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Data from: Community ecology in a bottle: Leveraging eDNA metabarcoding data to predict occupancy of co-occurring species

Cite this dataset

Tetzlaff, Sasha (2024). Data from: Community ecology in a bottle: Leveraging eDNA metabarcoding data to predict occupancy of co-occurring species [Dataset]. Dryad. https://doi.org/10.5061/dryad.866t1g1zr

Abstract

Detecting environmental DNA (eDNA) of numerous organisms from the same samples has been revolutionized by metabarcoding. However, utilizing the vast amounts of data generated from metabarcoding to predict occupancy probabilities for co-occurring species is currently rare. Here, we demonstrate how metabarcoding data can be used to advance community ecology research through a case study using replicate stream water samples and Bayesian occupancy models to test hypotheses of eDNA occurrence for a native fish (brook trout, Salvelinus fontinalis), its major ectoparasite (gill lice, Salmincola edwardsii), and an introduced potential competitor (brown trout, Salmo trutta). Gill lice DNA occupancy was positively associated with brook trout biomass determined via electrofishing conducted near eDNA sampling sites, suggesting gill lice occupancy is dependent on host density. Leveraging site-specific molecular operational taxonomic units identified from metabarcoding, DNA occupancy of trout and gill lice was often positively predicted by species richness of aquatic insect orders trout commonly feed on, which are also environmental quality indicators. Thus, high-quality habitat that environmentally sensitive salmonids and their primary prey rely on may promote higher fish occupancy rates, further facilitating the spread of fish parasites. An increasing amount of community-level data is being generated from global metabarcoding efforts, and we suggest our framework could be broadly implemented to enhance understanding of factors impacting distributions of co-occurring species, reveal new ecological phenomena, and support management and conservation efforts.

README: Data from: Community ecology in a bottle: Leveraging eDNA metabarcoding data to predict occupancy of co-occurring species

GENERAL INFORMATION

  1. Author Information Corresponding Investigator Name: Dr. Sasha Tetzlaff, https://orcid.org/0000-0001-5889-6573 Institution: U.S. Army Corps of Engineers, Engineer Research Development Center, Champaign, Illinois USA Email: Sasha.J.Tetzlaff@usace.army.mil Co-investigator 1 Name: Dr. Aron Katz, https://orcid.org/0000-0002-7810-9773 Institution: U.S. Army Corps of Engineers, Engineer Research Development Center, Champaign, Illinois USA Co-investigator 2 Name: Dr. Mark Johnson, https://orcid.org/0000-0002-0460-945X Institution: U.S. Army Corps of Engineers, Engineer Research Development Center, Champaign, Illinois USA Co-investigator 3 Name: Dr. Jinelle Sperry, https://orcid.org/ 0000-0003-0929-1900 Institution: U.S. Army Corps of Engineers, Engineer Research Development Center, Champaign, Illinois USA
  2. Date of data collection: 20-29 July 2021
  3. Geographic location of data collection: Fort McCoy (Monroe County, Wisconsin, USA)
  4. Funding sources that supported the collection of the data: U.S. Army
  5. Recommended citation for this dataset: Tetzlaff, Sasha, et al. (2024), Data from: Community ecology in a bottle: Leveraging eDNA metabarcoding data to predict occupancy of co-occurring species, Dryad, Dataset, https://doi.org/10.5061/dryad.866t1g1zr.

DATA & FILE OVERVIEW

  1. Description of dataset These data were generated to investigate occupancy patterns of a native fish (brook trout, Salvelinus fontinalis), its major ectoparasite (gill lice, Salmincola edwardsii), and an introduced potential competitor (brown trout, Salmo trutta) using environmental DNA metabarcoding.
  2. File list: File 1 Name: EDN3-2024-0053 Tetzlaff et al. trout and gill lice occupancy data.xlsx Tab 1 Name: EDN3-2024-0053 Tetzlaff et al. Tab 1 Description: Detection/non-detection data and covariates used to analyze occupancy of brook trout, brown trout, and gill lice METHODLOGICAL INFORMATION Replicate water samples were collected at 38 points on streams across Fort McCoy, WI. Samples were analyzed for vertebrate and invertebrate environmental DNA using metabarcoding. Detection/non-detection data for brook trout, gill lice, and brown trout eDNA from replicate water samples were used to simultaneously estimate occupancy and detection probability of these species. Occupancy covariates included site-specific biomass (g) of brook trout, brown trout, and all non-trout species combined; and species richness of Ephemeroptera (mayflies), Plecoptera (stoneflies), Trichoptera (caddisflies), and Diptera (true flies) known to have aquatic larval stages. DATA-SPECIFIC INFORMATION FOR: EDN3-2024-0053 Tetzlaff et al. trout and gill lice occupancy data.xlsx Tab 1: EDN3-2024-0053 Tetzlaff et al.
  3. Number of variables: 21
  4. Number of rows: 39
  5. Number of columns: 21
  6. Variable list: site: unique identifier for each sampled site (point on stream) latitude: latitude coordinate of sampled site longitude: longitude coordinate of sampled site X: Universal Transverse Mercator easting coordinate of sampled site Y: Universal Transverse Mercator northing coordinate of sampled site brook_L, brook_M, brook_R: detection (1) or non-detection (0) of brook trout environmental DNA at left (L), middle (M), or right (R) point on stream at each sampled site. brown_L, brown_M, brown_R: detection (1) or non-detection (0) of brown trout environmental DNA at left (L), middle (M), or right (R) point on stream at each sampled site. lice_L, lice _M, lice _R: detection (1) or non-detection (0) of gill lice environmental DNA at left (L), middle (M), or right (R) point on stream at each sampled site. brk_biomass: biomass (g) of brook trout from electrofishing station nearest a given environmental DNA sampling site brn_biomass: biomass (g) of brown trout from electrofishing station nearest a given environmental DNA sampling site tot_non_trout: biomass (g) of all non-trout species from electrofishing station nearest a given environmental DNA sampling site Diptera: Diptera species richness at each site, determined from environmental DNA sampling Ephemeroptera: Ephemeroptera species richness at each site, determined from environmental DNA sampling Plecoptera: Plecoptera species richness at each site, determined from environmental DNA sampling Trichoptera: Trichoptera species richness at each site, determined from environmental DNA sampling
  7. Missing data codes: None
  8. Abbreviations used: X: Universal Transverse Mercator easting coordinate Y: Universal Transverse Mercator northing coordinate brk: brook trout brn: brown trout tot_non_trout: total non-trout
  9. Other relevant information: None

Funding

United States Army