Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: Evidence from DNA metabarcoding, Molecular Ecology, vol.27, pp.815-825, 2018. ,
Promises and pitfalls of using high-throughput sequencing for diet analysis, Molecular Ecology Resources, vol.19, issue.2, pp.327-348, 2019. ,
Scrutinizing key steps for reliable metabarcoding of environmental samples, Methods in Ecology and Evolution, vol.9, pp.134-147, 2018. ,
Diet diversification shapes broad-scale distribution patterns in European bats, 2019. ,
Basic local alignment search tool, Journal of Molecular Biology, vol.215, issue.05, pp.80360-80362, 1990. ,
The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus, PLoS ONE, vol.14, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02627771
Why the COI barcode should be the community DNA metabarcode for the metazoa, Molecular Ecology, vol.27, pp.3968-3975, 2018. ,
Trophic requirements beyond foraging habitats: The importance of prey source habitats in bat conservation, Biological Conservation, vol.191, pp.512-519, 2015. ,
, GenBank. Nucleic Acids Research, vol.36, pp.25-30, 2008.
Novel insights into the diet of the Pyrenean desman (Galemys pyrenaicus) using next-generation sequencing molecular analyses, Journal of Mammalogy, vol.98, pp.1497-1507, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-02609535
Environmental DNA for wildlife biology and biodiversity monitoring, Trends in Ecology & Evolution, vol.29, pp.358-367, 2014. ,
Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure, Molecular Ecology Resources, vol.18, pp.1050-1063, 2018. ,
Molecular diet analysis of two African free-tailed bats (Molossidae) using high throughput sequencing, PLoS ONE, vol.6, 2011. ,
DNA metabarcoding of insects and allies: An evaluation of primers and pipelines, Bulletin of Entomological Research, vol.105, pp.1-11, 2015. ,
Metabarcoding a diverse arthropod mock community, Molecular Ecology Resources, vol.19, pp.711-727, 2019. ,
Molecular detection of trophic interactions: Emerging trends, distinct advantages, significant considerations and conservation applications, Evolutionary Applications, vol.7, pp.1144-1157, 2014. ,
Species on the menu of a generalist predator, the eastern red bat (Lasiurus borealis): Using a molecular approach to detect arthropod prey, Molecular Ecology, vol.18, pp.2532-2542, 2009. ,
The diet of Myotis lucifugus across Canada: Assessing foraging quality and diet variability, Molecular Ecology, vol.23, pp.3618-3632, 2014. ,
An inordinate fondness for beetles? Variation in seasonal dietary preferences of night-roosting big brown bats (Eptesicus fuscus), Molecular Ecology, vol.23, pp.3633-3647, 2014. ,
Environmental metabarcodes for insects: In silico PCR reveals potential for taxonomic bias, Molecular Ecology Resources, vol.14, pp.1160-1170, 2014. ,
A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies, Molecular Ecology Resources, vol.17, pp.146-159, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01681595
One-locus-several-primers: A strategy to improve the taxonomic and haplotypic coverage in diet metabarcoding studies, Ecology and Evolution, vol.9, pp.4603-4620, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02109732
Quantification of damage in DNA recovered from highly degraded samples -A case study on DNA in faeces, Frontiers in Zoology, vol.3, 2006. ,
DNA metabarcoding and the cytochrome c oxidase subunit I marker: Not a perfect match, Biology Letters, vol.10, 2014. ,
UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, vol.27, pp.2194-2200, 2011. ,
Validation of COI metabarcoding primers for terrestrial arthropods, PeerJ Preprints, vol.7, 2019. ,
PrimerMiner: An r package for development and in silico validation of DNA metabarcoding primers, Methods in Ecology and Evolution, vol.8, pp.622-626, 2016. ,
Validation and development of COI metabarcoding primers for freshwater macroinvertebrate bioassessment, 2017. ,
Scaling up DNA metabarcoding for freshwater macrozoobenthos monitoring, Freshwater Biology, vol.64, pp.380-387, 2019. ,
Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01780425
New environmental metabarcodes for analysing soil DNA: Potential for studying past and present ecosystems, Molecular Ecology, vol.21, pp.1821-1833, 2012. ,
FROGS: Find, rapidly, OTUs with galaxy solution, Bioinformatics, vol.34, pp.1287-1294, 2018. ,
Determining diet from faeces: Selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus), PLoS ONE, vol.13, 2018. ,
Coexistence of two sympatric cryptic bat species in French Guiana: Insights from genetic, acoustic and ecological data, BMC Evolutionary Biology, vol.18, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01936895
Conserved primers for PCR amplification of mitochondrial DNA from different invertebrate phyla, Molecular Marine Biology and Biotechnology, vol.3, pp.294-299, 1994. ,
Evaluating metabarcoding to analyse diet composition of species foraging in anthropogenic landscapes using Ion Torrent and Illumina sequencing, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02107284
Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis, Molecular Ecology Resources, vol.18, pp.474-489, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02626543
16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife. mSystems, vol.1, pp.32-48, 2016. ,
A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces, Mammalian Biology -Zeitschrift Für Säugetierkunde, vol.80, pp.505-509, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-02633337
Geoffroy's bat, Myotis emarginatus, preys preferentially on spiders in multistratified dense habitats: A study of foraging bats in the Mediterranean, Folia Zoologica, vol.60, pp.17-24, 2011. ,
A minimalist barcode can identify a specimen whose DNA is degraded, Molecular Ecology Notes, vol.6, pp.959-964, 2006. ,
Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods, Molecular Ecology, vol.25, pp.3101-3119, 2016. ,
Increasing the utility of barcode databases through high-throughput sequencing of amplicons from dried museum specimens, 2018. ,
, Biological Control, vol.122, pp.93-100, 2018.
Biological identifications through DNA barcodes, Proceedings of the Royal Society of London. Series B: Biological Sciences, vol.270, pp.313-321, 2003. ,
PCR protocols: A guide to methods and applications, 2012. ,
Prey selection by the greater horseshoe bat (Rhinolophus ferrumequinum): Optimal foraging by echolocation?, Journal of Animal Ecology, vol.59, pp.587-602, 1990. ,
An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals, Molecular Ecology Resources, vol.19, issue.1, pp.176-190, 2018. ,
Molecular detection of invertebrate prey in vertebrate diets: Trophic ecology of Caribbean island lizards, Molecular Ecology Resources, vol.15, pp.903-914, 2015. ,
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, pp.3059-3066, 2002. ,
Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces, Ecology and Evolution, vol.7, pp.8588-8598, 2017. ,
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, vol.28, pp.1647-1649, 2012. ,
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform, Nucleic Acids Research, vol.40, issue.1, pp.3-3, 2012. ,
Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples, New Zealand Journal of Ecology, vol.42, pp.10-50, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02302242
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: Application for characterizing coral reef fish gut contents, Frontiers in Zoology, vol.10, issue.1, p.34, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01268031
Fungal community analysis by high-throughput sequencing of amplified markers -A user's guide, New Phytologist, vol.199, pp.288-299, 2013. ,
FLASH: Fast length adjustment of short reads to improve genome assemblies, Bioinformatics, vol.27, pp.2957-2963, 2011. ,
Swarm: Robust and fast clustering method for amplicon-based studies, PeerJ, vol.2, 2014. ,
New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods, Molecular Ecology Resources, vol.19, issue.1, pp.90-104, 2019. ,
Establishing insect community composition using metabarcoding of soil samples, and preservative ethanol and homogenate from Malaise trap catches: Surprising inconsistencies between methods, 2019. ,
Creating error-proof indexes for high throughput sequencing, 2019. ,
Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet.journal, vol.17, pp.10-12, 2011. ,
Chirosurveillance: The use of native bats to detect invasive agricultural pests, PLoS ONE, vol.12, 2017. ,
How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis, Molecular Ecology, vol.28, pp.165-175, 2018. ,
Diet tracing in ecology: Method comparison and selection, Methods in Ecology and Evolution, vol.9, pp.278-291, 2018. ,
Molecular scatology: How to improve prey DNA detection success in avian faeces?, Molecular Ecology Resources, vol.11, pp.620-628, 2011. ,
Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies, PLoS ONE, vol.9, 2014. ,
The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative, Molecular Ecology, vol.28, pp.407-419, 2019. ,
Who is eating what: Diet assessment using next generation sequencing, Molecular Ecology, vol.21, 1931. ,
Evaluation of PCR-generated chimeras, mutations, and heteroduplexes with 16S rRNA gene-based cloning, Applied and Environment Microbiology, vol.67, pp.880-887, 2001. ,
ecoPrimers: Inference of new DNA barcode markers from whole genome sequence analysis, Nucleic Acids Research, vol.39, p.145, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00746852
VSEARCH: A versatile open source tool for metagenomics. PeerJ, 4, e2584, 2016. ,
From feces to data: A metabarcoding method for analyzing consumed and available prey in a bird-insect food web, Ecology and Evolution, vol.9, pp.631-639, 2019. ,
, , 2013.
, Noninvasive Method for a Statewide Survey of Eastern Hellbenders Cryptobranchus alleganiensis Using Environmental DNA [WWW Document, International Journal of Zoology, pp.1-6, 2013.
Carnivore diet analysis based on next-generation sequencing: Application to the leopard cat (Prionailurus bengalensis) in Pakistan, Molecular Ecology, vol.21, pp.1951-1965, 2012. ,
Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform, Scientific Reports, vol.5, pp.1-7, 2015. ,
Deciphering host-parasitoid interactions and parasitism rates of crop pests using DNA metabarcoding, Scientific Reports, vol.9, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02621788
DNA sequencing to help identify crop pests and their natural enemies in agro-ecosystems: The case of the millet head miner Heliocheilus albipunctella (Lepidoptera: Noctuidae) in sub-Saharan Africa, Biological Control, vol.121, pp.199-207, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02627984
, , 2012.
, Molecular Ecology, vol.21, pp.1789-1793
Towards next-generation biodiversity assessment using DNA metabarcoding, Molecular Ecology, vol.21, pp.2045-2050, 2012. ,
Short COI markers for freshwater macroinvertebrate metabarcoding, Metabarcoding and Metagenomics, vol.1, 2017. ,
Molecular dietary analysis of the endangered Ozark big-eared bat, 2016. ,
, Acta Chiropterologica, vol.18, pp.181-191
Table for five, please: Dietary partitioning in boreal bats, Ecology and Evolution, vol.8, pp.10914-10937, 2018. ,
Blocking primers to enhance PCR amplification of rare sequences in mixed samples -A case study on prey DNA in Antarctic krill stomachs, Frontiers in Zoology, vol.5, 2008. ,
Species from feces: Order-wide identification of chiroptera from guano and other non-invasive genetic samples, PLoS ONE, vol.11, 2016. ,
Guano morphology reveals ecological information in British bats, 2019. ,
Incidence and taxonomic richness of mosquitoes in the diets of little brown and big brown bats, Journal of Mammalogy, vol.99, pp.668-674, 2018. ,
Biodiversity soup: Metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring, Methods in Ecology and Evolution, vol.3, issue.4, pp.613-623, 2012. ,
Combining noninvasive genetics and a new mammalian sex-linked marker provides new tools to investigate population size, structure and individual behaviour: An application to bats, Molecular Ecology Resources, vol.18, pp.217-228, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01769650
Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces, Molecular Ecology Resources, vol.11, pp.236-244, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02650907