Creating a Genome Atlas could help save endangered species
Woolly mammoth herds once roamed the Northern Hemisphere, from the British Isles to the eastern shores of North America, across the Bering land bridge. The last mammoth died around 4000 years ago.
Enough of their remains were preserved in the icy tundra to reveal a sombre truth: the creatures vanished suddenly and catastrophically over a generational time scale. The jury is still out on whether a changing climate, human hunting, or something else is to blame—but we do know that the elephant, the mammoth's closest relative, is experiencing a similar population crash today, driven by similar threats.
According to the International Union for Conservation of Nature (IUCN), the number of living African savanna elephants has been reduced by 60% in the last century. African forest elephants, their sister species, have declined by an astounding 86% and are now classified as "critically endangered."
Humans have the ability to avert this extinction. But we need more data to do so.
“At the moment, we actually have more genomic data for woolly mammoths than we do for living elephants,” said Patrícia Pečnerová, an evolutionary biologist at the University of Copenhagen. “And that should change.”
Penerová completed her PhD thesis on mammoth paleogenomics and is now a Marie Skodowska-Curie Actions Fellow in the Department of Biology at the university as well as a National Geographic Explorer. To begin forming a partnership, she contacted Mrinalini Erkenswick Watsa, a conservation scientist with the San Diego Zoo Wildlife Alliance (SDZWA). Its goal is to create an atlas of elephant genome diversity across Africa, which will be used to develop field conservation tools for people and communities who have direct contact with the animals and thus the most power to help them.
A collaboration like this would necessitate several players: someone to collect biological samples, someone to sequence them, someone to analyze the data and create the atlas, and someone to deploy tools based on it in the field—and everyone involved must be aware of the challenges.
The world's largest land animal is the savanna elephant. They can weigh up to 6.5 tonnes (the weight of two Hummers) and live for up to 70 years. As a result, they require a large amount of space to roam in search of food and water, and they return to the same routes year after year. Unfortunately, humans frequently build over these routes without realizing it, and when wild elephants have their migration disrupted by humans, it often leads to confrontation and gives the animals a bad rap.
Dr. Stephen Chege, a wildlife veterinarian who oversees SDZWA conservation projects in northern Kenya, believes this is unjust.
“When everybody congregates to the only available water source, for example, there’s a high chance for conflict,” said Dr. Chege.
“People have the misconception that wildlife is there to bring chaos. But we need to change that thinking. For the health of wildlife populations and individual animals, we must say that they have a right to access what they need. We shouldn’t be selfish.”
If biologists could positively identify elephants based on their DNA and match them to records of where that herd has previously been, it could reveal their migration patterns and help people make decisions about where to build with coexistence in mind, ensuring the animals have enough space to pass by peacefully.
The loss of genetic diversity is another threat to elephants. Elephant herds are matriarchal, with females remaining with the herd and males frequently leaving or being forced out until they are old enough to mate. When reproductive males can mix between herds, the gene pool remains diverse, and the population maintains stronger defenses against disease, pests, climate change, and other environmental stresses.
However, current field observations show that approximately 70% of male elephants die before reaching reproductive age, and as herds become more isolated from one another, they exchange fewer individuals, resulting in older males dominating reproduction. When this occurs, the population's genetic diversity dwindles, making each successive generation more vulnerable.
Using genomic sequencing to determine how closely related each herd is, people will be able to prioritize which herds to conserve and even select individual animals for translocation.
And, despite international prohibition in 1989, illegal elephant poaching has only increased since then. It is the leading cause of death for forest elephants, according to the IUCN. However, forensic sequencing of recovered ivory could assist authorities in tracking where they are being hunted and intervening to protect them.
Obtaining samples
A vast collection of samples from across the animal's habitat range is required to create a genomic atlas. Fortunately, the collaboration did not have to start from scratch.
Nicholas Georgiadis collected over 400 biological samples from elephants across Africa during his tenure as director of the Mpala Research Centre in Nanyuki, Kenya, in the 1990s. Forest elephants were thought to be a subspecies of savanna elephants for the entire twentieth century, but Georgiadis, Alfred Roca, and other collaborators used these samples to show that they diverged into separate species millions of years ago.
“They’re as different as chimps and humans, more different than lions are from tigers,” says Roca, who’s now a professor with the Animal Sciences Laboratory at the University of Illinois. The distinction has real implications for conservation efforts: The two species have adapted to different habitats; they form different migration patterns and social structures. Roca’s research was central to the decision by conservation agencies to formally recognize African elephants as two distinct species. As a single species, African elephants had been considered merely “vulnerable” rather than “endangered” by the IUCN Red List. When the two species were assessed separately, the savanna elephant was determined to be endangered, while the forest elephant was found to be “critically endangered,” a category reserved for species at highest risk of extinction.
Roca was eager to join the collaboration and contribute this historic sample collection. Yasuko Ishida, a research scientist on his team, will be in charge of selecting a diverse set of populations from the collection and conducting several analyses on them. The fact that the samples are decades old makes no difference—DNA can still be extracted, sequenced, and mapped from them, and field biologists can use that information to study elephants that are still living in these populations.
Sequencing the samples
Previous elephant genetic studies focused on a few specific markers, such as microsatellites, which are short sections of DNA that repeat multiple times and can be used to trace family inheritance. The problem with this method is that different labs examine different sites, and their results cannot always be compared.
A project this large requires whole-genome sequencing, which is why it welcomed the Illumina iConserve partnership, whose mission is to accelerate environmental and wildlife conservation through genomics. This year, the iConserve team will use Illumina sequencers to delve into the depths of Roca's 400 samples, with 40x coverage. They will send the genome sequence data to Penerová in Denmark, where she will begin mapping it.
“Studying the whole genomes provides a lot more information at a much better resolution,” she said. “We can answer some questions that were really difficult or almost impossible to answer with the traditional markers.”
Generating the atlas
To map the genomic variation of elephants in Africa, the collaboration must first read the entire genetic code, then narrow it down to the sections that contain the most information.
Using the entire genetic code to study genetic variation provides unprecedented resolution. An individual's DNA is made up of pieces from both of its parents.
"We can reconstruct the entire population's demographic history, its changes in size over time, from one single individual's genome," explained Penerová .
Her job will be to sift through terabytes of genomic data to find the most informative positions in the genomes, which are each more than three billion "letters" long. SNPs (pronounced "snips") are differences in an individual's genetic code caused by a single letter that differs from the majority of its species. Instead of studying a dozen or two genetic markers, as researchers used to do, whole genomes provide them with millions. The team will identify which of the millions of SNPs are important in revealing local patterns and individual differences by analysing 400 elephants from across the continent.
With this information, the partnership should be able to map how elephant genetic diversity varies across their habitat range, determine how connected or isolated different populations are across Africa, and explain what factors contribute to the loss of that diversity.
Conservators could then identify potential conservation corridors and candidate populations for translocation. The data could be used to create a practical, low-cost genotyping tool for field teams, using SNPs that correlate with geography, species, sex, and individuals. Such a tool could aid in the construction of pedigrees for known individuals, the assessment of population numbers and dispersal in the landscape, and the rehabilitation of rescued animals back into the wild.
Deploying the atlas
Since the 1990s, when Georgiadis had to collect his samples using dart biopsy—a close-up, disruptive, and often dangerous method—field genotyping technology has come a long way (a defensive elephant once overturned his vehicle).
Now, viable samples can be collected from a less invasive (though less glamorous) source: dung. Modern sequencers can sift through the static of any other molecules present, such as gut microbes and digested plants, to extract only the elephant DNA.
“Technology is key to conservation,” said Dr. Chege , but he notes that taking these samples in the savanna presents another challenge: DNA quickly degrades with exposure to heat and ultraviolet light, especially if there’s limited electricity available to freeze it. Even liquid nitrogen evaporates every time you open the container, and biologists are often in the field for weeks at a time. They can no longer afford to wait and ship their samples overseas for analysis—so the partnership has a plan for that, too.
Everyone in the partnership agrees that the top priority is to empower conservationists on the ground to do this work themselves, wherever they are—even if they are not geneticists. Roca has always made it a point to involve local researchers in his work, but Watsa explains that, historically, members of the scientific community have often used samples imported from other countries.
"Today we work to flip that script. We're not going to bring samples to a lab; we're going to bring the lab to the samples."
By investing in training, ingredients, and equipment, those collecting future samples will be able to participate in a larger portion of the analysis and lead the research themselves.
As a proof of concept, the team hopes to test a new genotyping tool by creating a pedigree for the Save the Elephants population in Samburu, Kenya, as early as this year, before publicly disclosing all data and trial results.
“Besides making the atlas freely available,” said Pečnerová, “we hope that by implementing pilot runs in collaboration with colleagues in Kenya and Uganda, we will motivate and facilitate future research by conservationists across the range countries.” After all, elephants know no borders.
As Dr Chege admits, field kits are essential to this work, but "a lot of innovation research is based on developed countries. I understand that there is no market for such items; they do not provide a quick return on investment. However, wildlife conservation has far-reaching benefits."
When confronted with such alarming statistics about population decline, it is natural to question whether the investment is worthwhile. Why should we pay attention to this fire when there are a million others blazing?
“There are two ways of looking at it,” said Watsa. “One is that elephants are huge ecosystem engineers. When you remove them and no one’s eating what they ate, everything about the rest of that ecosystem—and ultimately, humans—changes. Because we’re all connected. Right?” As she says this, a half-smile crosses her face, as if her next words should be obvious. “But the simplest answer is that we all have a right to live on this planet.”
“There’s a message I would like to share with everybody. Elephants are wise, brilliant animals. They’re very intelligent, and they have emotions just like we do. They cuddle their little ones, and they mourn their family members for days. You find them using their trunk and tusks to investigate the carcass and turn it over. They must be asking so many questions. ‘What happened? Could we have done anything to not let you die?’” said Dr. Chege.
The end of the world is not unavoidable. We have the resources to prevent elephant extinction; all we need is the will to act.
Enough of their remains were preserved in the icy tundra to reveal a sombre truth: the creatures vanished suddenly and catastrophically over a generational time scale. The jury is still out on whether a changing climate, human hunting, or something else is to blame—but we do know that the elephant, the mammoth's closest relative, is experiencing a similar population crash today, driven by similar threats.
According to the International Union for Conservation of Nature (IUCN), the number of living African savanna elephants has been reduced by 60% in the last century. African forest elephants, their sister species, have declined by an astounding 86% and are now classified as "critically endangered."
Humans have the ability to avert this extinction. But we need more data to do so.
“At the moment, we actually have more genomic data for woolly mammoths than we do for living elephants,” said Patrícia Pečnerová, an evolutionary biologist at the University of Copenhagen. “And that should change.”
Penerová completed her PhD thesis on mammoth paleogenomics and is now a Marie Skodowska-Curie Actions Fellow in the Department of Biology at the university as well as a National Geographic Explorer. To begin forming a partnership, she contacted Mrinalini Erkenswick Watsa, a conservation scientist with the San Diego Zoo Wildlife Alliance (SDZWA). Its goal is to create an atlas of elephant genome diversity across Africa, which will be used to develop field conservation tools for people and communities who have direct contact with the animals and thus the most power to help them.
A collaboration like this would necessitate several players: someone to collect biological samples, someone to sequence them, someone to analyze the data and create the atlas, and someone to deploy tools based on it in the field—and everyone involved must be aware of the challenges.
The world's largest land animal is the savanna elephant. They can weigh up to 6.5 tonnes (the weight of two Hummers) and live for up to 70 years. As a result, they require a large amount of space to roam in search of food and water, and they return to the same routes year after year. Unfortunately, humans frequently build over these routes without realizing it, and when wild elephants have their migration disrupted by humans, it often leads to confrontation and gives the animals a bad rap.
Dr. Stephen Chege, a wildlife veterinarian who oversees SDZWA conservation projects in northern Kenya, believes this is unjust.
“When everybody congregates to the only available water source, for example, there’s a high chance for conflict,” said Dr. Chege.
“People have the misconception that wildlife is there to bring chaos. But we need to change that thinking. For the health of wildlife populations and individual animals, we must say that they have a right to access what they need. We shouldn’t be selfish.”
If biologists could positively identify elephants based on their DNA and match them to records of where that herd has previously been, it could reveal their migration patterns and help people make decisions about where to build with coexistence in mind, ensuring the animals have enough space to pass by peacefully.
The loss of genetic diversity is another threat to elephants. Elephant herds are matriarchal, with females remaining with the herd and males frequently leaving or being forced out until they are old enough to mate. When reproductive males can mix between herds, the gene pool remains diverse, and the population maintains stronger defenses against disease, pests, climate change, and other environmental stresses.
However, current field observations show that approximately 70% of male elephants die before reaching reproductive age, and as herds become more isolated from one another, they exchange fewer individuals, resulting in older males dominating reproduction. When this occurs, the population's genetic diversity dwindles, making each successive generation more vulnerable.
Using genomic sequencing to determine how closely related each herd is, people will be able to prioritize which herds to conserve and even select individual animals for translocation.
And, despite international prohibition in 1989, illegal elephant poaching has only increased since then. It is the leading cause of death for forest elephants, according to the IUCN. However, forensic sequencing of recovered ivory could assist authorities in tracking where they are being hunted and intervening to protect them.
Obtaining samples
A vast collection of samples from across the animal's habitat range is required to create a genomic atlas. Fortunately, the collaboration did not have to start from scratch.
Nicholas Georgiadis collected over 400 biological samples from elephants across Africa during his tenure as director of the Mpala Research Centre in Nanyuki, Kenya, in the 1990s. Forest elephants were thought to be a subspecies of savanna elephants for the entire twentieth century, but Georgiadis, Alfred Roca, and other collaborators used these samples to show that they diverged into separate species millions of years ago.
“They’re as different as chimps and humans, more different than lions are from tigers,” says Roca, who’s now a professor with the Animal Sciences Laboratory at the University of Illinois. The distinction has real implications for conservation efforts: The two species have adapted to different habitats; they form different migration patterns and social structures. Roca’s research was central to the decision by conservation agencies to formally recognize African elephants as two distinct species. As a single species, African elephants had been considered merely “vulnerable” rather than “endangered” by the IUCN Red List. When the two species were assessed separately, the savanna elephant was determined to be endangered, while the forest elephant was found to be “critically endangered,” a category reserved for species at highest risk of extinction.
Roca was eager to join the collaboration and contribute this historic sample collection. Yasuko Ishida, a research scientist on his team, will be in charge of selecting a diverse set of populations from the collection and conducting several analyses on them. The fact that the samples are decades old makes no difference—DNA can still be extracted, sequenced, and mapped from them, and field biologists can use that information to study elephants that are still living in these populations.
Sequencing the samples
Previous elephant genetic studies focused on a few specific markers, such as microsatellites, which are short sections of DNA that repeat multiple times and can be used to trace family inheritance. The problem with this method is that different labs examine different sites, and their results cannot always be compared.
A project this large requires whole-genome sequencing, which is why it welcomed the Illumina iConserve partnership, whose mission is to accelerate environmental and wildlife conservation through genomics. This year, the iConserve team will use Illumina sequencers to delve into the depths of Roca's 400 samples, with 40x coverage. They will send the genome sequence data to Penerová in Denmark, where she will begin mapping it.
“Studying the whole genomes provides a lot more information at a much better resolution,” she said. “We can answer some questions that were really difficult or almost impossible to answer with the traditional markers.”
Generating the atlas
To map the genomic variation of elephants in Africa, the collaboration must first read the entire genetic code, then narrow it down to the sections that contain the most information.
Using the entire genetic code to study genetic variation provides unprecedented resolution. An individual's DNA is made up of pieces from both of its parents.
"We can reconstruct the entire population's demographic history, its changes in size over time, from one single individual's genome," explained Penerová .
Her job will be to sift through terabytes of genomic data to find the most informative positions in the genomes, which are each more than three billion "letters" long. SNPs (pronounced "snips") are differences in an individual's genetic code caused by a single letter that differs from the majority of its species. Instead of studying a dozen or two genetic markers, as researchers used to do, whole genomes provide them with millions. The team will identify which of the millions of SNPs are important in revealing local patterns and individual differences by analysing 400 elephants from across the continent.
With this information, the partnership should be able to map how elephant genetic diversity varies across their habitat range, determine how connected or isolated different populations are across Africa, and explain what factors contribute to the loss of that diversity.
Conservators could then identify potential conservation corridors and candidate populations for translocation. The data could be used to create a practical, low-cost genotyping tool for field teams, using SNPs that correlate with geography, species, sex, and individuals. Such a tool could aid in the construction of pedigrees for known individuals, the assessment of population numbers and dispersal in the landscape, and the rehabilitation of rescued animals back into the wild.
Deploying the atlas
Since the 1990s, when Georgiadis had to collect his samples using dart biopsy—a close-up, disruptive, and often dangerous method—field genotyping technology has come a long way (a defensive elephant once overturned his vehicle).
Now, viable samples can be collected from a less invasive (though less glamorous) source: dung. Modern sequencers can sift through the static of any other molecules present, such as gut microbes and digested plants, to extract only the elephant DNA.
“Technology is key to conservation,” said Dr. Chege , but he notes that taking these samples in the savanna presents another challenge: DNA quickly degrades with exposure to heat and ultraviolet light, especially if there’s limited electricity available to freeze it. Even liquid nitrogen evaporates every time you open the container, and biologists are often in the field for weeks at a time. They can no longer afford to wait and ship their samples overseas for analysis—so the partnership has a plan for that, too.
Everyone in the partnership agrees that the top priority is to empower conservationists on the ground to do this work themselves, wherever they are—even if they are not geneticists. Roca has always made it a point to involve local researchers in his work, but Watsa explains that, historically, members of the scientific community have often used samples imported from other countries.
"Today we work to flip that script. We're not going to bring samples to a lab; we're going to bring the lab to the samples."
By investing in training, ingredients, and equipment, those collecting future samples will be able to participate in a larger portion of the analysis and lead the research themselves.
As a proof of concept, the team hopes to test a new genotyping tool by creating a pedigree for the Save the Elephants population in Samburu, Kenya, as early as this year, before publicly disclosing all data and trial results.
“Besides making the atlas freely available,” said Pečnerová, “we hope that by implementing pilot runs in collaboration with colleagues in Kenya and Uganda, we will motivate and facilitate future research by conservationists across the range countries.” After all, elephants know no borders.
As Dr Chege admits, field kits are essential to this work, but "a lot of innovation research is based on developed countries. I understand that there is no market for such items; they do not provide a quick return on investment. However, wildlife conservation has far-reaching benefits."
When confronted with such alarming statistics about population decline, it is natural to question whether the investment is worthwhile. Why should we pay attention to this fire when there are a million others blazing?
“There are two ways of looking at it,” said Watsa. “One is that elephants are huge ecosystem engineers. When you remove them and no one’s eating what they ate, everything about the rest of that ecosystem—and ultimately, humans—changes. Because we’re all connected. Right?” As she says this, a half-smile crosses her face, as if her next words should be obvious. “But the simplest answer is that we all have a right to live on this planet.”
“There’s a message I would like to share with everybody. Elephants are wise, brilliant animals. They’re very intelligent, and they have emotions just like we do. They cuddle their little ones, and they mourn their family members for days. You find them using their trunk and tusks to investigate the carcass and turn it over. They must be asking so many questions. ‘What happened? Could we have done anything to not let you die?’” said Dr. Chege.
The end of the world is not unavoidable. We have the resources to prevent elephant extinction; all we need is the will to act.
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