Sequencing the Aldabra giant tortoise genome

With all the talk of genome sequencing coming from last week's Nobel prizes, it seems apt that another member of the animal kingdom has had its genetic code sequenced: this time it’s the turn of the Aldabra giant tortoise, and this genetic data could come soon enough. As the name suggests, these gentle giants grow large: some get up to 300kg - as much as a grizzly bear - and they can live for 250 years. Regrettably, their numbers have plummeted since the 1800s as they came into contact with humans. Thankfully they are on the rise again thanks to conservation efforts, but restoring a population from such a small number of individuals means a lack of genetic diversity, making them vulnerable to diseases and environmental threats. So understanding their genome is vital in order to know who should mate with who, to minimise the risks of further inbreeding. Will Tingle spoke to the University of Zurich’s Gözde Çilingir...

Gözde - There are many Aldabra giant tortoise individuals all over the world. We don't actually know how much genetic variation remains outside of Aldabra. To understand such variation, we need a reference. And the only remaining wild population is the main information from the wild. But to understand what is remaining outside of their natural population is so important. First to understand overall diversity remaining out of a vulnerable species. Second, the zoos. There are some breeding efforts going on to increase the number of Aldabra giant tortoises and to better manage these breeding efforts, we need to understand which of the individuals come from which part of Aldabra, for example, and a reference genome and that population genetics analysis help us to understand and manage these breeding efforts.

Will - This study on a wider scale is about more than that because Aldabra giant tortoises act as ecosystem engineers to restore degraded island habitats. So understanding how better to conserve these tortoises should have knock on effects for the rest of their ecosystem as well.

Gözde - That's correct, because they are the largest herbivore of their ecosystems, they are basically one of the keystone species that have direct effects on the dynamics of the vegetation. There were many giant tortoise species living in the Western Indian Ocean Islands before, but only Aldabra giant tortoises were left in the wild. So Aldabra giant tortoises were effectively used for rewilding of the islands that once upon a time had their own giant tortoises and basically they substitute. The ecosystem rolls off that giant tortoise and helps resurrect the created habitats. So all the rewilding efforts mean another bottleneck for the species because basically a couple of individuals are chosen to be introduced into the wild. So if we could better manage these rewilded populations in terms of maximizing the genetic variation of these couple of individuals, then we could decrease the potential harmful effects of genetic drift, for example. And that may help us to ensure the long term survival of the rewilded populations where they were introduced.

Will - On a final point, could this sequencing extend to other tortoise species?

Gözde - Yes, it can. I mean, I think that's one of the things that amazes me a lot because at the end of the day, we produced a genomic tool that could be helpful not only for Aldabra giant tortoises, but also for other tortoise species that are endemic to Madagascar or East Africa or elsewhere. There are several reasons behind this. First of all in our work, in our paper, we show that the majority of the Aldabra giant tortoise genomics similar to other turtle species. And we also know that the evolutionary rate of tortoises is relatively lower than other vertebrates. So the Aldabra giant tortoise genome could be effectively used for other genomic conservation projects of these species, which is really exciting to me as a conservation geneticist because this tool could also be helpful for critically endangered tortoises in Madagascar, for example, and their genetic conservation.