How DNA from the Dead Is Helping To Boost Species on the Brink Aisling Irwin | January 22, 2024 When Evelyn Jensen visits a museum to scrape bone from a long-dead Galápagos tortoise, she has 2 hopes: The specimen’s genetic material is well-preserved, and it is from a Floreana tortoise — A species 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 US. But she has found only five from Floreana and 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 remarkably similar to the original Floreana tortoise to that specific Galápagos island, a project critical to restoring its depleted 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 advanced, both cheaper and faster, researchers now compare genomes of ancient museum specimens with living descendants. We are now using historic DNA to assess how much genetic diversity has been lost over time — an indicator of a population’s health and adaptability, and to make decisions about whether remnant populations should be combined, connected with others, or kept separate. In Africa, for example, scientists are using historic DNA to help guide critical conservation decisions for Black Rhino and Lion. In Europe, similar research informs a breeding program for Spain’s Bearded Vulture, and to assess current conservation strategies for Iberian Lynx and Imperial Eagle. In Australia and New Zealand, scientists are using historical DNA to assess the current genetic health of remnant and translocated populations of the marsupial Burrowing Bettong, and the Takahē, a flightless swamphen. In the Galápagos, similar work ihelps restore the most ecologically devastated island, Floreana, by repopulating it with species relatively well adapted to that particular island ecosystem. Starting in the 1800s, demand for tortoise oil and meat, plus the introduction of invasive species, drove 3 (of 15) Galápagos tortoise species and lineages to extinction, including those on Floreana Island. But 20 years ago, conservationists found tortoises with an unusual shell shape on north Isabela Island, about 125 miles from Floreana, and wondered if they were closely related to the extinct Floreana tortoise. A team led by Adalgisa Caccone, Director of Yale’s Center for Genetic Analyses of Biodiversity 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 Floreana caves, where they had lain possibly for thousands of years. Despite their age and condition,the team managed to extract mitochondrial DNA. They compared these DNA with those of the mystery tortoises and found a match: Floreanas had somehow reached Isabela and hybridized with its local species. 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. 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 historic genome, she says, but it does help to hone the selection of hybrids for the next breeding round. The guidance of breeding programs is just one way that historic 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, genetic diversity is lost. On average, wild populations have lost 6% of their genetic diversity over the last few hundred years. Comparing historic with present-day genomes can help quantify this erosion in a way that avoids making head counts of a species’ population. Historic genomes can also help conservationists avoid catastrophic mistakes. For example, if a threatened species lives in fragmented populations, managers have a choice of mixing or keeping them apart. If the populations separated as the result of gradual adaptation to differing environmental pressures, then maintaining that separation could promote genetic variety. But if they have separated quite recently for “unnatural” reasons — urbanization for example — then 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. “It’s a nightmare when populations are small and endangered because you know, just by virtue of not all animals breeding, you’re going to lose genetic diversity from one generation to the next, ”said Yoshan Moodley, an evolutionary biologist at the University of Venda in South Africa. It was just such a quandary that sent Moodley scouring museums for Black Rhino. Itused 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, the remainder were sparsely scattered and vulnerable. In the mid-1990s, the Kenyan Wildlife Service began concentrating them into secure reserves. Whether this approach was in the Black Rhino’s best long-term interests wasn’t clear, according to Moodley. His team extracted DNA from >100 museum samples and obtained 63 genomes dating from 1775 to 1981. The team then developed a picture of its decline. There had been 9 populations across sub-Saharan Africa, separated by rivers and mountains. “These unique genetic populations evolved due to separation by barriers,” says Moodley. Three populations have vanished in the last 40 years, taking their genetic variety with them. Moodley concludes that the Kenyans unknowingly mixed four populations together, but it was the right thing to do because extinction was imminent. Numbers have now risen, though at the cost of mingling different sets of genes. Kenya left intact a population of black rhino in the Maasai Mara : genetic analysis revealed it is the remnant of a distinct historic population and should 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 of a separate lineage anywhere in Africa: They should be kept apart until tested, said Moody. A fundamental challenge in mining historic 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. Still, they eventually retrieved good-quality samples from 245 specimens, then compared their DNAs with modern and ancient Iberian Lynx. Thousands of years ago, there was little genetic difference across the Lynx’s range. The larger population gradually became fragmented into smaller, genetically impoverished populations, with 2 quite different subpopulations remaining by 2002, one of which was in a genetically “critical” state, says Godoy. The scientists determined genetic drift, not adaptation to different habitats, had split the two populations., which supported decisions to combine them in a captive breeding population. In 2002, there were just 100 Lynx in the wild, but now there are >400. 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 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 but 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 . The thing that will save kākāpō will be more kākāpō, because there will be new mutations every generation .” Leigh agrees and 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 needed is now gone .Then, when a challenge arises — like climate change, or the introduction of an invasive species — the species is less resilient because it lacks genetic diversity and can’t easily adapt. This can have knockon effects on larger communities and entire ecosystems, even if the species itself doesn’t vanish. I call it the silent extinction .”
