The Bottlenose Dolphin Epigenetic Aging Tool (BEAT): A Molecular Age Estimation Tool for Small Cetaceans

Abstract

Age constitutes a critical parameter for the study of animal populations, providing information about development, environmental effects, survival, and reproduction. Unfortunately, age estimation is not only challenging in large, mobile and legally protected species, but often involves invasive sampling methods. The present work investigates the association between epigenetic modifications and chronological age in small cetaceans. For that purpose, DNA methylation at age-linked genes was characterized in an extensively studied, long-term resident common bottlenose dolphin (Tursiops truncatus) community from Sarasota Bay (FL, United States) for which sampled individuals have a known age. Results led to the identification of several CpG sites that are significantly correlated to chronological age in this species with the potential for sex to play a role in the modulation of this correlation. These findings have allowed for the development and validation of the "Bottlenose dolphin Epigenetic Age estimation Tool" (BEAT), improving minimally-invasive age estimation in free-ranging small cetaceans. Overall, the BEAT proved to be accurate in estimating age in these organisms. Given its minimally-invasive nature and potential large-scale implementation using skin biopsy samples, this tool can be used to generate age data from free-ranging small cetacean populations.

An epigenetic clock to estimate the age of living beluga whales

“…The LOOCV showed a pattern of age underestimation for older whales and overestimation of younger whales, a pattern that is present but less pronounced in the training dataset. This pattern could partially be driven by data scarcity of older and younger whales in our calibration dataset, but it is also observed in other epigenetic clocks (e.g., Beal et al, 2019;Polanowski et al, 2014).…”

“…In humans, clocks have been designed using varying numbers of CpG sites, from one site (e.g., an age predictor based on a CpG in the ELOVL2 gene; Garagnani et al, 2012) to several hundred sites (e.g., 353 sites; Horvath, 2013). Epigenetic clocks have also been developed for other species including the mouse (Stubbs et al, 2017;Petkovich et al, 2017;Thompson et al, 2018;Meer et al, 2018), chimpanzee (Ito et al, 2018), bat (Wright et al, 2018), canid (Ito et al, 2017;Thompson et al, 2017), humpback whale (Polanowski et al, 2014), minke whale (Tanabe et al, 2020), and bottlenose dolphin (Beal et al, 2019). Accurate age estimates can be valuable for conservation efforts and species management.…”

Health Assessments of Common Bottlenose Dolphins (Tursiops truncatus): Past, Present, and Potential Conservation Applications

“…Currently, sex and population structure of the animal can be determined from genetic analyses of skin (112), and contaminant concentrations and stress and reproductive hormone levels can be measured from blubber biopsy (33,116,136). Present efforts are working toward using skin to assess the epigenetics of the individual to give an estimation of age (137). The NMMF are expanding on this even further in line with recent human advancements to provide an indication of biological age (138).…”

Age determination of common bottlenose dolphins (Tursiops truncatus) using dental radiography pulp:tooth area ratio measurements

“…Thus, researchers have developed a variety of methods in an attempt to estimate age in marine mammals, each giving varying accuracy and precision. These techniques include, but are not limited to, long term photographic-identification (photo-ID) monitoring in live animals [1], morphometric comparisons in live and dead animals [2][3][4], dentinal growth layer groups from extracted teeth (GLGs) [1,3,5,6], bone GLGs in carcasses [7,8], skeletal ossification live dolphins [9], bone density [10][11][12], micro-CT scanning [13], radiometric aging in auditory bullae from carcasses [14], ear plug layers in mysticete carcasses [15], aspartic acid racemization in carcasses [16][17][18], baleen length or radiocarbon dating in carcasses [19,20], bomb radiocarbon dating in extracted teeth for animals alive in the 1960s [18,21], telomere sequence analysis in live animals [22][23][24], DNA methylation analysis in live animals [25], and fatty acid signatures in live or dead animals [26][27][28][29]. Unfortunately, many of the aforementioned techniques are inapplicable for use in studies with living dolphins, are unsuitable to be used in field studies, and/or provide poor precision.…”