eDNA webinars

CALeDNA research results were presented today to the USGS! Check out their numerous eDNA webinars here: https://my.usgs.gov/confluence/display/cdi/eDNA+Webinars

 

Desert eDNA results are online

Nearly a year ago, eDNA surveys took place from Oak Glen to deep in the Coachella Valley, meandering through Pioneertown, Anza Borrego, the Salton Sea, and Palm Desert. Results are in! We are looking for volunteers to help us analyze the data. https://data.ucedna.com/research_projects/6

As a botanist from Palm Desert (a desert rat, as we call ourselves), I can’t help but highlight that we get some really cool plants in the eDNA results, including one of my favorites that perfumes the desert, creosote bush (Larrea). Oh, and we got both black bears and water bears (Tardigrades) in the eDNA, too.

Image from the web, no author name given. Eat your hearts out, tardigrade lovers. California is full of them (58 sites and counting).

Image from the web, no author name given. Eat your hearts out, tardigrade lovers. California is full of them (58 sites and counting).

 

CALeDNA has its largest bioblitz ever! Surprise, it's at the UC Merced Vernal Pools

Fairy shrimp were all over the place, as were people of all ages, with their phones out, gloves on, and cryotubes handy. We got lucky with the weather, too! 41 people collected samples from 6 pools including the big playa. Teenagers took off their shoes to experience the squish of vernal pool mud. Two people celebrated their birthdays at the bioblitz; one birthday crew drove all the way up from Santa Barbara to join for the day. Afterwards, we met up with professor Michael Dawson and feasted on Indian food buffet.

I’m thrilled to pass along the amazing photographs and stories of the people who attended so you can read about the experience from their vantage points. Here’s Mr. Hollister’s blog post with photos and even a video of an endemic fairy shrimp!

http://www.mrhollisterphoto.com/home/uc-merced-vernal-pool-reserve-edna-collection

The full photo collection can be viewed here:

http://www.mrhollister.com/getout/vernal%20pool%20eDNA/

Here’s a screenshot of what you would see if you clicked that link.

Thanks to everyone who came out! We’ll do another bioblitz there in late April or May. Email us at uc.caledna@gmail.com if you want to join!

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Sampling the Santa Monica Mountains affected by the Woolsey Fire

It was wrenching to see the destruction and loss of life from the fire. Communities of organisms will reassemble somehow, and an important question to ask is will they be different than before (landscape conversion)? NASA Jet Propulsion Laboratories and CALeDNA want to understand this process by combining eDNA with remote sensing data. CALeDNA has 121 sites in the Santa Monica Mountains that are in the eDNA freezer — many of these areas burned and can be used to compare biodiversity before and after the fire. Volunteers, including JPL employees, set out to collect from burned sites. Some areas were dangerous with dead branches and debris, so we wore our helmets when hard hats weren’t available. We also thank Marti Witter from the Santa Monica Mountains Resource Conservation District for helping us access these sites. Photos below courtesy of Rachel Meyer and Natasha Stavros.

 
 

CALeDNA x NHMLA Tidepool bioblitz for Snapshot Cal Coast was like opening buried treasure!

Volunteers, researchers, and curators got to hop along algae-covered rocks, and peer into the rarely exposed world of the San Pedro Point Fermin intertidal zone at dawn. It was the second-to-lowest tide of the entire year. Every few minutes you could hear a burst of "oh what! wow!" as people found and gently scooped up animals, from slimy sponges to brittle starfish to the behemoth black sea hare. Regina Wetzer and Dean Pentcheff, long time collaborators now, also collected specimens to bring back to the lab and voucher for permanent archiving as well as DNA barcoding. With these species barcoded too, we can now track them more accurately with our CALeDNA environmental DNA metabarcoding. :)

 
 

California Naturalist Partner/Instructor Training Workshop

Rachel and Maura attended the California Naturalist Partner/Instructor Training Workshop for a future collaboration and we also trained/sampled with members from the Cabrillo Marine Aquarium, Community Nature Connection, and others at the Los Angeles County Arboretum & Botanic Garden in Arcadia, CA. We look forward to strengthening our connections at the local, state, national, and international level. Thank you for such an amazing opportunity!

 

Sampling the L.A. River

We successfully collected at the L.A. River this Memorial Day Weekend and made some new friends along the way. We made the news! Addriana Weingold from CBSLA asked us of our use of the L.A. River, go to (https://cbsloc.al/2sfxQpC) to find out our answers.  

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Welcome our two new postdocs!!!

Dr. Ana Garcia Vedrenne completed her Ph.D  at UC Santa Barbara in Ecology, Evolution and Marine Biology and  Dr. Maura Palacios Mejia obtained her Ph.D at Texas A&M University in Ecology & Evolution.

Together they will contribute their expertise to develop courses for the new Environmental DNA for Science Investigation and Education Program and pursue innovative eDNA research. 

Today, they were initiated by collecting sediment samples from the Mildred E. Mathias Botanical Garden at UCLA.

Welcome to the team!

 

Younger Lagoon Natural Reserve Bioblitz

Located adjacent to the UC Santa Cruz marine campus, Younger Lagoon Natural Reserve offers protection and access to a unique undisturbed coastal wetland and restored terrace. On April 28th, UCSC undergrads, UCSC alumni, UC Davis S.E.E.D.S, and local citizen scientists worked together to collect soil across the reserve, record flora and fauna with iNaturalist, and collect washed-in trash. 

Those collecting soil split into two groups. One group tackled the terrace, focusing their sampling on the three microhabitats (grassland, wetland, shrub) the terrace supports. Being raised on the terrace, this group was able to see a group of humpback whales breaching not too far off shore in the bay! The other group got a bit muddier, sampling from the sand bar in through the mixed and freshwater zones of the lagoons edge. This group was able to explore the beauty of an undisturbed and protected beach covered in drift wood, animal bones, and shells. 

Our trash collectors filled bags of water bottles, flip flops, candy wrappers, and other detritus that continues to wash in from the ocean. And our naturalists wandered both the terrace and lagoon taking pictures of native and invasive grasses, frogs, lizards, birds, and much more! 

The amazing turnout we had for this event allowed us to collect from 23 sites, record over 300 iNatualist observations, and remove several bags of trash from the Lagoon. 

iNat link for this event: https://www.inaturalist.org/projects/younger-lagoon-reserve-bioblitz-2018

Our sampling site: https://ucnrs.org/reserves/younger-lagoon-reserve/

eDNA collection sites: http://data.ucedna.com/field_data_projects/118

 

UC Davis S.E.E.D.S will collect eDNA on Mt. Diablo

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! 

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Our eDNA analysis pipeline is fast!

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!

 

And we're on for another 5 years!!

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

 

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UCLA graduate student Tiara Moore collects eDNA samples from SoCal lagoons

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!

 

Coastal CALeDNA bioblitz — Fall

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! 

A 5 mm diameter 6-rayed sea star ( Leptasterias ) recruit!

A 5 mm diameter 6-rayed sea star (Leptasterias) recruit!

Sunset at the last of our sites, Bodega Bay, for the Fall coastal eDNA Bioblitz.

Sunset at the last of our sites, Bodega Bay, for the Fall coastal eDNA Bioblitz.

What is in these waves, and from where did it come? &nbsp;CALeDNA sample K0307-LA-S1 will have some answers!

What is in these waves, and from where did it come?  CALeDNA sample K0307-LA-S1 will have some answers!

   And even in the darkest night, the Dawson lab was recording sea star counts in the tidepools. Check out the UCCGC Ochre sea star project here &lt; https://ucconservationgenomics.eeb.ucla.edu/projects/ochre-seastar/ &gt;&nbsp;

 

And even in the darkest night, the Dawson lab was recording sea star counts in the tidepools. Check out the UCCGC Ochre sea star project here <https://ucconservationgenomics.eeb.ucla.edu/projects/ochre-seastar/

 

From sea level to 14,000 feet in 36 hours

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!

 

Merced Vernal Pools and Grasslands sampling for eDNA (Summer)

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.