Lifespan estimation in marine turtles using genomic promoter CpG density

Legacy and emerging persistent organic pollutants in sea turtles from Korean waters: Levels, profiles, and interspecies differences

Sea turtles, as endangered species with their long lifespans, wide-ranging migration, and high trophic level, are effective bioindicators of marine pollution. Despite the importance of global monitoring of persistent organic pollutants (POPs) in sea turtles, research has been limited, especially in Asia. This study examined the accumulation of POPs in the livers of 44 sea turtles from Korean waters, including loggerhead (Caretta caretta) and green turtles (Chelonia mydas). The turtles accumulated the chemicals in the order PAHs > PCBs > DDTs > PBDEs > CHLs, HBCDs, hexachlorobenzene, HCHs > mirex, pentachlorobenzene. Loggerhead turtles had significantly higher levels of DDTs, HCHs, pentachlorobenzene, and PBDEs than green turtles (Wilcoxon rank sum test, p < 0.01), along with a higher proportion of bioaccumulative congeners and isomers, likely due to their primarily carnivorous diet compared to the predominantly herbivorous diet of green turtles. Conversely, HBCD levels were similar in both species, yet green turtles had a higher proportion of γ-HBCD-the dominant isomer in commercial HBCDs used as plastic additives, with lower bioaccumulation potential-likely reflecting their greater ingestion of plastic debris than loggerhead turtles. Notably, sea turtles had higher ratios of γ-HBCD to α-HBCD and HBCDs to PCBs than seabirds from Korean waters, implying greater exposure to plastic-derived POPs. This study highlights the widespread accumulation of legacy and emerging POPs, including plastic-associated chemicals, in Korean sea turtles. These findings underscore the need for global POP monitoring in sea turtles and further research on the environmental fate and impact of plastic-associated chemicals.

Genomic insights into marine environment adaptation and conservation of the threatened olive ridley turtle (Lepidochelys olivacea)

Sea turtles are marine flagship species and most of them are currently in a threatened state. Long-term surviving in the ocean has driven significant morphological and physiological changes for this group, which makes them an ideal model for studying adaptive evolution of marine environments. Herein, we present a chromosome-scale genome of Lepidochelys olivacea with a genome size of 2.22 Gb and a contig N50 of 97.3 Mb. Comparative genomic analyses uncovered a suite of adaptive changes in genes related to olfaction, vision, virus defense, and longevity, which may help explain the genetic underpinnings of its marine environment adaptation. We also observed that the genome-wide heterozygosity of L. olivacea was low (6.45e-4), consistent with its prolonged population decline. Overall, our study provides valuable genetic resources for understanding evolutionary adaptations to aquatic environment and for the conservation of this threatened species.

Biology, Nesting Behavior, Genetic Diversity, and Conservation of Leatherback Sea Turtles: Insights From Thailand and Global Perspectives

Sea turtles are large reptiles that inhabit the world's oceans and include seven extant species within two families: Cheloniidae and Dermochelyidae. These species are threatened globally, with several subpopulations listed as Endangered or Critically Endangered by the IUCN. Thailand hosts five sea turtle species, including leatherback turtles (Dermochelys coriacea ), which are significant for their nesting sites along the Andaman Sea coast. Conservation efforts in Thailand include beach patrols, hatcheries, and community education to mitigate threats such as poaching and habitat destruction. Leatherback turtles, classified as "Vulnerable" by the IUCN and listed in CITES Appendix I, face challenges in estimating global population size due to their highly migratory nature. They are the largest sea turtles, with distinct physical characteristics such as leathery skin, lack of scales, a hard shell, and backward-pointing spines in the throat that aid the passage of food. Leatherbacks reach sexual maturity at around 13-14 years of age and exhibit natal homing behavior for nesting. These turtles have low hatching rates; only 50% of eggs hatch, and just 2% of those hatchlings survive. Population genetic studies of leatherback turtles have been key to better understanding threats to survival, revealing low global mtDNA haplotype diversity, with notable recent radiation originating from the Indo-Pacific region. Despite this low diversity, there is significant population structuring, which hints at hidden nesting populations and foraging grounds that may contribute to genetic variability. For that reason, relocating nests to favorable locations is one possible conservation measure. Other strategies must address habitat loss, pollution, bycatch, and climate change in protection efforts for this species, as well as ensuring global population connectivity to maintain the genetic diversity of these highly migratory turtles.

A genomic predictor for age at sexual maturity for mammalian species

Age at sexual maturity is a key life history trait that can be used to predict population growth rates and develop life history models. In many wild animal species, the age at sexual maturity is not accurately quantified. This results in a reduced ability to accurately model demography of wild populations. Recent studies have indicated the potential for CpG density within gene promoters to be predictive of other life history traits, specifically maximum lifespan. Here, we have developed a machine learning model using gene promoter CpG density to predict the mean age at sexual maturity in mammalian species. In total, 91 genomes were used to identify 101 unique gene promoters predictive of age at sexual maturity across males and females. We found these gene promoters to be most predictive of age at sexual maturity in females (R 2 = 0.881) compared to males (R 2 = 0.758). The median absolute error rate was also found to be lower in females (0.427 years) compared to males (0.785 years). This model provides a novel method for species-level age at sexual maturity prediction without the need for long-term monitoring. This study also highlights a potential epigenetic mechanism for the onset of sexual maturity, indicating the possibility of using epigenetic biomarkers for this important life history trait.

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.

Hidden demographic impacts of fishing and environmental drivers of fecundity in a sea turtle population

Fisheries bycatch is a critical threat to sea turtle populations worldwide, particularly because turtles are vulnerable to multiple gear types. The Canary Current is an intensely fished region, yet there has been no demographic assessment integrating bycatch and population management information of the globally significant Cabo Verde loggerhead turtle (Caretta caretta) population. Using Boa Vista island (Eastern Cabo Verde) subpopulation data from capture-recapture and nest monitoring (2013-2019), we evaluated population viability and estimated regional bycatch rates (2016-2020) in longline, trawl, purse-seine, and artisanal fisheries. We further evaluated current nesting trends in the context of bycatch estimates, existing hatchery conservation measures, and environmental (net primary productivity) variability in turtle foraging grounds. We projected that current bycatch mortality rates would lead to the near extinction of the Boa Vista subpopulation. Bycatch reduction in longline fisheries and all fisheries combined would increase finite population growth rate by 1.76% and 1.95%, respectively. Hatchery conservation increased hatchling production and reduced extinction risk, but alone it could not achieve population growth. Short-term increases in nest counts (2013-2021), putatively driven by temporary increases in net primary productivity, may be masking ongoing long-term population declines. When fecundity was linked to net primary productivity, our hindcast models simultaneously predicted these opposing long-term and short-term trends. Consequently, our results showed conservation management must diversify from land-based management. The masking effect we found has broad-reaching implications for monitoring sea turtle populations worldwide, demonstrating the importance of directly estimating adult survival and that nest counts might inadequately reflect underlying population trends.

Age-specific growth and maturity estimates for the flatback sea turtle (Natator depressus) by skeletochronology

To address a major knowledge gap for flatback sea turtles (Natator depressus), a species endemic to Australia and considered ‘Data Deficient’ for IUCN Red List assessment, we present the first-ever skeletochronology-derived age and growth rate estimates for this species. Using a rare collection of bone samples gathered from across northern Australia, we applied skeletochronology and characterized the length-at-age relationship, established baseline growth rates from the hatchling to adult life stages, and produced empirical estimates of age-at- and size-at-sexual-maturation (ASM, SSM). We analyzed humeri from 74 flatback sea turtles ranging in body size from 6.0–96.0 cm curved carapace length (CCL), and recovered from Western Australia (n = 48), Eastern Australia (n = 13), central Australia (n = 8; Northern Territory n = 3, the Gulf of Carpentaria n = 5), and unknown locations (n = 5). We identified the onset of sexual maturity for 29 turtles, based on rapprochement growth patterns in the bones. Estimates for ASM ranged from 12.0 to 23.0 years (mean: 16.3 ± 0.53 SE), SSM ranged from 76.1 to 94.0 cm CCL (mean: 84.9 ± 0.90 SE), and maximum observed reproductive longevity was 31 years for a 45-year old male flatback. Growth was modeled as a smoothing spline fit to the size-at-age relationship and at the mean SSM (84.9 cm CCL) corresponded with a spline-predicted maturity age of 18 years (95% CI: 16 to 24), while mean nesting sizes reported in the literature (86.4 to 94 cm CCL) corresponded to estimated ages of 24+ years. A bootstrapped von Bertalanffy growth model was also applied and showed consistencies with the spline curve, yielding an estimated upper size limit, L_inf, at 89.2 ± 0.04 cm (95% CI: 85.5 to 95.9 cm) with the intrinsic growth rate parameter, k, at 0.185 ± 0.0004 (0.16 to 0.22); at the same mean SSM (84.9 cm CCL) the estimated ASM was 16.3 ± 0.05 years (95% CI: 12.8 to 27.7 years). Lastly, four of the samples analyzed were collected from deceased adult females that had previous sizes known from on-going mark/recapture studies at nesting sites in Western Australia. The paired CCL data (measured at nesting and back-calculated) did not significantly differ (p = 0.875). This first skeletochronology study for flatback sea turtles generates valuable empirical estimates for ongoing conservation and management efforts.

Sex-specific aging in animals: Perspective and future directions

Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age-associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer-lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well-characterized processes. In particular, understanding the role of sex-determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs.

Stress response markers in the blood of São Tomé green sea turtles (Chelonia mydas) and their relation with accumulated metal levels

Metals are persistent worldwide being harmful for diverse organisms and having complex and combined effects with other contaminants in the environment. Sea turtles accumulate these contaminants being considered good bioindicator species for marine pollution. However, very little is known on how this is affecting these charismatic animals. São Tomé and Príncipe archipelago harbours important green sea turtle (Chelonia mydas) nesting and feeding grounds. The main goal of this study was to determine metal and metalloid accumulation in the blood of females C. mydas nesting in São Tomé Island, and evaluate the possible impacts of this contamination by addressing molecular stress responses. Gene expression analysis was performed in blood targeting genes involved in detoxification/sequestration and metal transport (mt, mtf and fer), and in antioxidant and oxidative stress responses (cat, sod, gr, tdx, txrd, selp and gclc). Micronuclei analysis in blood was also addressed as a biomarker of genotoxicity. Present results showed significant correlations between different gene expressions with the metals evaluated. The best GLM models and significant relationships were found for mt expression, for which 78% of the variability was attributed to metal levels (Al, Cu, Fe, Hg, Pb and Zn), followed by micronuclei count (65% - Cr, Cu, Fe, Hg, Mn and Zn), tdx expression (52% - Cd, Fe, Mn, Pb and Se), and cat expression (52% - As, Fe, Se and Cd x Hg). Overall, this study demonstrates that these green sea turtles are trying to adapt to the oxidative stress and damage produced by metals through the increased expression of antioxidants and other protectors, which raises concerns about the impacts on these endangered organisms' fitness. Furthermore, promising biomarker candidates associated to metal stress were identified in this species that may be used in future biomonitoring studies using C. mydas' blood, allowing for a temporal follow-up of the organisms.

Cardiac Structures in Marine Animals Provide Insight on Potential Directions for Interventions for Pediatric Congenital Heart Defects

Despite recent advances in pediatric diagnosis and surgical intervention, mortality and morbidity continue to be a prevalent issue in both Tetralogy of Fallot (ToF) and Hypoplastic Left Heart Syndrome (HLHS). Therefore, novel approaches to studying both of these conditions is warranted. Investigating cardiac anatomical features of different species in the animal kingdom similar to the defects and complications present in ToF and HLHS (as well as others) could serve as a new avenue for improving the management of congenital heart diseases (CHD). This review reveals that although structures found in HLHS and ToF are pathological, similar structures are found in diving mammals and reptiles that are adaptive. Pathologic aortic dilation in CHD resembles the aortic bulb present in diving mammals, but the latter is more elastic and distensible compared to the former. The unrepaired HLHS heart resembles the univentricular heart of non-crocodilian reptiles. Right ventricle hypertrophy is pathological in HLHS and ToF, but adaptive in crocodilians and diving mammals. Lastly, the increased pulmonary resistance due to pulmonary stenosis in ToF is comparable to increased pulmonary resistance in crocodilians due to the presence of an active valve proximal to the pulmonary valve. Some of these anatomical structures could potentially be adapted for palliative surgery in children with HLHS or ToF. Moreover, further investigating the underlying molecular signals responsible for the adaptive tissue responses seen in other species may also be useful for developing novel strategies for preventing some of the complications that occur after surgical repair in both of these CHDs.

Trace Element Concentrations in Blood and Scute Tissues from Wild and Captive Hawaiian Green Sea Turtles (Chelonia mydas)

Sea turtles are exposed to trace elements through water, sediment, and food. Exposure to these elements has been shown to decrease immune function, impair growth, and decrease reproductive output in wildlife. The present study compares trace element concentrations in green turtles in captivity at Sea Life Park Hawaii (n = 6) to wild green turtles in Kapoho Bay, Hawaii, USA (n = 5-7). Blood and scute samples were collected and analyzed for 11 elements via inductively coupled plasma-mass spectrometry (ICP-MS). Selenium was significantly greater (p < 0.05) in the blood of captive turtles compared with wild turtles, whereas V, Ni, and Pb were significantly greater in the blood of wild turtles. In scute, V, Cu, Se, and Cr were significantly greater in captive turtles, whereas As was significantly greater in wild turtles. Pelleted food fed to the captive turtles and representative samples of the wild turtle diet were analyzed via ICP-MS to calculate trophic transfer factors and daily intake values. Wild turtles had greater estimated daily intake than captive turtles for all elements except Cu and Se. Because captive turtles are fed a diet very different from that of their wild counterparts, captive turtles do not represent control or reference samples for chemical exposure studies in wild turtles. No toxic thresholds are known for sea turtles, but rehabilitation and managed care facilities should monitor sea turtle elemental concentrations to ensure the animals' health. Environ Toxicol Chem 2021;40:208-218. © 2020 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.