Sunday, 17 November 2019

Don't Sleep with Your Sister

Conservation of mammals (or other animals) isn't simply a matter of providing enough suitable habitat for them to live in. One other consideration is that that habitat should not be overly fragmented - and this can be a problem as we build roads or other transport networks that cross otherwise wild terrain. The problem with fragmented habitats is that, even if there is enough space and food to support a small population of the animal in question, that population cannot reach and interact with other populations. And this leads to inbreeding.

We have known that inbreeding is a bad thing in animals since... well, probably at least since we started domesticating livestock. In our own species, there's a natural revulsion against incest, something that's reflected in moral teachings that go back at least as far as the Old Testament, and similar codes in other cultures. Animals too, avoid inbreeding when they can, perhaps finding the scent marks left by genetically similar individuals to be unpleasant.

On the other hand, you wouldn't need to make it a moral teaching if it never happened, and the reluctance of wild animals can also be overcome in the right circumstances - such as lack of alternatives. Initially spurred by its relevance to agriculture and animal husbandry, the study of inbreeding - how animals avoid it, and what happens when they don't - is something that likely goes back to pre-scientific times. A disproportionate amount of this research has been conducted on mammals, as is true of most similar topics, but, at least for this blog, that's not really a problem.

The history of the scientific study of inbreeding, however, really starts with Charles Darwin. Darwin noted that inbreeding was already known to cause issues with cats, dogs, and agricultural livestock., and conducted experiments on plants that supported this as a genuine phenomenon. The fact that genetics hadn't yet been discovered led him to some erroneous conclusions as to how it was happening and that it might not be quite as large a problem in humans as was generally thought. Even so, having married his own cousin, he had suspicions that the many health problems suffered by his children might not be coincidental... and he was probably right.

In the early 20th century, genetics entered the scientific mainstream with the rediscovery of Gregor Mendel's work. What is now the standard explanation for the deleterious effects of inbreeding was developed soon after, initially by Charles Davenport - who would go on to found the eugenics movement and, ironically when you think about it, denounce mixed-race marriages.

This "dominance theory", has been expanded and amended in the many years since Davenport first proposed it. In its modern form it essentially proposes that the majority of genetic mutations, if they do anything at all, are harmful, but that normally these are recessive, allowing a 'good' copy of the same gene to mask them. Inbreeding increases the chance that only harmful copies of the gene are inherited, unmasking them and bringing out their full effect. While any 'good' genes could similarly accumulate, those are typically dominant anyway, so having extra copies doesn't provide any further benefit - and anyway, there's less of them.

There's rather more to it than that, but that's the gist.

For much of the 20th century, studies on the effects of inbreeding relied on captive or domesticated species, where the pedigree of the animals in question was readily available. In the mid '60s, however, new techniques of protein analysis made it possible to assess whether a wild animal possessed multiple copies of a recessive gene, and thus, how related its ancestors were likely to be to one another. This sort of thing became a lot easier and more accurate in the '80s once it became possible to analyse DNA directly. Some modern techniques even allow us to scan whole genomes for runs of genes that all arise from a single common ancestor in the recent past, providing a direct measure of inbreeding.

Even by analysing pedigree information in captive zoo animals, rather than genetic information from those living in the wild, it became clear in the later 20th century just how much inbreeding can become a problem for species that are already endangered. This creates what's sometimes called an "extinction vortex", where the reduced breeding opportunities in an endangered species leads to more inbreeding, reduced fitness among the resulting offspring and thus further population loss, which leads in turn to even more reduced breeding opportunities and so on into an inescapable spiral of doom.

On the other hand, there are instances where small founder populations, sometimes just two individuals (or one pregnant one), can be isolated on an island and still create stable populations over the following years or decades. This may, in part, be due to the phenomenon of "purging" whereby the most lethal genetic mutations never get a chance to accumulate even in an inbred population because the individuals carrying most of them never get as far as breeding.

The reason that "purging" does not seem to be as helpful as one might hope may well be that not all harmful genes are necessarily lethal, and many contribute only a small amount to a reduction in fitness. By the time they build up to a lethal level, so that purging can kick in, it's too late, and they are already fixed in the population, with no source of healthy genes left to replace them.

As supporting evidence for this, for example, we can look at gorillas. Both species of gorilla are critically endangered, but the eastern gorilla (Gorilla beringei), which includes the mountain gorilla subspecies, is thought to have a far lower population than the western gorilla (Gorilla gorilla).  In line with this, it has been shown that mountain gorillas have fewer severely harmful mutations, but a higher number of mildly unhealthy mutations, than do typical western gorillas. In other words, the mountain gorillas have successfully purged the worst of their mutations from the population, but the others are building up, potentially leading to further problems down the line.

Just how serious might those problems be? Well, the extinction vortex certainly doesn't seem to be imaginary, and one way we can demonstrate that is by looking at species that are already extinct. Thanks to how far we have come with genetic analysis in recent years, these don't even need to be recently extinct species.

While woolly mammoths died out at the end of the Ice Ages in most parts of the world, the last population survived into historical times - 2,500 to 2,000 BC - on Wrangel Island off the north coast of Siberia. It has been possible to analyse the genetics of some of the last survivors and use the whole genome sequencing method I mentioned above to demonstrate remarkable levels of inbreeding among them. In fact, we can even look and see which genes it is that were most affected, showing that, among others, genes affecting their ability to smell and the quality of their coat had been effectively destroyed by accumulated mutations.

This sort of detail, once applied to species that have not yet gone extinct, might help us to understand, and hopefully to mitigate, the problems that inbreeding can pose for species already on the verge of extinction.

[Photo by "BluesyPete" from Wikimedia Commons.]

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