DNA sequencing to help save California’s plants and animals

In a dark, deep, and humid redwood forest, Max Genetti scans a trail for slime.

His career: Banana slugs, small but important contributors to the new California Conservation Genomics Projectan ambitious effort to find, catch, and genetically decode approximately 250 of the state’s most special species.

In the glow of a predawn headlamp, “you can spot the mucus trail, because it glows,” said Genetti, a bioinformatics specialist at UC Santa Cruz.

The slug’s DNA, extracted from a tiny slice of its tail, will tell a story. How this bright yellow Bay Area creature, one of Earth’s slowest animals, relates to its distant cousins, which look like Eureka bruised fruit and green fruit unripe in the foothills of the Sierra Nevada?

Like the people of California, the extended families of its plants and animals are extremely diverse, a mixture of different colors and customs. Some, like slugs, are separated by distance and weather changes. Others are fractured by urban development or have moved away in the relentless march of time.

By building a dataset of nearly 20,000 different genomes – representing carefully selected species from the arid Mojave Desert to the snow-capped Sierra Nevada Mountains – the $12 million state-funded project will create a unique map of the world. ‘State, providing leaders with current scientific data. and analyzes to help them make decisions about land use and conservation.

At a time of rapidly accelerating species decline, the map will reveal hotspots of diversity, which could serve as reservoirs of genetic variation to help species adapt to environmental change, said director Brad Shaffer of the UC Los Angeles The Kretz Center for California Conservation Science, who leads the 79 scientists in the effort. He could identify special landscape corridors, where creatures should connect.

“We protect pretty places,” Shaffer said. “We may not be protecting the most biologically important places.”

It will also stimulate research. For example, it could reveal which populations might be at risk due to inbreeding and low genetic diversity. It will help scientists understand how populatiWe have changed over time. It can link genes to physical appearance and behaviors. It could identify new species hidden within groups of identical-looking organisms.

To create this inventory, scientists from all 10 UC campuses – as well as Lawrence Berkeley and Los Alamos National Laboratories, UC Nature Preserves, several California State University campuses and some Federal and state regulators – scatter across the state in search of fins, feathers, fronds and other tissue.

Genetti aims to sample 150 banana slugs from 70 different locations. Once discovered, a slug is laid out on a board to be measured and photographed. Using a razor blade, Genetti cuts off a piece of tail the size of rice. With tweezers, he places the skin in a vial filled with alcohol and brings the tissue back to UCSC for freezing and processing in the laboratory of Professor Russ Corbett-Detig, principal investigator of the project.

“The more diverse a population, the healthier the population,” Genetti said. And because slugs are sensitive to moisture, “it also tells us about the health of the forest.”

To capture his creatures – golden eagles – Robert Fisher of the USGS must use bait.

Robert Fisher of the USGS releases a golden eagle in southern California after collecting a small DNA-rich blood sample for the California Conservation Genomics Project. (Photo courtesy of Robert Fisher)

Half-carcasses of dead calves, with stinging and dripping blood, are transported for miles along rugged trails to a remote location. When the eagle lands to eat, a soft snare in the shape of a “bow net” catches it. Fisher’s team, emerging from a nearby blind, subdues the bird by covering its head and wrapping gauze around its dangerous talons. Then they draw a drop of blood from a vein in its wing and release it.

Because genetic data can be linked to flight data, the project will help reveal the social structures, pedigrees and dispersal patterns of eagles, Fisher said.

It will also guide protection strategies, said Doug Bell, East Bay Regional Park district wildlife program manager. Different eagle populations face different pressures, from drought to development, he said.

“The project gives us a clearer picture of what conservation actions might be needed,” said Bell, who has contributed DNA from golden eagles captured at Sunol Wilderness, Crockett Hills and Mission Peak Regional Preserves.

The endangered Crotch’s bumblebee is the holy grail of entomologists. As UC Riverside collectors Blanca Ortega and Kaleigh Fisher slowly walked through Sequoia National Park last June, they were intrigued by a cloud of black bugs hovering around a flowering tree.

UC Riverside entomologists Blanca Ortega and Claudineia Costa catch bumblebees to contribute DNA to the California Conservation Genomics Project. (Photo courtesy of Blanca Ortega)

The pair quickly stopped, grabbed some nets and jumped off. Clinging to the edge of the steep hill, Fisher took a hit – and caught one.

“We couldn’t believe it. It was worth risking our lives,” Ortega said. The rare bee, with a distinctive thick yellow abdomen, was placed in liquid nitrogen and brought back over 250 miles to the lab.

Emma Steigerwald of UC Berkeley’s Evolab found Tetragnatha spiders at the edge of Marin County’s Lagunitas Creek at night when the spiders are active. The spiders are well camouflaged — but when she beat the vegetation with a stick, the arachnids fell on a white sheet.

On the beaches, Dan Costa and his team sneak up on their target species: northern elephant seals. There’s a brief window of time – March through May – when the pups are alone on the sand, so it’s safe to get close. The team is sampling four animals from each of the state’s 14 colonies, from the Channel Islands to Humboldt’s Punta Gorda.

Año Nuevo Reserve director Patrick Robinson, left, and UC Santa Cruz student Wade Matern take a sample of fin tissue from a baby elephant seal as part of the California Conservation Genomics Project . (Photo courtesy of Dan Costa, UCSC)

“We can sneak up to them with little pliers and get a piece of tissue, from the fin. It’s like getting your ear pierced,” said Costa, director of UCSC’s Institute of Marine Science. “The animal will wake up, look at us and go back to sleep. It’s only dangerous if you don’t know what you’re doing.

The elephant seal project, led by Roxanne Beltran, assistant professor of ecology and evolutionary biology at UCSC, will help scientists better understand the recovery of this species, once nearly extinct due to hunting. Today’s 200,000 elephant seals are all descended from fewer than 25 individuals.

From a genetic bottleneck from long ago, “Are all colonies the same?” Costa asked. “Over time, will they diverge from each other?”

Back in the labs, the DNA from each sample is sequenced and passed through a computer analysis pipeline that converts the raw data into a format that can be more easily analyzed. The goal is to understand the molecular code that provides an “instruction manual” on the development of any living organism.

The project is made possible by dramatic improvements in genetic sequencing technologies, with huge advances in computing power and plummeting costs. All data is stored at the NIH National Center for Biotechnology Information.

Despite challenges, such as COVID-19 and drought, the effort is progressing rapidly. So far around 15,000 samples have been collected. Of these, DNA has been extracted from more than 5,000. In a year or two, the project should be complete.

“We’re in a triage situation,” Costa said, racing against time as species are stressed by climate change.

“I’m proud that itLifornia recognizes the need for this fundamental science,” Costa said, “to give us the best information we can get, to make the decisions necessary to protect what we have.