Biology subjects

Petit, E. J.

Publications and source records attributed to Petit, E. J..

8 recordsLinked to original sources

bioRxiv2026

Variable performances of commercial eDNA inventories challenge their use for surveying stream fish communities

1. Environmental DNA (eDNA) metabarcoding of water samples is increasingly used to detect fish species in streams. Several studies have concluded that it can outperform traditional inventory methods and recommend using it at large scales for fish-based ecological assessments. However, there is no standard protocol that can guarantee sufficient detection rates and repeatability, despite companies offering an extensive range of analyses. 2. We compared eDNA metabarcoding performed by four companies. Following their guidelines, samples were collected in a small tropical stream in the Maroni River (French Guiana) that hosts a species-rich fish community. We compared their inventories to each other and to a list of species captured during an extensive fish inventory performed immediately after sampling eDNA, as well as to current data on the species distributions. 3. The number of species detected by eDNA metabarcoding ranged from 5 to 48 among the companies, but these inventories contained many inaccuracies. All companies combined, 63 species were detected, of which 10 (16%) had never been reported in the Maroni River. The extensive inventory identified 50 species in the local fish community, of which 16-46 were not detected by eDNA metabarcoding (i.e. false negative detection rate of 32%-92% among the companies). 4. Reanalysis of raw sequencing data decreased differences among companies greatly, highlighting the importance of using a comprehensive and accurate DNA barcode database to assign species. Dissimilarity indices, calculated to compare the local fish community (based on presence/absence or fish catches) to eDNA detection, revealed large differences regardless of the company. 5. Summary and applications. The large percentage of species not detected by eDNA metabarcoding of water samples could strongly bias fish-diversity inventories in streams that host species-rich communities. This issue is not well documented in the literature, and we recommend that similar studies in the future focus on other stream contexts. The large differences between commercial eDNA inventories and the local fish community challenge the use of eDNA metabarcoding for fish-based ecological assessments of streams. The variable performance of eDNA companies indicates the need for a standard protocol and access to a comprehensive DNA database before beginning large-scale eDNA programmes. Highlights- eDNA metabarcoding of water samples is widely used to detect species in streams - Detection performances of 4 private companies were compared to an exhaustive fish inventory - The number of undetected species varies from 32 to 92% depending on the company - Such discrepancies challenge the use of eDNA for fish-based ecological assessments

ecology↗

bioRxiv2024

The geometry of gametic dispersal in a flying mammal, Rhinolophus hipposideros

Dispersal influences population and evolutionary dynamics, with effects that depend on the dispersal strategies through which gene flow occurs. In some species, mating partners move exclusively for mating, dispersing genes but not individuals. This is the case in many bat species, of which the lesser horseshoe bat (Rhinolophus hipposideros) shows a genetic structure at a fine spatial scale suggesting restricted dispersal. We investigated how natal and mating dispersal shape gene flow in this species in two metapopulations using paternity and population assignments. Half of the inferred paternities were intra-colonial and gave an estimate of the mean mating dispersal distance of around 11 km, explaining the observed genetic structure. Complete gametic dispersal distances were further estimated by combining natal with mating dispersal distances. The resulting gametic dispersal kernels showed a mean distance of around 20 km and a fat-tailed distribution typical of an excess of long-distance dispersal movements. It is the first time that natal and mating dispersal distances have been separately estimated and then combined in animals, documenting quantitatively how mating dispersal decorrelates gene and individual flows. It is important to consider this mechanism to explain dispersal evolution.

evolutionary biology↗

bioRxiv2024

Reproductive modes of polyploid Ludwigia grandiflora subsp. hexapetala in western Europe: the effects of a late-acting self-incompatibility system and its absence on genetic diversity within populations

Reproductive mode, i.e., the proportion of individuals produced by clonality, selfing and outcrossing in populations, determines how hereditary material is transmitted through generations. It shapes genetic diversity and its structure over time and space, which can be used to infer reproductive modes. Ludwigia grandiflora subsp. hexapetala (Lgh) is a partially clonal, polyploid, hermaphroditic, and heteromorphic plant that recently colonized multiple countries worldwide. In western Europe, individuals are either self-incompatible caused by a late-acting self-incompatibility (LSI) system developing long-styled flowers, or self-compatible (SC), with short-styled flowers. In this study, we genotyped 53 long- and short-styled populations newly colonizing France and northern Spain using SNPs to estimate rates of clonality, selfing and outcrossing. We found that populations reproduced mainly clonally but with a high diversity of genotypes along with rates of sexuality ranging from 10% up to 40%. We also found evidence for local admixture between long- and short-styled populations in a background of genetic structure between floral morphs that was twice the level found within morphs. Long- and short-styled populations showed similar rates of clonality but short-styled populations presented significantly higher rates of selfing, as expected considering their breeding system, and despite the small rates of failure of the LSI system. Within the 53 studied populations, the 13 short-styled populations had fewer effective alleles, lower observed heterozygosity, and higher inbreeding coefficients, linkage disequilibrium and estimates of selfing than what was found in long-styled populations. These results emphasize the necessity to consider the variation of reproductive modes when managing invasive plant species. The overall maintenance of higher genetic diversity with the possibility of maintaining populations clonally in the absence of compatible partners may explain why long-styled individuals seem to be more prevalent in all newly expanding populations worldwide. Beyond Lgh, our methodological approach may inspire future studies to assess the reproductive modes in other autopolyploid populations.

evolutionary biology↗

bioRxiv2022

Determinants of survival and dispersal along the range expansion of a biological invasion

Projecting and managing the future response of biological systems to global change requires a mechanistic understanding of how climate and ecology jointly drive species demography and range dynamics. Such knowledge is particularly crucial when it comes to invasive species, which expansion may have far-reaching consequences for recipient ecosystems. Here, we use mark recapture in replicated outdoor mesocosms to examine how survival and dispersal, two key drivers of population and range dynamics, respond to climate and ecology in the invasive red swamp crayfish (Procambarus clarkii) along an invasion gradient. We show that crayfish survival probability increased with (i) increasing body size at high (but not low) crayfish density and (ii) with warmer temperatures, and decreased (i) with increasing body condition and (ii) under higher crayfish density. Overland dispersal probability by crayfish increased with increasing (i) body-size, (ii) body condition and (iii) temperatures. In contrast, crayfish from range-edge and range-core habitats had similar survival and overland dispersal probabilities, suggesting no evolution of the crayfish expansion potential along the invasion gradient. Our results highlight that species population dynamics and range shifts in a changing world are driven by joint contributions from both climate and ecology. In P. clarkii, global warming will simultaneously promote both a demographic increase and a geographic range expansion, especially in populations dominated by large-bodied individuals. In already-invaded ecosystems, selective harvesting of large-bodied crayfish can potentially reduce the dispersal potential of populations and, after a few generations, might further induce an evolutionary decline in fitness traits that is desirable from a management perspective. Open research statementUpon acceptance of this manuscript, data and codes will be made publicly available online on the INRAE data repository (https://entrepot.recherche.data.gouv.fr/dataverse/inrae).

ecology↗

bioRxiv2022

Mark loss can strongly bias demographic rates in multi-state models: a case study with simulated and empirical datasets

O_LIThe development of methods for individual identification in wild species and the refinement of Capture-Mark-Recapture (CMR) models over the past few decades have greatly improved the assessment of population demographic rates to address ecological and conservation questions. In particular, multi-state models, which offer flexibility in analysing complex study systems, have gained popularity within the ecological community. In this study, we focus on the issue of mark loss and the associated recycling of remarked individuals, which requires further exploration given the increasing use of these models. C_LIO_LITo fill this knowledge gap, we employed a wide range of simulation scenarios that reflect commonly encountered real case studies, drawing inspiration from the survival rates of 700 vertebrate species. Using a multi-state, Arnason-Schwartz (AS) modelling framework, we estimated the effects of mark loss and recycled individuals on parameter estimates. We assessed parameter bias by simulating a metapopulation system with varying capture and survival rates. Additionally, we demonstrated how mark loss can be easily estimated and accounted for using a 10-year empirical CMR dataset of bats. The bats were individually identified using Passive Integrated Transponder (PIT) tag technology as potentially lost marks and multi-locus genotypes as permanent marks. C_LIO_LIOur simulation results revealed that the occurrence of bias and the affected parameters were highly dependent on the study system, making it difficult to establish general rules to predict bias a priori. The model structure and the interdependency among parameters pose challenges in predicting the impact of bias on estimates. C_LIO_LIOur findings underscore the importance of assessing the effect of mark loss when using AS models. Ignoring such violations of model assumptions can have significant implications for ecological inferences and conservation policies. In general, the use of permanent marks, such as genotypes, should always be preferred when modelling population dynamics. If that is not feasible, an alternative is to combine two independent types of temporary marks, such as PIT tags and bands. C_LIO_LIAnalysis of our empirical dataset on Myotis myotis bats revealed that tag loss is higher in juveniles than in adults during the first year after tagging. The use of surgical glue to close the injection hole reduces tag loss rate from 28% to 19% in juveniles, while it has no effect on the tag loss rate in adults ([~]10%). The main bias observed in our metapopulation system appears in the survival rate, with up to a 20% underestimation if tag loss is not accounted for. C_LI

ecology↗

bioRxiv2019

Population-level sensitivity to landscape variables reflects individual-based habitat selection in a woodland bat species

Understanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat quality is generally only investigated at the individual scale, as it is the case for the lesser horseshoe bat (Rhinolophus hipposideros), a species of conservation concern. Using a statistical modelling approach and census data of 94 lesser horseshoe bat colonies located in Brittany (France), we analysed the effect of landscape composition and configuration on the demographic components of surveyed maternity colonies (i.e. colony size, fecundity and growth rate), and compared our result to those provided by individual-based studies. Our results validated that the landscape in a 500-meter buffer around colonies (core foraging area) is crucial for population size and dynamics, and confirmed the positive influence of broadleaved woodland proportion on bat colony size. We revealed a positive effect of lakeshores and riverbanks on colony size and growth rate, underlying the importance of these habitats for the long-term conservation of this non-migratory forest species. Importantly, our results refine previous knowledge concerning the threat posed by the intensification of human activities (e.g. urbanization, agriculture, habitat fragmentation), and highlight the negative effect of large and regular patches of artificial and crop lands and of open land patches shape complexity on all demographic variables investigated. While our results support the dependence of population dynamics and associated conservation management to individual behaviour and sensitivity, environmental responses differed between the population metrics investigated, showing that efficient range prediction will require to fully grasp the complexity of the interaction between landscape and the different population dynamic parameters.

ecology↗

bioRxiv2018

Measuring genetic differentiation from Pool-seq data

The recent advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many non-model species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator of FST for Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased, and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Last, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpin Cottus asper, we show how the use of an unbiased FST estimator may question the interpretation of population structure inferred from previous analyses.

evolutionary biology↗

bioRxiv2017

Effective population size and durability of plant resistances in the potato cyst nematode Globodera pallida

O_LIThe effective size of a population is the size of an ideal population which would drift at the same rate as the real population. The balance between selection and genetic drift depends on the population size expressed as the genetically effective population size (Ne), rather than the real numbers of individuals in the population (N).\nC_LIO_LIThe objectives of the present study were to estimate Ne in the potato cyst nematode Globodera pallida using artificial populations and to explore the link between Ne and the durability of plant resistances.\nC_LIO_LIUsing a temporal method on 24 independent pairs of initial and final populations, the median Ne was 58 individuals.\nC_LIO_LINe is commonly lower than N but in our case the Ne/N ratio was extremely low because G. pallida populations deviate in structure from the assumptions of the ideal population by having unequal sex-ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a low Ne could be important for the control of phytoparasitic nematodes because G. pallida populations will have a low capacity to adapt to changing environments unless selection intensity is very strong, which could be greatly beneficial for long-term use of plant resistances.\nC_LI

evolutionary biology↗