Thanks, S.E.E.D.S, for staying committed to the CALeDNA program and offering to collect on your upcoming excursion to Mt. Diablo! Hope 2018 is a great year for you with lots of new recruits. If anyone is interested in eDNA research internships this coming summer, let us know!
We'll be there and chairing the Citizen Science session. Let us know if you'll be there too. https://www.facebook.com/events/1387097401303773/
UCLA postdoc Dr. Emily Curd, who spearheaded the development of a new software pipeline and top quality DNA reference databases, has streamlined the pipeline to run fast. In just about two days, we've gone from 200 samples in raw fastq files to lists of species, abundance, and confidence level of the species assignment. We've processed close to 1000 samples on the pipeline, which will called Anacapa, and will soon be published and publicly available. Congratulations, Emily, Jesse, Gaurav, Bao-Chen, Zack, Rachel, and Bob!
HHMI funded Beth Shapiro (UCSC) and Bob Wayne (UCLA), two PIs behind the UC Conservation Genomics Consortium, to build out CALeDNA into a three tiered environmental science program that begins with citizen science and leads to placement in a research lab and a science career!
Read the full article about the HHMI grants here: http://www.hhmi.org/news/fourteen-hhmi-professors-take-important-challenges-science-education
Ever wonder what precious lagoon ecosystems hold? Fong Lab doctoral student Tiara Moore and undergraduate volunteers went to Malibu, Newport, and Carpinteria to observe species and sample for eDNA, chemistry, and biological indicators of stress on the ecosystem (to be tested with the new and awesome GeoChip). Check out the photos! We are lucky she went on fieldwork December 1, just before the big fires broke out (that are still burning near Carpinteria).
eDNA from these areas and Tiara's samples could be and important marker for comparing before and after the fire to understand how fire affects California lagoon systems.
Flip through the slideshow!
After an hugely successful Spring coastal eDNA bioblitz <http://www.ucedna.com/blog/2017/5/9/coastal-caledna-bioblitz-team-dawson-labs-experience> the teams from Humboldt U, UC Davis, UC Santa Cruz, UC Merced, CalPoly + UCNRS, CSU Channel Islands, UC Los Angeles, CSU Los Angeles, & UC San Diego headed to California's shores again to repeat eDNA sampling between 30 Nov - 17 Dec.
We again sampled sites covering the latitudinal extent and biogeographic changes of California’s diverse coastal marine, estuarine, and terrestrial biota. We bumped into a SCUBA Search & Rescue team practice at Gaviota State Park, helped return a passport lost at Van Damme State Park so it’s owner could head back to Spain, and re-visited the invaluable UC Natural Reserves at Cambria <http://www.ucnrs.org/reserves/kenneth-s-norris-rancho-marino-reserve.html> and Bodega <http://www.ucnrs.org/reserves/bodega-marine-reserve.html>. At Bodega, we also spent time chatting with Jackie Sones about sea stars, recovery from wasting disease, and finding and identifying millimeter-sized new recruits along tens of kilometers of coastline. It might seem like an impossible task, but keen eyes and commitment yield amazing results … which you can see below and also read about on Jackie’s outstanding blog The Natural History of Bodega Head <http://bodegahead.blogspot.com/> see <http://bodegahead.blogspot.com/2017/12/another-little-one.html> and <http://bodegahead.blogspot.com/2017/12/little-ones.html>.
All the eDNA samples are now on the way to UCLA for analyses!
By the CALeDNA laboratory technician extaordinare, Teia Schweizer
Last weekend, 23 adventurous spirits headed to the White Mountains to collect soil and sediment samples. The sampling locations, carefully chosen by CALeDNA’s Emily Curd, spanned a 10,000 foot elevational gradient and represented a number of habitat types. We spent Friday night at the beautiful facilities at White Mountains Research Station in Bishop. Early Saturday, our citizen scientists got briefed on details and split into five cars to head into the mountains. We made our way up a steep and narrow 4wd canyon road to our destination: the summit. After several hours and a number of unexpected challenges, we hiked and drove to our highest sampling point just shy of the summit at about 14,000ft.
Seeing the diversity of species as we drove ever higher to the summit was quite remarkable. The shrub/scrubland at lower elevation was replaced by pines (including the famous Bristlecone Pines that are thousands of years old--just see the photos!), which then gave way to grasses. As we approached the summit on foot, gasping and feeling the effects of altitude, we noticed that even the grass could no longer hang on, replaced by piles of tumbled rock and the last patches of snowpack from last year. We collected our last sample just as the sun was setting and had the thrill of watching the temperature on our soil meter drop every couple of seconds.
In less than 36 hours, we went from Los Angeles (close to sea level) to the summit of the third highest peak in California! We hit 28 sites in total, which were all spaced far apart, and we left some kits with local citizen scientists who will continue to collect some samples. Can't wait to go back!
Sexton & Dawson labs at UC Merced
Back at the end of April, as the winds and sun were picking up after one of the wettest winters in recent memory, and the vernal pools were lush with green grassses and white & yellow flowers, we completed our first vernal pool eDNA sampling on a beautiful spring morning. Now, in mid-summer, we’re back out there again, resampling some pools and adding other pools into the study design. It has the sense of a completely different landscape. Golden grasses stretch as far as the eye can see. The flowers are long gone. But among the mostly dormant plant life are a few hidden surprises: a praying mantis, a horned lark nest. And one or two green Orcuttia grasses in the dry pool bottoms indicated some residual moisture below the hard-baked surface. We’ll be back out in November-December to see the change of another season. CLICK THE PHOTOS TO SCROLL THROUGH THEM.
Reseda High School students were involved with CALeDNA from start to finish. A) Twenty five Reseda High School students, ages 15 – 17, used CALeDNA kits to collect samples at Stunt Ranch. B) They collect samples from general areas on a map that land managers chose. C) Indicates the relative abundance of plant taxa sequencing reads recovered for a single site sampled. D-L) The plants recovered in eDNA results were confirmed to be growing at Location C. Examples include D) Bromus, E) Tribulus, F) Medicago, G) Lupinus, H) Marah, I) Fraxinus, J) Eucrypta chrysanthemifolia, H) Artemesia, L) Centaurea melitensis. Bromus, Tribulus, and Centaurea are invasive species targeted for removal; DNA may indicate the presence of these species in the seedbank even if they are not visibly growing in an area. The results from the Reseda High School soil collections, observations, and other fieldwork activities are helping scientists understand the limitations and utility of eDNA samples, which inform the design of state-wide investigations.
In our October-November bioblitz, CALeDNA is eager to get more data from inland California. Specifically, we want data from montane and desert ecosystems and will be recruiting citizen scientists to participate! You can go ahead and register and we will contact you with more information closer to bioblitz time.
Loved visiting the UC Reserves? Don't worry! We'll be sampling more at the reserves as well.
More information to come!
UCLA's Research Immersion Laboratory in Microbiology hit a home run after two quarters of hands-on exploration, by delivering powerful oral presentations and posters. These highlighted the capacity of eDNA to rapidly address ecological questions spanning plant growth, human impact on the environment, temporal variation in climate, and community interactions. The eDNA data were collected by the class during a field outing to Sedgwick Reserve, where they used ecological experimental plots set up by the Kraft Lab and graduate student Gaurav Kandlikar to carefully choose their question and samples of focus.
The CALeDNA program funded by the UC Conservation Genomics Consortium sequenced the eDNA in the soil samples and provided data back to the students in the form of tables consisting of species names and the number of DNA reads that were a match. Students formed hypotheses about the role of the organisms in the environment based on the observed differences among sites, and then cultured microbes to test in vitro if the organisms may have those proposed functional roles. A small group of honors students even went one step further to do sophisticated informatics analysis on the samples, which illuminated patterns of biodiversity that could inform the UCLA researchers in the Kraft lab.
On April 29th, after about two months of planning, 9 teams (Humboldt U, UC Davis, UC Santa Cruz, UC Merced, CalPoly + UCNRS, CSU Channel Islands, UC Los Angeles, CSU Los Angeles, & UC San Diego) all headed out to sample around the Saturday morning low tide. Together, we sampled an impressive 20 places, from Arcata to San Diego (~850 miles, 1100 km, coastal distance), within a little over 24 hours.
Together, this teams, totaling 21 people, collected 312 samples
The sampling sites were carefully chosen to reflect different elements of California’s coastal habitats: sand beach, tidepools, dune bluff, estuaries, harbors, swashs, creeks, and bays, were targeted multiple times.
Q: Where’s Waldo? Where’s eDNA!?
A: Pretty much everywhere?
Despite colleagues at almost a dozen institutions pooling their resources, one or two long stretches of coastline were still not covered by coastal CALeDNA. The team from UC Merced decided to gap-fill what we think might be several interesting sites along the California coast. It was also a great excuse for Lauren, who’d been cooped up for months writing her thesis and defended on 27th, to get back in the field (what better way to celebrate!) and for Dannise, our most recent addition to the team, from Puerto Rico, to see something of California. 1200 miles later, we’re looking back on a great road trip. Here’s a brief recap of the highlights … including collecting samples from 4 very different places!
The tide is early in the morning, and it’s a 4 hour drive from Merced to Bodega, so we leave at 6:00 p.m. We hit Petaluma at 9-ish, so decide to stop for dinner; this is what becomes the first of three ‘goat’ stops, as we share sliders, a pretty decent sweet potato and quinoa fritter, and salad at the Wild Goat Bistro. Replenished, we carry on to Bodega Marine Lab where we’re staying the night. As we pull up at 11:30 p.m., we spy Steve Dudgeon who’s leading a class field trip from Cal State Northridge – they’re just back from the field, and are heading back out to the mudflats for the morning low-tide. That’s commitment! Kudos to our next generation of marine scientists!
We move up to the nearby bluff to sample the coastal scrub habitat, where the soil is caked and baked, and then repeat about 150 m along the shore. We then find the nearest bay, creek, or estuary—which in this case is Bodega Harbor—where we take another pair of samples, about 12 ml total of sediment, while dozens of folk nearby are pulling all kinds of invertebrates out of their burrows in the mud. So, that is our basic study design, which we’ll repeat 3 more times, over 600 miles apart, and colleagues are replicating throughout California at exactly this time. How cool is that? What an amazing team effort!
By 8:00 a.m. we’re heading north on Hwy 1, with Dramamine or a tight focus on the road or the distant views to take the edge off wildly winding road as it weaves around the coastal hills and headlands and drops and climbs steeply through river valleys. By 11 a.m., a little later than hoped, we’re arriving at Van Damme State Park, our second place for sampling eDNA site. SCUBA divers are entering and exiting the water, diving in the kelp. There are some bubbles in the middle of the bay; maybe Waldo is down there? But, it’s too cold for our tired souls, so we won’t be getting a visual. We wrap up and head along the beach to sample our eDNA; maybe we will pick up what the divers are seeing, or the divers’ DNA (and Waldo)?
With sampling finished for the day, we make a short detour north to Fort Bragg, to the Glass Fire Gallery where we marvel at the blown glass and get a quick tour of the kilns. They’ve some remarkable jellyfish lamps (though Mike can’t identify the species) and glass sea stars—none other than Pisaster, one of the stars of Lauren’s thesis! We watch sand turn to glass (no DNA in that sample!) at over 2000ºC. Then, at a little after noon, we start the long trek south, the longest leg of our trip. We marvel at the coastal redwoods along Hwy 128, blur thousands of rows of grapes in the Williamette valley, and pull off for a few minutes in Booneville to pick up lunch. This is when Lauren realizes she left debit card at the bistro last night, so in 2 hrs we swing through Petaluma for our second encounter with ‘the goat’, retrieve the card, and with spending power back in hand, our next road-stop is the Gilroy outlets, where the boss tries, and fails, to pick up some new sandals for the coming summer. We stretch, and get back in the car for another 3.5 hrs to San Simeon. Nine hours after leaving Fort Bragg, we crash, metaphorically, in the hotel, and with a wireless connection at last, upload some of our valuable data.
5:30 a.m. Rise & Shine! Feeling distinctly less shiney than yesterday, and with some bad hotel coffee in hand, our first stop today is the Kenneth S. Norris Rancho Marino Reserve; at 6:43:43 AM, our third set of samples is underway. Rancho Marino is a gem, extending from sea level to 700-foot elevation, harboring one of the three remaining naturally occurring stands of Monterey pine forest in CA. The reserve manager is Don Canestro, who comes to greet us at around 7:00. Don was out yesterday morning, collecting samples from just up the coast at Morro Bay for the CALeDNA project, so we trade notes. We conclude several things: iPhones are great but nothing beats the reliability of pencil, water proof paper, and a clipboard for taking field notes; it’s just an amazing privilege to be able to do this kind of fieldwork; and one of life’s truisms is that sometimes great conversation will have to end when “I’ve got to go milk a goat!” Don heads up the hill, we finish sampling, and grab his samples from Morro Bay on the way out.
This is where Lauren’s five years of graduate field work experience really comes into play. She guides us faultlessly to the very excellent Linn’s bakery in Cambria, where we stock up for the penultimate leg of the journey, and then charts a route that takes us past the Los Osos Oaks State Natural Reserve where we take 15 minutes to wander through a beautiful copse of live oaks (and not so beautiful swarms of mosquitos).
Because of Robert Parker and other hybrid citizen scientists and naturalists, we have really great observation data to match up with eDNA samples. CALeDNA is almost at 500 observations!
Zack Gold is a PhD student in Professor Paul Barber's lab at UCLA currently researching the spatial and temporal variation of environmental DNA and the ability to use eDNA to assess the effects of multiple human stressors including chronically impaired water quality and fishing pressures on marine ecosystems. He received his B.S. in marine biology with Honors from Stanford University in 2015 where gained a background in coral reef ecology, ocean acidification, and marine policy. As an avid surfer, former ocean lifeguard, and underwater photographer, Zack has a deep passion for the marine environment and its protection from environmental impacts. Zack hopes to gain more experience at the intersection of research and policy, with a focus on understanding the interplay of local (pollution, overfishing, habitat destruction) and global (climate change and ocean acidification) stressors on marine ecosystems.
Why reinvent the wheel and ask for species observations in a totally separate app when we can encourage people to link their observations with those of thousands of people around the world with iNaturalist, run by our friends at the California Academy of Sciences. We love using iNaturalist, and are showing you what it's like. Here's Dr. Emily Curd using it on UCLA campus.
We love the webform and Kobo Toolbox, the really great program that let's people make such survey tools for free. But not all phones act alike. Here's some basic tips to make sure you have an easy experience with the webform and successfully upload that precious data.
UCSC Fort Ord Natural Reserve - Spring eDNA Survey
April 28 - May 7
The Spring eDNA survey is a chance to use citizen science to help build a California soil museum with emphasis on UC Reserves. We are fortunate that the CALeDNA group has chosen UCSC Fort Ord Natural Reserve for a large sampling project. Participants will use provided kits and apps to take samples in different habitat types across the reserve. Then the group will use the DNA sequences in soil to inventory biodiversity of microbes, plants, and animals.
Learn more about this project at www.ucedna.com.
Anyone who is interested should sign up by emailing firstname.lastname@example.org ASAP!
Spring 2017 Bioblitz - UCSC Fort Ord Natural Reserve
Saturday, May 6, 9am-2pm
Info and sign-up here: https://www.inaturalist.org/projects/ucsc-fort-ord-natural-reserve-spring-2017-bioblitz
A bioblitz is a community event that brings together a variety of people to rapidly inventory the living organisms found in a particular place. UCSC Fort Ord Natural Reserve's unique maritime chaparral habitat and setting have resulted in a wonderful diversity of species that call the reserve home.
UC Santa Cruz Fort Ord Natural Reserve is a UCNRS site in Marina, CA. We focus on research, teaching, and public service. We work with students from local schools, CSUMB, Hartnell College, UCSC, as well as researchers from all over to learn and teach about our wonderful local habitat. On May 6, 2017 We'll be using iNaturalist to photograph and geographically pinpoint our findings and will come back together at the end of the day to upload our records, share stories, and help each other with identifications. We hope to grow our reserve species lists, but most importantly celebrate our fellow creatures and each other. This will be a great way to introduce the reserve to community members and students that have yet to visit UCSC Fort Ord Natural Reserve!
We will meet at the main reserve gate at the end of Neeson Road (adjacent to Marina Municipal Airport). The physical address of this gate is 711 Neeson Rd. Marina, CA 93933 (this is not the office/mailing address for UCSC Fort Ord Natural Reserve). Light refreshments will be served at a break, and at the end of the event.
Reserve waivers must be signed before accessing and using UCSC Fort Ord Natural Reserve. These will be available the morning of the event. All attendees must get an RSVP e-ticket for the event, so that we can successfully plan ahead for this fun day!
I am a PhD student in David Jacobs' lab at UCLA, and I am broadly interested in evolution and biogeography. Currently, I am involved in many different projects involving population genomics, ancient DNA of threatened fauna, as well as eDNA. Together with the CALeDNA team I hope to use this exciting technique to study communities and ecosystems, and how they are impacted by human activities. In the future, I wish to work at a museum where I can expand my research on aDNA and also engage in the popularization of science.
In early 2017, the UC Davis SEEDS group (that stands for Strategies for Ecology Education, Diversity and Sustainability) connected with us with a will to help. They held several Skype meetings with our team and brought a CALeDNA workshop to the UC Davis campus. We were worried that being largely in southern California, the CALeDNA core team wouldn't be able to recruit citizen science help up north. Boy were we wrong! SEEDS has organized trips to several UC Natural Reserves and has facilitated training on how to use the app and the kit, while managing the distribution of supplies. SEEDS members have brought in their partners, family, and friends to sample for CALeDNA, and hearing their responses to the program has shaped our strategy forward. We thank UC Davis SEEDS and hope that other campuses develop such proactive and integrative student groups!