Biology subjects

Buso, P.

Publications and source records attributed to Buso, P..

3 recordsLinked to original sources

bioRxiv2026

Decoupling epigenetic variation from genetic variation reveals complementary dimensions of coral eco-evolutionary dynamics

Understanding how intraspecific diversity is structured is essential for predicting the eco-evolutionary trajectories of populations, especially under rapid environmental change. While such diversity has been extensively studied from a genetic perspective, much less is known about the distribution and ecological relevance of epigenetic variation within natural populations. To address this question, we focused on two species of reef-building corals belonging to distinct functional groups, Pocillopora acuta and Acropora hyacinthus, sampled across the South Pacific (New Caledonia, Fiji, French Polynesia). Using genome-wide Enzyme-Methyl sequencing, we jointly analyzed genetic (SNPs) and DNA methylation (CpGs) variation, while explicitly disentangling genetically associated from genetically independent epigenetic variation. Genetic and epigenetic structure showed contrasting spatial patterns, reflecting distinct temporal and ecological components of population dynamics. Genetic structure was strongest between archipelagos and followed an isolation-by-distance pattern consistent with long-term evolutionary processes. In contrast, epigenetic variation converged between colonies from different archipelagos. At finer spatial scales within archipelago, genetically independent epigenetic variation exhibited stronger structure than both genetic and genetically associated epigenetic variation, likely reflecting local environmental conditions. Together, our results show that genetic and epigenetic variation provide complementary insights into the eco-evolutionary processes shaping intraspecific diversity.

evolutionary biology↗

bioRxiv2025

Non-invasive eDNA reveals the ecological and genetic status of the Western Capercaillie (Tetrao urogallus aquitanicus) in the Eastern Pyrenees

The Anthropocene era is expected to bring about significant biodiversity and habitat loss for many species. These geographical changes, whether driven by climatic or anthropogenic factors, are likely to lead to considerable alterations in population size, structure, and genetic diversity. Monitoring natural populations is therefore essential to assess these impacts and enable informed conservation strategies for threatened species. The Western Capercaillie (Tetrao urogallus, L. 1758) has a widespread distribution in Boreal forests but fragmented in mountainous regions of the Palearctic, and is locally threatened by climate change, habitat destruction, and human disturbance. Our study focused on the eastern population of the subspecies T. u. aquitanicus, which is endemic to the Pyrenees mountains. The monitoring of this population has relied on direct methods and no genetic information had been generated so far. Here, we conducted a molecular study based on 229 non-invasive samples (faeces) to assess the ecological and genetic status of local population in the Catalan Nature Reserves of the Pyrenees-Orientales (Occitanie region, France). At the individual level, we assessed multi-locus genotypes, sexing, levels of inbreeding, stress level (Fecal Corticosterone Metabolites; FCMs) and diet. At the population level, we assessed sex ratio, genetic diversity and structure. We identified 62 individuals with a balanced sex ratio and estimated a census size of 79 individuals [95%CI = 68-92] in the study area. Genetic diversity was low and suggested significant inbreeding levels. FCM levels were lower in birds of areas considered as disturbed by humans and metabarcoding approach indicated a geographical structuring of diet composition at the reserve scale, with individuals exhibiting feeding behavior upon only one or few plant species. Our estimate of population census size was higher with figures assessed from lek counts, and the genetic approach provided additional insights on this population, establishing a baseline that will support conservation management plans.

ecology↗

bioRxiv2024

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

Aquaculture has a considerably shorter history compared to the domestication of plants and animals. Among aquatic species, those that have undergone whole genome duplication events (WGD) seem particularly successful. This suggests that genetic redundancy from WGD is important for domestication, possibly similar to plant domestication. Atlantic salmon (Salmo salar), which has experienced a lineage-specific WGD, has undergone rapid domestication through intensive breeding since the 1960s. Here, we examined the genomic responses to the domestication of Atlantic salmon, including the impacts of WGD, by comparing the whole genome sequence data of aquaculture and wild populations from two lineages: the Eastern and Western Atlantic (Western Norway and North America). Our analysis revealed shared selective sweeps on identical SNPs in major histocompatibility complex (MHC) genes across distinct aquaculture populations compared to their wild counterparts. This SNP level parallelism suggests that a combination of long-term balancing selection and recent human-induced selection has significantly shaped the evolutionary trajectory of MHC genes. In addition, we observed selective sweeps on gene pairs in the homeologous regions originating from WGD, highlighting WGDs role in maintaining genomic variation and potentially reducing pleiotropy through sub-functionalization. This unique type of "parallel" selection contributes to adapting to the intensive artificial conditions of aquaculture. These findings provide valuable insights into the genetic mechanisms of domestication and adaptive responses in Atlantic salmon, suggesting that the salmonid whole genome duplication has underpinned their successful rapid domestication. Our research emphasizes the importance of maintaining genetic diversity to support sustainable aquaculture practices.

genomics↗