Biology subjects

Le Floch, G.

Publications and source records attributed to Le Floch, G..

8 recordsLinked to original sources

bioRxiv2026

Switching to one or the other : Shorebirds behavioural flexibility in food transport mechanisms

Shorebirds provide an excellent model for investigating the relationship between bill morphology and food acquisition. Food acquisition comprises three successive behavioural stages: foraging (locomotion and prey capture), feeding (food handling and transport), and swallowing. During food transport, these birds use two non-lingual mechanisms, surface-tension transport (ST) and ballistic transport (BT), whose characteristics depends on the kinematics of head and beak movements and the physical properties of the food. We investigated the behavioural flexibility of these transport mechanisms in captive and free-ranging individuals of two species with contrasting beak morphologies: the Pied avocet (Recurvirostra avosetta) and the Black-winged stilt (Himantopus himantopus). Although these species have beaks of a similar size, avocets are distinguished by their upward-curved beaks, whereas stilts have a rather straight beak. We examined the effects of food water content and the presence or absence of water in the beak on food transport by quantifying maximum gape, maximum head displacement, and maximum head velocity. Transport kinematics were jointly influenced by food properties and water availability in the beak. Moist food improved transport performance in both species, whereas dry food required compensatory increases in gape amplitude and head movements, demonstrating that neither ST nor BT constitutes a fixed behavioural sequence. Species also differed consistently in their transport strategies: Black-winged stilts relied on slower, larger-amplitude head movements, whereas Pied Avocets exhibited faster, more precise movements, particularly when water was present. These findings demonstrate that ST and BT share common biomechanical foundations while being governed by rapid kinematic adjustments to changing environmental conditions that probably correspond to flexible motor control. This behavioural flexibility in food transport is therefore likely to enhance feeding performance and ecological resilience in the heterogeneous habitats occupied by shorebirds, suggesting that context-dependent modulation of transport behaviour represents an important adaptive feature of these shorebirds.

animal behavior and cognition↗

bioRxiv2026

Adaptive genomic compartments shaped by giant mobile elements underpin the ancient emergence of fungal pathogenicity

The emergence of new fungal pathogens often depends on the acquisition of complex adaptive traits, yet the mechanisms by which such traits arise remain poorly understood. Here we show that a biosynthetic gene cluster required for pathogenicity in the lupin pathogenic fungus Colletotrichum lupini was acquired within a genomic region derived from a giant Starship transposable element. Comparative and population genomic analyses reveal that the C. lupini genome contains multiple regions derived from ancestrally active Starship elements, enriched in lineage-specific genes and strongly induced during plant infection. One such region harbours a hybrid polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) gene cluster that is conserved in pathogenic isolates but absent from closely related non-pathogenic species and from a non-pathogenic strain. Phylogenetic analyses of the PKS-NRPS backbone gene reveal incongruence with species relationships and a distribution across deeply divergent fungal lineages, consistent with horizontal acquisition. Disruption of the PKS-NRPS backbone gene abolishes pathogenicity, demonstrating that this cluster is required for host infection. Phylogenomic analyses further indicate that lupin pathogenicity emerged once within the C. lupini lineage prior to its diversification. Together, these findings identify a Starship-associated virulence determinant and support a model in which giant cargo-mobilizing mobile elements generate genomic novelty by facilitating the acquisition, assembly and integration of adaptive traits during the emergence of fungal pathogenicity.

genetics↗

bioRxiv2025

Character displacement in shorebirds

Modification of phenotypic traits induced by character displacements allow species to coexist by reducing interspecific competition. This study explores if and how shorebirds partition feeding ressources by foraging at different water depths outside the breeding season. During this period, communities of up to dozen shorebird species coexist on suitable habitats at land-water interfaces. By video recording 22 species of migrating and wintering shorebirds in different sites, we show that their distribution according to the water height at which they forage is not random but follows a gradient of increasing water height according to increasing species body size. Species-specific beak and tarsus lengths are positively correlated with the water height at which the different species forage. Our data do not support a trade-off in investment between beak length and tarsus length in our study species set. Congeneric species that are expected to be morphologically and ecologically more similar forage at contrasted water heights. Altogether, our findings supports the idea of resource partitioning, and consequently of competition relaxation, by morphological and/or by behavioral character displacements.

evolutionary biology↗

bioRxiv2025

Beak elongation as key innovation in shorebird adaptive radiation

Adaptive radiations are often associated with phenotypic innovations that broaden ecological opportunity and bias subsequent ecological divergence. In shorebirds (Charadriiformes), variation in beak length has long been linked to resource partitioning, yet its role as a functional innovation has remained largely untested. Here, we integrate behavioural, morphological, and phylogenetic data from 29 Western Palearctic shorebird species to evaluate whether beak elongation fulfils key expectations of a candidate innovation by being repeatedly associated with ecological and functional transitions. Species with longer than expected beaks relative to body size consistently exhibit distinct locomotor, prey-capture, and food-transport strategies. These integrated morphological-behavioural syndromes recur across independent lineages, suggesting convergent evolution driven by shared ecological constraints. Phylogenetic analyses indicate multiple independent origins of relative beak elongation, supporting its role as a repeated evolutionary solution. Together, our results support a functionally integrated view of adaptation, in which coordinated changes in morphology, sensory investment, and behaviour facilitate access to alternative foraging microhabitats and enable repeated ecological transitions within shorebirds. More broadly, this study provides a testable framework for identifying candidate innovations based on replicated trait-niche associations. O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/671984v2_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@185f912org.highwire.dtl.DTLVardef@a33baforg.highwire.dtl.DTLVardef@a37b35org.highwire.dtl.DTLVardef@ee0831_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2025

A population genetic study of Fusarium graminearum, the causal agent of Fusarium Head Blight, provides insights into patterns of inoculum dispersal in wheat fields at a regional scale

Fusarium graminearum is the primary pathogen responsible for Fusarium Head Blight (FHB) in cereals, causing yield losses and mycotoxin contamination. The present study investigated the genetic diversity and population structure of F. graminearum from wheat grains and maize residues, which were the primary inoculum sources of FHB. A total of 588 isolates from four different fields were genotyped using a sequence-based microsatellite genotyping method of 34 SSR markers (SSRseq) and characterized for chemotype distribution. The results revealed high genetic diversity with 453 distinct multilocus genotypes (MLGs) without significant genetic differentiation by geographic location or substrate, suggesting a single metapopulation at the regional scale. This absence of substrate genetic differentiation strongly supports the fact that residue-borne inoculum contributed to FHB infection, although we failed to demonstrate any field-specific dispersal pattern from residues to grains. The findings underscore the importance of maize residues as a critical inoculum source and highlight the need to consider both local and regional sources in FHB management.

genetics↗

bioRxiv2025

Etiology and epidemiology of branch dieback and fruit blight and necrosis of English walnut in France

English walnut (Juglans regia L.) is an economically-important fruit crop worldwide, particularly in France, where it is the second most important fruit crop after apples in terms of cultivated area. Walnut orchards are targeted by numerous diseases, but new symptoms have been widely observed since 2015 in France, consisting in typical branch dieback and fruit blight and necrosis. Herein, both symptomatic and asymptomatic twigs and husks were collected from 12 commercial French walnut orchards from the two main production areas located in the South of France from 2020 to 2022. Overall, Botryosphaeriaceae, Colletotrichum, Diaporthe, and Fusarium species were consistently isolated from symptomatic husks and twigs. Among these taxa, B. dothidea and C. godetiae were significantly more associated with symptomatic husks, contrary to D. eres and F. juglandicola, more frequently isolated from symptomatic twigs, as also confirmed by ITS2 metabarcoding sequencing. Tissue type was the primary factor significantly impacting the composition of the fungal communities (R{superscript 2} = 16.6%), followed by sampling campaign and production area (R{superscript 2} = 11.6% and 4.6%, respectively). We also found that Neofusicoccum and Diaporthe were significantly more associated with warm and dry years, unlike Colletotrichum. Pathogenicity tests revealed that only Botryosphaeriaceae and Diaporthe species were pathogenic on walnut fruits and twigs, with B. dothidea and N. parvum being the most aggressive species. Several significant positive and negative correlations were identified based on SparCC co-occurrence networks and correlograms based on prevalence data. In particular, the positive correlation between Colletotrichum and Fusarium species on symptomatic twigs was highlighted by both methods. This work is the first comprehensive etiological and epidemiological study of branch dieback and fruit blight and necrosis of English walnut in France. Author SummaryEnglish walnut is an economically important crop, mainly produced in China, in the United States and in Turkey while in Europe, France is one of the biggest producers. Although widespread in nut orchards abroad, new symptoms, including fruit necroses and branch dieback, were observed for the first time in 2015 in France. We then conducted sampling campaigns between 2020 and 2022 to collect walnut husks and twigs in the two main French production areas. Exploration of the associated microbiota revealed the presence of six predominant fungal species, even in samples without symptoms. We then investigated the capacity of these species to cause lesions on twigs and fruits. Among all species, Neofusicoccum parvum was the most aggressive on both organs while other species were mainly aggressive on only twigs or husks. In addition, we evidenced that the presence of some species was favored by warm and dry weather or inversely cold and wet weather. We also found negative correlations between certain species (in particular between N. parvum and Diaporthe eres), suggesting that some species probably prevented the other from further colonization. Overall, we identified the species specifically associated with the disease in France and the factors influencing the disease risk. This work will enable us to better identify the best strategies to combat this disease.

microbiology↗

bioRxiv2022

Genome evolution and transcriptome plasticity associated with adaptation to monocot and eudicot plants in Colletotrichum fungi

Colletotrichum fungi infect a wide diversity of monocot and eudicot hosts, causing plant diseases on almost all economically important crops worldwide. In addition to its economic impact, Colletotrichum is a suitable model for the study of gene family evolution on a fine scale to uncover events in the genome that are associated with the evolution of biological characters important for host interactions. Here we present the genome sequences of 30 Colletotrichum species, 18 of them newly sequenced, covering the taxonomic diversity within the genus. A time-calibrated tree revealed that the Colletotrichum ancestor diverged in the late Cretaceous around 70 million years ago (mya) in parallel with the diversification of flowering plants. We provide evidence of independent host jumps from eudicots to monocots during the evolution of this pathogen, coinciding with a progressive shrinking of the degradative arsenal and expansions in lineage specific genes. Comparative transcriptomics of four reference species with different evolutionary histories and adapted to different hosts revealed similarity in gene content but differences in the modulation of their transcription profiles. Only a few orthologs show similar expression profiles on different plant cell walls. Combining genome sequences and expression profiles we identified a set of core genes, such as specific transcription factors, involved in plant cell wall degradation in Colletotrichum.Together, these results indicate that the ancestral Colletotrichum were associated with eudicot plants and certain branches progressively adapted to different monocot hosts, reshaping part of the degradative and transcriptional arsenal.

microbiology↗

bioRxiv2019

Maize residues changes soil fungal composition and decrease soil microbial co-ocurrence networks complexity.

Fusarium graminearum (Fg) can cause different diseases in cereals and maize crops worldwide, and a correct management of previous crop residues could decrease disease incidence and/or severity. Bacterial, fungal and Fusarium communities were studied by metabarcoding approach in 8 agricultural fields with wheat-maize rotation system in Brittany, France, during three years. Additionally, shift in microbial communities were evaluated under mesocosm experiments in soils amended or not with maize residues and/or Fg isolate. Bacterial communities composition were highly influenced by crop soil origin in both environmental and mesocosm soils, while bacteria co-occurrence network complexity was decreased by maize residues in environmental samples and Fg treatment in mesocosm samples. Maize residues altered slightly bacteria-fungi co-occurrence networks, while all treatments on mesoscosm experiments showed lower complexity in bacteria-fungi networks than Control Soil treatment. A clear input of fungal genera Epicoccum, Fusarium, Vishniacozyma, Articulospora, Papiliotrema, Sarocladium, Xenobotryosphaeria, Ramularia, Cladosporium, Cryptococcus and Bullera from maize residues to soil were observed for both environmental and mesocosm samples. Moreover, an increase of F. graminearum and F. avenaceum was observed in soils whe maize residues were presented. Finally, microbial co-occurrence networks reported some OTUs significant correlated to Fusarium spp. OTUs, such as those assigned to Epicoccum, Vishniacozyma and Sarocladium fungal genera, previously reported as efficient biocontrol agents versus Fusarium spp. Moreover, a decrease of complexity was observed for soil bacterial and bacterial-fungal networks due to maize addition in both environmental and mesocoms communities.

microbiology↗