Stepping into the entomology department at the California Academy of Sciences, a crisp chill greets you as towering white vaults stand like guardians of history. The vaults hold one of the state’s largest insect collections, amassed over 200 years. In each tray in these vaults, a dazzling array of colors bursts to life. Thousands of tiny pins glint under the light, each holding an insect like a jewel— their colourful wings shimmering like stained glass, their bodies glowing like polished armor.

One floor below, where these insect specimens are stored, Anna Holmquist, a postdoctoral researcher at the California Academy of Science’s Center for Comparative Genomics, applies state-of-the-art technology to uncover genetic clues in the delicately preserved century-old insects of California.

“I was just amazed by how you could just turn over a rock and see so many different animals right there,” Holmquist said, holding up a tray of carefully labelled insects, some collected long before she was born. These tiny time capsules contain valuable genetic information that can help scientists track biodiversity and understand how insect populations are changing.

Insects are nature’s tiny building blocks, holding together nearly every land and freshwater ecosystem. Yet, more than 40% of insect species are declining, and a third are at risk of disappearing. Scientists know the numbers are shrinking, but with millions of species—many still undiscovered —it may seem like counting the number of stars in the night sky. For accurate species identification, DNA-based methods are remarkably reliable for identifying insect species and estimating biodiversity. Instead of relying on experts and microscopes to identify insects by their morphology, DNA tests read an insect’s genes to quickly tell what it is. This makes identification easier, especially when the insects are hard to tell apart. However, even with this method, there are still issues with identifying species at large.

While researchers can collect and sequence insect DNA, no complete reference guides them in identifying the insect. So sequencing DNA from one insect is like finding a puzzle piece without the box cover showing where that piece could go in the overall picture. In an effort to create such a reference, Holmquist and her team at the California Academy of Sciences are sequencing DNA from carefully identified specimens — some collected centuries ago and stored across seven California institutes. The results of this project will serve as a biological “cheat sheet,” helping scientists use genetic sequences to quickly identify species, track biodiversity, and spot changes in ecosystems.

Museums simply don’t have the room to house every insect from every part of the world, but we must continue to discover and collect new species to understand our world, said Professor Brian Fischer, the curator of entomology at the California Academy of Sciences. “This method is the best guide for documenting and studying the diversity of insects.”

DNA barcoding comes of age 

“Entomology may seem like an obscure field, but it influences everything.”

With over one million species, insects make up around two-thirds of all animal species on Earth. They’re found everywhere, buzzing through the air, burrowing in the soil and skimming across ponds.

Insects are also vital to our ecosystems, as they support life by pollinating plants, recycling nutrients, and serve as food for countless animals. They also have the power to take life away, as some carry harmful diseases or can decimate the plant life they feed on.

“Entomology may seem like an obscure field, but it influences everything,” Professor Emerita of Entomology Lynn S Kimsey from the University of California Davis said.

Data from the International Union for Conservation of Nature from 2024 show that researchers have estimated the conservation status of only about 14% of the roughly 1 million known insect species. This means that scientists do not know whether the vast majority of insect species populations are stable or declining. Globally, there are about 5.5 million species of insects, according to recent scientific estimates. This means that among one million insect species described, 80 per cent are still undiscovered. Among this immense diversity of insects, even if we look at just 1% of all insect species, that tiny slice would include as many species as every bird on Earth—and that’s twice as many species as all the mammals that scientists have studied.

Many reports over the recent years have drawn attention to the dropping abundance of insects, and scientists have warned that humans are causing insect extinctions. But because most insect species have not been studied, scientists aren’t entirely sure which insects are most at risk.  To tackle this, scientists use genetic data to identify and study insect biodiversity because DNA—the fundamental genetic blueprint of all life—uniquely defines every species. Since the early 2000s, scientists have been developing a concept called “DNA barcoding” that attempts to use snippets of genetic sequences to identify and study species. Just like a supermarket scanner reads the black stripes of a barcode to identify products, this unique DNA sequence can be used to tell different species apart.

The barcoding effort began in 2003 when Paul Hebert, founder and director of the Centre for Biodiversity Genomics at the University of Guelph in Ontario and his team introduced the barcoding method, which samples a small section of DNA from a specific part of the genome. Data from this small section is compared across individuals, yielding information on how closely these individuals are related to each other or other species. Scientists can use this DNA barcode data to determine whether one individual organism belongs to an existing species or an as-yet undiscovered one.

“Barcoding democratizes taxonomy, makes it a lot easier for somebody to say what lives in this environment,” Christopher C. Grinter, collection manager of entomology at the California Academy of Sciences, said. He adds that DNA barcoding has evolved to the point where what once cost hundreds of dollars can now be done for just pennies, making it an increasingly useful tool for studying biodiversity.

Mapping the unknown 

California serves as a hotspot for insect biodiversity, but how many insects and species call the state home is still a big question. We’ve long recognised that insects are facing significant challenges, but our knowledge about them is surprisingly limited—we’re still uncertain about the total number of insect species that inhabit our planet said Daniel Gluesenkamp, the president of the California Institute for Biodiversity, a non-profit organisation in Berkeley. “We don’t know how many [insects] there are in California, where we have essentially as much resources, money, brilliant scientists capacity as you’re going to find anywhere on the planet.”

Natural history museums in California hold millions of specimens that likely include many new species, but most of them are still not officially identified, meaning that scientists don’t know which of these specimens belong to new species or existing ones.  The California Academy of Sciences collection holds about 17 million insect specimens, making it one of the four largest and oldest insect specimen collections in the United States. Scientists hope to catalogue the genetic information in these existing specimen collections and use it to construct large-scale DNA barcode libraries.

In an attempt to do so, California Academy researchers and a team of scientists across seven Californian institutes secured funding of  $6 million in 2022 to launch the California Insect Barcoding Initiative (CIBI).  The project is funded by the California State Legislature, and administered through the California Institute for Biodiversity, a non-profit organization.

The California Academy of Sciences is working with several institutions, including the California Department of Food and Agriculture, UC Berkeley, UC Riverside, the San Diego Natural History Museum, and the Natural History Museum of Los Angeles County, on two major projects under the statewide barcoding initiative. One involves discovering and collecting new insect species from the field to send to the Canadian Center of DNA Barcoding in Guelph, Canada. The other focuses on barcoding insect specimens already housed in museums across California to build a reliable reference library. The resulting data will be uploaded to the online database, the International Barcode of Life. 

This database is regularly updated by scientists from more than 40 nations who use DNA barcoding to study species around the world. “There are thousands of people around the world using the DNA barcoding approach to learn more about biodiversity, and I think it’s one of the great science bargains of our time,” Hebert said.

This global endeavour is mirrored by equally ambitious regional targets. “The project is a big encompassing project to DNA barcode, not just insects, but pretty much all of the understudied taxa across California,” said Austin Baker, the postdoctoral fellow leading the Natural History Museum’s efforts in the initiative.

Decoding the past   

Traditional barcoding techniques rely on high-quality, non-destructive fresh DNA samples. For instance, a scientist might collect DNA barcode data from trace amounts of genetic material found in animal scat left in the woods. While these methods have been effective for sequencing recently collected specimens, such as for the samples being sent to Guelph, they fail when applied to degraded DNA, such as that found in older collections, which may contain samples that have sat in drawers for centuries.

“The age continues to degrade the DNA, so even though the technology gets cheaper, it doesn’t mean we can get an accurate DNA out of it,” Grinter said. Fortunately, Holmquist and her team have developed solutions to these challenges.

“The field of entomology has evolved from just collections into thinking about more focused questions,” said Athena Lam, director of the Center for Comparative Genomics, who leads the all-women DNA barcoding team in the academy.

Today, she works with Anna Holmquist and lab technician Holly Tavris, to decode ancient insect DNA in the quiet, white genomic laboratory of the California Academy of Sciences. Their challenge: to construct smooth, linear DNA barcodes out of the tiny fragments of DNA that remain after museum specimens have broken down after years in storage. And to do so at a fraction of the current cost.

“I had learned through my own work how important it was to have these barcode types, and it was just kind of a perfect method development opportunity for me in line with what I am passionate about,” Holmquist said.

A typical day in the lab starts with Holmquist scooping tiny metallic beads, each about the size of a poppy seed, into trays with compartments that are each no bigger than a grain of rice. Inside each well of the tray sits the leg of a century-old insect specimen. Holmquist uses a machine to grind up the insect legs, which results in a thick fluid of ground-up DNA and tissue. The DNA in this mixture sticks to the metallic beads, allowing Holmquist to pull out just the DNA while leaving unwanted material behind like a magnet pulling iron filings out of a batch of sand.

The researchers then scoop up the beads and the DNA fragments attached to them, ready for the next step: creating copies of the DNA fragments using a method called Polymerase Chain Reaction or PCR, which works like a photocopier for DNA. The research team then combines all the amplified insect DNA from every specimen into one tiny tube—just a few drops holding the genetic material of thousands of insects. Each tube contains DNA fragments from just one species.

The team then loads these tiny drops carefully into a high-technology DNA reader, similar to plugging a USB drive into a computer. This DNA reader called a nanopore sequencer, small enough to fit in a human palm, and can read thousands of DNA samples in a few seconds.

By reading thousands of DNA fragments from one species, the team determines the final, most accurate DNA sequence for each species. The team uploads the data to the International Barcode of Life, making information stored in museums for decades accessible to everyone in the world.

Building a blueprint

Six months after optimising the protocol, the team is making strides. “A year and a half ago this could not be done, and we’ve done it,” Lam said. “It’s been rewarding working with the team and doing these things that could not have been done before.”

As of February 2025, the team has generated 2500 barcodes from the 5000 ancient DNA samples sent by the collaborators of the project. And they’ve cut the cost of processing each sample from $4-5 dollars to 11 cents. The oldest specimen the team deciphered in their last sequencing run in February 2025 was 115 years old.

This challenge of identifying cryptic species — those that look alike but are genetically distinct — is one of the reasons why the project is so important. The team recently helped Severyn Korneyev, an environmental scientist at the California Department of Food and Agriculture, by analyzing the DNA of some flies that he assumed all belonged to the same species. Holmquist sequenced the DNA of the flies he collected, which revealed that they were genetically distinct from R. juniperina, the species Korneyev initially thought they belonged to.

For accurate species identification in the field, appearances can be misleading at times. “A lot of flies look identical, and then you DNA sequence them and you’re like, ‘Oh, that’s not the same thing after all,'” said Julia Betz, entomology curatorial assistant at the California Academy of Sciences, who supplies Holmquist with the ancient insect samples from the museum’s collections.

“If we had a barcode library already,” entomologist Fischer said, “whenever I go to the field, I could easily just take a sample and sequence it.”

For Hebert, the father of DNA barcoding, this project represents a crucial step toward achieving the broader objective of barcoding—to “register every species, preserve its DNA, and read its genome for the long term.”

The California Insect Barcoding Initiative’s funding will take it through June 2026, at which point the researchers hope to have completed the sequencing of 100,000 ancient insect samples from California.

“With our first bioinformatic pipeline now established”, Holmquist said, “now we’ll just be cruising and that’ll definitely improve our success and we’ll start getting a lot more barcodes.”

While it may be impossible to identify and barcode every insect species in California through this project alone, since there are still thousands to document and describe, this project represents an enormous advance in our knowledge of what insect species are out there and where they live.

By rigorously documenting and preserving California’s extensive biodiversity—from established specimens in collections to newly discovered life from uncharted sites—Gluesenkamp said, “we will know humankind saved some specimens of these things that we know will not be there in the future.”

 © 2025 Mahima Samraik / UC Santa Cruz Science Communication Program