The golden eagle genome has landed

The golden eagle is undoubtedly one of the UK’s most iconic birds. With an impressive 2 metre wingspan and striking yellow feathered legs, it’s a stirring sight if you’re lucky enough to spot one soaring over the Scottish Highlands and Islands.

While golden eagles may not be critically endangered – the IUCN’s Red List of Threatened Species lists them as being of ‘least concern’ – their habitat is shrinking. Many of the already small populations around the world are continuing to decline, scattered through Europe, Japan and other areas, which is why today’s announcement of a new golden eagle genome is so important.

The eagle genome has been completed as part of our 25 genomes project, sequencing the genomes of 25 significant UK species ranging from pipistrelle bats and Eurasian otters to spiders, starfish and summer truffles. But while the announcement of a newly-sequenced species is undoubtedly exciting to fans of genomics, having a complete golden eagle genome is also a vital tool to help conservationists protect and manage these fabulous birds.

Genetics meets conservation

Conservation geneticist Dr Rob Ogden at the University of Edinburgh has been using simple DNA profiling and sequencing to monitor the genetic makeup of animal populations for at least 20 years, studying species as diverse as endangered gazelles, manta rays and (of course) golden eagles.

But, as Rob explains, while these tests can provide useful information about a population – such as how genetically diverse it is, and how individuals are related – it can only tell us so much.

“This basic information can help us when we come to make decisions about how to manage populations, but it’s based on looking at differences in small ‘snapshots’ of DNA scattered throughout the genome,” he says. “What we don’t really understand is what any of these genetic differences relate to in biological terms. If you keep a couple of populations separate for multiple generations, parts of their DNA will gradually drift apart, but we don’t know if they have any biological relevance at all.”

To draw an analogy with language, a simple alteration in spelling – for example, switching recognise to recognize – makes no difference to the meaning of the word. But more significant changes might alter the meaning of a word altogether, like changing ‘recognise’ to ‘organise’.

The simple DNA tools that Rob and his team have been using up until now can spot that individual ‘letters’ have changed, but they can’t identify the context of the biological ‘words’ in order to tell whether the difference is meaningful. And to read the ‘words’ in DNA (genes), you need to read the full genome.

The DNA that was used to create the new golden eagle genome came from a chick that was found dead in a Scottish nest during a raptor health study and was read using PacBio SMRT technology. Unlike other DNA reading methods, PacBio’s technique generates very long, high-quality stretches of sequence from which it’s easier to build a whole genome. This allowed the researchers to build what’s known as a ‘reference genome’, against which DNA from other golden eagles around the world can be compared.

Adapting to a changing world

The full genome sequence for the golden eagle will help conservation efforts. Having a high-quality full genome sequence for the golden eagle opens up a treasure trove of biological information that conservationists can use to manage species more effectively in the wild.

“Now we have the whole genome we can identify specific genes and work out what they do, so we can see whether a specific change is likely to affect what happens in a cell or in a whole animal,” he says.

“Golden eagles are spread around the world in lots of different habitats and climates – there are hot weather birds and cold ones, eagles in forests and others in the hills – so are their genes adapted to their local environment? Do the genetic differences we see relate to important differences in the physiology of the animals which are related to how they can best survive in that particular environment?”

This knowledge is vital for managing endangered populations effectively as the global climate changes. One conservation tool is land management – generating certain types of habitats that will encourage particular species. Another option is translocation, moving animals from one area to another or releasing captive animals back into the wild. But if those creatures are poorly adapted to the environment they’re being put into, then there’s a good chance they’ll fail to thrive.

As temperatures across Europe are expected to increase over the next century and habitats change, it’s unlikely that large species like eagles will be able to adapt fast enough to cope. Instead, the most likely solution is for populations to move north in search of cooler climes.

“We know that Mediterranean golden eagles are genetically quite different from the Scottish birds, so perhaps we might see a situation where eagles from warmer climates become better adapted to a changing habitat type in northern Europe than the existing population that’s there now,” Rob explains.

“But if it’s taken 10,000 years to evolve a particular trait, there's no way that's going to adapt to climate change in the next hundred years, so understanding how these locally adapted populations have come about is really important for predicting how we can manage species in the future.”

Taking flight

The completion of the golden eagle genome as part of the 25 genomes project is only the first part of the story. The golden eagle has been selected as one of the species to go forward into the Genome 10K project, carrying out detailed analysis of DNA from around 10,000 vertebrate species. Researchers will be using a technique called optical mapping to get an even more detailed picture of how the eagle genome is organised and to make sure they haven’t missed any bits.

“The golden eagle has been promoted up to the Premier league in terms of the quality of genome that we are going to obtain for it in the future,” Rob says. “The genome we have now is more detailed than anything that has been done before with golden eagles by quite a long way, but the next step is to make it way better – the best of all wild bird species.”

Having been lucky enough to watch a pair take flight in the hills on the Scottish island of Skye, watching with rapt attention as they swooped and circled round each other in a charming courtship dance, it’s easy to argue that golden eagles themselves are better than a lot of other birds.

“They certainly are very cool!” laughs Rob. “They’re an iconic species in the UK – people recognise them and are proud of them, but that's true in every culture where you find golden eagles. It’s something that helps with conservation education because people can really relate to these animals and support projects that focus on saving them. They’re fantastic birds to work on.”