The OBGP’s Emily Dziedzic had the opportunity to present at the annual Fisheries Society of the British Isles conference this past week in Hull, UK. It was a true meeting of the greatest environmental DNA minds from around the world. Keynote speakers included Christopher Jerde, Didier Pont, Kristy Deiner, Alice Valentini, and Masaki Miya, with additional talks given by Louis Bernatchez and Bob Hanner. Over 25 nations were represented at the conference and it was an honor to have the opportunity to spread the word about the work being done by the OBGP in Oregon. Many thanks, FSBI, and congratulations on putting together such an inspirational conference!
OBGP Acquires ARF Seed Funding for Pollinator Project
The Agricultural Research Foundation at Oregon State University (OSU) has awarded the OBGP with a small grant to begin sequencing genomic regions in bees and to develop molecular detection tools for these insect pollinators within the state of Oregon. This is the start of what we hope will be a long and productive collaboration between the OBGP, the Jim Rivers and Sandy DeBano laboratories at OSU, the Oregon State University Arthropod Collection, and the Oregon Bee Atlas.
Extending our scope to develop molecular tools to detect bees may not seem an obvious progression but both groups are experiencing major population declines worldwide and would benefit from the creation of improved monitoring tools. The most recent WWF Living Planet Report reports that populations of freshwater species have declined by 83% since 1970 and a study by Sánchez-Bayo and Wyckhuys (2019) suggests that more than 50% of bee species are experiencing significant population declines.
Developing methods to more rapidly and efficiently monitor these groups is essential given their population shifts and the prospect of mining the nuclear genome for bee detection is an exciting one. This is possible with bees because monitoring them involves capturing whole insects and not just environmental DNA samples. These are exciting times and the OBGP is looking forward to harnessing the molecular tools at our fingertips to enhance wildlife detection and monitoring.
First Round of OBGP Mitogenome Assembly is Complete
Our collective field to lab to data analysis pipeline has reaped its first rewards. The mitogenomes of 137 specimens comprising 57 uniquely identified species, subspecies, and one known hybrid is now complete. Mitogenome data for Redband Trout, Rainbow Trout, Steelhead Trout, Westslope Cutthroat Trout, Coho Salmon, Reticulate Sculpin, Torrent Sculpin, Prickly Sculpin, Riffle Sculpin, Klamath Lake Sculpin, Klamath Marbled Sculpin, Marbled Sculpin, and Slender Sculpin have been sent off to researchers at USFS PNW Research Station and the Levi Lab at Oregon State University for analysis. Colleagues at USFS Rocky Mountain Research Station are using OBGP mitogenome data for Sacramento Sucker and Modoc Sucker to develop tools for environmental detection of these species in aquatic environments using eDNA. The future is now!
This is an amazing accomplishment on the part of everyone involved. Congratulations everyone! Now for phase 2: The final push to finish sequencing the mitogenomes of all of Oregon's resident fishes. We are already well on our way and should be done by this time next year. Engage!
Wildlife Applications for eDNA Sampling with Contributions from Some of OBGP's Own
A recent article published in The Wildlife Society's November/December 2017 issue of The Wildlife Professional is coauthored by our very own Brooke Penaluna and highlights some of the work she has done with two more OBGP people: Rich Cronn and Laura Hauck. It's an exciting time for eDNA and Not Just for Fisheries Biologists Anymore: Environmental DNA Sampling Makes Strides in Wildlife provides an excellent overview of the field-to-lab eDNA pipeline. It also touches on potential applications for terrestrial wildlife. This is one of the reasons the OBGP is interested in developing a library of genomic material from all of Oregon's animal species. We don't know what the future holds so it makes sense for us to lay the groundwork for tool development targeting any and all of Oregon's animal species.
An Excellent Overview of eDNA Metabarcoding in Molecular Methods
Kristy Deiner has contributed significantly to the eDNA literature over the past few years and is the lead author on an article that was published in Molecular Ecology in September 2017. Environmental DNA metabarcoding: Transforming how we survey animal and plant communities provides an excellent review of how eDNA metabarcoding is used to survey animal and plant species richness. It also details the various challenges involved with using metabarcoding to calculate abundance. This is an excellent overview of what can be accomplished with this technology and is a very accessible read. It touches on some of what we plan to explore and accomplish with the OBGP as we work to evolve these methods. I highly recommend checking it out if you have the time and—being that Kristy Deiner is a hero of mine—I'm always excited to see what she's been up to.
There's also a project up on ResearchGate that I'm currently following that has brought together a lot of the stars of the eDNA world. They're all involved with DNAqua-Net with the goal of identifying the best available genomic tools for biodiversity assessments and biomonitoring in aquatic systems in Europe. They've had several meetings over the past couple of years and I hope I can make it to the next one as a representative of OBGP.
Fun Piece in the Smithsonian Magazine about eDNA
It's cool to see that eDNA is going mainstream with this article on Smithsonian.com. It's definitely taking a few liberties—tales of the possibility of a Loch Ness monster discovery with eDNA are used as a way to hook people in—but it's great to have it out there. Definitely worth a read.
Future of Conservation: How Scientists Use Teeny Bits of Leftover DNA to Solve Wildlife Mysteries