MinION Lichen Workshop
We plan to test the MinION Nanopore platform as a transformative tool for lichen community research, bridging traditional morphology-based surveys with modern DNA sequencing, while fostering collaboration between nonprofits, professionals, and community scientists. The goal of the field event is to conduct strategic sampling, extract the material for DNA, and get at least preliminary results, all in one long weekend! Can it be done?
The Forest Service (Mt Hood NF, Zigzag) has camping space plus very limited housing and is providing room for processing samples and scope work.
Possible spots to visit include:
- Lava flows and surroundings at Old Maid Flats (low elevations near the ranger station)
- Bull Run Watershed
- Some areas that we plan to visit are gated, so independent access is not possible.
- We will carpool to study areas.
Who should come:
Professionals, pre-professionals, and serious amateurs. This event is tailored to people who are already competent with lichen identification and who wish to learn methods associated with DNA sequencing, in particular Nanopore technologies. We will not provide formal lichen training, but we are partnering with FUNDIS to train participants in MinION workflows, and integrate FUNDIS methodologies.
If you are uncertain if this is for you, it would be best to give others a chance to register first. If you would like to participate, please contact the secretary for a registration code.
Facilities:
- Room for microscope and lab work: we will use the large room on the North Compound across Highway 26 from the Zigzag Ranger Station. This has a numerical key-pad lock. The main gate to enter the North Compound has a combination lock on it. You’ll get the gate lock number and door code when you arrive.
- Camping space at Mc Neil, Riley, and Lost Creek Campgrounds are potential sites; all are close to the ranger station.
- Four beds are available at the ranger station. First come first served at registration where you can choose your option.
- Nearby motels if you prefer that.
- Bring your own food or arrange to cooperate with others. There are also numerous restaurants nearby.
- Bring your own scopes, reference books, collecting materials, and tools, or cooperate with others on these.
Approach
We will be led by Lalita Calabria (Evergreen and NWL) overall, with Harte Singer (FUNDIS) teaching us the Nanopore technology and data management.
We envision two main approaches, depending on goals of cooperators.
- Comparative study: Conduct side-by-side surveys of FIA-style plots using both morphology-based methods and MinION sequencing of epiphytic macrolichens. Compare species representation, overlap, and blind spots.
- Habitat-focused inventories: Apply MinION sequencing to intensive studies of lichens in a selected habitat, such as streamside mosaics, old lava flows, and other special habitats.
- Targeted searches for rare, threatened and endangered species: If found, specimens will form the basis for a conservation-focused genetic reference library.
We propose to contribute to each of the four major global repositories of lichen biota information, treating our outputs as “extended specimens” that integrate across platforms:
- Museums and herbaria provide permanent records of the tangible features of organisms, preserving physical and chemical properties that cannot be captured in photographs or DNA sequences.
- Academic publications (journals and books) present logical and conceptual frameworks, offering synthesis and interpretation of available data within a broader scientific context.
- GenBank serves as a vast, searchable repository of genetic information, enabling comparative analyses and molecular data on individual organisms.
- iNaturalist is an exponentially growing collection of georeferenced photographic records contributed by both amateurs and professionals, providing unparalleled geographic coverage and fine-scale detail that surpasses other repositories.
Fees: There is no registration fee but we expect everyone involved to contribute to the field work, sample processing, and at least one of the follow-up products. You must be a member of NWL to register. Because we will be carpooling with private vehicles, it is up to you to contribute to that, either with a vehicle or sharing expenses.
Size limit: 15 registrants; with additional slots in waitlist.
More specifics will be distributed to registrants as the time approaches.
Funding: NWL is funding the instructional costs of the workshop, but we are hoping to use crowdfunding (Zeffy) to support the follow-up work. Donate to NWL Lichen Barcoding Project! Contribute to exploring the next lichen frontier and nurturing the next generation of lichenologists in the Pacific NW.
The purpose of this fundraiser is to support the followup activities: data and specimen management and dissemination of our results through Genbank, iNat, and CLH, as well as publications.
Please note that all of your contribution goes to NWL, but our crowdfunding platform, Zeffy, will ask for a "tip" as a percentage of your donation, to help cover their costs and credit card fees. Zeffy suggests 15% by default, but you can choose "Other", then any amount you want, including 0.
Thank you for supporting our mission!
