Automating the use of citizen scientists’ biodiversity surveys in iNaturalist to facilitate early detection of species’ responses to climate change

Dates

Release Date: 2017-10-01

Summary

A BioBlitz is a field survey method for finding and documenting as many species as possible in a specific area over a short period. The National Park Service and National Geographic Society hosted the largest BioBlitz survey ever in 2016; people in more than 120 national parks used the iNaturalist app on mobile devices to document organisms they observed. Resulting records have Global Positioning System (GPS) coordinates, include biological accuracy assessments, and provide an unprecedented snapshot of biodiversity nationwide. Additional processing and analysis would make these data available to inform conservation and management decisions. This project developed a process to integrate iNaturalist data with existing species lists from [...]

Summary

A BioBlitz is a field survey method for finding and documenting as many species as possible in a specific area over a short period. The National Park Service and National Geographic Society hosted the largest BioBlitz survey ever in 2016; people in more than 120 national parks used the iNaturalist app on mobile devices to document organisms they observed. Resulting records have Global Positioning System (GPS) coordinates, include biological accuracy assessments, and provide an unprecedented snapshot of biodiversity nationwide. Additional processing and analysis would make these data available to inform conservation and management decisions. This project developed a process to integrate iNaturalist data with existing species lists from national parks (fig. 2). This cross-referencing of citizen science data with species inventories helps to update taxonomic and species occurrence information and may detect species range shifts or new invasions. Further, this process can serve as the basis for incorporating other online databases and to increase engagement of the public in biodiversity stewardship.

Principal Investigator : Erin E Boydston
Cooperator/Partner : Vijay Barve, Lena Lee
Co-Investigator : Toni Lyn Morelli, Jenny S Briggs

Project Report
1. Developed and tested new computer code, named TaxaTaxi

The TaxaTaxi code compares taxonomic observations from online biodiversity databases to information about known biodiversity for a particular area. The code outputs information on potential taxonomic updates, proportions of biodiversity observed, and potential new species detections for national parks or other defined areas that may indicate species range expansion. For this CDI-awarded project, we focused on iNaturalist and NPSpecies databases.
To test and refine our code, we compared TaxaTaxi output to results for 9 national parks for which we ‘manually’ compared NPSpecies and iNaturalist through close inspection of records. We also used the taxonomic expertise within our collaboration to inspect outputs from TaxaTaxi for possible further refinements.
We encountered several challenges inherent in working with species information from so many different park units. One of the solutions was to build in more flexibility to our TaxaTaxi code, to allow end-users to filter and query based on their particular information needs.
That online biodiversity databases are updated and grow through a wide community of users is one of the reasons to access and utilize such publicly-available information. Challenges from using online data though include that internal rules for accuracy assessments or other definitions may change, or there can be greater restructuring that could prevent automated code functions from accessing the data.
Next steps in the development of TaxaTaxi include:
1. Continued testing and refinement of the code, and potential migration to R
2. Further discussion with (1) NPS partners about NPSpecies and BioBlitzes to verify TaxaTaxi outputs and understand park-specific inputs (2) developers and data managers for iNaturalist and ITIS (3) developers of the R-package Taxize for how to best incorporate Taxize into TaxaTaxi (4) USFWS developers of similar code
3. Building a front-end, user friendly tool for determining inputs and filtering / querying outputs.

2. Coordination with DOI partners

Met with existing park partners for feedback on TaxaTaxi and information about park resources
Developed new NPS partners at local and national levels, including NPSpecies managers
Communicated with USFWS about code recently developed for National Wildlife Refuges species information that incorporates online public databases such as iNaturalist.
Wrote USGS-NPS ServiceFirst grant stemming from this project “Using Citizen Science to Enhance Natural Resource Stewardship: a Collaboration between NPS and USGS” (not awarded)

3. Obtained and explored National Park Service visitor usage data, to relate to BioBlitz efforts and findings.

4. Presentations given

Boydston, Briggs, Morelli, Lee. 2017. Public presentation. Preliminary Biodiversity Results of the Centennial BioBlitz, including Santa Monica Mountains National Recreation Area. Santa Monica Mountains NPS Science Day, Thousand Oaks, CA.
Morelli, Boydston, Briggs, Lee. 2017. Contributed oral presentation. One Hundred Parks and Counting: Biodiversity Findings and Outreach Impacts from a Nationwide BioBlitz. George Wright Society Conference, Norfolk, VA.
Boydston, Backiel, Barve, Blackburn, Briggs, Morelli. Poster. 2017. Using input from citizen scientists to monitor biodiversity and detect species range shifts. CDI Annual Meeting, Federal Center, Denver, CO.

5. Began draft of a manuscript, draft title “Public involvement in biodiversity stewardship of national parks”

6. Related links

NPSpecies: https://irma.nps.gov/NPSpecies/
iNaturalist 2016 BioBlitz data: https://www.inaturalist.org/projects/2016-national-parks-bioblitz-nps-servicewide

Figure caption for attached figure:

Graphic depicting TaxaTaxi Computer Code: TaxaTaxi compares online biodiversity databases to find species in common and unique to each database. Here, the inputs for comparison were (A) species lists for National Parks, called NPSpecies, and (B) observations of organisms from the 2016 National Park Service-National Geographic BioBlitz that were recorded in iNaturalist. The first filter (white oval with gray dots at top) checked if species in iNaturalist were present in NPSpecies for the park where the observations in iNaturalist were made. Records output by this filter as unique to iNaturalist (red container on right) were checked for taxonomic synonyms through comparison to ITIS and incorporation of R-package Taxize. Because scientific names often change, identifying taxonomic updates can assist curators of biodiversity information. After aligning taxonomies between lists, filtering the inputs a second time narrows the output to species not present in NPSpecies (orange container on right). These may be records of species not known to occur and could signal important ecological changes. TaxaTaxi also identifies species in NPSpecies that were not recorded in the 2016 BioBlitz (green container, left). These results can indicate modifications to consider for future citizen science efforts. Species in common (gray container, right) verify organisms from NPSpecies present in the 2016 BioBlitz and show the proportion of a park’s biodiversity recorded through citizen science effort.

Contacts

Contact :: Erin E Boydston
CMS Group :: Community for Data Integration - CDI

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boydston-fy17cdi-image.png “Graphic depicting TaxaTaxi Computer Code”		643.88 KB	image/png

Project Extension

projectProducts

productDescription	One manuscript that will be a methods paper about the R-scripts tool (nickamed “TaxaTaxi”) developed through this proposal and demonstration of it using iNaturalist and NPSpecies and the potential to expand beyond these datasets
status	Expected

productDescription

One manuscript that will describe the findings from comparison of the 2016 NPS BioBlitz results in iNaturalist with NPSpecies with a focus on all newly-documented species, how many were outside their known range, and the implications for climate change understanding of these taxa and regions. An appendix in this manuscript will include all species’ mismatch information from the data integration.

status

Expected

productDescription	Records subset from iNaturalist during this process will all have geographic coordinates and can be easily provided as shapefiles, and these will all be available in ScienceBase
status	Expected

productDescription	The code and relevant user guides for TaxaTaxi will be available via GitHub and a USGS Bitbucket Repository
status	Expected

projectStatus

Completed

Automating the use of citizen scientists’ biodiversity surveys in iNaturalist to facilitate early detection of species’ responses to climate change

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