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Museum specimen DNA in conservation

Aisling Irwin, How DNA from the Dead Is Helping Boost Species on the Brink, Yale Environment 360, 22 January 2024

Historical and ancient DNA from museum specimens is enabling scientists to establish baselines of genetic diversity for species in decline. That information is guiding key decisions on how best to protect imperiled wildlife, from Galápagos tortoises to African rhinos.

The shell of a Floreana tortoise, extinct for 180 years, at the Field Museum in Chicago. MARC SCHLOSSMAN.

When Evelyn Jensen visits a museum to scrape bone from a long-dead Galápagos tortoise, she has two hopes in mind.

First, that the specimen’s genetic material will be well-preserved. Second, that she will find that it is a Floreana tortoise — a species that has been extinct for 180 years.

A lecturer in molecular ecology at Newcastle University, Jensen has, over the last four years, studied 78 Galápagos tortoises at museums in Britain and the United States. But she has found only five from Floreana. Only one yielded high-quality DNA.

“It just kills me that after all of this — just one,” she says.

Nevertheless, that single sample is helping to guide the restoration of giant tortoises that are remarkably similar to the original Floreana tortoise to that Galápagos island, a project that is critical to restoring its depleted ecosystem.

Historical DNA is helping conservationists repopulate the island of Floreana with a tortoise that’s well adapted to the ecosystem.

When 19th century hunters, explorers, and naturalists killed fauna across continents, some of their trophies and specimens went to museums and private collections, forming a record of wildlife before many of their populations drastically declined. As the power of genetic sequencing technology has advanced, and become both cheaper and faster, researchers have begun to compare the genomes of ancient and museum specimens with those of their living descendants. Scientists are now using historical DNA to establish baselines for assessing how much genetic diversity has been lost over time — an indicator of a population’s health and its ability to adapt to a changing world. They’re using it to identify the genealogical continuity of populations and to make decisions about whether remnant populations should be combined, connected with others, or kept separate.

A team led by Adalgisa Caccone, director of the Center for Genetic Analyses of Biodiversity at Yale University, turned to museums for an answer. The American Museum of Natural History and Harvard’s Museum of Comparative Zoology kept boxes of bones and shell fragments gathered from caves in Floreana, where they had lain possibly for thousands of years. Despite the age and condition of the fragments, the team managed to extract some maternal DNA, large quantities of which float in structures known as mitochondria in every cell. They compared segments of this DNA with those of the mystery tortoises and found a match: Floreanas had somehow reached Isabela and hybridized with its local species.

The discovery of the genetic signature of a long-extinct species was “a unique conservation situation,” says Jensen.

On average, wild populations have lost 6 percent of their genetic diversity over the last few hundred years, says a geneticist.

The scientists used this genetic reference material to choose the most Floreana-like of the Isabela hybrids and are now selectively breeding them in captivity. The goal is to push the genome more toward Floreana and away from Isabela. This is important because the Floreana tortoise is a keystone species — it shapes its ecosystem — and is therefore critical to the larger project of restoring the island, says Jensen. Early this year, some 300 offspring will be released into Floreana’s interior.

Since they had only maternal DNA, the scientists could identify only hybrids whose mothers had Floreana ancestry. That is why Jensen continues to look for more recent and better-preserved specimens, like the one she found in London’s Natural History Museum, in the hope of accessing full genomes, tucked away in the cell’s nucleus. It’s not ideal to have only a single historical genome, she says, but it is helping to hone the selection of hybrids for the next breeding round.

Guiding breeding programs is just one way that historical DNA may help to conserve species. Every member of a species has a slightly different genetic code. This diversity is critical if a population is to adapt over generations to environmental change. But as population sizes decline, they lose their genetic diversity. On average, wild populations have lost 6 percent of their genetic diversity over the last few hundred years, estimates Deborah Leigh, an ecological geneticist at the Swiss Federal Institute for Forest, Snow and Landscape Research. Comparing historical genomes with present-day genomes can help quantify this erosion in a way that simply making head counts of a species’ population cannot.

An Iberian lynx being released into the Sierra de Arana range in southern Spain as part of an effort to connect disparate groups of lynx. Genetic analysis shows the historical population of lynx had been fragmented. JORGE GUERRERO / AFP VIA GETTY IMAGES.

Historical genomes can also help conservationists avoid catastrophic mistakes. For example, if a threatened species lives in fragmented populations, managers have a choice of mixing them together or keeping them apart. If the populations separated as the result of gradual adaptation to differing environmental pressures, then maintaining these divisions could preserve genetic variety. But if they divided quite recently for “unnatural” reasons — the building of a city in their midst, perhaps — the resulting smaller populations may be at risk of extinction as their genetic diversity dwindles due to genetic drift. Drift occurs when a random event like a lightning strike killing a breeding female, for example, or an overly dominant male preventing some individuals from mating, constrains which genes get passed down.

“When populations are small and endangered it’s a nightmare,” says Yoshan Moodley, an evolutionary biologist at the University of Venda in South Africa, “because you know that, just by virtue of not all animals breeding, you’re going to lose genetic diversity from one generation to the next.”

It was just such a quandary that sent Moodley scouring museums for black rhinos. The animals used to inhabit a vast area of sub-Saharan bushland, grassland, and desert. Now, just over 6,000 remain, in five countries. Poaching has driven their most recent declines, and countries have responded differently. In Kenya, where poaching slashed the black rhino population from 20,000 in the 1970s to just 400 in the 1990s, those that remained were sparsely scattered across the country, and vulnerable. In the mid-1990s, the Kenyan Wildlife Service began concentrating them into secure reserves.

In East Africa, the remaining black rhino populations are precariously inbred: They urgently need fresh blood.

Whether this approach was in the black rhino’s best long-term interests wasn’t clear, according to Moodley. His team extracted DNA from more than 100 museum samples of preserved rhino skin and obtained 63 genomes dating from 1775 to 1981. With this DNA, the team developed a picture of the black rhino’s decline based on genes rather than on population numbers. There had been nine populations across sub-Saharan Africa, separated by rivers and mountains. “We have these unique genetic populations evolving because of these dispersal barriers,” says Moodley.

East Africa, and in particular Kenya, now hold the greatest genetic diversity of black rhino, and if the differences between the existing populations arose from local adaptations — which is not proven — it might have been better to keep them apart. “Mixing them with another population may undermine all of what evolution has been doing for the last few hundred thousand years,” says Moodley. But his work also showed that some of today’s groupings are precariously inbred: They urgently need fresh blood.

Moodley concludes that the Kenyans unknowingly mixed four different black rhino populations together, but it was the right thing to do because extinction was imminent. Numbers have risen, though at the cost of mingling different sets of genes.

A black rhino mother with her calf in Maasai Mara, Kenya. UWE SKRZYPCZAK / ALAMY STOCK PHOTO.

Kenya left intact a population of black rhino in the Maasai Mara: genetic analysis revealed they are the remnant of a distinct historical population and should, says Moodley, remain separate. It also left undisturbed a population in Chyulu National Park, in the south of Kenya. It’s possible that these are the last remaining members anywhere in Africa of a separate lineage: until they are tested, says the scientists, they should be kept apart.

As for the combined rhino populations, Moodley says, “We need to now make sure [they don’t] drift towards one or the other set of [genes].” This can be done by controlling who breeds with whom.

A fundamental challenge in mining historical specimens is finding them: individual owners, schools, and government offices often regard them as “ugly” and dispose of them, as José Godoy, a conservation geneticist with the Spanish National Research Council, and his team discovered when searching for Iberian lynx specimens across Spain and Portugal.

In 2002, there were just 100 Iberian lynx in the wild: DNA-informed breeding programs helped boost the population to more than 400.

Still, the team eventually retrieved good-quality samples from 245 specimens from museum and private collections, then compared their DNA with that of both modern Iberian lynx and ancient, archaeological discoveries. In this way they reconstructed the genetic history of a wild cat that once roamed freely across the Iberian peninsula and beyond. Thousands of years ago, there was little genetic difference across the lynx’s range. DNA comparisons showed how the larger population gradually became fragmented into genetically impoverished populations, ending with two, quite different subpopulations by 2002, one of which was in a genetically “critical” state, says Godoy.

The scientists found that it was genetic drift, not adaptation to different habitats, that had split the two populations. This provided scientific support for decisions to combine them in a captive breeding program and by translocating lynx from one wild population into the other wild population. In 2002, there were just 100 Iberian lynx in the wild: now there are more than 400.

Historical DNA is not the only thing conservationists need: they also require a reference genome — a representative example of one typical representative of a species. When scientists pull the DNA out of an ancient specimen, they don’t retrieve an intact genome. Rather, they extract thousands of small stretches of DNA, a bit like a jumble of jigsaw pieces that are of similar colors; some will overlap with each other or share bits that are identical. Scientists need a template, in the form of an intact genome, against which to set them out.

Bird specimens at the National Museum of Natural History in Washington, D.C.. Scientists have used the museum’s specimens to sequence bird genomes as part of the Earth Biogenome Project. CHIP CLARK / SMITHSONIAN.

There are now thousands of reference genomes for humans, but for other creatures the work has been slow to begin. As costs fall and sequencing technologies advance, the Earth Biogenome Project, an international consortium, aims to fix this. Its members are sequencing the genomes of thousands of species, says Ian Barnes, a genomics researcher who runs the U.K.’s contribution to the project, called the Darwin Tree of Life.

Another obstacle to using museum or ancient DNA is its quality. If samples aren’t well preserved, says Peter Dearden, an evolutionary biologist at Otago University in New Zealand, “you end up with genomes that are fragmented and a bit dodgy. … You want to be sure you are looking at real genetic loss rather than problems associated with using ancient [or historical] DNA.”

Dearden helps with the rescue of the kākāpō, a nocturnal, ground-dwelling parrot in New Zealand whose numbers fell to 50 in the mid-1990s and are now rising. But Dearden doubts that working with museum DNA will help with the bird’s conservation. Dramatic situations with tiny population numbers like the kākāpō are, he says, “ambulance time. You don’t need historic DNA to tell you that they need safe habitat and more breeding,” he says. “The thing that will save kākāpō will be more kākāpō.” The population’s genetic diversity will increase over time, he added, “because every generation there will be new mutations.”

Leigh agrees that “in some cases conservation really is a numbers game.” But it depends on a species history, she adds: “There can [sometimes] be very little correlation between census size and genetic diversity. You [might] see this species and it looks fine, but actually a lot of the diversity that species needs is gone.”