News - January 17, 2019

Inbreeding threatens Veluwe boar

Roelof Kleis

Groups of wild boar in the Veluwe nature area are fairly isolated from one another despite the wildlife overpasses. The result is inbreeding, as a study by Joost de Jong shows. He advocates vigorous measures. ‘After all, what’s so wild about our wild boars now? We’re long past that stage.’

texst Roelof Kleis  photos Yorick Liefting, Shutterstock, Hollandse Hoogte

Researcher Joost de Jong thinks wildlife managers should do more to combat inbreeding, for example through breeding programmes.
Researcher Joost de Jong thinks wildlife managers should do more to combat inbreeding, for example through breeding programmes.

The wild boar in the Veluwe are doing well, in the sense that there are enough of them. So many, in fact, that every year some have to be culled to keep numbers within manageable limits. But it is misleading to focus simply on numbers as in genetic terms they are suffering an insidious decline. Genetic diversity, which is necessary for a healthy population, is falling. Population geneticists call this ‘genetic erosion’. Joost de Jong, a lecturer in the Resource Ecology chair group, obtained his doctorate in December for a detailed study of this issue

Genetic boar map

It should be noted that De Jong’s study was not limited to the Veluwe. To be able to say something about local populations, it is essential to have a detailed picture of the natural genetic variation, in this case among boar throughout Europe. To get this picture, De Jong used SNPs — pronounced ‘snips’ — which are little genetic markers on the genome (see inset). Every genome has millions of them. Taken together, the markers form a kind of genetic fingerprint that can also reveal information about relationships. De Jong used it to draw a European boar map.

To do this, he worked with the Animal Breeding and Genetics chair group to collect DNA material from dozens of populations of wild boar across Europe. He ended up with about 500 samples. If you think De Jong must have travelled a lot to get this, you are much mistaken. ‘The samples were sent by fellow scientists I’d met at conferences, for example, and by hunters and wildlife managers. I did most of my work at my desk,’ laughs De Jong. ‘In principle, any piece of tissue can be used to get DNA. I chose the ear because that is usually a part that nobody is interested in so it gets left over. Incidentally, not a single boar was killed specifically for this study. These were all animals that were culled for population management purposes.’

Natural barriers

Analysis of the SNPs revealed an interesting pattern. De Jong: ‘You’d expect neighbouring populations to be genetically very similar, but that’s not always the case at all. For example, there are big differences within Central Europe. Genetically, the boars belong either to a western group or to an eastern group.’ The standard explanation for such patterns is that they are due to the Ice Ages. The argument goes that the differences arose due to repopulation following the retreat of the ice. The arrival of humans is also often cited as a cause. The differences are said to be explained by the loss and fragmentation of habitats, hunting, extermination and the displacement of boar.

But De Jong does not agree. He conducted a model study of the spread of wild boar based purely on the topography of Europe. How does the very shape of Europe and its natural barriers — mountain ranges — affect the genetic variation? De Jong: ‘What kind of geographical genetic structure do you get then? Which populations are similar to one another thousands of generations later?’ And that gives the same genetic boar map that he had already drawn on the basis of the SNP analysis. De Jong personally finds this the best part of his thesis. ‘It’s not empirical proof because it is a simulation. But I’m personally convinced that the topography is the main cause. I don’t need Ice Ages or human behaviour to explain the genetic profiles of boar.’

Half-brothers and half-sisters

Back to the Netherlands. What is the genetic variation like in a relatively isolated and fragmented area such as the Veluwe? It was already known that the Veluwe boar do not form a homogeneous group. De Jong: ‘An initial impression was obtained decades ago from protein studies. Three years ago, Alterra mapped the boar populations with genetic research. I’ve now added far more detail to that picture with the SNPs. It shows that dispersion is rare; the animals hardly change location at all and are very isolated.’

The wild boar hardly change location at all and are very isolated

On top of that, there is a lot of inbreeding. De Jong found boar populations where every animal had inbred pieces of DNA, traceable to recent forebears, on 10 per cent of the genome. In this case, ‘recent’ means going back 10 generations or less. ‘To put this in perspective, the values I find are often higher than the expected inbreeding for descendants of cousins and can be as high as the inbreeding for descendants of half-brothers and half-sisters.’

Prince Hendrik

Another conclusion is that the Veluwe boar are closely related to the boar in northeast Germany. That probably is the result of human intervention. ‘There were hardly any wild boars in the Veluwe a century ago,’ explains De Jong. That changed when Prince Hendrik, great-grandfather of King Willem Alexander, and Anthony Kröller, the man behind the Kröller-Müller Museum, introduced wild boar in their fenced parks — now the Crown lands and the Hoge Veluwe National Park. ‘Sometimes boars would escape and start new populations on the other side of the fence. That probably explains why they are genetically different to the wild boar in Western Europe.’

Would a wildlife manager want their animals to be so inbred?

De Jong says it is worrying to see genetic erosion among the boar in the Veluwe. That is why he feels management of the wild boar populations should be based much more on genetics. De Jong: ‘Opponents point to the fact that the populations are doing well despite the inbreeding, or argue that other threats deserve more attention. They also say we know too little about how inbreeding affects the genome to worry about it. But I absolutely disagree. I’m an advocate of the precautionary principle. The populations might be doing well in terms of growth but you shouldn’t be happy with so much inbreeding. It’s a welfare issue. Would a wildlife manager want their animals to be so inbred?’

The wildlife crossing over the A50 motorway at Woeste Hoeve.

Wildlife overpasses

What about the wildlife overpasses, known as ecoducts? Don’t they encourage migration and therefore genetic variation? De Jong has a nuanced opinion about them. ‘The wildlife overpasses are a nice gesture to nature by humans and they help prevent isolation. You can see that clearly in the populations on either side of the A50 motorway. When the road was turned into a motorway, a wildlife crossing was built at Woeste Hoeve. Now you see little genetic difference between the populations on the two sides of the motorway. So a wildlife overpass can prevent isolation.’

‘But it’s more difficult to end isolation than to prevent it,’ continues De Jong. ‘You need much more migration to introduce genetic variation back into an isolated population that is suffering from genetic erosion. That means that if you build a wildlife overpass to connect areas that have been separated for a long time, it will be a while before this has an effect. A connection is soon broken but nature doesn’t recover overnight. It takes time.’

Breeding programmes

De Jong believes we sometimes need to do more than just build wildlife overpasses. His PhD thesis includes a detailed decision schedule with measures that could be taken for different degrees of inbreeding. One such measure is the sterilization of dominant males. Another is introducing new boars from elsewhere. De Jong: ‘But you then need to think hard about which animals you bring in to end the inbreeding.’ De Jong is aware that this is a sensitive topic. ‘Some people think such breeding programmes go too far and are not compatible with the concept of wildlife. But what’s so wild about the wild boars in the Veluwe now? We’re long past that stage.’

Detecting genetic patterns with ‘snips’

SNP, pronounced ‘snip’, stands for single nucleotide polymorphism. The term refers to pieces of genetic code that are found in a single position. You can imagine them as a typo in the long genetic letter code. The human genome has millions of such SNPs. Each individual person has their own unique pattern of SNPs — a kind of genetic fingerprint. Nowadays there are techniques that make examining a DNA sample for SNPs a fast, routine job. Researcher Joost de Jong had his samples from nearly 500 boars scanned for 30,000 known SNPs for boar. That let him detect geographical genetic patterns in great detail and make precise estimates of the degree of inbreeding and relationship.