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eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.)

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Habitat degradation and land-use change severely threaten the survival of fairy shrimp and the vernal pools in which they live. Limiting effective fairy shrimp conservation management efforts is the ability to readily identify species without the capture and sacrifice of individuals for microscopy. Here we demonstrate that eDNA metabarcoding is an effective non-invasive tool for monitoring fairy shrimp. Results from ten Southern California vernal pools comparing eDNA and traditional dip-net methods showed that eDNA metabarcoding with 16S rDNA provides exceptional species-level resolution. Importantly, while the two methods were concordant during early hydroperiods where adults were present, eDNA detected fairy shrimp for up to 2 months after dip-nets failed to detect any adults, expanding the time period for vernal pool monitoring. Together, these results provide resource managers a simple, cost-effective, and non-invasive method for biomonitoring endangered fairy shrimp species.

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Data availability

Sanger sequence 16S rDNA barcode data generated for this study has been submitted to the GenBank database under accession number. MN982235–MN982294. Supplemental Table 1 lists GenBank for all 16S rDNA sequences used in the study. Metabarcode generated sequencing data is available on dryad link: and

Code availability

Code used to analyze the data presented in this project are publicly available here:


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We gratefully acknowledge David Hogon and The Chaparral Lands Conservancy for conserving the lands that made this research possible. We thank Rocks Biological Consulting, Inc. for collecting and preserving invertebrate samples used in this study. For help with field collections and invertebrate sample processing, sorting, and identifications, we thank colleagues Jenessa Wall and Kathy Omura at the Natural History Museum. We thank Benoit Goossens and the anonymous reviewer for their detailed and thoughtful input on this manuscript. We also thank Onny Marwayana, Taylor Ely, Keira Monuki, Markus Min, Bridget Foy, and McKenzie Koch for assistance with processing eDNA lab samples at UCLA. This publication is DISCO number 4 of the Diversity Initiative for the Southern California Ocean.


Support came from the University of California President’s Research Catalyst Award [CA-16-376437]. ZG was supported by the US-NSF Graduate Research Fellowship [DEG No. 1650604].

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Contributions could include, but are not limited to: Conceptualization ARW, ZG, NDP, RW, LR, PHB. Investigation ARW, ZG, EEC, RK. Funding Acquisition ARW, ZG, PHB, RW, NDP. Data Curation ARW, NDP, LR, RW, RK. Formal Analysis ARW, ZG, EEC, RK. Resources LR. Writing – Original Draft Preparation ARW, ZG, PHB, EEC, RK, LR, NDP, RW.

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Correspondence to Zachary Gold.

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No ethics approval was needed for this study. All samples were collected under USFWS permit TE-221290-4.

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Gold, Z., Wall, A.R., Curd, E.E. et al. eDNA metabarcoding bioassessment of endangered fairy shrimp (Branchinecta spp.). Conservation Genet Resour 12, 685–690 (2020).

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