Biology subjects

Caron, F.

Publications and source records attributed to Caron, F..

7 recordsLinked to original sources

bioRxiv2026

RuHere (Are You Here?): An R package to obtain, validate, and clean species records using metadata and specialist range information

O_LISpecies occurrence data are fundamental to understanding, predicting, and conserving global biodiversity. However, biodiversity datasets remain affected by substantial data-quality issues, particularly erroneous or imprecise geographic coordinates. Most available tools for identifying problematic records rely primarily on automated spatial or metadata-based checks and rarely integrate expert-curated species range information, which can reveal introductions or geographic errors that often escape standard validation procedures. C_LIO_LIHere, we introduce RuHere, an R package designed to manage species occurrence data, flag potential errors, and support the iterative exploration of problematic records. RuHere streamlines the data-cleaning process by integrating six main steps: (1) obtaining species occurrence records; (2) merging datasets and standardizing spatial information; (3) flagging records based on metadata; (4) flagging records using expert-derived distribution data; (5) visualizing, investigating, and summarizing flagged issues in the final datasets; and (6) exploring and reducing sampling bias. C_LIO_LIWe demonstrate the applicability of RuHere using occurrence data for a plant species (Araucaria angustifolia) and an animal species (Cyanocorax caeruleus). Nearly 75% of records were flagged as potentially problematic, including records identified exclusively by functions relying on specialist range information. C_LIO_LIThe main strengths of RuHere lie in its integrated and computationally efficient workflow, its tools for exploring and evaluating flagged records, and its ability to incorporate expert-derived distribution data to identify occurrences outside a species known natural range. By combining metadata-based checks, coordinate validation, and specialist knowledge, RuHere provides a robust and reproducible framework for improving the quality of species occurrence datasets. C_LI

ecology↗

bioRxiv2025

The evolution of Hutchinsonian climatic niche hypervolumes in gymnosperms

AimThe niche is a fundamental concept in theoretical and experimental ecology and is used to describe a wide range of ecological processes from species interaction with the environment to community assemblies. A common way to represent the niche is through a multidimensional geometry known as the Hutchinsonian niche hypervolume. Ecological theory predicts that niche hypervolumes have properties such as holes with broader eco-evolutionary significance, but we lack a comprehensive empirical study of niche hypervolume properties and their evolutionary significance. LocationGlobal Time periodHolocene Major taxa studiedGymnosperms MethodsWe conducted for the first time a systematic and comprehensive test of the evolution of Hutchinsonian niche hypervolume properties (volume and holes) across 65 genera and 12 families of gymnosperms, which includes many species that are endangered or threatened. Using cutting-edge computational algorithms, we measured the evolution of geometric (i.e. volume) and topological (i.e. holes) properties of gymnosperm hypervolumes across a comprehensive calibrated phylogeny. ResultsOur comparative analysis revealed weak evidence of the non-independent evolution of niche hypervolume volume and no evidence of the non-independent evolution of hypervolume holes. We also found that genera and families with low hypervolume volume such as monotypic groups like Gingko, likely experienced shifts in hypervolume evolutionary rates. Main conclusionsOur results show that geometric and topological properties of gymnosperm climatic niche hypervolumes evolve independently. This agrees with competitive exclusion hypothesis in ecological theory where extant groups are likely to be the ones which minimise niche overlap and competition.

ecology↗

bioRxiv2024

No evidence that proteome composition is associated with realised thermal limit and dietary niche breadth in butterflies

Amino acids are the building blocks of proteins that perform essential physiological functions. Theory suggests that the proteome composition, the amino acid frequencies across all proteins in a genome, is associated with an organisms optimal growth temperature, offering insights into species temperature limits. However, this hypothesis, based on prokaryotes, has not been tested in complex multicellular eukaryotes where many amino acids are strictly acquired through diet. Here, we analysed amino acid frequencies in the proteomes of orthologous and non-orthologous genes from 35 butterfly species to test for correlations with maximum observed temperatures and diet breadth. Using a comparative approach, we found no evidence that proteome composition correlates with temperature or diet breadth. Our findings suggest that animal proteome composition is likely shaped more strongly by energetic and biophysical constraints rather than by ecological factors.

zoology↗

bioRxiv2024

In vitro activity of hydroxychloroquine in combination with antibiotics against intracellular uropathogenic Escherichia coli

BackgroundTwo pathophysiological concepts may explain recurrent UTI: a reinfection by a bacterial strain from the digestive microbiota or a relapse from Escherichia coli persisting within the superficial urothelial cells as intracellular bacterial communities (IBC). Hydroxychloroquine (HCQ)-antibiotic combination is effective against intracellular adherent-invasive E. coli isolated from patients with Crohns disease. We hypothesized that HCQ may enhanced antibiotic efficacy against E. coli IBC. MethodsUTI89 reference strain and two clinical E. coli strains forming IBCs (VITALE#2157, VITALE#2206) were used in this study. MIC, MBC and time killing curves (4xMIC) were performed for AZYTHROMYCIN (AZT), CIPROFLOXACIN (CIP), DOXYCYCLINE (DC), FOSFMOMYCIN (FF) and HCQ. In vitro activity of antibiotics alone and combined with HCQ was evaluated on intracellular bacterial survival assay using a model of urothelium cells (HTB-9). ResultsTime-killing curves showed that CIP has a bactericidal activity at H6 (-4.6 log10 CFU/mL) with regrowth at H24 against 2157, and a bactericidal activity at H6 without regrowth at H24 against 2206 (-3.3 log10 CFU/mL) and UTI89 (-3.4 log10 CFU/mL); DC, AZT and FF demonstrated bacteriostatic activity at H24 regardless of the strain. We observed a significant decrease in the number of intracellular bacteria at H42 with CIP (-1.83 log10 / 106 cells). DC, FF, and AZT exposure did not reduce IBC formation at H42 (P>0.05). IBC formation after HCQ-antibiotic combination exposure was not significantly different (P>0.05) from antibiotic exposure alone, regardless of the antibiotic or strain studied. ConclusionsIn conclusion, HCQ exposure does not enhance antibiotics activity against intracellular uropathogenic E. coli. HighlightsO_LIUsing an in vitro model of superficial urothelium monolayer, we observed a significant decrease in intracellular uropathogenic Escherichia coli in response to ciprofloxacin exposure. C_LIO_LIHydroxychloroquine exposure does not enhance antibiotics activity against intracellular uropathogenic Escherichia coli. C_LI

microbiology↗

bioRxiv2023

Are Escherichia coli causing recurrent cystitis just ordinary Uropathogenic E. coli (UPEC) strains?

Specific determinants associated with Uropathogenic Escherichia coli (UPEC) causing recurrent cystitis are still poorly characterized. The aims of this study were (i) to describe genomic and phenotypic traits associated with recurrence using a large collection of recurrent and paired sporadic UPEC isolates, and (ii) to explore within-host genomic adaptation associated with recurrence using series of 2 to 5 sequential UPEC isolates. Whole genome comparative analyses between 24 recurrent cystitis isolates (RCIs) and 24 phylogenetically paired sporadic cystitis isolates (SCIs) suggested a lower prevalence of putative mobile genetic elements (MGE) in RCIs, such as plasmids and prophages. The intra-patient evolution of the 24 RCI series over time was characterized by SNP occurrence in genes involved in metabolism or membrane transport, and by plasmid loss in 5 out of the 24 RCI series. Genomic evolution occurred early in the course of recurrence, suggesting rapid adaptation to strong selection pressure in the urinary tract. However, RCIs did not exhibit specific virulence factor determinants and could not be distinguished from SCIs by their fitness, biofilm formation, or ability to invade HTB-9 bladder epithelial cells. Taken together, these results suggest a rapid but not convergent adaptation of RCIs that involves both strain- and host-specific characteristics. Author summaryThe recurrence of cystitis is a frequent but poorly understood phenomenon. There are currently many hypotheses trying to explain recurrence, but data on large collections of well-characterized clinical isolates are lacking. In order to identify specific recurrence-associated markers, we conducted a large genomic and phenotypic study involving 48 well-characterized cystitis isolates: 24 recurrent cystitis isolates (RCIs) and 24 pairs of isolates causing sporadic cystitis (SCIs). Moreover, we were able to explore intra-host overtime RCI evolution, by analyzing up to 5 sequential UPEC isolates per RCI series. Our results suggest that RCI rapidly adapt to their host through mobile genetic elements loss and SNP accumulation in genes involved in metabolism and membrane transport. However, no convergent genomic nor phenotypic evolution was observed between isolates collected from distinct patients. Taken together, these results suggest a host-shaped evolution of RCIs, highlighting a need for future studies focused on the host-pathogen relationships.

microbiology↗

bioRxiv2023

Substantial variation in species ages among vertebrate clades

Ecological and evolutionary studies traditionally assume that species are comparable units of biodiversity. However, not only this assumption is rarely tested, but also there have been few attempts even to assess variation in most emergent, species-level traits and their corresponding underlying mechanisms. One such trait is species age, here defined as the time since the most recent common ancestor between a given species and its sister lineage. In this study, we demonstrate that different terrestrial vertebrate clades vary considerably in the age of their constituent species. In particular, species ages were youngest in mammals and birds as opposed to squamates and amphibians, although considerable variation was found within those clades as well. Sensitivity analyses showed that these results are unaffected by phylogenetic uncertainty or incomplete taxonomic sampling. Interestingly, there was little geographical correspondence in mean species age across taxa, as well as with temperature and precipitation stability over the past 21,000 years. We discuss candidate mechanisms that might explain differences in species ages among clades, and explore the implications of these findings in relation to recent advances in age-dependent speciation and extinction models of diversification.

evolutionary biology↗

bioRxiv2020

The diversification of termites: inferences from a complete species-level phylogeny

Termites play a major role in a variety of ecological processes in tropical and subtropical biomes worldwide, such as decomposition, soil formation and aeration, and nutrient cycling. These important ecosystem services were achieved through their highly complex societies and remarkable adaptations, including the evolution of sterile worker castes, the acquisition of endosymbionts, and the capacity for extensive environmental engineering, yet the causes and consequences of their ecological success are still poorly understood. The goals of our study were (1) to provide the first complete, species-level phylogeny of all currently recognized termite species by integrating the available genetic and taxonomic data, as well as methods of phylogenetic imputation and divergence time estimation; and (2) to explore variation in speciation rates among termite lineages. We provide the inferred relationships as a set of 1,000 pseudo-posterior trees, which can be used in future comparative analyses. We demonstrate that speciation rates have been relatively constant throughout the history of termites, with two positive shifts in speciation rates: one at their origin of Euisoptera and the other concordant with evolution of Termitidae. On the other hand, there was no obvious trend towards deceleration in speciation rates for termites as a whole, nor within the most species-rich families. The provided trees might represent a valuable resource for termite comparative studies by summarizing the available phylogenetic information, while accounting for uncertainty in the inferred topologies.

evolutionary biology↗