Biology subjects

Jacquin, L.

Publications and source records attributed to Jacquin, L..

4 recordsLinked to original sources

bioRxiv2025

WISER: an innovative and efficient method for correcting population structure in omics-based prediction and selection

This work introduces WISER (whitening and successive least squares estimation refinement), an innovative and efficient method designed to enhance phenotype estimation by addressing population structure. WISER outperforms traditional methods such as least squares (LS) means and best linear unbiased prediction (BLUP) in phenotype estimation, offering a more accurate approach for omics-based selection and having the potential to improve association studies. Unlike existing approaches that correct for population structure, WISER provides a generalized framework applicable across diverse experimental setups, species, and omics datasets, including single nucleotide polymorphisms (SNPs), metabolomics, and near-infrared spectroscopy (NIRS) used as phenomic predictors. Central to WISER is the concept of whitening, a statistical transformation that removes correlations between variables and standardizes their variances. Within its framework, WISER extends classical methods that use eigen-information as fixed-effect covariates to correct for population structure, by relaxing their assumptions and implementing a true whitening matrix instead of a pseudo-whitening matrix. This approach corrects fixed effects (e.g., environmental effects) for the genetic covariance structure embedded within the experimental design, thereby minimizing confounding factors between fixed and genetic effects. To support its practical application, a user-friendly R package named wiser has been developed. The WISER method has been employed in analyses for genomic prediction and heritability estimation across four species and 33 traits using multiple datasets, including rice, maize, apple, and Scots pine. Results indicate that genomic predictive abilities based on WISER-estimated phenotypes consistently outperform the LS-means and BLUP approaches for phenotype estimation, regardless of the predictive model applied. This underscores WISERs potential to advance omics analyses and related research fields by capturing stronger genetic signals.

genetics↗

bioRxiv2025

Behavior Outpaces Form when Linking Traits to Ecological Responses within Populations: A Meta-Analysis

Intraspecific variability is fundamental to ecology, yet we still know remarkably little about what governs the strength of the associations between traits expressed by individuals and ecological dynamics. To explore this overlooked aspect of diversity, we asked whether the strength of correlations between traits and a wide spectrum of ecological responses could differ (i) between intraspecific levels (among vs. within populations), (ii) among ecological responses across levels of biological organization (from ecological performance to ecosystem functioning), and (iii) among trait types (morphology, physiology, and behavior). We performed a meta-analysis synthesizing over a thousand effect sizes from nearly two hundred studies spanning approximately a hundred animal species across a broad range of traits and ecological responses. The average effect size was |r| = 0.26 (95% confidence interval: 0.21 - 0.30). At the individual level, effect sizes were larger for ecological performance (foraging, diet) than for fitness (reproduction), and tended to be larger for community responses (e.g., community composition of surrounding organisms). Physiology and behavior showed larger effect sizes than morphology. Our meta-analysis not only confirms that intraspecific trait variability is central to ecological dynamics, but also highlights physiology and behavior as key traits for unraveling the ecological consequences of individual variability.

ecology↗

bioRxiv2024

When does a parasite become a disease? eDNA unravels complex host-pathogen dynamics across environmental stress gradients in wild salmonid populations

Infectious diseases stem from disrupted interactions among hosts, parasites, and the environment. Both abiotic and biotic factors can influence infection outcomes by shaping the abundance of a parasites infective stages, as well as the hosts ability to fight infection. However, disentangling these mechanisms within natural ecosystems remains challenging. Here, combining environmental DNA analysis and niche modeling at a regional scale, we uncovered the biotic and abiotic drivers of a lethal infectious disease of salmonid fish, triggered by the parasite Tetracapsuloides bryosalmonae. We found that the occurrence and abundance of the parasite in the water--i.e., the propagule pressure-- were mainly correlated to the abundances of its two primary hosts, the bryozoan Fredericella sultana and the fish Salmo trutta, but poorly to local abiotic environmental stressors. In contrast, the occurrence and abundance of parasites within fish hosts--i.e., proxies for disease emergence--were closely linked to environmental stressors (water temperature, agricultural activities, dams), and to a lesser extent to parasite propagule pressure. These results suggest that pathogen distribution alone cannot predict the risk of disease in wildlife, and that local anthropogenic stressors may play a pivotal role in disease emergence among wild host populations, likely by compromising the hosts ability to fight the parasite. Our study sheds light on the intricate interplay between biotic and abiotic factors in shaping pathogen distribution and raises concerns about the effects of global change on disease emergence.

ecology↗

bioRxiv2017

Effects of confinement on body mass and site fidelity of feral pigeons during the setting-up of pigeon houses.

Feral pigeons can reach high densities in the urban environments and have thus been subject to various regulation programs. Recently, an alternative ethical regulation strategy based on the installation of artificial breeding facilities has been tested in European cities. In Paris (France), pigeons are first confined for several weeks within the pigeon house before being released. According to authorities, this method allows to retain confined pigeons in this new habitat and to attract more conspecifics. This study aims at evaluating the efficiency and potential side-effects of this method by assessing pigeon fidelity behaviour and pigeon welfare after release. Results show that confinement in pigeon houses induced a significant body mass loss in birds. Only 19% of confined pigeons became faithful to their new habitat. This fidelity depended on the origin of birds suggesting that pigeons captured closer to the pigeon houses are more likely to stay in the vicinity of the pigeon house one year after. Investigations on methods of regulation on animal behavior may help to improve management procedures.

ecology↗