Pioneering new test can predict extinction risk in mammals

Single genome reflecting species' history over millions of years can provide a rapid, cost-effective conservation risk assessment

The Zoonomia Project is an international effort that compares the genetic blueprints of an array of animals, including the Chinese pangolin. AP

Genomic information can help predict which mammal species are more likely to face extinction, a study has shown.

The study found that species with smaller historical populations carry higher burdens of damaging mutations and have an elevated extinction risk.

The findings, which could change how conservation actions and resources are strategically applied to help save endangered wildlife, are part of a series of papers from the Zoonomia Consortium that will be published this spring in a special issue of the journal Science.

The planet is experiencing rapid biodiversity loss, with tens of thousands of species at risk of dying out, and identifying the ones in most urgent need is a long and costly process.

But there is little known about thousands of species, which makes it difficult to allocate limited conservation resources to help those closest to the brink.

To help circumvent these limitations, the scientists — led by researchers at San Diego Zoo Wildlife Alliance and University of California, Santa Cruz — examined 240 mammal species, from tiny tree shrews to towering giraffes, killer whales and even humans.

They found that the DNA encoded within a single genome — reflecting the species' history over millions of years — can provide a rapid, cost-effective conservation risk assessment, even when we know little about the animals' physiological, behavioural and life history characteristics, or even how many remain.

Aryn Wilder, a conservation scientist at San Diego Zoo Wildlife Alliance and one of the paper’s two lead authors said: “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 on the ground.”

Megan Supple, a research scientist with the UCSC Paleogenomics Lab and co-lead of the project, said: “The limited resources available for the conservation of wildlife species requires 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 towards species most in need.”

The research was used to train models that quickly distinguish between threatened and non-threatened species based on demography, diversity and mutations that affect biological fitness.

This will help assess extinction risk and identify which of the thousands of threatened species stand to benefit the most from conservation support, especially as the number of sequenced genomes grows and the models continue to improve.

Three species — the Upper Galilee Mountains blind mole rat, lesser chevrotain and orca — are highlighted as only three examples of the thousands of species lacking information on whether they are threatened.

The scientists applied their models to these “data-deficient” species to demonstrate how a genomic risk assessment could work.

The overall number of species included in the study is the largest of its kind. By examining 240 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.

That led the paper’s authors to call for genomic information to be included in conservation status assessments of species to bridge the gap between geneticists and conservation managers and provide a framework for using money and resources for species at the highest risk.

Beth Shapiro, professor of Ecology and Evolutionary Biology at UC Santa Cruz, said: “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.

“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.”

Conservation geneticist Oliver Ryder said that genomics is a powerful tool that can be used to protect animals and plants from extinction

“We are in an unprecedented era of discovery — a whole new way of seeing the world,” he said.

“We’ve long thought this potential existed, but it’s profound to see it crystallise into a catalyst that will help conservationists make crucial decisions that may save the world as we know it.”

The genomics manuscript is part of the work of the Zoonomia Consortium, the largest comparative mammalian genomics resource in the world.