DOI: 10.5281/zenodo.14967375
title: Metabarcoding arthropods in agroecosystems in Southern Ontario, Canada

description: This dataset was generated as part of the Food from Thought ecosystem genomics project (2019-2022) which’s overarching goal was to develop innovative ways to link reliable field estimates of organismal abundance with evidence of biodiversity obtained through metabarcoding (this dataset), eDNA, and image analysis of bulk samples.

By gathering data through metabarcoding of malaise trap samples across sites in southern Ontario that span the gradient of from intense and highly productive corn-soybean farming to alternative land use farms with varying amounts natural restoration of marginal lands, this work generated one of deepest datasets available for comparison with factors influencing arthropod biodiversity in relation to farming practices, climatic variation, physical features, and landscape heterogeneity. This work established elements of a standardized methodology for biodiversity monitoring and environmental impact assessment, identified key uncertainties with respect to field metrics based on DNA-based methodologies, and outlined a framework for early warning of insect pest outbreaks and/or decline of beneficial insect species.

The two datasets represent DNA-based occurrences in Darwin Core Format (dwc). The first is a dwc occurrence dataset and the second the corresponding DNA-derived extension table based on GBIF recommendations. 






Column label



Column description





basisOfRecord



Nature of data record - “MaterialSample”





occurrenceID (Occurrence core)



A unique identifier for the occurrence.





eventID (Occurrence core)



An identifier for the set of information associated with an Event (sample number).





eventDate (Occurrence core)



Date when the sample was retrieved from trap.





recordedBy (Occurrence core)



Organization or persons responsible for recording occurrence “Centre for Biodiversity Genomics”





organismQuantity (Occurrence core)



Number of reads of this OTU in this sample.





organismQuantityType (Occurrence core)



"DNA sequence reads".





sampleSizeValue (Occurrence core)



Total number of reads in sample





sampleSizeUnit (Occurrence core)



“DNA sequence reads”





materialSampleID (Occurrence core)



Biosample ID obtained from NCBI SRA





samplingProtocol (Occurrence core)



Sampling method“Malaise Trap”





decimalLatitude (Occurrence core)



The geographic latitude where the dwc:Event occurred (exact locality of the sample collection).





decimalLongitude (Occurrence core)



The geographic longitude where the dwc:Event occurred (exact locality of the sample collection).





country (Occurrence core)



A name of the country where the sampling occurred ("Canada").





stateProvince (Occurrence core)



A name of the province where the sampling occurred ("Ontario").





locationID (Occurrence core)



Code for a specific location





geodeticDatum (Occurrence core)



The geodetic datum ("WGS84").





scientificName (Occurrence core)



identifier from BOLD (BIN)





kingdom (Occurrence core)



The full scientific name of the kingdom in which the taxon is classified.





phylum (Occurrence core)



The full scientific name of the phylum in which the taxon is classified.





class (Occurrence core)



The full scientific name of the class in which the taxon is classified.





order (Occurrence core)



The full scientific name of the order in which the taxon is classified.





family (Occurrence core)



The full scientific name of the family in which the taxon is classified.





subfamily (Occurrence core)



The full scientific name of the subfamily in which the taxon is classified.





genus (Occurrence core)



The full scientific name of the genus in which the taxon is classified.





verbatimIdentification (Occurrence core)



The full scientific name of the species in which the taxon is classified.





habitat (Occurrence core)



A category or description of the habitat in which the dwc:Event occurred ("ALUS” - Alternative Landuse Farming, “CONV” - Conventional Farming, ”CONS” - Conservation Area, “MID” - mid-impact Farming).





ID (DNA-derived extension)



A unique identifier for the occurrence refers to the occurrence table (occurrenceID).





sop (DNA-derived extension)



Standard operating procedures used in assembly and/or taxonomic annotation of reads.





target_gene (DNA-derived extension)



Targeted gene or marker name for marker-based studies (COI).





target_subfragment (DNA-derived extension)



Name of subfragment of a gene (COI-barcoding region).





pcr_primer_forward (DNA-derived extension)



Forward PCR primer ("TTATAATTGGDGGWTTTGGWAATTG""CCHGAYATRGCHTTYCCHCG").





pcr_primer_reverse (DNA-derived extension)



Reverse PCR primer ("TAAACTTCTGGATGTCCAAAAAATCA""TCDGGRTGNCCRAARAAYCA").





pcr_primer_name_forward (DNA-derived extension)



Name of the forward PCR primer ("AncientLepF3", "BF3").





pcr_primer_name_reverse (DNA-derived extension)



Name of the reverse PCR primer ("LepR1", "BR2").





pcr_primer_reference (DNA-derived extension)



Reference for the primers ().





lib_layout (DNA-derived extension)



The configuration of reads ("paired").





seq_meth (DNA-derived extension)



Sequencing method used ("Ion Torrent", "Illumina NextSeq").





otu_class_appr (DNA-derived extension)



Approach/algorithm and clustering level ("mBRAVE").





otu_seq_comp_appr (DNA-derived extension)



Tool and thresholds used to assign "species-level" names to OTUs ("mBRAVE").





otu_db (DNA-derived extension)



Reference database: Canadian Reference library (Pentinsaari et al.)“DS-CANREF22”