Biology subjects

Ambrosini, R.

Publications and source records attributed to Ambrosini, R..

7 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

The end of the American dream: a hard to Swallow reality - How the Barn Swallow (Hirundo rustica) returned from America, a complete mtDNA phylogeny

The barn swallow (Hirundo rustica, H.r.) is one of the most iconic and fascinating migratory birds since ancient times, their philopatry and pair bonding have been the symbol of travellers and lovers throughout history. The barn swallow subspecies complex has been the main focus of many latest papers, focusing mainly on the Eurasian and Levant subspecies (H.r. rustica and H.r. transitiva). The remaining subspecies have either not been studied or few complete mitogenome sequences have been obtained. We present a comprehensive phylogeographic analysis of 580 complete mitochondrial genomes of barn swallows representing all recognized subspecies. We identified 553 unique haplotypes, 166 of which are novel, with high haplotype diversity and notable nucleotide diversity among subspecies. Phylogenetic analysis by maximum parsimony supports a single maternal ancestor and reveals five main haplogroups, confirming and refining prior classifications. A novel, distinct haplogroup (E) was identified for H.r. tytleri, previously classified as a sub-branch of H.r. erythrogaster. The inclusion of 66 hybrid individuals confirmed extensive maternal introgression and revealed multiple cases of mitogenome-subspecies mismatches, notably in savignii, transitiva, and tytleri populations. We further integrated 13 mitogenomes from 12 other Hirundo species, three of which are newly sequenced, to contextualize H. rustica evolution within the genus. Our findings support a southern African origin with subsequent diversification and a northward expansion. This study significantly enhances resolution of barn swallow mitogenomic diversity, revises phylogenetic relationships, identifies new haplogroups, hints at inter-subspecies gene flow and refines coalescent-based divergence times, offering key insights into the evolutionary history and hybridisation patterns of this iconic migratory species.

evolutionary biology↗

bioRxiv2022

Eco-evolutionary drivers of avian migratory connectivity

Understanding how individuals redistribute after migration assists in the conservation and management of mobile species, yet the eco-evolutionary drivers of migratory connectivity remain unclear. Taking advantage of an exceptionally large (~150,000 individuals, 83 species) and more-than-a-century long dataset of bird ringing encounters, we investigated determinants of avian migratory connectivity on both short- and long-distance migrants. Most species exhibited significant connectivity likely due to the large intraspecific variability in migration strategies, which often led to the identification of distinct migratory populations. Migratory connectivity was strongly predicted by geography, especially migration distance, but it was evolutionary labile and weakly influenced by biological traits due to flexibility in migratory behaviour. By unravelling determinants of migratory connectivity we improve knowledge about the resilience of migrants to ecological perturbations. Also, our population-level analysis provides a critical tool to inform transboundary conservation and management strategies by explicitly considering the large intraspecific variability of avian migration.

ecology↗

bioRxiv2022

Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2, with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF, a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.

genomics↗

bioRxiv2021

Diel transcriptional pattern contributes to functional and taxonomic diversity in supraglacial microbial communities

Despite the harsh environmental conditions, glacier surfaces host metabolically active bacterial communities, especially in cryoconite holes, small ponds filled with melting water and with a fine-grained sediment at the bottom. We investigated the daily changes in transcript profiles of the microbial community of a cryoconite hole on an Alpine glacier. Using a metatranscriptomic shotgun sequencing, we observed different level of expression of the main carbon and energy metabolisms along the day. Oxygenic and anoxygenic photosynthesis peaked their activity at the sunrise and sunset, respectively, and showed an inhibition at midday, in response to high solar radiation. Carbon fixation genes were expressed all day long with the lowest coverage at night. Different microbial populations were responsible for this metabolic function along the day. Cyanobacteria and Algae were the most active primary producers at the sunrise and the sunset, whereas at night and at noon chemosynthetic proteobacteria, likely hydrogen oxidisers, were most active. Furthermore, the observed temporal cascade of transcript peaks of photosynthesis and respiration recalls those occurring in both coastal and open waters in ocean, thus supporting the hypothesis that conserved temporally phased biotic interactions are ubiquitous among aquatic communities worldwide.

ecology↗

bioRxiv2021

Geographical variability of bacterial communities of cryoconite holes of Andean glaciers

Cryoconite holes, ponds full of melting water with a sediment on the bottom, are hotspot of biodiversity of glacier surface. They host a metabolically active bacterial community that is involved in different dynamics concerning glacier ecosystems. Indeed, they are responsible of organic matter production and with other microorganisms establish a real microecosystem. Cryoconite holes have been described in different areas of the world (e.g., Arctic, Antarctic, Alps, Himalaya), and with this study we will provide the first description of bacterial communities of cryoconite holes of the Andes in South America. We collected samples on three high elevation glaciers of the Andes (Iver, Iver East and Morado glaciers) and two Patagonian glaciers located at sea level (Exploradores glacier and Perito Moreno). Results show that the most abundant orders are Burkholderiales, Cytophagales, Sphingobacteriales, Actinomycetales, Pseudomonadales, Rhodospiarillales, Rhizobiales, Sphingomonadales and Bacteroidales, which have been reported on glaciers of other areas of the world, Bacterial communities change from one glacier to another and both water pH and O2 concentration affect bacterial communities composition.

ecology↗

bioRxiv2020

Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. As part of the Vertebrate Genomes Project (VGP) we have developed mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (>10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline led to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We have observed that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we have identified errors, missing sequences, and incomplete genes in those references, particularly in repeat regions. Our assemblies have also identified novel gene region duplications, shedding new light on mitochondrial genome evolution and organization.

genomics↗