Plants and other eukaryotes detected in herbivore faeces (collected 2018) from Iberá National Park, Argentina; inferred from ITS2 DNA metabarcoding data

Occurrence
Dernière version Publié par Ecoinformatics & Biodiversity, Department of Biology, Aarhus University le avr. 30, 2024 Ecoinformatics & Biodiversity, Department of Biology, Aarhus University
Date de publication:
30 avril 2024
Licence:
CC0 1.0

Téléchargez la dernière version de la ressource en tant quArchive Darwin Core (DwC-A), ou les métadonnées de la ressource au format EML ou RTF :

Données sous forme de fichier DwC-A (zip) télécharger 11 505 enregistrements dans Anglais (1 MB) - Fréquence de mise à jour: quand cela est nécessaire
Métadonnées sous forme de fichier EML télécharger dans Anglais (13 KB)
Métadonnées sous forme de fichier RTF télécharger dans Anglais (11 KB)

Description

DNA metabarcoding was used to identify plant diet contents of the faeces in a diverse herbivore community in Argentina's Iberá National Park. The sequence data was generated by sequencing amplicons of the nuclear ribosomal internal transcribed spacer region 2 (ITS2) amplified with the primers S2F and ITS4. The results indicate that despite concerns, there is minimal resource competition between native, reintroduced, and non-native herbivores. Analysis of their diets through DNA metabarcoding of fecal samples revealed varied feeding strategies and significant dietary differentiation among species, indicating that these herbivores are partitioning resources effectively. This suggests that the coexistence of different herbivores might contribute positively to ecosystem restoration without significant competition for resources. PCR reactions contained 0,04 U/μl AmpliTaq Gold (Life Technologies), 0.6 μM of each primer, 0.8 mg/ml bovine serum albumin (BSA), 1X Gold Buffer, 2.5 mM of MgCl, 0.2 mM of each dNTPs and 1 μl DNA extract in a 25 μl total reaction volume. For the plant extracts 2 µl template was used. Thermocycling conditions for plant ITS were: 95°C 5 min; (95°C 30s; 55°C 30s; 72°C 1 min) x 35 cycles; 72°C 7 min, 4°C forever. Both forward and reverse primers were designed with 80 or 96 unique tags (MID/barcodes) of 6 bp at the 5’ end using a restrictive dual-indexing approach. No primer tag (forward or reverse) was used more than once in any sequencing library and no combination of forward and reverse primer was reused in the study. For each multiplex sequencing library, PCR products were pooled (5 µl of each product), for a total of 8 to 9 pools/libraries per marker with up to 80 PCR products per pool. Each pool contained extraction blanks and PCR negatives. Prior to pooling a random selection of 25-50 PCR products were checked for amplification success and measured with Qubit dsDNA HS (High Sensitivity) Assay Kit (Invitrogen). PCR pools were purified with MinElute PCR purification kit (QIAGEN GmbH) and the length of PCR amplicons was verified on Bioanalyzer High-Sensitivity Chip (Agilent Technologies, Inc., Santa Clara, California, USA). Each pool was built into a sequencing library. Libraries were built using the TruSeq DNA PCR-Free Library Preparation Kit (Illumina), replacing all the manufacturer suggested clean-up step with MinElute purification. A final library purification was carried out to remove adapter dimers with HighPrep™ PCR Clean-up System (Magbio). Sequencing was carried out on MiSeq (Illumina Inc., San Diego, CA, USA), at the Danish National High-throughput DNA Sequencing Centre, using two 300 bp paired-end run. The ITS2 was allocated one full run, and trnL and CO1 were pooled in equimolar concentrations on another run. The data mediated in this dataset includes all detections passing the bioinformatic quality filtering. The data used for the associated scientific publication was filtered to exclude the following types of detections: non-plant, low specificity (less than 97% query coverage and/or less than 98% sequence identity with best match in ncbi), low read-abundance detections (fewer than 25 reads or less than 0.5% relative read-abundance in a sample), more than 1000 km outside of their known range. Samples only containing on plant species were also removed. Thus the data here is more complete, contains unidentified sequences and potential errors and contaminants. [This dataset was processed using the GBIF eDNA converter tool.]

Enregistrements de données

Les données de cette ressource occurrence ont été publiées sous forme dune Archive Darwin Core (Darwin Core Archive ou DwC-A), le format standard pour partager des données de biodiversité en tant quensemble dun ou plusieurs tableurs de données. Le tableur de données du cœur de standard (core) contient 11 505 enregistrements.

1 tableurs de données dextension existent également. Un enregistrement dextension fournit des informations supplémentaires sur un enregistrement du cœur de standard (core). Le nombre denregistrements dans chaque tableur de données dextension est illustré ci-dessous.

Occurrence (noyau)
11505
dnaDerivedData 
11505

Cet IPT archive les données et sert donc de dépôt de données. Les données et métadonnées de la ressource sont disponibles pour téléchargement dans la section téléchargements. Le tableau des versions liste les autres versions de chaque ressource rendues disponibles de façon publique et permet de tracer les modifications apportées à la ressource au fil du temps.

Versions

Le tableau ci-dessous naffiche que les versions publiées de la ressource accessibles publiquement.

Comment citer

Les chercheurs doivent citer cette ressource comme suit:

Mata J C, Davison C, Buitenwerf R, Svenning J, Broman Nielsen I, Frøslev T G (2024). Plants and other eukaryotes detected in herbivore faeces (collected 2018) from Iberá National Park, Argentina; inferred from ITS2 DNA metabarcoding data. Version 1.2. Ecoinformatics & Biodiversity, Department of Biology, Aarhus University. Occurrence dataset. https://danbif.au.dk/ipt/resource?r=plants_other_eukaryotes_from_herbivore_faeces_argentina&v=1.2

Droits

Les chercheurs doivent respecter la déclaration de droits suivante:

L’éditeur et détenteur des droits de cette ressource est Ecoinformatics & Biodiversity, Department of Biology, Aarhus University. En vertu de la loi, léditeur a abandonné ses droits par rapport à ces données et les a dédié au Domaine Public (CC0 1.0). Les utilisateurs peuvent copier, modifier, distribuer et utiliser ces travaux, incluant des utilisations commerciales, sans aucune restriction.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède lUUID GBIF suivante : e94f1b8b-671f-4ca4-9e4d-ffef194430da.  Ecoinformatics & Biodiversity, Department of Biology, Aarhus University publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec lapprobation du DanBIF - Danish Biodiversity Information Facility.

Mots-clé

Occurrence

Contacts

Julia Carolina Mata
  • Créateur
Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) & Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University
  • Ny Munkegade 114
DK-8000 Aarhus C
DK
Charles Davison
  • Créateur
Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) & Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University
  • Ny Munkegade 114
DK-8000 Aarhus C
DK
Robert Buitenwerf
  • Créateur
Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) & Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University
  • Ny Munkegade 114
DK-8000 Aarhus C
DK
Jens-Christian Svenning
  • Créateur
  • Director
Center for Biodiversity Dynamics in a Changing World (BIOCHANGE) & Center for Ecological Dynamics in a Novel Biosphere (ECONOVO), Department of Biology, Aarhus University
  • Ny Munkegade 114
DK-8000 Aarhus C
DK
Ida Broman Nielsen
  • Créateur
Globe Institute, University of Copenhagen
  • Oester Voldgade 5-7
1350 Copenhagen K
DK
Tobias Guldberg Frøslev
  • Personne De Contact
Globe Institute, University of Copenhagen
  • Oester Voldgade 5-7
1350 Copenhagen K
DK
Tobias Guldberg Frøslev
  • Personne De Contact
GBIF
DK
Isabel Calabuig
  • Distributeur
  • Node Manager, Data Curator
DanBIF, Natural History Museum of Denmark
Copenhagen
DK

Couverture géographique

Argentina

Enveloppe géographique Sud Ouest [-28,689, -57,469], Nord Est [-28,583, -57,243]

Métadonnées additionnelles

Identifiants alternatifs e94f1b8b-671f-4ca4-9e4d-ffef194430da
https://danbif.au.dk/ipt/resource?r=plants_other_eukaryotes_from_herbivore_faeces_argentina