DNA-based trends for the arrival of new non-indigenous taxa
This workflow aims to detect non-indigenous species entering pelagic habitats early on by using environmental DNA metabarcoding. The biological samples used to develop the index are those collected using Autonomous Reef Monitoring Structures (ARMS;
Kuwahara et al. 2013) by the EMOBON network. Samples are processed through the PEMA pipeline (Zafeiropoulos et al 2020), which produces a metabarcoding matrix of operational taxonomic units (OTUs). The resulting sequences are lists for each sampling station and these lists are then cross-checked against the WoRMS (Costello et al. 2013) catalogue of historical and regional occurrence records to pinpoint taxa absent from prior observations in the area from the WRiMS invasive checker web service (https:/www.marinespecies.org/introduced/news.php?p=showamp;id=8942). Newly detected non-indigenous species are flagged, yielding a time series that tracks the rate at which novel taxa appear.
Default
- Date ( Publication)
- 2025-08-01
- Status
- Completed
- Version
-
1.0.0
- Keywords
-
DNA-base
- Keywords
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metabarcoding
- Keywords
-
pelagic habitats
- Keywords
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ARMS
- Keywords
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EMOBON
- Keywords
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PEMA
- Keywords
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WoRMS
- Keywords
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taxonomy
- Keywords
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WRiMS
- Keywords
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non-indigenous species
- Access constraints
- License
- Use limitation
- OnLine resource
-
Link to the workflow
(
WWW:LINK-1.0-http--link
)
- Service Name
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PEMA Runner
- Service Description
-
This service aims at running PEMA on all the sequences passed as input. It also requires a parameter file (a tsv file).
- Service Reference (id)
- Service Name
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PEMA Converter
- Service Description
-
This service aims to reformat and produce final output in various formats for human and machine2machine reading.
- Service Reference (id)
- Service Name
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PEMA Sequences Retriever
- Service Description
-
This service aims to download the sequences files (fasq files) in order to run PEMA.
- Service Reference (id)
- Service Name
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ARMS OTU Unifier
- Service Description
-
This service aims at creating an OTU table with species information that can be processed by WoRMS and WRIMS.
- Service Reference (id)
- Service Name
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ARMS WoRMS Taxonomic Checker
- Service Description
-
WoRMS taxon match webservice to check for the WoRMS match.
- Service Reference (id)
- Service Name
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ARMS WRiMS Invasive Checker
- Service Description
-
WRIMS taxon match webservice to check the known distribution of the species.
- Service Reference (id)
- Service Name
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Metamds Observations
- Service Reference (id)
- Workflow Helpdesk
metadataMetadata
- File identifier
- 7fadba9a-dcc3-40c8-b359-c07f094be68c XML
- Metadata language
- en
- Hierarchy level
- Workflow
- Metadata Schema Version
-
1.0
Overviews
Spatial extent
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