Environmental DNA (eDNA for short) occurrence records are created from DNA contained in various types of samples (soil, water, stomach contents) rather than DNA directly taken from the organisms themselves.
Virtually all species have unique DNA sequences at a number of “DNA Barcode” genes. To identify the species represented in an eDNA sample a search for matches is made between the DNA barcode sequences found in the samples and in a reference library of DNA sequences from known species (e.g. GenBank, BOLD). This blog article provides more information on eDNA records.
Sampling and surveying methodologies differ and eDNA occurrence records may have limitations on their taxonomic or geospatial level of granularity depending on methodology, but eDNA records can provide a valuable indication of the presence or absence of organisms.
Default filtering
eDNA studies often result in very large datasets. These records can overwhelm the numbers of records provided by more conventional means. In addition, most ALA data users do not expect eDNA records to be provided in search results. As a result, when the ALA General data profile is used, eDNA records are excluded by default and must be consciously included when required.
However, in the spatial portal eDNA records are included by default and must be filtered out if not required.
How can I find eDNA records?
eDNA records can be found through the search interface, by querying the APIs or via the spatial portal.
Search interface
To include eDNA records in a search with the ALA general data profile active, untick the checkbox to exclude records based on record type.
This will include eDNA and fossil specimens in your search.
Clicking on the "(1,034,609 records excluded)" option next to this checkbox, will limit your search results to the excluded records, in this case eDNA and fossil specimen records.
Find ONLY eDNA records
To only see eDNA records, follow the steps below.
1. Disable the ALA default profile.
2. Look for the search facet Content types in the Record category
Note: If you are unable to see this group of facets, this article shows you how to turn facets off and on.
3. Select the facet EnvironmentalDNA. This will limit search results to those datasets with eDNA in them. However, these datasets may also include conventional observation records.
4. To ensure you only get eDNA records select the facet Record type = MaterialSample.
The records displayed will now be eDNA only records.
Query using the APIs
This query will fetch all eDNA records:
Spatial portal
When using the spatial portal the facets allow you to filter the overall search results to include only eDNA records.
For detailed information on using facets in the spatial portal see this article.
You will need to select the facets Record Type = Material Sample, Content type = EnvironmentalDNA
You can also use the Content types facet to exclude records from the spatial portal.
What eDNA records does the ALA hold?
The ALA holds several eDNA datasets. Data resources containing eDNA records are identified with the content type: EnvironmentalDNA.
You can see the data resources with eDNA records in the search interface by following these steps.
1. Turn off the ALA Default data profile.
2. Select the Content types = EnvironmentalDNA
The data resources with eDNA records are displayed as facet options in the Attribution group of facets.
3. To see the list of data resources, click on the choose more... link at the bottom of the group.
4. The names of the data resources with eDNA records will be displayed.
