The meltwater stonefly has adapted to a very specific and extreme niche — the cold, clear water that pours off of the melting ice and snow from the glaciers in Glacier National Park in Montana. This bug is on the leading edge of climate change because its frigid mountain habitat is rapidly disappearing. Since 1850, 85 percent of the ice in Glacier has disappeared, and all of it is forecast to vanish completely by 2020.

In a study published in 2016, researchers found the cold-loving insect in trouble. “Their physiology requires really, really cold water, and they can’t survive once the water gets above an average of 9 degrees Centigrade during August,” said Joe Giersch, a biologist with the U.S. Geological Survey (USGS), who has studied this and a similar insect, the western glacier stonefly.

Meltwater stoneflies and western glacier stoneflies move upstream to find cold water as things warm, and because of steeper mountain topography, populations become separated. This has interrupted gene flow, causing some genetics to disappear. As genes dwindle, the species is losing genetic variation and likely “adaptive capacity” — the genetics that give species the ability to evolve needed traits as habitat conditions change. It’s a big part of why the meltwater stonefly (Lednia tumana) is being considered for listing as threatened under the federal Endangered Species Act.

And many of its fellow high-altitude insects are in trouble too. This stonefly, Giersch and his co-authors wrote, “likely represents a guild of species facing similar threats in alpine headwaters worldwide.”

There is a huge unknown when it comes to protecting the meltwater stonefly and other species. Biologists are missing a huge piece of the puzzle — knowing which genetics will give species the evolutionary lift that allows them to adapt successfully to a warmer world. This hidden DNA and the possibly important traits it represents are known as “cryptic diversity,” and much of it is being lost, experts say, as the range of species contracts, fragments, and otherwise changes. Yet this DNA is vital because it contains information on different lineages and on species that are emerging, the cutting edge of evolution. Losing it will greatly complicate the task of assessing how climate change will affect biodiversity and what to protect.

What disappears before we know it could have far-reaching consequences. A long-term research project on the genetic variations in cottonwood trees, called the Cottonwood Ecology Group, found that the genotype of a tree affects the communities of some 700 insect species that depend on it, as well as chemical emissions, microbes, bacteria, lichens, beavers, and birds that feed on the insects. Should important genotypes disappear, whole ecological communities could change in unpredictable ways. “Genetic diversity in foundational plant species — alpine flowers, cottonwoods, or tall grass prairie — drive hundreds if not thousands of other species,” said Thomas Whitham who heads the project at Northern Arizona University. “That’s why climate change is an evolutionary event.”

Often where the climate is changing fastest is where species are affected most. The bull trout, a threatened species that depends on very cold water in the Pacific Northwest, is also being impacted by warming. “What we found is that genetic diversity is lowest in those locations that are going to experience the greatest climate change and the most stressful environmental conditions,” said Ryan Kovach, a USGS fisheries biologist in Glacier National Park who has published papers on the subject of bull trout and climate. “In other words they don’t have genetic diversity where they are most likely to need it.” That’s because there are fewer fish in these habitats because of already stressful conditions.

These kinds of genetic studies are a race against climate warming that is happening far faster than predicted. “Although genetic diversity is literally the fundamental building block for all life, it is almost completely ignored in the context of climate change,” said Kovach.

Carsten Nowak, a conservation biologist at the Senckenberg Research Institute and Natural History Museum in Gelnhausen, Germany, has also studied the genetics of climate change response in alpine insects, as well as in wolves and other species.

In 2011 Nowak and his colleagues conducted research in high-country Europe that looked at seven species of caddis fly and one species each of mayfly and stonefly, which like the stoneflies in Glacier National Park are cold-loving bugs. The scientists examined the species’ genetics and divided them into a finer scale, populations within the species that are genetically distinct from each other, something known as Evolutionary Significant Units (ESUs).

If the climate scenario doesn’t change, according to their work, 79 percent of the ESUs will go extinct by 2080, decimating hidden genetic diversity. If greenhouse gas emissions are reduced by the amount needed to cap global warming at 2 degrees Celsius, as the Intergovernmental Panel on Climate Change has urged, then 59 percent of the ESUs are projected to disappear.

Nowak’s study predicted that the loss of genetic diversity in Europe would be most marked in the Mediterranean region of southern Europe, which is also the area of the continent with the greatest genetic diversity. Even if populations disappear, no one knows what the loss represents. “We need to know if there are ten populations and nine disappear does that matter?” Nowak said.

Portuguese researchers forecasted in a paper published in February of 2016 that many lineages of amphibians and reptiles on the Iberian peninsula, which is expected to be hardest hit by warmer and drier weather, could disappear or contract within the next half century, causing a loss of cryptic diversity “with implications to evolutionary processes.”

These losses are important because a species, for example, that is exposed to a new disease, might not be able to evolve resistance to it because the genetics that govern immune response are gone. Or the genes that allow a fish or stonefly to regulate its temperature in warmer water might disappear.

The good news is that there has been a revolution in the ability to sequence DNA — it’s now much faster and far cheaper than ever. The goal of many conservation scientists is to sequence the genomes of a species and then understand which section is responsible for adaptation, including such traits as migratory abilities, dispersal, and the ability to adapt to warmer temperature. Once that’s done, it allows managers to allocate scarce resources to protect the populations most essential for adapting to changing conditions.

Nowak cited the example of the Siberian tiger, whose population has dwindled to a few hundred. “Can we use the Indian tiger to repopulate Siberia?” he asked rhetorically. “If you have a lot of Evolutionary Significant Units and know what they represent, you might want some that are better at cold adaptation or fish catching,” to repopulate Siberia. “You can’t just protect the species, you have to protect the populations,” the small units of a species that might have the genes necessary for adaptation. Knowing what they represent is the hard part.

As ecologically important species come on line with their adaptation capacity mapped, it will give managers a powerful tool to triage species to protect the adaptation genetics. They might even affect “gene rescues” by focusing on the populations with the most vital genes. “One of the options we have for the stonefly is translocation — moving one population to a different location,” said Giersch. “That’s after we investigate the hidden adaptations within the DNA to figure out which ones have the ability to adapt to warmer temperatures. That’s a ways down the road.”

Two species of trees have recently had their climate genes mapped and adaptive capacity located. A study published in September of 2016 found that two distantly related trees — interior spruce and lodgepole pine — use the same set of 47 genes to deal with temperature, precipitation and other climate variables. Knowing about these adaptations trees is important because they migrate slowly, over generations, and assisted migration efforts with trees are already underway. “We have to understand climate adaptation in other conifers so we can address trees that are becoming mismatched” to their environment, said Sally Aitken, a professor of forest and conservation science at the University of British Columbia. That will inform better management strategies, she said, and enable us “to plant trees that are more likely to thrive and adapt more quickly to climate change.”