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

Occurrence
Versão mais recente published by Ecoinformatics & Biodiversity, Department of Biology, Aarhus University on abr 30, 2024 Ecoinformatics & Biodiversity, Department of Biology, Aarhus University
Publication date:
30 de abril de 2024
Licença:
CC0 1.0

Baixe a última versão do recurso de dados, como um Darwin Core Archive (DwC-A) ou recurso de metadados, como EML ou RTF:

Dados como um arquivo DwC-A download 11.505 registros em English (1 MB) - Frequência de atualização: quando necessário
Metadados como um arquivo EML download em English (13 KB)
Metadados como um arquivo RTF download em English (11 KB)

Descrição

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.]

Registros de Dados

Os dados deste recurso de ocorrência foram publicados como um Darwin Core Archive (DwC-A), que é o formato padronizado para compartilhamento de dados de biodiversidade como um conjunto de uma ou mais tabelas de dados. A tabela de dados do núcleo contém 11.505 registros.

Também existem 1 tabelas de dados de extensão. Um registro de extensão fornece informações adicionais sobre um registro do núcleo. O número de registros em cada tabela de dados de extensão é ilustrado abaixo.

Occurrence (core)
11505
dnaDerivedData 
11505

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Versões

A tabela abaixo mostra apenas versões de recursos que são publicamente acessíveis.

Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

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

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

O editor e o detentor dos direitos deste trabalho é Ecoinformatics & Biodiversity, Department of Biology, Aarhus University. To the extent possible under law, the publisher has waived all rights to these data and has dedicated them to the Public Domain (CC0 1.0). Users may copy, modify, distribute and use the work, including for commercial purposes, without restriction.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: e94f1b8b-671f-4ca4-9e4d-ffef194430da.  Ecoinformatics & Biodiversity, Department of Biology, Aarhus University publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por DanBIF - Danish Biodiversity Information Facility.

Palavras-chave

Occurrence

Contatos

Julia Carolina Mata
  • Originador
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
  • Originador
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
  • Originador
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
  • Originador
  • 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
  • Originador
Globe Institute, University of Copenhagen
  • Oester Voldgade 5-7
1350 Copenhagen K
DK
Tobias Guldberg Frøslev
  • Ponto De Contato
Globe Institute, University of Copenhagen
  • Oester Voldgade 5-7
1350 Copenhagen K
DK
Tobias Guldberg Frøslev
  • Ponto De Contato
GBIF
DK
Isabel Calabuig
  • Distribuidor
  • Node Manager, Data Curator
DanBIF, Natural History Museum of Denmark
Copenhagen
DK

Cobertura Geográfica

Argentina

Coordenadas delimitadoras Sul Oeste [-28,689, -57,469], Norte Leste [-28,583, -57,243]

Metadados Adicionais

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