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Data-deficient species are a conservation blind spot. Geneticists found a way to see through it.

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Data-deficient species are a conservation blind spot. Geneticists found a way to see through it.

They discovered that single animal’s DNA contains clues to the extinction risk of the entire species.
May 3, 2023

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In the universe of endangered species, there is a blind spot. These are the organisms called “data deficient,” by the International Union for Conservation of Nature (IUCN), whose Red List is the gold standard for tracking the fate of species. In more colloquial terms, the phrase means “We don’t know what the heck is going on.”

This is not a small oversight. All told, there are more than 20,000 such species, nearly 14% of all Red List organisms. There’s Savage’s earth snake, a slender brown creature found in Costa Rica. There’s Retrophyllum piresii, a Brazilian conifer with fern-like leaves. There’s the humpnose unicornfish, the southern Honduran spiny-tailed iguana, the Central American red brocket (a kind of small deer), and on, and on.

Behind this “data deficient” label is a bigger story about a lack of basic information about lots of species: how many there are, where they are found, and whether their numbers are declining. Being stuck in this data-free limbo means it’s easier for species to be overlooked by environmentalists, policymakers and the general public, even if they are on the verge of disappearing.

It also highlights the challenge scientists face to collect enough information about these species to figure out what’s happening to them. Too many species, too few scientists.

Now, geneticists hope to help tackle the problem by harnessing the burgeoning library of genetic data about species, the increasing ease with which we can decipher entire animal genomes and the growing computer power available to make sense of it all.

“The limited resources available for the conservation of wildlife species requires triage,” said Megan Supple, a genomics expert at the University of California, Santa Cruz (UCSC). “Our genomic assessment provides a relatively inexpensive method to rapidly identify species at risk of becoming endangered in the future, even when little else is known about that species.”

Supple was part of a bigger initiative called Zoonomia. That project, which involved more than 30 labs at several dozen research institutions, aimed to learn more about what makes the world’s mammals tick – on a genetic level – by comparing the genomes of 240 mammal species ranging from a tiny shrew to a bus-sized killer whale. The group recently unveiled discoveries about everything from the genetic underpinnings of the athletic feats of the famed sled dog Balto to ways to zero in on the genetic origins of some human diseases.

When it comes to biodiversity, the scientists set out to see if DNA from a single animal contained clues about whether an entire species was at greater risk of extinction.

The basic idea is that an animal’s genome bears evidence about the health of a species. Generally, a larger number of animals in a species contributes to health and resilience, because it provides more genetic diversity. Harmful genetic mutations are less likely to become dominant from one generation to the next, for example, because they will be diluted as animals carrying that mutation mate with others that don’t.

 Overall, the researchers found that out of the 240 mammals, threatened species were more likely to have a variety of genetic risk factors. Their genomes bore evidence of smaller ancient populations, had more mutations in parts of their DNA considered important for telling the body how to make new proteins, and showed more genetic similarity between parents.

When the researchers plugged 13 different genetic variables into a computer model designed to predict extinction risk, it accurately predicted whether or not the species was threatened with extinction between 69 and 82% of the time, depending on the particular model, the researchers reported last week in Science.

While that’s better than the 50% that would come with a coin flip, it’s worse than when the model was fed detailed ecological data about a species, such as the age when an animal is weaned, the age it first gives birth and the age it reaches sexual maturity. Then, the computer got the correct answer 88% of the time.

But, as the saying goes, don’t let the perfect be the enemy of the good. In this case, the scientists noted that while the genomic analysis is imperfect, it could give scientists an indication of which species warrant a closer look, the kind of look that can produce this ecological information.

To illustrate, they compared the extinction risks culled from the genomes of the Upper Galilee Mountains blind mole rat, the killer whale and the Java lesser chevrotain, a kind of rabbit-sized deer. All these species are listed as “data deficient” by the IUCN. According to the genome-based models, the mole rat had the lowest probability of being threatened (11 to 44%) while the whale had the highest (35 to 68%).  

“Our results show that a genome from a single individual can be sufficient to identify the most threatened of these ‘data deficient’ species, enabling us to focus our limited resources,” said Beth Shapiro, a UCSC scientists involved in the work.

Perhaps that can help tell scientists where to shine a bit more light on those species in the shadows.

Wilder et. al. “The contribution of historical processes to contemporary extinction risk in placental mammals.Science. April 27, 2023.

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