A one-day meeting (hosted by the Southeast Alaska Watershed Coalition and Southeast Alaska Fish Habitat Partnership) took place April 1 of 2019 bringing together state and federal agencies, university researchers, Tribes, and NGOs for a regional discussion about the state of eDNA research and existing and future applications across Alaska. The agenda, brief synopsis and presentations are included below. Presentations and discussion touched on topics of interest garnered in early outreach efforts including: 

• desire for a primer on the science of eDNA sampling, including methodology issues related to
  • single and multiple species sampling
  • laboratory practices and locations in Alaska and Pacific Northwest
  • field sample collection protocols
  • abundance vs presence/absence methods
  • freshwater/marine environment/terrestrial sampling considerations
  • assessing overall biodiversity using metabarcoding approaches
• interest in using eDNA for habitat mapping endangered species, invasive species and anadromous species and associated relevance to nominations to the Anadromous Waters Catalog
• overview of existing sampling efforts taking place across Alaska (freshwater/marine/terrestrial)
• recommendations for developing sampling protocols/cost considerations

Meeting Agenda

eDNA Terminology Resource

Meeting Synopsis

Workshop Presentations

Session 1. Primer on science status of eDNA, considerations for Alaska

eDNA Primer & USFWS Perspectives – Ora Russ (USWFS Genetics Lab)

An Ecologists Guide to eDNA: Examples from Oregon – Brooke Penaluna (USFS, PNWRS)

eDNA at AFSC: Environmental DNA at the Alaska Fisheries Science Center – Chris Kondzela (NOAA Genetics Lab)

Alaska Department of Fish and Game’s Anadromous Waters Catalog and Position on eDNA Sampling Methods – J Johnson (ADFG AWC), Chris Habicht (ADFG Genetics Lab)

ADFG Anadromous Waters Catalog Information

ADFG AWC Guidelines and Position on eDNA Sampling

Session 2. Field applications utilizing eDNA sampling

Auke Creek salmon eDNA – David Tallmon (UAS)

Using Environmental DNA to Monitor Eulachon (Thaleichthys pacificus) Abundance Northern Southeast Alaska (aka hooligan, Saak) – Meredith Pochardt (Takshanuk)

Identifying distribution boundaries at the upper extent of fish in forested streams with electrofishing and eDNA – Brooke Penaluna (USFS, PNWRS)

A Rapid Assessment Method to Estimate the Distribution of Juvenile Chinook Salmon (Oncorhynchus tshawytscha) in Tributary Habitats Using eDNA and Occupancy Estimation – Jeff Falke (UAF) for Allison Matter (see additional publication resource noted below)

Using eDNA (single species qPCR assays) for aquatic invasive species in Alaska – Ora Russ (USFWS Genetics Lab)

Multispecies/Metabarcoding with eDNA – Damian Menning (USGS)

eDNA Resources

• Washington State University eDNA Resources Hub: https://www.ednaresources.com/
• new journal: Environmental DNA https://onlinelibrary.wiley.com/journal/26374943
• Critical considerations for the application of environmental DNA methods to detect aquatic species (Goldberg et al. 2016) https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12595
• A Rapid-Assessment Method to Estimate the Distribution of Juvenile Chinook Salmon in Tributary Habitats Using eDNA and Occupancy Estimation (Matter et al. 2018) https://afspubs.onlinelibrary.wiley.com/doi/10.1002/nafm.10014
• ADFG invasive species in Alaska information and resources: http://www.adfg.alaska.gov/index.cfm?adfg=invasive.main
• Potential of Environmental DNA to Evaluate Northern Pike (Esoxlucius) Eradication Efforts: An Experimental Test and Case Study (Dunker et al. 2016) https://s3-us-west-1.amazonaws.com/akssfapm/APM_Uploads/2014/44168/.pdf/dunkeretal2016.pdf
• Validation of PCR-Based Assays and Laboratory Accreditation for Environmental Detection of Aquatic Invasive Species (ISAC White Paper 2012)
• https://www.doi.gov/sites/doi.gov/files/uploads/isac_pcr_white_paper.pdf
• Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus) (Harper et al. 2017) https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.4013
• Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG (2013) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10:57–59. https ://doi.org/10.1038/nmeth.2276
• Greiman SE, Cook JA, Tkach VV, Hoberg EP, Menning SM, Hope AG, Sonsthagen SA, Talbot SL (2018) Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time. Int J Parasitol doi. https ://doi.org/10.1016/j.ijpar a.2018.08.001
• Longmire JL, Maltbie M, Baker RJ (1997) Use of “Lysis Buffer” in DNA isolation and its implication for museum collections. Museum of Texas Tech University https://www.biodiversitylibrary.org/item/242562
• Menning DM, Simmons T, Talbot S (2018) Using redundant primer sets to detect multiple native Alaskan fish species from environmental DNA. Conservation Genet Resour https ://doi.org/10.1007/s1268 6-018-1071-7
• Taberlet P, Coissac E, Pompanon F, Gielly L, Miguel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E (2007) Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Res 35(3):e14. https://doi.org/10.1093/nar/gkl938
• Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA.  Plant Mol Biol 17: 1105-1109. https://doi.org/10.1007/BF00037152
• Zeglin LH, Wang B, Waythomas C, Rainey F, Talbot S (2016) Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska. Env Micro https://doi.org/10.1111/1462-2920.12924