Biological clocks as age estimation markers in animals: a systematic review and meta-analysis

Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.

The use of telomeric length as authenticity marker in fish and seafood - a new perspective in the detection of adulteration

In this review we propose the use of telomeric length (TL) as an authenticity marker that could provide an alternative method for differentiating fish and seafood samples or detecting fraud. Considering the ever-growing number of incidents of economically motivated fish and seafood adulteration using even more sophisticated methods to overcome current authenticity markers, the need to identify novel authenticity markers becomes essential. The TL of fish and seafood depends on individual characteristics (e.g., sex, age) and the environmental stimuli (e.g., temperature, water quality) to which these are exposed. Hence, both wild marine and freshwater populations occupying different geographical origin habitats might differ substantially because of the environmental cues affecting them. Moreover, the implementation of various rearing practices in aquaculture, such as different levels of fish and seafood density and increased ambient noise combined with site-specific environmental cues could affect TL, providing regulatory authorities with valuable information by distinguishing wild from reared populations and organic from conventional ones. In the present review the effects of both the environmental conditions and individual characteristics on the telomeric stability of fish and seafood telomeres are discussed, suggesting TL as a potential prospect authenticity marker that could be used to prevent fish and seafood adulteration.

Decline in telomere length with increasing age across nonhuman vertebrates: A meta-analysis

The prediction that telomere length (TL) shortens with increasing age is a major element in considering the role of telomeres as a key player in evolution. While telomere attrition is found in humans both in vitro and in vivo, the increasing number of studies reporting diverse age-specific patterns of TL challenges the hypothesis of a universal decline of TL with increasing age. Here, we performed a meta-analysis to estimate the relationship between TL and age across 175 estimates encompassing 98 species of vertebrates. We found that, on average, TL does decline with increasing age during adulthood. However, this decline was weak and variable across vertebrate classes, and we also found evidence for a publication bias that might weaken our current evidence of decreasing TL with increasing age. We found no evidence for a faster decline in TL with increasing age when considering the juvenile stage (from birth to age at first reproduction) compared to the adult stage. Heterogeneity in TL ageing rates was explained by the method used to measure telomeres: detectable TL declines with increasing age were found only among studies using TRF with in-gel hybridisation and qFISH methods, but not in studies using qPCR and Southern blot-based TRF methods. While we confirmed that TL declines with increasing age in most adult vertebrates, our results identify an influence of telomere measurement methodology, which highlights the need to examine more thoroughly the effect of the method of measurement on TL estimates.

Development in the European flounder (Platichthys flesus) of a q-PCR assay for the measurement of telomere length, a potential biomarker of pollutant effects for biomonitoring studies

Telomeres protect the coding sequence of chromosome ends and Telomere Length (TL) has been proposed as a biomarker of cellular aging, cumulative stress exposure and life-span in humans. With the aim to propose new biomarkers, a q-PCR protocol was adapted for the measurement of TL in the European flounder Platichthys flesus. The protocol was then applied in 2-year-old flounders from the Seine Estuary. The absolute TL in the flounder is 54 ± 13 kbp per genome (mean ± standard error). Considering relative or absolute TL, no correlation was observed with DNA damage and any of the measured contaminant concentrations (trace elements, metabolites of polycyclic aromatic hydrocarbons, polychlorobiphenyls, organochlorinated pesticides, polybrominated diphenyl ethers, perfluoroalkyl substances). Because sampling was limited, further investigations are required to state a possible impact of chemical pollution on flatfish telomeres. This is motivated by correlations observed with organochlorinated compounds when decreasing statistical significance (p ≤ 0.10).

Short-term exposure to unmanned aerial vehicles does not alter stress responses in breeding tree swallows

Recent studies suggest that visual and acoustic anthropogenic disturbances can cause physiological stress in animals. Human-induced stress may be particularly problematic for birds as new technologies, such as drones, increasingly invade their low-altitude air space. Although professional and recreational drone usage is increasing rapidly, there is little information on how drones affect avian behavior and physiology. We examined the effects of drone activity on behavior and physiology in adult, box-nesting tree swallows (Tachycineta bicolor). Specifically, we monitored bird behavior during drone flights and in response to a control object and measured telomere lengths and corticosterone levels as indicators of longer-term physiological stress. We predicted that drone-exposed tree swallows would habituate behaviorally after multiple flights, but that telomeres would shorten more quickly and that baseline corticosterone levels would be altered. One significant and two strong, non-significant trends in behavioral assays indicated that adult swallows acted more aggressively towards drone presence compared to a control object, but were slower to approach the drone initially. Swallows were also more reluctant to use nest boxes during drone activity. Tree swallows habituated to drone presence as expected, although the rate of habituation often did not differ between drone-exposed and control groups. Contrary to our prediction, drone activity did not affect telomere length, corticosterone levels, body mass or fledging rates. Overall, our results indicate that a small number of short, targeted, drone flights do not impact tree swallow health or productivity differently than a non-invasive control object. Minor behavioral differences suggest that increasing the frequency of drone use could impact this species. We provide some of the first results addressing how drone activity alters behavioral, physiological and molecular responses to stress in songbirds. A better understanding of these impacts will allow ecologists to make more informed decisions on the use and regulation of new drone technologies.

Telomere Dynamics in the Diploid and Triploid Rainbow Trout (Oncorhynchus mykiss) Assessed by Q-FISH Analysis

Changes of telomere length with age were assessed in diploid and triploid rainbow trout (Oncorhynchus mykiss) females in the cross-sectional study using Q-FISH technique. Triploid trout as sterile do not invest an energy in gametogenesis and continue to grow, whereas fertile diploid individuals suffer from declines in growth and survival during sexual maturation. However, triploid and diploid specimens exhibited similar patterns of telomere dynamics. Telomere length in the embryos, larvae and one-year-old juveniles did not change significantly. In the second year after hatching, subadults exhibited substantially shortened telomeres, while significant increase of the telomere length was reported in the three-year-old adults. On the other hand, correlation between telomere length and body size was observed in the triploid, but not in the diploid rainbow trout. Telomere shortening observed in two-year-old subadults may have been associated with the premature period of the fast growth in rainbow trout. Similar pattern of the telomere dynamics reported in the fertile diploids and sterile triploids indicated processes related to reproduction did not affect telomere dynamics in this species. Unexpected increase of the telomere length reported during the third year of life confirmed that in rainbow trout telomeric DNA shortens and lengthens, depending on the developmental stage.

DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird

Most seabirds do not have any outward identifiers of their chronological age, so estimation of seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular age biomarker to estimate age in short-tailed shearwaters (Ardenna tenuirostris). We quantified DNA methylation in several A. tenuirostris genes that have shown age-related methylation changes in mammals. In birds ranging from chicks to 21 years of age, bisulphite treated blood and feather DNA was sequenced and methylation levels analysed in 67 CpG sites in 13 target gene regions. From blood samples, five of the top relationships with age were identified in KCNC3 loci (CpG66: R² = 0.325, p = 0.019). In feather samples ELOVL2 (CpG42: R² = 0.285, p = 0.00048) and EDARADD (CpG46: R² = 0.168, p = 0.0067) were also weakly correlated with age. However, the majority of markers had no clear association with age (of 131 comparisons only 12 had a p-value < 0.05) and statistical analysis using a penalised lasso approach did not produce an accurate ageing model. Our data indicate that some age-related signatures identified in orthologous mammalian genes are not conserved in the long-lived short tailed shearwater. Alternative molecular approaches will be required to identify a reliable biomarker of chronological age in these seabirds.

Molecular biomarkers for chronological age in animal ecology

The chronological age of an individual animal predicts many of its biological characteristics, and these in turn influence population-level ecological processes. Animal age information can therefore be valuable in ecological research, but many species have no external features that allow age to be reliably determined. Molecular age biomarkers provide a potential solution to this problem. Research in this area of molecular ecology has so far focused on a limited range of age biomarkers. The most commonly tested molecular age biomarker is change in average telomere length, which predicts age well in a small number of species and tissues, but performs poorly in many other situations. Epigenetic regulation of gene expression has recently been shown to cause age-related modifications to DNA and to cause changes in abundance of several RNA types throughout animal lifespans. Age biomarkers based on these epigenetic changes, and other new DNA-based assays, have already been applied to model organisms, humans and a limited number of wild animals. There is clear potential to apply these marker types more widely in ecological studies. For many species, these new approaches will produce age estimates where this was previously impractical. They will also enable age information to be gathered in cross-sectional studies and expand the range of demographic characteristics that can be quantified with molecular methods. We describe the range of molecular age biomarkers that have been investigated to date and suggest approaches for developing the newer marker types as age assays in nonmodel animal species.

Does Reproductive Investment Decrease Telomere Length in Menidia menidia?

Given finite resources, intense investment in one life history trait is expected to reduce investment in others. Although telomere length appears to be strongly tied to age in many taxa, telomere maintenance requires energy. We therefore hypothesize that telomere maintenance may trade off against other life history characters. We used natural variation in laboratory populations of Atlantic silversides (Menidia menidia) to study the relationship between growth, fecundity, life expectancy, and relative telomere length. In keeping with several other studies on fishes, we found no clear dependence of telomere length on age. However, we did find that more fecund fish tended to have both reduced life expectancy and shorter telomeres. This result is consistent with the hypothesis that there is a trade-off between telomere maintenance and reproductive output.

Molecular cloning and measurement of telomerase reverse transcriptase (TERT) transcription patterns in tissues of European hake (Merluccius merluccius) and Atlantic cod (Gadus morhua) during aging

Telomerase is a reverse transcriptase ribonucleoprotein that maintains the ends of linear chromosomes. This enzyme plays a major role in cell processes like proliferation, differentiation and tumorigenesis, being associated with aging and survival of species. In this study, the gene coding for TERT (Telomerase Reverse Transcriptase) of two commercial fish species, European hake (Merluccius merluccius) and Atlantic cod (Gadus morhua), has been partially cloned. A fragment of 1581bp (hake) and 633bp (cod) showed high homology (identity 74%, query cover 99%, E-value=0) with known Perciformes TERT sequences. TERT transcription patterns were assessed by qRT-PCR in different tissues of hake (brain, ovary, testis, muscle, skin, gills, liver and kidney) and cod (brain, muscle and skin) of different sizes/ages in order to understand its role in the physiological aging of teleosts. TERT was found to be ubiquitously transcribed in all tissues and size/age groups studied in both species. Significantly higher relative transcription levels (p<0.05) were found with increasing size/age of M. merluccius in the kidney, muscle, skin and gonad, the latter exhibiting particularly high relative transcription levels. Male hakes showed higher TERT relative transcription levels in the brain, gonad and liver than females, although these differences were not statistically significant (p<0.05). In G. morhua, higher TERT relative transcription levels were recorded in the muscle and brain of fry and juvenile individuals. Therefore, TERT relative transcription pattern exhibited a higher telomerase demand in early developmental stages and also in mature stages, suggesting tissue renewal or regeneration processes as a conserved mechanism for maintaining long-term cell proliferation capacity and preventing senescence. Thus, it can be concluded that TERT relative transcription level was species and tissue specific and changed with the age of fishes.

Telomere-independent ageing in the longest-lived non-colonial animal, Arctica islandica

The shortening of telomeres as a causative factor in ageing is a widely discussed hypothesis in ageing research. The study of telomere length and its regenerating enzyme telomerase in the longest-lived non-colonial animal on earth, Arctica islandica, should inform whether the maintenance of telomere length plays a role in reaching the extreme maximum lifespan (MLSP) of >500years in this species. Since longitudinal measurements on living animals cannot be achieved, a cross-sectional analysis of a short-lived (MLSP 40years from the Baltic Sea) and a long-lived population (MLSP 226years Northeast of Iceland) and in different tissues of young and old animals from the Irish Sea was performed. A high heterogeneity of telomere length was observed in investigated A. islandica over a wide age range (10-36years for the Baltic Sea, 11-194years for Irish Sea, 6-226years for Iceland). Constant telomerase activity and telomere lengths were detected at any age and in different tissues; neither correlated with age or population habitat. Stable telomere maintenance might contribute to the long lifespan of A. islandica. Telomere dynamics are no explanation for the distinct MLSPs of the examined populations and thus the cause of it remains to be investigated.

Inheritance of telomere length in a bird

Telomere dynamics are intensively studied in human ageing research and epidemiology, with many correlations reported between telomere length and age-related diseases, cancer and death. While telomere length is influenced by environmental factors there is also good evidence for a strong heritable component. In human, the mode of telomere length inheritance appears to be paternal and telomere length differs between sexes, with females having longer telomeres than males. Genetic factors, e.g. sex chromosomal inactivation, and non-genetic factors, e.g. antioxidant properties of oestrogen, have been suggested as possible explanations for these sex-specific telomere inheritance and telomere length differences. To test the influence of sex chromosomes on telomere length, we investigated inheritance and sex-specificity of telomere length in a bird species, the kakapo (Strigops habroptilus), in which females are the heterogametic sex (ZW) and males are the homogametic (ZZ) sex. We found that, contrary to findings in humans, telomere length was maternally inherited and also longer in males. These results argue against an effect of sex hormones on telomere length and suggest that factors associated with heterogamy may play a role in telomere inheritance and sex-specific differences in telomere length.