Surprises From the Past: The Revelations of Ancient DNA

Forest Tundra on the Taymyr Peninsula between Dudinka and Norilsk near Kayerkan, Russia, taken in 2016. Was it always look like this? Should it look like this?
Image Credit: Ninaras, CC BY 4.0, Image Cropped

Although obtaining ancient DNA can be quite a headache, it is a very rewarding headache. After all the work that goes into obtaining DNA from a bone, fur, hair, or Viking’s leftover meal, researchers have to make sense of the apparent random sequence of nucleotide bases. But once that’s taken care of, there are a series of really interesting questions we can start to answer. Were DNA strands that are present in the modern times inherited from the past? How similar are today’s species to their forebears? Where is my pet velociraptor?

The fundamental research question around ancient DNA is this: what is the difference between DNA in the past and DNA in the present?

The first thing to keep in mind when we answer this question, is that DNA is inherited in quite a dynamic way, and modern DNA is unlikely to represent what happens in the past accurately. For starters, our DNA replication machinery is not always going to be 100% accurate. Inter-generation difference in DNA sequences due to our enzymes inserting the wrong bases purely by chance is inevitable, like a typo from an exhausted writer (not me). This is the main source of what we often call “random mutation”, one of the driving forces of evolution. There is also recombination, the exchange of chromosomal segments between homologous chromosomes, when our body produces gamete cells that will deliver DNA to the next generation. Whilst, again, these are key forces behind evolution, sometimes these processes make it hard to determine exactly what a species’ ancestors looked like.

Despite these problems, there is still a great degree of information we can glean from analysing ancient DNA. Often, that information is closely linked to the source of the DNA and the context. For example, fossilised fish bones will allow us to not only answer questions about past population history of the fish but also the past landscape of coastal hunther-fisher-gatherers’ residences, if for example you got the fossils from an ancient inhabitation. We’ve recently been able to track past ivory trade in Greenland from walrus bones stored in local museums… the list goes on.

From a permutation of body parts, geographic locations, habitat types, archeological context, and species identity, you may already guess that there is a plethora of ecological insights we can gain from ancient DNA. Sometimes it is just an extension or a confirmation of what we expect, sometimes it is an inconvenient truth. Here are four such examples.

Some Natives are Colonizers

One of the more inconvenient truths is the conundrum around the conservation of the yellow-eyed penguin (Megadyptes antipodes), known to be an endemic species of New Zealand. This bird, also called the “Hoiho”, is a major attraction for tourists and popular among the citizens of New Zealand. Conservation efforts and ecotourism have focused on preserving this species as they were predicted to extinct in a decade or two.

As researchers collected ancient bird bones from the local coastal banks, however, they found that there was another penguin species that had lived in the vicinity. It is called the Waitaha penguin (Megadyptes waitaha), not even known to be native to the island until this discovery. Analysis on the DNA extracted from these ancient bird bones revealed that the Hoihos are a recent invader that experienced population expansion shortly after the extinction of the Waitahas, possibly due to the latter failing to adapt to past climate change while being intensely hunted by Polynesian voyagers. 

The Hoihos are said to be “self-introduced”, which means they dispersed naturally, but they flourished and outcompeted a native due to human intervention. Again, this brings back the question of what we mean by ‘natural’, a classic question in conservation biology that I will bring up again at the end. Should the Hoihos cease from being New Zealand conservation icon?

Some Wild Species Apparently Had Been Domesticated

Speaking of wild species, Przewalski’s horses (Equus ferus ssp. przewalskii) are said to be the last surviving subspecies of wild horses because their ancestors were never domesticated. Other wild horses we usually see in the US or Australia are feral horses. These kinds of horses are horses that have gone through domestication but then went wild. You can easily see this from the similarities between their genome and that of modern domesticated horses.

An analysis of the whole genome sequences of Przewalki’s horses and domestic horses showed Przewalski’s horses do not share any genetic material with domestic horse lineages that isn’t ancestral DNA. So while they may share some DNA, it’s from an ancestor far back enough that they remain a distinct subspecies. In other words, the Przewalski’s are legit. Reintroduction efforts to its natural habitat in the steppes in Central Asia have been ongoing to preserve them and interbreeding with domestic lineage is actively prohibited.

przewalskis_horse_02

Photo of reintroduced Przewalski’s horse taken at the “Seer” release site, managed by the Association pour le cheval de Przewalski:TAKH, in the Khar Us Nuur National Park Buffer Zone. Image Credit: Claudia Feh, CC BY-SA 4.0

When researchers sequenced the remains of the earliest domestic horse in northern Kazakhstan, ancient DNA of these horses were grouped together with the genome of Przewalski’s horses. The Przewalski’s horses apparently escaped from the Botai settlements in the past, crashing the narrative of “last surviving wild horse” that has been imposed on them for the last decades. Interestingly, these ancient domestic horses were not the source of most domestic horse lineages that currently exist, explaining the distinctiveness of Przewalski’s genome in comparison to that of domestic horses.

Should We Revive Extinct Species?

The possibility to isolate ancient DNA of course brings a surge of more sensationalist questions. Indeed, ancient DNA can be said as “celebrity science” as its popularity in society fuels its development. People are interested in the possibility of reviving dinosaurs and mammoths. People want to know how far related we are to the ancient pharaohs, and which past diseases in Neanderthals may or may not have made them extinct. People want to know the ancient history of today’s endangered species.

Let’s discuss dinosaurs. In theory, isolating DNA from fossils is possible, but the older your fossils, the more fragmented they are, and there may not be any DNA at all left from the Jurassic dinosaurs, which died out 145 million years ago. Even if we miraculously got a very decent extract, we cannot assemble a whole genome sequence of a dinosaur as there are no reference genomes reliable enough to help construct them (read here on why it is important). 

If we can get the dinosaurs’ DNA and somehow revive them through cloning closely related birds and reptiles, those gigantic lizards may not be able to cope with current climatic conditions (imagine how many carbon biomass are needed to keep those sizes). Also, there are a few little-known cult 90s movies that suggest this may not be a good idea. 

How About the Pleistocene Park?

The Pleistocene Park is a nature reserve in Siberia aimed to bring back ancient Siberian steppe. Although the sedimentary ancient DNA isolated from local lakes showed that the grassland steppe gradually changed to forest in the past, bringing back the ancient steppe was considered a global importance. Research has shown that green grass reflects more sunlight than forests that are currently crowding the landscape. Thus, it absorbs less heat; an important feature of high-latitude ecosystems with permafrost in the midst of global warming. Animal-trampled snow in such grassy areas will also insulate the permafrost further, further locking a nightmarish vault of greenhouse gas emission. 

You cannot maintain a steppe without megafauna, and that is what the park is looking for: megafauna big enough to maintain the steppe and survive the Arctic winter. The park management is currently “importing” such fauna from all over the world as Siberia is lacking them. They are filling the park with reindeer, elk, yak, muskox, and other more sensible Holarctic fauna (it got Yakutian horses last April!), but getting a mammoth is still on the agenda.

In conclusion…

Whether we should pursue a new directive with ancient DNA depends on the moral development around the issue. In the case of Przewalski’s horse and Hoiho penguin not an “original” species, does that mean we should stop their conservation efforts? Again, this is another issue of what we consider natural and what conservation actually aims to do.  The Pleistocene Park has certainly pursued the extent of “natural ecosystem” down to half a million years ago. 

The facts are one thing, what to do with the facts is another thing. With more research on how nature works in the past and present, I hope we can more easily answer moral and ethical questions in biodiversity conservation and understand more on how to use all the information we have.


Sabhrina Gita Aninta is a conservation geneticist currently pursuing her PhD at Queen Mary University of London to understand how genome-wide variation of the endemic pigs and buffalos from Southeast Asia could assist their conservation. Follow her Twitter here for an update of her work, along with a mix of conservation, biodiversity, evolution, but mostly various rants and random stuffs in Indonesian and English. You can find more of her work at Ecology for the Masses at her profile.

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