Humans find the idea of incest disgusting and thus avoid mating with close relatives. Most people have a vague understanding that children born to closely related parents are likely to have physical or mental abnormalities, like the royal family of years gone by and some of that dodgy village down the road. This is known as inbreeding depression. But why does it occur? Surely it is beneficial to give children not only half of your set of genes, but also some that your sibling or parent shares with you, thus passing more than 50% of your genes to the next generation. Inbreeding ought to allow you to maximise the proportion of your genes in the next generation, the ‘goal’ of reproduction. Unfortunately, for most animals on this planet there are severe problems with inbred offspring that outweigh any benefits in terms of propagating their genes.
To understand inbreeding depression you must first have some basic knowledge of errors that occur when genes are copied or repaired incorrectly, called mutations. Every time cells divide they must copy all of their genetic material using microscopic ‘machinery’, and these are subject to the occasional error, which can result in a new version of a gene. Additionally, mutations can arise due to environmental damage through radiation, heat or chemical agents. These mutations become permanent features in the genetic lineage of a given cell, hence those that appear in the germ line (egg and sperm cells) are passed from parent to offspring eternally down the generations.
Within a single cell a mutation happens at a completely random point in the genome, effecting any of the ~25,000 genes. In most cases the mutation is not expressed, as there are two copies, called alleles, of each gene. And mutations usually result in a recessive allele, meaning it is submissive and masked by the ‘normal’, dominant allele, which works as usual. Therefore, any person with a random recessive mutation is unaffected and a ‘carrier’ for the genetic disorder associated with faults in that particular gene.
Most individuals inherit between 3-5 random recessive mutations and when they mate with an unrelated person in the population there is a very low probability that they are both carriers of the same mutation. This means that their children are pretty much guaranteed to inherit at least one healthy, working version of each gene. However, when closely related people mate they are likely to share mutations they’ve inherited from a common ancestor, meaning each of their children would have a 1 in 4 chance of receiving both faulty versions of a particular gene, giving them a genetic disorder. As most people carry multiple mutations (and these are likely to be shared by related parents) the chance that their child will have genetic abnormalities becomes seriously high.
So that is inbreeding depression: the accumulation of faulty versions of genes in descendants of closely related sexual partners, where they are shared through common ancestry.
Note: Not all mutations are harmful; most are in fact neutral, producing no effect on the protein and function of the gene. And while some mutations are harmful, a small but important subset result in improved function of a gene, and this is a crucial way in which new adaptations can arise.