="https://github.com/celsohlsj/gee_brazil_sv">https://github.com/celsohlsj/gee_brazil_sv</a> Dataset usage: It is free to use, but if you use this dataset in your work, please make sure to cite the repository and our paper properly. We also welcome users to invite us for collaboration. For the use of this dataset, please cite: Silva Junior, C.H.L., Heinrich, V.H.A., Freire, A.T.G., Broggio, I.S., Rosan, T.M., Doblas, J., Anderson, L.O., Rousseau, G.X., Shimabukuro, Y.E., Silva, C.A., House, J.I., Aragão, L.E.O.C. Benchmark maps of 33 years of secondary forest age for Brazil. Scientific Data (2020). <a href="https://doi.org/10.1038/s41597-020-00600-4">https://doi.org/10.1038/s41597-020-00600-4</a>

Data from: Age influences the thermal suitability of Plasmodium falciparum transmission in the Asian malaria vector Anopheles stephensi

Models predicting disease transmission are vital tools for long-term planning of malaria reduction efforts, particularly for mitigating impacts of climate change. We compared temperature-dependent malaria transmission models when mosquito life history traits were estimated from a truncated portion of the lifespan (a common practice) to traits measured across the full lifespan. We conducted an experiment on adult female Anopheles stephensi, the Asian urban malaria mosquito, to generate daily per capita values for mortality, egg production, and biting rate at six constant temperatures. Both temperature and age significantly affected trait values. Further, we found quantitative and qualitative differences between temperature-trait relationships estimated from truncated data versus observed lifetime values. Incorporating these temperature-trait relationships into an expression governing the thermal suitability of transmission, relative R0(T), resulted in minor differences in the breadth of suitable temperatures for Plasmodium falciparum transmission between the two models constructed from only An. stephensi trait data. However, we found a substantial increase in thermal niche breadth compared to a previously published model consisting of trait data from multiple Anopheles mosquito species. Overall, this work highlights the importance of considering how mosquito trait values vary with mosquito age and mosquito species when generating temperature-based suitability predictions of transmission.

Data from: Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages

Ectomycorrhizal fungi are key players in terrestrial ecosystems yet their mating systems and population dynamics remain poorly understood. We investigated the fine-scale relatedness structure and genetic diversity of Boletus edulis, one of the world's most commercially important wild mushrooms. Microsatellite genotyping of fruiting bodies from 14 different sites around Bielefeld in Germany revealed little in the way of population structure over a geographic scale of several kilometers. However, on a more local scale we found evidence for elevated relatedness as well as inbreeding. We also observed a significant negative association between the genetic diversity of fruit and the age of the trees under which they were sampled. Taken together, our results suggest that as genets mature, they compete and potentially create conditions under which further spores struggle to become established. By implication, even though this species is widely picked, propagules remain common enough to create strong competition when new habitats become available.

opencc-zeroDec 2018View details →

Data from: One and two year visual outcomes from the Moorfields age-related macular degeneration database: a retrospective cohort study and an open science resource

Objectives: To analyse treatment outcomes and share clinical data from a large, single-center, well-curated database (8174 eyes / 6664 patients with 120,756 single entries) of patients with neovascular age related macular degeneration (AMD) treated with anti-vascular endothelial growth factor (VEGF). By making our depersonalised raw data openly available, we aim to stimulate further research in AMD, as well as setting a precedent for future work in this area. Setting: Retrospective, comparative, non-randomised electronic medical record (EMR) database cohort study of the UK Moorfields AMD database with data extracted between 2008 and 2018. Participants: Including one eye per patient, 3357 eyes/patients (61% female). Extraction criteria were ≥ 1 ranibizumab or aflibercept injection, entry of "AMD" in the diagnosis field of the EMR, and a minimum of one year of follow-up. Exclusion criteria were unknown date of first injection and treatment outside of routine clinical care at Moorfields before the first recorded injection in the database. Main outcome measures: Primary outcome measure was change in VA at one and two years from baseline as measured in Early Treatment Diabetic Retinopathy Study (ETDRS) letters. Secondary outcomes were the number of injections and predictive factors for VA gain. Results: Mean VA gain at one-year and two years were +5.5 (95%CI:5.0,6.0) and +4.9 (95%CI:4.2,5.6) letters respectively. Fifty-four percent of eyes gained ≥5 letters at two years, 63% had stable VA (±≤14 letters), forty-four percent of eyes maintained good VA (≥70 letters). Patients received a mean of 7.7 (95%CI:7.6,7.8) injections during year one and 13.0 (95%CI:12.8,13.2) injections over two years. Younger age, lower baseline VA, and more injections were associated with higher VA gain at two years. Conclusion: This study benchmarks high quality EMR study results of real life AMD treatment and promotes open science in clinical AMD research by making the underlying data publicly available.

Data from: Telomere attrition with age in a wild amphibian population

Telomere shortening with age has been documented in many organisms, but few studies have reported telomere length measurements in amphibians, and no information is available for growth after metamorphosis, nor in wild populations. We provide both cross-sectional and longitudinal evidence of net telomere attrition with age in a wild amphibian population of natterjack toads (Epidalea calamita). Based on age-estimation by skeletochronology and qPCR telomere length measurements in the framework of an individual-based monitoring programme, we confirmed telomere attrition in recaptured males. Our results support that toads experience telomere attrition throughout their ontogeny, and that most attrition occurs during the first 1–2 years.We did not find associations between telomere length and inbreeding or body condition. Our results on telomere length dynamics under natural conditions confirm telomere shortening with age in amphibians and provide quantification of wide telomere length variation within and among age-classes in a wild breeding population.

opencc-by-4.0Jul 2020View details →

Surveyed terrace profiles and terrace radiocarbon ages, western Jumgal basin, Tien Shan, Kyrgyz Republic

This archive contains survey data and radiocarbon ages from deformed terraces in the western Jumgal basin, Kyrgyz Republic. These data support analysis by Coddington and Burgette (2020) to be published in Tectonics: “Fold kinematics and fault slip rates from progressively deformed terraces: Implications for structural evolution of basins in the Kyrgyz Tien Shan”

opencc-zeroAug 2020View details →

Data from: Age-dependent changes in infidelity in Seychelles warblers

Extra-pair paternity (EPP) is often linked to male age in socially monogamous vertebrates, i.e. older males are more likely to gain EPP and less likely to be cuckolded. However, whether this occurs because males improve at gaining paternity as they grow older, or because 'higher quality' males that live longer are preferred by females, has rarely been tested, despite being central to our understanding of the evolutionary drivers of female infidelity. Moreover, how extra-pair reproduction changes with age within females has received even less attention. Using 18 years of longitudinal data from an individually-marked population of Seychelles warblers (Acrocephalus sechellensis), we found considerable within-individual changes in extra-pair reproduction in both sexes, i.e. an early-life increase and a late-life decline. Furthermore, males were cuckolded less as they aged. Our results indicate that in this species age-related patterns of extra-pair reproduction are determined by within-individual changes with age, rather than differences among individuals in longevity. These results challenge the hypothesis – based on longevity reflecting intrinsic quality – that the association between male age and EPP is due to females seeking high quality paternal genes for offspring. Importantly, EPP accounted for up to half of male reproductive success, emphasising the male fitness benefits of this reproductive strategy. Finally, the occurrence of post-peak declines in extra-pair reproduction provides explicit evidence of senescence in infidelity in both males and females.

opencc-by-4.0Aug 2020View details →

Online supplement for "T cell costimulation blockade blunts age-related heart failure"

ONLINE SUPPLEMENT FOR: Research Letter: T cell costimulation blockade blunts age-related heart failure

opencc-zeroJan 2020View details →

Data for: Evaluating the impact of physical frailty during ageing in wild chimpanzees (Pan troglodytes schweinfurthii)

While declining physical performance is an expected consequence of aging, human clinical research has placed increasing emphasis on physical frailty as a predictor of death and disability in the elderly. We examined non-invasive measures approximating frailty in a richly-sampled longitudinal dataset on wild chimpanzees. Using urinary creatinine to assess lean body mass, we demonstrated moderate but significant declines in physical condition with age in both sexes. While older chimpanzees spent less of their day in the trees and feeding, they did not alter activity budgets with respect to travel or resting. There was little evidence that declining lean body mass had negative consequences independent of age. Old chimpanzees with poor lean body mass rested more often but did not otherwise differ in activity. Males, but not females, in poor condition were more likely to exhibit respiratory illness. Poor muscle mass was associated acutely with death in males, but it did not predict future mortality in either sex. While there may be some reasons to suspect biological differences in the susceptibility to frailty in chimpanzees versus humans, our data are consistent with recent reports from humans that lean, physically active individuals can successfully combat frailty.

opencc-zeroAug 2020View details →

An age-dependent ovulatory strategy explains the evolution of dizygotic twinning in humans

Dizygotic twinning, the simultaneous birth of siblings when multiple ova are released, is an evolutionary paradox. Twin bearing mothers often have elevated fitness1-5; but despite twinning being heritable6, twin births only occur at low frequencies in human populations7. We resolve this paradox by showing that twinning and non-twinning are not competing strategies, instead dizygotic twinning is the outcome of an adaptive conditional ovulatory strategy of switching from single to double ovulation with increasing age. This conditional strategy when coupled with the well-known decline in fertility as women age, maximizes reproductive success and explains the increase and subsequent decrease in twinning rate with maternal age that is observed across human populations8-10. We show that the most successful ovulatory strategy would be to always double ovulate as an insurance against early fetal loss, but to never bear twins. This finding supports the hypothesis that twinning is a byproduct of selection for double ovulation rather than twinning.

opencc-by-4.0Aug 2020View details →

The Ubiquitin Ligase WWP1 Contributes to Shifts in Matrix Proteolytic Profiles and a Myocardial Aging Phenotype with Diastolic Heart Failure

Aims. Ubiquitylation is a key event that regulates protein turnover, and induction of the ubiquitin ligase E3 WWP1 has been associated with age. Left ventricular hypertrophy (LVH) commonly occurs as a function of age and can cause heart failure with a preserved ejection fraction (EF; HFpEF). We hypothesized that overexpression (O/E) of WWP1 in the heart would cause LVH as well as functional and structural changes consistent with the aging HFpEF phenotype. Methods and Results. Global WWP1 O/E was achieved in mice (n=11) and echocardiography (40 MHz) performed to measure LV mass, EF, Doppler velocities (early-E, late/atrial-A), myocardial relaxation (E’), and isovolumetric relaxation time (IVRT) at 4, 6, and 8 weeks. Age matched wild type animals (n=15) were included as referent controls. LV EF was identical (60+1% vs 60+1%, p>0.90) with no difference in LV mass (67+3 vs 75+5, p>0.25) at 4 weeks. However, at 8 weeks of age, LV mass increased by over two-fold, E/A fell (impaired passive filling), and E/E’ was lower and IVRT prolonged (impaired LV relaxation) - all p<0.05. Collagen percent area increased by over two-fold and fibrillar collagen expression (rtPCR) by over 1.5 fold (p<0.05) with WWP1 O/E. WWP1 with an anti-WWP1 antibody could be identified in isolated cardiac fibroblasts with WWP1 increased by over two-fold in O/E fibroblasts (p<0.05). Conclusion. Inducing WWP1 expression caused LVH, preserved systolic function, but impaired diastolic dysfunction, consistent with the HFpEF phenotype. Targeting the WWP1 pathway may be a novel therapeutic target for this intractable form of HF associated with aging.

opencc-zeroAug 2020View details →

Data from: Evaluating tooth strontium and barium as indicators of weaning age in Pacific walruses

A dataset of calcium-normalized 88Sr and 137Ba concentrations from laser ablation transects across the cementum layer of 107 (female: n = 84, male: n = 23) Pacific walrus (Odobenus rosmarus divergens) teeth. Dataset includes spreadsheets containing elapsed time of laser ablation transect in seconds (ElapsedTime_s; laser transect speed = 5μm/s), calcium-normalized strontium concentrations (Sr_ppm_m88; values below limit of detection replaced with 1/2*limit of detection, see methods), and calcium-normalized barium concentrations (Ba_ppm_m137; values below limit of detection replaced with 0.5*limit of detection). Photos (in .tif format) of tooth cementum used to estimate the positions of cementum growth layer groups are included for each animal. For teeth where more than one laser ablation scar is visible in the photo, an arrow is included to indicate the laser ablation scar that corresponds with the included trace element data. Finally, a Word document containing metadata (Catalog Number/ID, Sex, Median Age Est., Coll. Year, Est. Birth Year), weaning age estimates produced by both a visual and mathematical method (Sr Vis. Est., Sr Math. Est., Ba Vis. Est., Ba Math. Est.), and a descriptive grouping of the patterns of accumulation of Sr and Ba (Sr Pat., Ba Pat.) are included. See methods and accompanying paper in Methods in Ecology and Evolution for more details.

opencc-zeroSep 2020View details →

Data from: Age and sex prevalence estimate of Joubert Syndrome in Italy

Objective: To estimate the prevalence of Joubert syndrome (JS) in Italy applying standards of descriptive epidemiology, and to provide a molecular characterization of the described patients cohort. Methods: We enrolled all patients with a neuroradiologically confirmed diagnosis of JS and resident in Italy in 2018, and calculated age and sex prevalence, assuming a Poisson distribution. We also investigated the correlation between proband chronological age and age at diagnosis, and performed Next-Generation Sequencing (NGS) analysis on probands' DNA when available. Results: We identified 284 JS patients: the overall, female- and male-specific population-based prevalence rates were 0.47 (95% CI 0.41-0.53), 0.41 (95% CI 0.32-0.49) and 0.53 (95% CI 0.45-0.61) per 100,000 population, respectively. When considering only patients in the age range from 0 to 19 years, the corresponding population-based prevalence rates rose to 1.7 (95% CI 1.49-1.97), 1.62 (95% CI 1.31-1.99) and 1.80 (95% CI 1.49-2.18) per 100,000 population. NGS analysis allowed identifying the genetic cause in 131 out of 219 screened probands. Age at diagnosis was available for 223 probands, with a mean of 6.67 ± 8.10 years, and showed a statistically significant linear relationship with chronological age (r2=0.91; p<0.001). Conclusions: We estimated for the first time the age and sex prevalence of JS in Italy, and investigated their genetic profile. The obtained population-based prevalence rate was approximately 10 times higher than that available in literature for children population.

opencc-zeroSep 2021View details →

Maternal and paternal age effects on male antler flies: a field experiment

In many species, parental age at reproduction can influence offspring performance and lifespan, but the direction of these effects and the traits affected vary among studies. Data on parental age effects are still scarce in non-captive populations, especially insects, despite species such as fruit flies being models in laboratory-based aging research. We performed a biologically relevant experimental manipulation of maternal and paternal age at reproduction of antler flies (Protopiophila litigata) in the laboratory and tracked the adult lifespan and reproductive success of their male offspring released in the wild. Increased paternal, but not maternal, age somewhat increased sons' adult lifespan, while parental ages did not influence sons' mating rate or reproductive senescence. Our results indicate that while parental age effects do exist in an insect in the field, they may be beneficial in such a short-lived animal, in contrast to results from most wild vertebrates and laboratory invertebrates.

opencc-zeroSep 2020View details →

R code for Snyder, Ellner, and Hooker, "Time and chance: using age partitioning to understand how luck drives variation in reproductive success"

Over the course of individual lifetimes, luck usually explains a large fraction of the between- individual variation in lifespan or lifetime reproductive output (LRO) within a population, while variation in individual traits or "quality" explains much less. To understand how, where in the life cycle, and through which demographic processes luck trumps trait variation, we show how to partition by age the contributions of luck and trait variation to LRO variance, and how to quantify three distinct components of luck. We apply these tools to several empirical case studies. We find that luck swamps effects of trait variation at all ages, primarily due to randomness in individual state dynamics ("state trajectory luck"). Luck early in life is most important. Very early state trajectory luck generally determines whether or not an individual ever breeds, likely by ensuring that they are not dead or doomed quickly. Less early luck drives variation in success among those breeding at least once. Consequently, the importance of luck often has a sharp peak early in life, or two peaks. We suggest that ages/stages where the importance luck peaks are potential targets for interventions to benefit a population of concern, different from those identified by eigenvalue elasticity analysis.

opencc-by-4.0Sep 2020View details →

Silvicultural and economic dataset for even-aged and coppice-with-standards managements in France.

Data set from DEFIFORBOIS project "Development and sustainability of the forest-wood sector in the Centre region", PSDR 4 project Centre-Val de Loire Region, France. This study has been carried out also with financial support from the French National Research Agency (ANR) in the frame of the Investments for the future Programme, within the Cluster of Excellence COTE (ANR-10-LABX-45) through the Project LUCAS.

Data from: Changes in age-structure over four decades were a key determinant of population growth rate in a long-lived mammal

1. A changing environment directly influences birth and mortality rates, and thus population growth rates. However, population growth rates in the short-term are also influenced by population age-structure. Despite its importance, the contribution of age-structure to population growth rates has rarely been explored empirically in wildlife populations with long-term demographic data. 2. Here, we assessed how changes in age-structure influenced short-term population dynamics in a semi-captive population of Asian elephants (Elephas maximus). 3. We addressed this question using a demographic dataset of female Asian elephants from timber camps in Myanmar spanning 45 years (1970-2014). First, we explored temporal variation in age-structure. Then, using annual matrix population models, we used a retrospective approach to assess the contributions of age-structure and vital rates to short-term population growth rates with respect to the average environment. 4. Age-structure was highly variable over the study period, with large proportions of juveniles in the years 1970 and 1985, and made a substantial contribution to annual population growth rate deviations. High adult birth rates between 1970-1980 would have resulted in large positive population growth rates, but these were prevented by a low proportion of reproductive-aged females. 5. We highlight that an understanding of both age-specific vital rates and age-structure is needed to assess short-term population dynamics. Furthermore, this example from a human-managed system suggests that the importance of age-structure may be accentuated in populations experiencing human disturbance where age-structure is unstable, such as those in captivity or for endangered species. Ultimately, changes to the environment drive population dynamics by influencing birth and mortality rates, but understanding demographic structure is crucial for assessing population growth.

opencc-zeroOct 2020View details →

Data from: Social selectivity in aging wild chimpanzees

Humans prioritize close, positive relationships during aging, and socioemotional selectivity theory proposes that this shift causally depend on capacities for thinking about personal future time horizons. To examine this theory, we tested for key elements of human social aging in longitudinal data on wild chimpanzees. Aging male chimpanzees have more mutual friendships characterized by high, equitable investment, whereas younger males have more one-sided relationships. Older males are more likely to be alone, but they also socialize more with important social partners. Further, males show a relative shift from more agonistic interactions to more positive, affiliative interactions over their life span. Our findings indicate that social selectivity can emerge in the absence of complex future-oriented cognition, and they provide an evolutionary context for patterns of social aging in humans.