Biology subjects

Jarman, S.

Publications and source records attributed to Jarman, S..

4 recordsLinked to original sources

bioRxiv2026

The BEAC, an epigenetic clock for birds

Epigenetic clocks are powerful tools for estimating both chronological and biological age, enabling the integration of age information into population monitoring, demographic modelling, and research on the ecophysiology and evolution of ageing. Most epigenetic clocks so far have been developed for mammals: here, we present the Bird Epigenetic Ageing Clock (BEAC) for estimating chronological age in avian species. BEAC was established based on genome-wide enzymatic methylation sequencing data of known-age king penguins (Aptenodytes patagonicus), and validated in nine other bird species. The BEAC collects age-informative signals into a bisulfite amplicon sequencing panel of 24 primer pairs, providing a highly accurate and cost-effective alternative to sequencing-intensive approaches. It achieved strong predictive performance in independent king penguin training (R{superscript 2}=0.88; MAE=1.7 years, n=78) and testing data (R{superscript 2}=0.79; MAE=2.3 years, n=41), with negligible batch effects, high longitudinal consistency, and resilience to reduced sample size or missing loci. Importantly, cross-species validation across 180 samples showed that BEAC reliably captures age-associated methylation signals in nine additional bird species across seven clades, demonstrating that a single set of loci can be predictive of ageing across multiple different bird species. BEAC offers a flexible, empirically validated tool and a transferable framework for developing epigenetic clocks in avian species, providing a highly valuable resource for eco-evolutionary studies of ageing in wild species.

molecular biology↗

bioRxiv2025

Population genetic assessment of marine megafauna using seawater environmental DNA: a case study of whale sharks from the Ningaloo Coast World Heritage Area.

There is a growing need for scalable and cost-effective genetic monitoring tools to support the management of species and populations of conservation importance, driven by the increasing biodiversity loss, need for long-term population data and limitations of invasive genetic sampling. Whale sharks (Rhincodon typus), along with other Endangered, elusive and highly migratory species, spend the majority of their lives in offshore ocean waters. This behaviour poses logistical and ethical challenges to invasive genetic sampling of the species, which is traditionally done via tissue biopsy. Here, we develop a genetic toolkit to study populations of whale sharks from seawater environmental DNA using short segments of nuclear DNA (100-300bp) containing two or more SNPs called "microhaplotypes". Amplifying these markers from seawater collected in 1L bottles behind sharks showed that we can reliably genotype sharks from water samples taken immediately behind the animal. Moreover, we observed a strong relationship between population-level allele frequencies and estimates of genetic diversity between eDNA and tissue-derived samples, demonstrating the capability of eDNA in capturing population-level genetic information with high fidelity. We also analysed a tissue dataset of 72 sharks that attended the Ningaloo Coast World Heritage Area over six-years to showcase the utility of our SNP panel to study temporal processes in these populations. Our data revealed patterns of genetic variation through time that were consistent with whole genome techniques. Contributor estimation from mock environmental samples using various combinations of tissue-derived sequence data to estimate abundance of animals in a mixed DNA sample was shown to accurately identify the number of contributors in mixtures containing [≤] 10 individuals, beyond which biases were too large. Our findings illustrate the viability of using microhaplotype markers from seawater eDNA as a tool to study conservation genetics of whale sharks, with the potential for broader expansion of eDNA-based genetic assessments to other marine megafauna and aquatic species.

genetics↗

bioRxiv2025

Towards population genetic assessments and species abundance from environmental DNA: A case study with zebrafish in controlled aquaria

Developing robust methods for amplifying and analysing highly-polymorphic nuclear genetic markers from environmental samples could assist in the reliable and scalable long-term monitoring of elusive, threatened or invasive species that are otherwise challenging to observe. In this study, we used zebrafish in controlled aquaria to apply forensic science approaches and demonstrate that microhaplotypes, which are short segments of nuclear DNA (100-300bp) containing two or more single nucleotide polymorphisms (SNPs), can be amplified from trace DNA in water samples to accurately estimate population genetic diversity and species abundance. We successfully amplified a panel of 17 microhaplotypes that comprised 69 SNPs which could reliably estimate population-level allele frequencies and genetic diversity estimates from water DNA. The panel of microhaplotypes amplified from water samples from replicate tanks strongly matched allele frequency estimates from corresponding tissue samples, and could also be used for estimating number of contributors from multi-individual samples. Our research demonstrates the effectiveness and potential of amplifying microhaplotype panels from eDNA as a non-invasive and scalable tool for population genetic studies of aquatic species.

ecology↗

bioRxiv2020

An epigenetic clock to estimate the age of living beluga whales

IntroductionDNA methylation data facilitate the development of accurate molecular estimators of chronological age, or epigenetic clocks. We present a robust epigenetic clock for the beluga whale, Delphinapterus leucas, developed for an endangered population in Cook Inlet, Alaska, USA. Methods and ResultsWe used a custom methylation array to measure methylation levels at 37,491 cytosine-guanine sites (CpGs) from skin samples of dead whales (n = 67) whose chronological ages were estimated based on tooth growth layer groups. Using these calibration data, a penalized regression model selected 23 CpGs, providing an R2 = 0.92 for the training data; and an R2 = 0.74 and median absolute age error = 2.9 years for the leave one out cross-validation. We applied the epigenetic clock to an independent data set of 38 skin samples collected with a biopsy dart from living whales between 2016 and 2018. Age estimates ranged from 11 to 27 years. We also report sex correlations in CpG data and describe an approach of identifying the sex of an animal using DNA methylation. DiscussionThe epigenetic estimators of age and sex presented here have broad applications for conservation and management of Cook Inlet beluga whales and potentially other cetaceans.

developmental biology↗