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Cristofari, R.

Publications and source records attributed to Cristofari, R..

12 recordsLinked to original sources
bioRxiv2026

An epigenetic palimpsest: the King penguin's blood methylome reveals conserved hematopoietic ageing

Age-associated DNA methylation is conserved across vertebrates, but whether epigenetic ageing reflects cellular ageing programmes or age-dependent shifts in cell composition remains unresolved. Here, using 126 whole-blood methylomes from known-age King penguins (Aptenodytes patagonicus), we exploit a vertebrate system in which nucleated erythrocytes dominate peripheral blood, minimizing the influence of leukocyte heterogeneity. We identify a core set of 409 ageing-associated genes showing lifelong, clock-like methylation change. These genes are strongly enriched for regulators of hematopoietic stem and progenitor cell (HSPC) function and niche communication. Integration of methylome, transcriptome and chromatin-accessibility data reveals that many of the strongest ageing signals derive from genes inactive in mature erythrocytes, consistent with the persistence of epigenetic states from ancestral hematopoietic progenitors. A comparison with methylation profiles from 1,501 humans identified a conserved cross-species subset of ageing genes, and a human epigenetic age model constructed solely from orthologues of penguin ageing genes predicts chronological age with high accuracy while remaining largely insensitive to blood cell composition. We propose that blood epigenetic ageing signatures contain a long-lived cellular memory of stem-cell ageing, that may represent an evolutionarily ancient layer of the vertebrate ageing process.

systems biology↗
bioRxiv2025

Multiannual environmental forcing shapes breeding phenology and success in a subantarctic seabird

Climate-driven phenological mismatches threaten avian reproduction by disrupting food availability during critical breeding stages. In marine ecosystems, time lags between environmental changes and their effects on food webs are challenging to model, yet they can have a profound impact on top-predator reproduction. We disentangle how oceanic and climatic variability influence the breeding phenology and success of a keystone seabird of the Southern Ocean drawing on 24 years of data from 17,000 marked king penguins. We document an exceptional 19-day advancement in breeding phenology, alongside increased breeding success (44% in 2000, 62% in 2023). A sliding-window analysis reveals that sea temperature and primary production in key foraging zones predict both phenology and breeding success, with lags ranging from several weeks to two years. While king penguins appear to be keeping pace with current changes, their dependence on multi-year environmental conditions underscores the vulnerability of top predators to unpredictable, fast-changing, and more frequent extreme conditions.

ecology↗
bioRxiv2025

Early-life stress as a potential resilience factor in king penguins

Climate change-driven environmental variability can cause species to shift their phenology, leading to an increase in phenological mismatches. Whether the fitness cost of such mismatches can be mitigated by plasticity remains poorly understood, especially in the context of wild populations. In this study, we quantified responses to phenological mismatch using capture-mark-recapture, morphological, and transcriptomic data from king penguins hatching during and after the seasonal peak of food availability (i.e., born early and late in the breeding season, respectively). Late-born chicks showed reduced survival to fledging and fledged smaller and in slightly poorer body condition than chicks born during the seasonal peak in food availability. Yet post-fledging return rates did not differ between late- and early-born chicks, suggesting that early-life stress was effectively mitigated among individuals that survived to fledging, with no detectable carryover effects in the first years post-fledging. Genes involved in oxidative stress response, homeostasis, and nutrient-sensing were differentially expressed between early- and late-born chicks, consistent with stress mitigation and homeostasis maintenance at the expense of growth in late-born chicks. A co-expression gene cluster whose primary expression pattern was associated with hatching phenology also contained central genes involved in stress mitigation. Together, our findings highlight molecular mechanisms that buffer the fitness costs of phenological mismatch, which may allow species to tolerate mismatch to some extent. Despite higher winter mortality of individuals born in mismatch, the plastic response observed in survivors hints towards molecular adaptations that could allow species resilience under increasing climate-driven environmental unpredictability.

genomics↗
bioRxiv2025

Flexible foraging effort shapes Adelie penguin reproductive success across Antarctica and sea ice conditions

Understanding how species deal with diverse environmental conditions is crucial for predicting their future responses to climate change. In Antarctica, changing sea ice dynamics threaten ice-dependent species. Whilebehavioural adjustmentscould help mitigate these threats, their effectiveness under future environmental conditions and potential thresholds remain unclear. Long-term studies and circumpolar approaches could address this challenge. Our 15-year study (2010-2024) of over 23,000 foraging trips from Adelie penguins (Pygoscelis adeliae) in East Antarctica, identified a non-linear relationship between sea ice concentration (SIC) and foraging effort when landfast ice was absent, a situation anticipated to define the species future habitat during chick-rearing. Minimal effort occurred at 10-20% SIC, but more than doubled with the presence of landfast ice or heavy pack-ice, with females showing greater sensitivity to these ice changes. Acircumpolar analysis of similar data demonstrated that foraging effort during chick-guarding predicted reproductive success across ten Adelie penguin populations. Reproductive success remained high until foraging trips exceeded approximately 29 hours, after which performance declined sharply. This indicates that while behavioural flexibility can buffer against moderate environmental changes, it has clear limits. Our findings establish foraging trip duration as a valuable early warning indicator for population responses to environmental change.

ecology↗
bioRxiv2025

A chromosome-level genome of the King penguin (Aptenodytes patagonicus): an emerging model-in-the-wild for studying evolution

The King penguin (Aptenodytes patagonicus) is an iconic species of the Southern Ocean and is currently being developed as a model-in-the-wild for understanding evolution. We present a high-quality, haplotype-resolved 1.35 Gb chromosome-level genome of an adult female King penguin - Pen/Se-guin - from the Crozet Archipelago, assembled using PacBio HiFi long-read sequencing and Hi-C proximity data. 94.93% of the assembly is assigned to 34 chromosomes (32 autosomes, plus the Z and W chromosomes), with a BUSCO completeness of 97.2%, a k-mer completeness of 99.7%, and a quality value (QV) of 63.8. We also assembled a circularised mitogenome (20,520 bp), which includes the avian tandem duplication (TD). Annotation of repetitive sequences revealed that 16.3% of the genome comprises repetitive elements, with LINEs being the most abundant transposable element class (5.6%). Gene prediction using an extensive multi-tissue RNA-seq dataset resulted in 18,081 predicted protein-coding genes, of which 17,081 were functionally annotated, with a BUSCO completeness of 98.4% and an OMArk completeness of 97.3%. The presented assembly substantially improves the quality of a previous draft genome, showing a 28-fold increase in assembly contiguity and a significantly improved genome annotation, exceeding the standards of the Earth BioGenome Project (EBP) and Vertebrate Genomes Project (VGP). This high-quality genome will enable ongoing and future studies harnessing the King penguin as a model-in-the-wild to test hypotheses on the genotype-to-fitness link, ageing, life-history trait evolution, and adaptation.

genomics↗
bioRxiv2024

Sedentary life accelerates epigenetic ageing in King penguins

Introductory paragraphAdvances in medicine and food security have contributed to an increase in human lifespan1. Yet, the associated rise in sedentary behaviour and in obesity2,3 already threatens these gains4. Indeed, a growing body of evidence supports the central role of nutrient sensing and energy management pathways in regulating ageing rate and healthspan5,6, but the diversity of human lifestyles challenges our ability to identify the genetic and epigenetic drivers of this age acceleration. Here, we examine how the transition of wild King penguins to zoo husbandry can closely mimic the shift to a Western lifestyle in humans, and shed light on evolutionarily conserved epigenetic changes in responses to sedentary conditions. We show that, just like modern humans, zoo-housed King penguins experience an extended lifespan, but this comes at the cost of accelerated epigenetic ageing throughout life. This accelerated ageing is associated with differential methylation in key growth and maintenance pathways including the mTOR and PI3K/Akt networks, as well as in specific pathways of lipid-rich diet adaptation and heart-function. Our results demonstrate the deeply conserved link between sedentary behaviour and food availability on the one hand, and age acceleration on the other. Such evolutionary evidence may in turn help us to improve risk detection and, ultimately, therapeutics for lifestyle-induced age acceleration in humans7.

genomics↗
bioRxiv2024

Declining juvenile survival of Adelie penguins in Antarctica

As summer sea ice around Antarctica reaches modern lows, quantifying the demographic response of polar species to such environmental changes becomes critical. To achieve this, synthesizing results across species ranges and elucidating the environmental factors driving population dynamics are key. Adelie penguins are considered reliable indicators of changes in Antarctica but the processes through which sea ice and other environmental factors shape their population dynamics are still unclear, especially for critical age groups such as juveniles. Using a 17-year dataset of Adelie penguins electronically tagged in Adelie Land (Antarctica), we found that juvenile survival probability was most impacted by sea ice concentration near their natal colony right after fledging, with lower ice concentrations detrimental to survival. Importantly, we found that juvenile survival declined by 32% from 2007 to 2020, mirroring trends at other distant colonies. The emergence of similar patterns at opposite ends of the continent may be an early signal for shifts in population trends expected from climate change.

ecology↗
bioRxiv2024

Human reproduction comes at the expense of faster aging and a shorter life

Evolutionary theories suggest a trade-off between resources allocated to reproduction and those allocated to self-maintenance, and predict that higher reproductive output entails a shorter lifespan. This study investigates the impact of childbearing on aging and lifespan using data from contemporary Finnish twin women. We model the association between reproductive trajectories and survival in 17,080 women, and assess biological aging in a subset of participants (N=1,117) using the PCGrimAge clock, an algorithm trained to predict biological aging and mortality risk from DNA methylation. Our findings suggest that early childbearing, numerous pregnancies or nulliparity all contribute to accelerated aging and increased mortality risk. These results provide strong evidence for the existence of a trade-off between reproduction, aging and lifespan in modern humans, and provide novel insights into the genetic and lifestyle determinants of healthspan.

evolutionary biology↗
bioRxiv2023

Remote sensing of emperor penguin abundance and breeding success

Emperor penguins (Aptenodytes forsteri) are under increasing environmental pressure. Monitoring colony size and trends of this Antarctic seabird relies primarily on satellite imagery recorded near the end of the breeding season, when illumination levels are sufficient to capture images, but colony occupancy is highly variable. To correct population estimates for this variability, we develop a phenological model that accurately predicts the number of breeding pairs and fledging chicks, as well as key phenological events such as arrival, hatching and foraging times, from as few as six data points from a single season. The ability to extrapolate occupancy from sparse data makes the model particularly useful for monitoring remotely sensed animal colonies where ground-based population estimates are very rare or unavailable. TeaserThe Emperor penguin becomes the Southern Oceans canary in a coal mine through remote sensing its annual breeding success.

ecology↗
bioRxiv2023

RFIDeep: Unfolding the Potential of Deep Learning forRadio-Frequency Identification

O_LIAutomatic monitoring of wildlife is becoming a critical tool in the field of ecology. In particular, Radio-Frequency IDentification (RFID) is now a widespread technology to assess the phenology, breeding, and survival of many species. While RFID produces massive datasets, no established fast and accurate methods are yet available for this type of data processing. Deep learning approaches have been used to overcome similar problems in other scientific fields and hence might hold the potential to overcome these analytical challenges and unlock the full potential of RFID studies. C_LIO_LIWe present a deep learning workflow, coined "RFIDeep", to derive ecological features, such as breeding status and outcome, from RFID mark-recapture data. To demonstrate the performance of RFIDeep with complex datasets, we used a long-term automatic monitoring of a long-lived seabird that breeds in densely packed colonies, hence with many daily entries and exits. C_LIO_LITo determine individual breeding status and phenology and for each breeding season, we first developed a one-dimensional convolution neural network (1D-CNN) architecture. Second, to account for variance in breeding phenology and technical limitations of field data acquisition, we built a new data augmentation step mimicking a shift in breeding dates and missing RFID detections, a common issue with RFIDs. Third, to identify the segments of the breeding activity used during classification, we also included a visualisation tool, which allows users to understand what is usually considered a "black box" step of deep learning. With these three steps, we achieved a high accuracy for all breeding parameters: breeding status accuracy = 96.3%; phenological accuracy = 86.9%; breeding success accuracy = 97.3%. C_LIO_LIRFIDeep has unfolded the potential of artificial intelligence for tracking changes in animal populations, multiplying the benefit of automated mark-recapture monitoring of undisturbed wildlife populations. RFIDeep is an open source code to facilitate the use, adaptation, or enhancement of RFID data in a wide variety of species. In addition to a tremendous time saving for analyzing these large datasets, our study shows the capacities of CNN models to autonomously detect ecologically meaningful patterns in data through visualisation techniques, which are seldom used in ecology. C_LI

ecology↗
bioRxiv2016

Climate-driven range shifts in fragmented ecosystems

Range shift is the primary short-term response of species to rapid climate change but it is hampered by natural or anthropogenic habitat fragmentation. Fragmented habitats expose different critical areas of a species niche to heterogeneous environmental changes resulting in uncoupled effects. Modelling species distribution under complex real-life scenarios and incorporating such uncoupled effects has not been achieved yet. Here we identify the most vulnerable areas and the potential cold refugia of a top-predator with fragmented niche range in the Southern ocean by integrating genomic, ecological and behavioural data with atmospheric and oceanographic models. Our integrative approach constitutes an indispensable example for predicting the effect of global warming on species relying on spatially and ecologically distinct areas to complete their life-cycle (e.g., migratory animals, marine pelagic organisms, central-place foragers) and, in general, on species constrained in fragmented landscapes due to continuously-growing anthropogenic pressure.

evolutionary biology↗