What genetic sequencing can reveal about the secret lives of bees

Bees are, in many ways, the darlings of the insect world. Not only do they play a crucial role in thriving ecosystems, but they’re also harbingers of the worsening consequences of climate change.

To bolster our knowledge of bee biology and behavior, a new effort dubbed the “Beenome100 Project” is building a first-of-its-kind library of dozens of different bee genomes. Researchers can use that information to tackle big picture questions like how to protect these tiny creatures, and how they’ve evolved alongside us over time.

Beenome is just one of the many initiatives affiliated with the Earth BioGenome Project (EBP), an ambitious international effort to sequence the genomes of nearly 2 million named eukaryotic species. Eukaryotes have cells that contain nuclei and other organelles, setting them apart from other life forms like bacteria. This domain covers all plants, fungi, and animals, including bees.

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First launched in 2018, EBP aims to sequence the genomes of those species over the course of 10 years, housing them in a public database so that all researchers can have unfettered access to this extensive, unprecedented data. The sweeping project is largely made possible thanks to advancements in the field of genomic sequencing technology, which has made this work faster, cheaper and more accessible in recent years.

Bees face myriad threats in a warming world, including population decline, a loss of synchronicity with the flowers they pollinate and increased susceptibility to disease. In general, insects are vulnerable to climate change because being coldblooded makes them uniquely sensitive to temperature fluctuations, said Michael Branstetter, a research entomologist at the United States Department of Agriculture.

The extinction rate of insect species is eight times faster compared to mammals, birds and reptiles, according to the United Nations Environment Program, and if the total mass of insects continues to drop at its current annual rate, these creatures could “vanish within a century.” Bees are no exception – to our own peril. Around a third of the crops we eat rely on animal pollinators, according to the USDA. Without bees, birds and other creatures, our pantries and refrigerators would look dramatically different.

“If you picked any insect group to disappear, you wouldn’t want to start with bees, because we would feel the effects for sure,” Branstetter said.

The United States is home to approximately 4,000 native bee species, and the aim of Beenome is to help researchers answer such questions as the genetic underpinnings that make different species susceptible to climate change. The project has a goal of unlocking the “blueprint” for at least 100 species, and eventually sequencing more over time, said Jay Evans, a research entomologist at the USDA and co-lead of the project.

The broader Earth BioGenome Project will help map a massive branch on the tree of life, with many potential uses, like significantly improving our understanding of evolution and ecology. It will also inform research in fields like agriculture, medicine, biotechnology and more. But the reality of climate change is putting researchers’ feet to the fire.

Around 1 million animal and plant species face extinction, several potentially within the next few decades, due to forces like habitat loss and rising global temperatures, the United Nations estimates. That means Earth could lose up to 50 percent of its total biodiversity by 2100 without human intervention, according to the University of California, Davis.

For pollinator species, shifting temperatures and weather patterns shift also affect the natural timetables long adhered to by flowering plants – a serious disadvantage to both the plant and the insects.

There are many reasons why genomes are useful tools for scientific research, Branstetter said, including assessing the genetic diversity of a species and identifying potential “genomic signatures” of sociality that underpin some species’ hive mentality. But the very real threat of losing entire species to environmental changes is also a consideration.

Should a species go extinct, “it’s at least nice to know that we’ve documented the genome of that species,” Branstetter added.

Anna Childers co-leads the USDA’s Ag100Pest Initiative sequencing arthropods like ticks, flies and weevils. She noted that it’s crucial to understand how bees, as “sentinel insects of climate change,” may be responding to fluctuating temperatures and seasons in order for us to protect potentially endangered species.

“We kind of need to know how climate change might affect them, and having their genome is one way of learning this,” she said.

What does it take to put together a genome?

So how does genetic code, gibberish to the untrained eye, help answer major questions?

Childers knows that people’s eyes tend to glaze over once you get into the alphabet soup (adenine, guanine, thymine and cytosine — or A, G, T and C) that comprises genomes. That’s why she likes to use the metaphor of a map.

Genomes are like the most bare-boned map, where the basic geographic features are laid out but not much else. With a little more information, Childers said, you can start to add details like the locations of homes and businesses, or the traffic patterns of the busiest neighborhoods that differ depending on the time of day.

“By bringing it all together in one place and having that map on which to place [other information,] it allows us to have a much more intricate understanding of what’s happening,” Childers said.

So far, members of 40 species are on their way to having their genomes sequenced. These bees were picked out of their natural environments, then frozen and sent to Hawaii-based labs tasked with extracting their DNA. It may sound counterintuitive to sacrifice the bees scientists aim to preserve, but don’t worry — they don’t take enough individuals to harm the species as a whole.

Sample collection can be tricky — first researchers have to actually find a member of the bee species they’re seeking to sample in the wild. For larger bees, a single part of their body — like the thorax — is usually enough to get a whole genome. But the tinier the bee, the more you need to retrieve genetic code.

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“For the small bees, there’s only enough DNA if you do the whole bee. We just grind up wings, everything all together,” Evans said.

Sometimes researchers can also take multiple bees from the same colony or location and pool them together to generate a genome, Branstetter noted.

Once DNA is extracted from Beenome bees in Hawaii, researchers there or in Mississippi (both locations have the technology) feed it to a sequencing machine in smaller portions.

“You break that DNA down a little bit to maybe 20,000 base pair chunks. Then you put tags on the ends of each of those chunks, and then those are what go into this sequencing machine,” Evans said.

After that, those sequenced chunks get stitched together in a process called assembly. The annotation phase comes next. That’s when a combination of researchers and automated analyses interpret stretches of genetic code to figure out which genes they correspond to.

The process, which concerns about a tenth of the total genome, cross references the genomes of other species to identify the genes that are shared across different forms of life. Other parts of the genome are assessed as well, including non-coding RNA and sites that regulate how genes are turned on.

The process of annotating is akin to noting those traffic patterns or key landmarks on a map. Once it’s complete, the seemingly endless series of four letters is transformed into a key that connects an organism’s DNA to what researchers can observe about how a living member of the species’ goes about its daily life.

What researchers are learning

Bees captivate researchers for almost as many reasons as there are kinds of bees. For one, their behavior varies wildly across species. Some are social — like the famously hive-minded honeybees and bumblebees — but the majority lead solitary lives. There’s even variation within the same species in terms of living a social or solo life depending on external factors, noted Branstetter, who is involved with Beenome.

In the U.S., the Mojave poppy bee is native to a small, arid range across parts of Utah, Nevada and California. This tiny, solitary bee — which belongs to a family that had not been sequenced previously— specializes in pollinating local poppies that really only grow in certain conditions, and bloom for a short period during the spring.


Perdita meconis, otherwise known as the Mojave poppy bee, is pictured beside a dime to indicate its small size. Photo by Chelsey Ritner/USDA-ARS.

Their symbiosis is a prime example of how specialized the relationship between certain bees and plants can become, and just how crucial their mutual survival is. Both the bee and one of the flowers it frequents are under consideration for the endangered species list and face the threats of urbanization in their native habitat.

When Branstetter’s team sent the bee’s genome for sequencing, he said the result was one of the best genomes of a solitary bee generated thus far. He noted that the species’ unique biology and habitat “checks a lot of boxes” when it comes to the study of bees and their conservation.

“It’s a really tiny bee, so it was sort of challenging methodologically to see, ‘Can we get a good genome from it?'” he said. “And it’s from the desert Southwest, so it covers a geographic region and a habitat that we don’t have many representatives of for bees.”

The researchers intend to collect more Mojave poppy bees in order to improve their understanding of the population’s genetic diversity, but last year they didn’t find a single specimen, illustrating just how tricky that field work can be. Branstetter hopes that’s an example of “bet hedging,” when bees skip a season of poor, dry weather conditions so that they can reappear the following year.

Can bee genomes help save us?

Bee genomes can also help us map humans’ shared history with the rest of the natural world. Margarita López-Uribe, an associate professor of entomology at Penn State University, worked with her team to sequence the squash bee genome, a species that specializes in the pollination of members of the cucurbita genus, including squash and pumpkins.

Although squash bees can be found across the U.S. today, they were originally native to southwestern parts of the country, plus modern-day Mexico. They happily feasted on wild cucurbita plants that Indigenous populations in those regions began domesticating 10,000 years ago. But as people migrated away from that region and the scale of agriculture increased over the course of millennia, they brought their cultivated “cucurbits” with them, and the squash bees followed suit.

“This bee had been moving with the cultivation of crops and the movement of humans throughout North America,” López-Uribe said.


Squash bees are pictured collecting nectar inside a squash blossom. Photo courtesy Laura Jones.

By using a combination of different genomic information, she and her team estimated when geographically separated squash bees split off from each other. The squash bees that now live in the Northeast are genetically “highly divergent,” López-Uribe said, compared to the ancestral populations that still live in the southwest and Mexico. That means that squash bees have gone through “major adaptive processes” in their journey across land and time.

It’s clear that genomes can help us solve mysteries of evolution and ecology. But we can also call on them to help solve some of the most pressing crises facing humanity. Childers pointed to a beetle whose genomic sequence allowed researchers to understand how it’s able to break down wood. That kind of information, she noted, could help us identify more efficient ways to do the same thing in order to develop alternate fuels, or clean up environmental damage caused by catastrophes like oil spills.

“It’s hard to know what species we’re going to pluck out of the environment” that lead us to the innovations that will transform the future, Childers said. Having a bank of genomes at our fingertips is key to unlocking that wealth.