DNA analysis can predict which animals are at risk of extinction

In a fascinating new discovery, a team of scientists from the San Diego Zoo Wildlife Alliance and the University of California, Santa Cruz has found that animals’ genomic information can help predict which mammal species are more likely to face extinction. 

The researchers found that species with smaller historical populations tend to carry higher burdens of damaging mutations and have elevated extinction risk. This indicates that long-term demographic statistics play a crucial role in understanding a species’ current conservation status and resiliency.

As our planet experiences rapid biodiversity loss, tens of thousands of species are at risk of dying out. Identifying the species in most urgent need of conservation is a challenging and expensive process, especially given the limited information available for many of them. This makes it difficult to allocate scarce conservation resources to target the species closest to the brink of extinction.

To address these limitations, the scientists examined the genomes of 240 mammal species, ranging from tiny tree shrews to towering giraffes, killer whales, and even humans. 

What the researchers discovered

The experts discovered that the DNA encoded within a single genome – reflecting a species’ history over millions of years – can provide a rapid, cost-effective conservation risk assessment. This information is useful even when we know little about the animals’ physiological, behavioral, and life history characteristics, or how many individuals remain in the population.

“These results show that genetic information, even if only from a single individual for a given species, offers immediate, actionable guidance for scientists designing conservation strategies as well as those with boots in the field,” said co-lead author Dr. Aryn P. Wilder, a conservation scientist at San Diego Zoo Wildlife Alliance.

“The limited resources available for the conservation of wildlife species require triage. 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. This genomic triage enables managers to target limited resources toward species most in need,” explained Megan Supple, a research scientist with the UCSC Paleogenomics Lab.

How the study was done

The researchers used the genomic information to train models that quickly distinguish between threatened and non-threatened species, based on demography, diversity, and mutations that impact fitness. 

This will help assess extinction risk and identify which of the thousands of threatened species stand to benefit the most from conservation support. As the number of sequenced genomes grows and the models continue to improve, this approach will become increasingly valuable.

To demonstrate the potential of this genomic risk assessment, the scientists applied their models to three “data-deficient” species: the Upper Galilee Mountains blind mole rat, the lesser chevrotain, and the orca. 

These are just a few examples of the thousands of species lacking information on whether they’re threatened or not.

Why this study is groundbreaking

The researchers examined the genomes of 240 species, revealing the potential for genomic information to play a vital role in conservation efforts. 

By analyzing such a vast number of species, scientists were able to estimate the genomic characteristics that best predict extinction risk and build genomic risk assessment models that can be used when other information is lacking.

The authors of the paper are advocating for the inclusion of genomic information in conservation status assessments of species. This would bridge the gap between geneticists and conservation managers, providing a framework for deploying money and resources to species at the highest risk.

“Many potentially endangered species are classified as ‘data deficient,’ meaning that we simply have too little information to determine whether immediate conservation action is required,” said Dr. Beth Shapiro. “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 where they can be most impactful.”

Study co-senior author Dr. Oliver Ryder emphasized the importance of genomics in conservation efforts: “Our rapidly changing world threatens animal and plant species worldwide – but the use of genomics in conservation is a massive, underappreciated opportunity to protect them.”

“We are in an unprecedented era of discovery – a whole new way of seeing the world. We’ve long thought this potential existed, but it’s profound to see it crystallize into a catalyst that will help conservationists make crucial decisions that may save the world as we know it,” said Dr. Ryder.

More about the study

The study is part of the work of the Zoonomia Consortium, the largest comparative mammalian genomics resource in the world, involving more than 150 people worldwide. 

A series of papers recently published in the journal Science also demonstrate how comparative genomics can shed light on how certain species achieve extraordinary feats and help scientists better understand the functional parts of our genome and how they might influence health and disease. 

Additionally, the researchers identified part of the genetic basis for rare mammal traits, such as the ability to sniff faint scents from miles away.

Many of the genetic samples for the DNA analyses were provided by the San Diego Zoo Wildlife Alliance’s “Frozen Zoo,” the largest repository of genetic material of its kind. The Frozen Zoo, or Wildlife Biodiversity Bank, contains viable cell cultures and reproductive material from approximately 10,000 animals representing over 1,100 species and subspecies.

More about species extinction

Many scientists believe that we are currently in the midst of a mass extinction event, often referred to as the Sixth Mass Extinction or the Holocene Extinction. This ongoing extinction event is primarily driven by human activities, such as habitat destruction, pollution, climate change, and the introduction of invasive species.

In Earth’s history, there have been five major mass extinction events:

Ordovician-Silurian Extinction (about 443 million years ago)

This event resulted in the loss of around 85% of marine species, likely due to glaciation and subsequent changes in sea levels and ocean chemistry.

Late Devonian Extinction (about 359 million years ago)

This extinction event eliminated about 75% of all species, primarily affecting marine life. Possible causes include global cooling, changes in ocean chemistry, and asteroid impacts.

Permian-Triassic Extinction (about 252 million years ago)

Also known as the “Great Dying,” this was the most severe extinction event in Earth’s history, resulting in the loss of approximately 90-96% of all species. The cause of this event is still debated, but likely factors include volcanic activity, climate change, and ocean anoxia (a lack of oxygen).

Triassic-Jurassic Extinction (about 201 million years ago)

This event led to the extinction of around 75-80% of all species, including many marine and land-dwelling reptiles. The exact cause is uncertain, but it may have been related to volcanic activity or asteroid impacts.

Cretaceous-Paleogene Extinction (about 66 million years ago)

This well-known extinction event resulted in the loss of approximately 75 percent of all species, including the non-avian dinosaurs. The primary cause is believed to be an asteroid impact, although volcanic activity might have also played a role.

The current mass extinction event, if it continues at its current rate, could have devastating consequences for biodiversity on Earth, ultimately affecting human societies that depend on healthy ecosystems for survival.

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