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118 results for “Age estimation”
Data from: How to date a crocodile – estimation of neosuchian clade ages and a comparison of four time-scaling methods
<p>Clade ages within the crocodylomorph clade Neosuchia have long been debated. Molecular and morphological studies have yielded remarkably divergent results. Despite recent advances, there has been no comprehensive relative comparison of the major time calibration methods available to estimate clade ages based on morphological data. We used four methods (cal3, Extended Hedman [EH], smoothed Ghost-Lineage-Analysis [sGLA] and the Fossilised Birth-Death model [FBD]) to date clade ages derived from a published crocodylomorph supertree and a new neosuchian phylogeny. All time-scaling methods applied here agree on the origination of Neosuchia during the Late Triassic/Early Jurassic, and the presence of the major extant eusuchian groups (Crocodyloidea, Gavialoidea, Alligatoroidea, and Caimaininae) by the end of the Late Cretaceous. The number of distinct lineages present before the K/Pg boundary is less certain, with support for two competing scenarios in which Crocodylinae, Tomistominae and Diplocynodontinae either: 1) diverged from other eusuchian lineages before the K/Pg boundary; or 2) evolved during a 'burst' of diversification after the K/Pg event. Cal3 and FBD are identified as the most suitable methods for time-scaling phylogenetic trees dominated by fossil taxa. Extended Hedman estimates are substantially older than the others, with larger standard deviations and a strong vulnerability to taxon sampling and topological changes. sGLA has similar problems and cannot be recommended either. We conclude that a detailed understanding of phylogenetic relationships, tree reconstruction methods, and good taxonomic coverage (in particular the inclusion of the oldest taxon in each clade) is essential when evaluating the results of such dating analyses.</p>
Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals
<p><span>The popularity of relaxed clock Bayesian inference of clade origin timings has generated several recent publications with focal results considerably older than the fossils of the clades in question. Here we critically examine two such clades: the animals (with focus on the bilaterians); and the mammals (with focus on the placentals). Each example displays a set of characteristic pathologies which, although much commented on, are rarely corrected for. We conclude that in neither case does the molecular clock analysis provide any evidence for an origin of the clade deeper than what is suggested by the fossil record. In addition, both these clades have other features (including, in the case of the placental mammals, proximity to a large mass extinction) that allow us to generate precise expectations of the timings of their origins. Thus, in these instances the fossil record can provide a powerful test of molecular clock methodology, and why it goes astray; and we have every reason to think these problems are general. </span></p>
Figure 3 in Age estimation of Anatololacerta anatolica (Werner, 1902) in the vicinity of Çanakkale by skeletochronology
Figure 3. Age (years)–SVL relationship of females.
Figure 2 in Age estimation of Anatololacerta anatolica (Werner, 1902) in the vicinity of Çanakkale by skeletochronology
Figure 2. The relationship between age and SVL of A. anatolica specimens.
Figure 4 in Age estimation of Anatololacerta anatolica (Werner, 1902) in the vicinity of Çanakkale by skeletochronology
Figure 4. Age (years)–SVL relationship of males.
The crater detection results (necessary data for making Figs 6 and 7) for areas A2, A4 and A7 to estimate the ages of RMDS-overlapped craters in Figs 2a-2c
<p>To estimate the ages of RMDS-overlapped craters in Figs 2a-2c ( located in areas A2, A4 and A7, respectively) with a locally calibrated Monte Carlo model, the NAC-DEM-based crater detection results are provided here, as the basis input and necessary data to make Figs 6 and 7.</p> <p>They have been introduced in the following publication, where more details can be found:</p> <p>F. Zhang, J. W. Head, C. Wöhler, A. T. Basilevsky, L. Wilson, M. Xie, R. Bugiolacchi, T. Wilhelm, S. Althoff, Y. L. Zou.</p> <p>The Lunar Mare Ring-Moat Dome Structure (RMDS) Age Conundrum: Contemporaneous with Imbrian-Aged Host Lava Flows or Emplaced in the Copernican?</p> <p>Journal of Geophysical Research: Planets, 126, e2021JE006880. https://doi. org/10.1029/2021JE006880</p>
Age estimation based on blood DNA methylation levels in brown bears
<p><span>Age is an essential trait for understanding the ecology and management of wildlife. A conventional method of estimating age in wild animals is counting annuli formed in the cementum of teeth. This method has been used in bears despite some disadvantages, such as high invasiveness and the requirement for experienced observers. In this study, we established a novel age estimation method based on DNA methylation levels using blood collected from 49 brown bears</span><span> </span><span>of known ages living in both captivity and the wild. We performed bisulfite pyrosequencing and obtained methylation levels at 39 cytosine-phosphate-guanine (CpG) sites adjacent to 12 genes. The methylation levels of CpGs adjacent to four genes showed a significant correlation with age. The best model was based on DNA methylation levels at just four CpG sites adjacent to a single gene, SLC12A5, and it had high accuracy with a mean absolute error of 1.3 years and median absolute error of 1.0 year after leave-one-out cross-validation. This model represents the first epigenetic method of age estimation in brown bears, which provides benefits over tooth-based methods, including high accuracy, less invasiveness, and a simple procedure. Our model has the potential for application to other bear species, which will greatly improve ecological research, conservation, and management.</span></p>
Mark-recapture dataset to estimate age-specific reproductive rates of Steller sea lions in Southeast Alaska
<p>Age, region, and year-specific estimates of reproduction are needed for monitoring wildlife populations during periods of ecosystem change. Population dynamics of Steller sea lions (<em>Eumetopias jubatus</em>) in Southeast Alaska varied regionally (with high population growth and survival in the north versus the south) and annually (with reduced adult female survival observed following a severe marine heatwave event), but reproductive performance is currently unknown. We used mark-resighting data from 1,006 SSL females marked as pups at age ~3 weeks of age from 1994–1995 and 2001–2005 and resighted from 2002–2019 (to a maximum age of 25) to examine age-, region-, and year-specific reproduction. In the north versus the south, age of first reproduction was earlier (beginning at age 4 versus age 5, respectively) but annual birth probabilities of parous females were reduced by 0.05. In an average year pre-heatwave, the proportion of females with pup at the end of the pupping season peaked at ages 12–13 with ~0.60/0.65 (north/south) with pup, ~0.30/0.25 with juvenile, and ~0.10 (both regions) without a dependent. In both regions, reproductive senescence was gradual after age 12: ~0.40, 0.40, and 0.20 of females were in these reproductive states, respectively, by age 20. Correcting for neonatal mortality, true birth probabilities at peak ages were 0.66/0.72 (north/south). No cost of reproduction on female survival was detected, but pup production remained lower (-0.06) after the heatwave event, which if sustained would result in population decline in the south. Reduced pup production and greater retention of juveniles during periods of poor prey conditions may be an important strategy for Steller sea lions in Southeast Alaska, where fine-tuning reproduction based on nutritional status may improve the lifetime probability of producing pups under good conditions in a variable and less productive environment. </p>
Diagnostic Accuracy of a Novel Machine Learning Algorithm to Estimate Gestational Age
ClinicalTrials.gov study NCT05433519. IPD Sharing: YES. Countries: 2. Publications: 1.
Integrating multiple field measurements in a Bayesian parallel regression framework to estimate Tasmanian devil age
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Data from: Age and sex prevalence estimate of Joubert Syndrome in Italy
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Data from: How to date a crocodile – estimation of neosuchian clade ages and a comparison of four time-scaling methods
Open the record for dataset details and reuse information.
Mark-recapture dataset to estimate age-specific reproductive rates of Steller sea lions in Southeast Alaska
Open the record for dataset details and reuse information.
Age estimation based on blood DNA methylation levels in brown bears
Open the record for dataset details and reuse information.
Two notorious nodes: A critical examination of relaxed molecular clock age estimates of the bilaterian animals and placental mammals
Open the record for dataset details and reuse information.
Figure 1 in Estimating the young evolutionary age of marbled crayfish from museum samples
Figure 1. Geographical origin and sex distribution of Procambarus fallax samples in the USNM collection. Figures in circles indicate number of lots collected in the respective county. Both sexes were found in 194 lots in 39 counties. Pure female samples with>3 specimens were found in 7 lots in 7 counties and pure male samples>3 specimens were found in 2 lots in 1 county. The circles marked by H and V indicate counties not represented in the USNM collection. They were collected by Hendrix et al. (2000) and Van der Heiden and Dorn (2017), respectively. These samples included both sexes.
Estimation of environmental, genetic and parental age at conception effects on telomere length in a wild mammal
<p class="MsoNoSpacing">Understanding individual variation in fitness-related traits requires separating the environmental and genetic determinants. Telomeres are protective caps at the ends of chromosomes that are thought to be a biomarker of senescence as their length predicts mortality risk and reflect the physiological consequences of environmental conditions. The relative contribution of genetic and environmental factors to individual variation in telomere length is however unclear, yet important for understanding its evolutionary dynamics. In particular, the evidence for transgenerational effects, in terms of parental age at conception, on telomere length is mixed. Here, we investigate the heritability of telomere length, using the 'animal model', and parental age at conception effects on offspring telomere length in a wild population of European badgers (<i>Meles meles</i>). While we found no heritability of telomere length and low evolvability (<0.001), our power to detect heritability was low and a repeatability of 2% across individual lifetimes provides a low upper limit to ordinary narrow-sense heritability. However, year (25%) and cohort (3%) explained greater proportions of the phenotypic variance in telomere length. There was no support for cross-sectional or within-individual parental age at conception effects on offspring telomere length. Our results indicate a lack of transgenerational effects through parental age at conception and a low potential for evolutionary change in telomere length in this population. Instead, we provide evidence that individual variation in telomere length is largely driven by environmental variation in this wild mammal.</p>
Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: How old are you? Genet age estimates in a clonal animal
Foundation species such as redwoods, seagrasses and corals are often long-lived and clonal. Genets may consist of hundreds of members (ramets) and originated hundreds to thousands of years ago. As climate change and other stressors exert selection pressure on species, the demography of populations changes. Yet, because size does not indicate age in clonal organisms, demographic models are missing data necessary to predict the resilience of many foundation species. Here, we correlate somatic mutations with genet age of corals and provide the first, preliminary estimates of genet age in a colonial animal. We observed somatic mutations at five microsatellite loci in rangewide samples of the endangered coral, Acropora palmata (n = 3352). Colonies harboured 342 unique mutations in 147 genets. Genet age ranged from 30 to 838 years assuming a mutation rate of 1.195−04 per locus per year based on colony growth rates and 236 to 6500 years assuming a mutation rate of 1.542−05 per locus per year based on sea level changes to habitat availability. Long-lived A. palmata genets imply a large capacity to tolerate past environmental change, and yet recent mass mortality events in A. palmata suggest that capacity is now being frequently exceeded.
Data from: A function-valued trait approach to estimating the genetic basis of size at age and its potential role in fisheries induced evolution
Natural selection is inherently a multivariate phenomenon. The selection pressure on size (natural and artificial) and the age at which selection occurs is likely to induce evolutionary changes in growth rates across the entire life history. However, the covariance structure that will determine the path of evolution for size-at-age has been studied in only a few fish species. We therefore estimated the genetic covariance function for size throughout ontogeny using Atlantic silversides (Menidia menidia) as the model system. Over a 3-year period, a total of 542 families were used to estimate the genetic covariance in length at age from hatch through maturity. The function-valued trait approach was employed to estimate the genetic covariance functions. A Bayesian hierarchical model was used to account for the unbalanced design, unequal measurement intervals, unequal sample sizes, and family-aggregated data. To improve mixing, we developed a two-stage sampler using a Gibbs sampler to generate the posterior of a well-mixing approximate model followed by an importance sampler to draw samples from posterior of the completely specified model. We found that heritability of length is age-specific and there are strong genetic correlations in length across ages that last 30d or more. We used these estimates in a hypothetical model predicting the evolutionary response to harvesting following a single generation of selection under both sigmoidal and unimodal patterns of gear selectivity to illustrate the potential outcomes of ignoring the genetic correlations. In these scenarios genetic correlations were found to have a strong effect on both the direction and magnitude of the response to harvest selection.
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