How You Can Help Ancient Ungulate Conservation Using Ancient DNA

We write so much here on Ecology for the Masses about the danger that countless species face in today’s world. So every now and then we need to give tangible solutions and talk about how to actually save an endangered species. It’s not an easy task, and every one comes at it from a different angle. But right now, I want to talk about the fate of two amazing species, the work my colleagues and I have been doing to try and save them using DNA from museum collections, and how you can help. Yes, you. Our awesome readers. Here is a story about my research.

First of all, I need you to look at these magnificent beasts, the anoa (left) and the babirusa (right). Anoa comes from the local language and literally means “dwarf buffalo” while babirusa is the Indonesian word for “pig-deer”. They have a range of different names across their different ranges, but I can guarantee you that local people all know what an “anoa” and a “babirusa” are.

Anoa (left) and babirusa (right) at Chester Zoo (Twitter @chesterzoo) taken in 2015.

What is so special about these pig- and cow-looking animals?

These ancient ungulates lives in the archipelago of Wallacea, named after a British naturalist Alfred Russel Wallace who came up with the theory of natural selection around the same period as Charles Darwin. Babirusa is the only lineage remaining from an ancient lineage of pigs that once roamed the Asian continent tens of millions of years ago, while the anoa diverged from the lineage of common water buffalo around one million years ago.

Not taller than human adult hips, the anoa is the LARGEST native animal species in Wallacea, followed by the babirusa. They are natural forest-dwellers; you can see that anoa’s horn grow quite flat backwards compared to other Bovid relatives, which ease stheir movement within the rainforest where they live. Their relatives in the Philippines, the tamaraw, have more or less the same thing.

These two taxa are thought to consist of more than one species each, considering their morphological and genetic diversity, which remains to be tested. If you look at the IUCN Red List, there are two recognised species for anoa and three for babirusa, each are thought to be distinct due to difference in the habitat they live in (mountain vs lowland, small islands vs large islands, etc).

Evolutionary history of babirusa (top) and anoa (bottom)

An interesting thing I note every time I introduce these guys to a lot of people is that the Westerners tend to favour the babirusa while Indonesian people care more about the anoa. That being said, these two taxa are generally considered “low-profile species” in the world of conservation biology. They aren’t thought of as charismatic or bearers of unique awesome features (and setting aside the fact that charisma is somewhat of an outdated concept, you may realise that the photos beg to differ).

Low-profile endemics need more awareness work because not only are people typically not interested in their look, but also have a hard time relating to them. How many people have seen a real life buffalo or wild boar their entire life? How can people see peace-loving plant-eating animals as anything other than another form of livestock?

This is why some of the attempts in conserving them involve zoos all around the world. The picture you see of anoas and babirusas are mostly from the captivity because they are SO HARD to find in the forest. Zoos and other conservation organisations are also working on breeding them in captivity so that when *God forbid* their native population crashes in the wild, we can bring them back. Much like what people have been doing with the Tasmanian devils.

The love for horns and tusks

As low-profile as they might be, people are still interested in what happens to be in their head.  Specifically the horns on the anoa’s head, and the tusks on the babirusa’s snout. In the 19th century when exotic natural collections were commodities that cost a fortune, wealthy socialites would try to increase their exotic collections, forming their own cabinet of curiosity. The oldest mention of “horned pigs” in such collections was found in a Portuguese text from 1555. Please have a look at the early attempts to record babirusa here

A screenshot of an auction for what they claim as anoa’s horn killed around 1900 I randomly found on Google when looking at “anoa horns”.
A screenshot of an auction for what they claim as anoa’s horn killed around 1900 I randomly found on Google when looking at “anoa horns”.

Additionally, when we were looking for available museum specimens for anoa and babirusa, we found 644 records from GBIF and the most abundant collections belong to a museum in Sweden and The Netherlands, and most dated around the early 1900s. Meaning, there are plenty of samples of individuals that were living in the past, way before anthropogenic threats hit their peak in the habitats of these hooved animals.

These old ancestors can help their descendants.

Solving the shifting baseline syndrome with museum collections

In 1995, a fisheries scientist realised that every generation of scientists use a different baseline to evaluate annual capture because they see different numbers of captures every period. He named this phenomenon the ‘shifting baseline syndrome’. This is what could happen to anoa and babirusa as conservation baseline also changes with years as they evaluate the change in numbers of individuals observed. We need a *real* baseline, and genetic information from museum collections can help.

Illustration on Shifting Baseline Syndrome by Cameron Shepherd made for Earth Day on 22nd of April 2019 (Twitter @cameron_jms)
Illustration on Shifting Baseline Syndrome by Cameron Shepherd made for Earth Day on 22nd of April 2019 (Twitter @cameron_jms)

We cannot estimate how many individuals of these species existed in the wild directly from the abundance of museum collections. It is just too biased on collectors’ capacity, and every museum collected data using different methods. Sampling for babirusa was also biased to males as they have those amazing overgrown canines; so even if we get an accurate count on the males, we don’t know how many females or babies there were. What should we do? Here is where the concept of genetic diversity comes in handy.

Although the chances vary, tissues sampled from ~1,000 years ago can still contain short DNA fragments. You need to consider a lot of things to get them, and the ability of next generation sequencing to tell us the sequence of DNA in these fragments base by base has proven to increase our understanding of many things about the extinct animals.

Yet what these samples allow us to do is determine where these two species are most threatened. My team and I can use genetic information from older populations to figure out how badly these species’ genetic diversity have been depleted over the last two centuries. In Indonesia, this scenario (genomic erosion) is highly likely as logging the forest for mining, agriculture, settlement, and road building has been increasing in rate since the start of the New Order in the 1950s. The New Order was a historical period during the Indonesian government tried to make everyone in the country eat rice, hence logging was especially high as many rice paddy fields were established. 

Using this information, we hope to influence land-use policy in the anoa’s and babirusa’s habitats in the future. We might get surprises that I or the policy makers like or not like, but it’s a chance we are taking.

How you can help us getting the ancient DNAs

If you want to know the results, you can actually help us! I and my team are currently maintaining a crowdfunding campaign linked here to increase the quality of the DNA sequences from the samples we already have, and get a better picture of where the babirusa and anoa are in the most trouble. There are also plans to sample museums in Indonesia, but coronavirus obviously makes this difficult. The money will be used for doing whole genome sequencing of the ancient samples and all the things you need to get ancient DNAs.

Project Link: Building a Time Machine From Museum Collections

You do not need a lot to help; just $1 coming from many people will add a lot to this! If you cannot help directly through backing, I would really appreciate it if you spread the word around so many more people who could contribute will know. The deadline is the 9th of February 2021 on 17:00 PST to be counted as booster backers, but you can still contribute after that until 12th of February 2021.

If you decide to back us, you will get updates about this project straight to your inbox! I will tell you more about how these two animals fare in the wild, (as much as my friends on the field update me of course), how far we are in the lab works, the sequencing process and results, and you will be one of the first to know about the genetic diversity of the ancient DNA when we get it!

Learn more about our project at the link above and feel free to ask more in the Discussion page or just comment on this post below.

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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