Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fie...
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Language: | English |
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Dryad
2017
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Online Access: | https://doi.org/10.5061/dryad.kv02g |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::23f98d67e7d469f495bcbe4f6b34f573 2023-05-15T15:37:52+02:00 Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis Galan, Maxime Pons, Jean-Baptiste Tournayre, Orianne Pierre, Eric Leuchtmann, Maxime Pontier, Dominique Charbonnel, Nathalie 2017-12-27 https://doi.org/10.5061/dryad.kv02g en eng Dryad http://dx.doi.org/10.5061/dryad.kv02g https://dx.doi.org/10.5061/dryad.kv02g lic_creative-commons 10.5061/dryad.kv02g oai:easy.dans.knaw.nl:easy-dataset:98049 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:98049 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 Myotis emarginatus high-throughput sequencing (HTS) Rhinolophus ferrumequinum Myotis bechsteinii Predator-prey interactions Plecotus auritus False positives Barbastella barbastellus Myotis myotis Miniopterus schreibersii Myotis alcathoe Rhinolophus euryale Arthropoda Pipistrellus kuhlii Myotis daubentonii Myotis mystacinus Eptesicus serotinus Pipistrellus pipistrellus Environmental DNA (eDNA) Chiroptera Myotis nattereri Rhinolophus hipposideros Life sciences medicine and health care Western France Poitou-Charentes envir geo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2017 fttriple https://doi.org/10.5061/dryad.kv02g 2023-01-22T17:23:15Z Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the ‘all at once’ taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing ‘chirosurveillance’ and conservation strategies. MiSeq raw sequences of the COI minibarcode from the faecal pellets of 357 bats from Western France (part 1 to 2)This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each faecal pellet in triplicate using the MiSeq platform. The 1162 multiplexed PCR products were ... Dataset Barbastella barbastellus Myotis nattereri Pipistrellus pipistrellus Unknown |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
Myotis emarginatus high-throughput sequencing (HTS) Rhinolophus ferrumequinum Myotis bechsteinii Predator-prey interactions Plecotus auritus False positives Barbastella barbastellus Myotis myotis Miniopterus schreibersii Myotis alcathoe Rhinolophus euryale Arthropoda Pipistrellus kuhlii Myotis daubentonii Myotis mystacinus Eptesicus serotinus Pipistrellus pipistrellus Environmental DNA (eDNA) Chiroptera Myotis nattereri Rhinolophus hipposideros Life sciences medicine and health care Western France Poitou-Charentes envir geo |
spellingShingle |
Myotis emarginatus high-throughput sequencing (HTS) Rhinolophus ferrumequinum Myotis bechsteinii Predator-prey interactions Plecotus auritus False positives Barbastella barbastellus Myotis myotis Miniopterus schreibersii Myotis alcathoe Rhinolophus euryale Arthropoda Pipistrellus kuhlii Myotis daubentonii Myotis mystacinus Eptesicus serotinus Pipistrellus pipistrellus Environmental DNA (eDNA) Chiroptera Myotis nattereri Rhinolophus hipposideros Life sciences medicine and health care Western France Poitou-Charentes envir geo Galan, Maxime Pons, Jean-Baptiste Tournayre, Orianne Pierre, Eric Leuchtmann, Maxime Pontier, Dominique Charbonnel, Nathalie Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis |
topic_facet |
Myotis emarginatus high-throughput sequencing (HTS) Rhinolophus ferrumequinum Myotis bechsteinii Predator-prey interactions Plecotus auritus False positives Barbastella barbastellus Myotis myotis Miniopterus schreibersii Myotis alcathoe Rhinolophus euryale Arthropoda Pipistrellus kuhlii Myotis daubentonii Myotis mystacinus Eptesicus serotinus Pipistrellus pipistrellus Environmental DNA (eDNA) Chiroptera Myotis nattereri Rhinolophus hipposideros Life sciences medicine and health care Western France Poitou-Charentes envir geo |
description |
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the ‘all at once’ taxonomic identification of bats and their arthropod preys for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity, and amplification biases. Our parallel identification strategy of predators and preys reduces the risk of mis-assigning preys to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing ‘chirosurveillance’ and conservation strategies. MiSeq raw sequences of the COI minibarcode from the faecal pellets of 357 bats from Western France (part 1 to 2)This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each faecal pellet in triplicate using the MiSeq platform. The 1162 multiplexed PCR products were ... |
format |
Dataset |
author |
Galan, Maxime Pons, Jean-Baptiste Tournayre, Orianne Pierre, Eric Leuchtmann, Maxime Pontier, Dominique Charbonnel, Nathalie |
author_facet |
Galan, Maxime Pons, Jean-Baptiste Tournayre, Orianne Pierre, Eric Leuchtmann, Maxime Pontier, Dominique Charbonnel, Nathalie |
author_sort |
Galan, Maxime |
title |
Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis |
title_short |
Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis |
title_full |
Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis |
title_fullStr |
Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis |
title_full_unstemmed |
Data from: Metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis |
title_sort |
data from: metabarcoding for the parallel identification of several hundred predators and their preys: application to bat species diet analysis |
publisher |
Dryad |
publishDate |
2017 |
url |
https://doi.org/10.5061/dryad.kv02g |
genre |
Barbastella barbastellus Myotis nattereri Pipistrellus pipistrellus |
genre_facet |
Barbastella barbastellus Myotis nattereri Pipistrellus pipistrellus |
op_source |
10.5061/dryad.kv02g oai:easy.dans.knaw.nl:easy-dataset:98049 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:98049 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 |
op_relation |
http://dx.doi.org/10.5061/dryad.kv02g https://dx.doi.org/10.5061/dryad.kv02g |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.kv02g |
_version_ |
1766368542649745408 |