Pierre Taberlet

Pierre Taberlet
Université Grenoble Alpes · Laboratoire d'Ecologie Alpine

PhD

About

671
Publications
251,185
Reads
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62,457
Citations
Introduction
Additional affiliations
October 1994 - present
French National Centre for Scientific Research
Position
  • Senior Researcher
September 1988 - present
Université Grenoble Alpes
Position
  • Senior Researcher

Publications

Publications (671)
Article
Full-text available
Ice‐free areas are expanding worldwide due to the dramatic glacier shrinkage and undergo rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. It has been proposed that colonization dynamics of deglaciated terrains is different between surface and deep soils, but that the heterogeneity between...
Article
Full-text available
Ecological niche differences are necessary for stable species coexistence but are often dif- ficult to discern. Models of dietary niche differentiation in large mammalian herbivores invoke the quality, quantity, and spatiotemporal distribution of plant tissues and growth forms but are agnostic toward food plant species identity. Empirical support f...
Article
Full-text available
Vertebrate animals are known to consume other species' faeces, yet the role of such coprophagy in species dynamics remains unknown, not least due to the methodological challenges of documenting it. In a large-scale metabarcoding study of red fox and pine marten scats, we document a high occurrence of domestic dog DNA in red fox scats and investigat...
Article
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Assessing biodiversity loss and species extinction is necessary to warn society and raise awareness of the impacts of ongoing climate change. Prioritizing protected areas is the pragmatic and applicable management measure under the pressure of ongoing climate change and limited resources to conserve species at risk of extinction. We developed a nov...
Article
We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome‐b sequences of wi...
Preprint
Ice-free areas are increasing worldwide due to the dramatic glacier shrinkage and are undergoing rapid colonization by multiple lifeforms, thus representing key environments to study ecosystem development. Soils have a complex vertical structure. However, we know little about how microbial and animal communities differ across soil depths and develo...
Article
Diet studies are essential to understand animal ecology and ecosystem dynamics, especially in the case of large omnivores. These studies are particularly relevant in areas where human disturbance is intense and, thus, species dietary patterns might change due to the easy accessibility of food resources of human origin, which may hinder the ecosyste...
Article
Full-text available
Biodiversity assessments are indispensable tools for planning and monitoring conservation strategies. Camera traps (CT) are widely used to monitor wildlife and have proven their usefulness. Environmental DNA (eDNA)-based approaches are increasingly implemented for biomonitoring, combining sensitivity, high taxonomic coverage and resolution, non-inv...
Preprint
Full-text available
The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. It would help assessing the relative role of historical contingencies versus determinism in evolution. To bring new insights to this debate we set up a framework which aimed to compare the adaptive t...
Article
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Increasing evidence suggests that agricultural intensification is a threat to many groups of soil biota, but how the impacts of land-use intensity on soil organisms translate into changes in comprehensive soil interaction networks remains unclear. Here for the first time, we use environmental DNA to examine total soil multi-trophic diversity and fo...
Article
Freshwater macroinvertebrates provide valuable indicators for biomonitoring ecosystem change in relation to natural and anthropogenic drivers. DNA metabarcoding is an efficient approach for estimating such indicators, but its results may differ from morphotaxonomic approaches traditionally used in biomonitoring. Here we test the hypothesis that des...
Article
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Freshwater ecosystems are the most vulnerable worldwide and freshwater bivalves rank amongst the most threatened animals in the world. Surveying and monitoring freshwater bivalves are difficult tasks: they are difficult to find, hard to identify (taxonomic expertise is needed), and working underwater is technically challenging. It is therefore cruc...
Conference Paper
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Since the seminal paper in 1998 (Coolen and Overmann), sedimentary ancient DNA (sedaDNA) has become a powerful tool in paleoecology to reconstruct past changes in terrestrial and aquatic biodiversity. Still, sedaDNA is an emerging tool and there is a need for calibrations and validations to ensure the reliability of sedaDNA as a proxy to reconstruc...
Article
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Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. While the identification of food components of plant and animal origin has traditionally been conducted by macro- and microscopical approaches in case of incomplete digestion, molecular methods provide the potential to increase sensitivity and tax...
Article
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Les inventaires d’espèces dulçaquicoles par analyse de l’ADN environnemental (ADNe) se sont développés depuis une dizaine d’années. Nous présentons ici l’application de cette méthode à l’inventaire des Bivalves d’eau douce de France. De 2015 à 2018, nous avons réalisé plusieurs tests de terrain en France, en choisissant différentes conditions envir...
Article
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With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently be...
Article
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The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building...
Article
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Primary Biogenic Organic Aerosols (PBOA) were recently shown to be produced by only a few types of microorganisms, emitted by the surrounding vegetation in the case of a regionally homogeneous field site. This study presents the first comprehensive description of the structure and main sources of airborne microbial communities associated with tempo...
Article
Macroinvertebrate assemblages are the most common bioindicators used for stream biomonitoring, yet the standard approach exhibits several time‐consuming steps, including the sorting and identification of organisms based on morphological criteria. In this study, we examined if DNA metabarcoding could be used as an efficient molecular‐based alternati...
Article
Full-text available
The moose (Alces alces) is a dominant large mammalian herbivore in the world’s boreal zones. Moose exert significant browsing impacts on forest vegetation and are therefore often at the centre of wildlife-forestry conflicts. Consequently, understanding the drivers of their foraging behaviour is crucial for mitigating such conflicts. Management of m...
Article
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Leaf litter habitats shelter a great variety of organisms, which play an important role in ecosystem dynamics. However, monitoring species in leaf litter is challenging, especially in highly diverse environments such as tropical forests, because individuals may easily camouflage themselves or hide in the litter layer. Identifying species based on e...
Article
Metabarcoding of bulk or environmental DNA has great potential for biomonitoring freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensiv...
Article
Full-text available
DNA metabarcoding from the ethanol used to store macroinvertebrate bulk samples is a convenient methodological option in molecular biodiversity assessment and biomonitoring of aquatic ecosystems, as it preserves specimens and reduces problems associated with sample sorting. However, this method may be affected by errors and biases, which need to be...
Article
Full-text available
Knowledge of how animal species use food resources available in the environment increases our understanding of ecological processes. However, obtaining this information using traditional methods is a hard task for species feeding on a large variety of food items in highly diverse environments. We amplified the DNA of plants for 306 scat and 40 soil...
Data
Commented maps of all the freshwater bivalve species in France with distinction between traditional data and eDNA data
Article
Full-text available
Primary biogenic organic aerosols (PBOAs) represent a major fraction of coarse organic matter (OM) in air. Despite their implication in many atmospheric processes and human health problems, we surprisingly know little about PBOA characteristics (i.e., composition, dominant sources, and contribution to airborne particles). In addition, specific prim...
Chapter
The rainforests of the Neotropics shelter a vast diversity of plant, animal and microscopic species that provide critical ecosystem goods and services for both local and worldwide populations. These environments face a major crisis due to increased deforestation, pollution, and climate change, emphasizing the need for more effective conservation ef...
Preprint
Full-text available
Abstract. Primary biogenic organic aerosols (PBOA) represent a major fraction of coarse organic matter (OM) in air. Despite their implication in many atmospheric processes and human health problems, we surprisingly know little about PBOA characteristics (i.e., composition, dominant sources, and contribution to airborne-particles). In addition, spec...
Book
The rainforests of the Neotropics shelter a vast diversity of plant, animal and microscopic species that provide critical ecosystem goods and services for both local and worldwide populations. These environments face a major crisis due to increased deforestation, pollution, and climate change, emphasizing the need for more effective conservation ef...
Article
Full-text available
The ecological requirements of brown bears are poorly known in the Himalaya region, which complicates conservation efforts. We documented the diet of the Himalayan brown bear (Ursus arctos isabellinus) by combining classical scat analysis and a newly developed molecular genetic technique (the trnL approach), in Deosai National Park, Pakistan. Brown...
Article
Full-text available
The origin of modern disjunct plant distributions in the Brazilian Highlands with strong floristic affinities to distant montane rainforests of isolated mountaintops in the northeast and northern Amazonia and the Guyana Shield remains unknown. We tested the hypothesis that these unexplained biogeographical patterns reflect former ecosystem rearrang...
Article
The origin of modern disjunct plant distributions in the Brazilian Highlands with strong floristic affinities to distant montane rainforests of isolated mountaintops in the northeast and northern Amazonia and the Guyana Shield remains unknown. We tested the hypothesis that these unexplained biogeographical patterns reflect former ecosystem rearrang...
Article
Full-text available
High‐throughput sequencing of amplicons from environmental DNA samples permits rapid, standardized and comprehensive biodiversity assessments. However, retrieving and interpreting the structure of such datasets requires efficient methods for dimensionality reduction. Latent Dirichlet Allocation (LDA) can be used to decompose environmental DNA sampl...
Article
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Over the last decade, an increasing number of studies have used lake sediment DNA to trace past landscape changes, agricultural activities or human presence. However, the processes responsible for lake sediment formation and sediment properties might affect DNA records via taphonomic and analytical processes. It is crucial to understand these proce...
Article
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The sociopolitical acceptance necessary for the conservation of controversial species requires scientific knowledge that disentangles empirical facts from myth and misinformation. An epitome of such, the grey wolf (Canis lupus), had been eradicated from most of Western Europe by the early 20th century. However, a few mysteriously re-appeared in the...
Article
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Soil microbial communities play a key role in ecosystem functioning but still little is known about the processes that determine their turnover (β‐diversity) along ecological gradients. Here, we characterize soil microbial β‐diversity at two spatial scales and at multiple phylogenetic grains to ask how archaeal, bacterial and fungal communities are...
Article
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Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However WGS can still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by te...
Article
Large herbivores that survived the Pleistocene/Holocene transition are hypothesized to have been forced to take refuge, as a result of environmental changes and human pressure, into forest habitats. Today, there is an open question of the degree to which extant large herbivores are well adapted to the forests that allowed for the herbivores’ persis...
Article
Full-text available
A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical...
Article
Full-text available
In the last decade, eDNA and metabarcoding have opened new avenues to biodiversity studies; amphibians and reptiles are animals for which these new approaches have allowed great leaps forward. Here we review different approaches through which eDNA can be used to study amphibians, reptiles and many more organisms. eDNA is often used to evaluate the...
Article
Full-text available
Pellet counts are widely used to monitor ungulates but rely on the assumption that pellets of different species are correctly identified in the field. Recent studies question this assumption using DNA barcoding techniques to check field identification rates. For Europe, which is undergoing a rapid shift towards more diverse ungulate assemblages, su...
Article
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Environmental DNA (eDNA) metabarcoding is a promising tool to estimate aquatic biodiversity. It is based on the capture of DNA from a water sample. The sampled water volume, a crucial aspect for efficient species detection, has been empirically variable (ranging from few centiliters to tens of liters). This results in a high variability of sampling...
Article
Full-text available
Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent ex...
Article
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Tropical forests shelter an unparalleled biological diversity. The relative influence of environmental selection (i.e. abiotic conditions, biotic interactions) and stochastic‐distance dependent neutral processes (i.e. demography, dispersal) in shaping communities has been extensively studied for various organisms, but has rarely been explored acros...
Article
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Environmental DNA retrieved from modern soils (eDNA) and late-Quaternary palaeosols and sediments (aDNA and sedaDNA) promises insight into the composition of present and past terrestrial biotic communities, but few studies address the spatial relationship between recovered eDNA and contributing organisms. Svalbard’s vascular plant flora is well kno...
Article
Full-text available
Life history changes may change resource use. Such shifts are not well understood in the dung beetles, despite recognised differences in larval and adult feeding ability. We use the flightless dung beetle Circellium bacchus to explore such shifts, identifying dung sources of adults using DNA metabarcoding, and comparing these with published account...