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Answer by Justin Ma, Ph.D. student in plant breeding and genetics:
Inbreeding the is the sexual reproduction between related individuals. However, since we're all related in some manner, geneticists define inbreeding more technically and quantitatively. I also want to discuss the effects of inbreeding in more detail. There's a common assumption that inbreeding is always bad, which is far from the truth.
The usual measure for inbreeding is the inbreeding coefficient (F). It is a measure of the probability that two alleles at a given locus are identical by descent, or in other words, homozygous. Similarly, it's also proportion of the genome that is homozygous. (Very strictly speaking, the three things I have described are actually slightly different, but for most purposes, they can be understood to be synonymous.)
To put a number on inbreeding and estimate F, the first step to set a baseline. The baseline is what you consider to be unrelated. For example, in most human populations, two strangers are sixth to eighth cousins, so you could consider that to be unrelated; in other cases, you would just use as much pedigree (family tree) information as you have available, and your baseline is established by the data you have on hand. This matters because about 99.5 percent of our human genomes are identical and therefore homozygous if you consider nonvariable (i.e., non-polymorphic) loci. However, setting that baseline effectively makes those 99.5 percent of no interest; we are only interested in the 0.5 percent.
The inbreeding coefficient is estimated by various means, most traditionally through simple pedigrees with the math based on Mendelian principles. However, estimates based on pedigrees are not a perfect reflection of what actually happens in our genomes. In modern times, “realized inbreeding coefficients,” which are more accurate, can be more directly estimate inbreeding based on our genetics (although this leads to some funky results like inbreeding coefficients below zero and above one—the simple explanation for this is because of the baseline and scaling).
Inbreeding matters most because of inbreeding depression. As there are many examples of this, it's most simply understood as the increase in the likelihood that you'll get two deleterious recessive alleles of, say, a major genetic disease. However, this works across many other genes (loci) of smaller effects as well. Fitness is generally decreased with inbreeding depression.
However, inbreeding is not always bad. Higher animals have a very low tolerance for inbreeding, but inbreeding is common in other life forms like certain worms, and extremely common in the plant world. And in these cases, I am talking about selfing, which, by human standards, is an extreme form of inbreeding.
There are many advantages of inbreeding but it can be boiled down to:
- The same advantages of , which are numerous. These include far faster and more efficient reproduction, lower search costs, improves kin selection, undesired variability over generations, reduced risk of disease.
- Increasing the frequency and/or fixation of desired alleles. In the same way that deleterious alleles are more likely to be unmasked, you can fix desired alleles and purge those deleterious alleles more effectively.
On average, this doesn't work well in species with high inbreeding depression, but with selection and sufficient populations, the problems can be overcome. This is commonly done by animal and plant breeders.
In animal and plant breeding, we target specific traits, and it makes sense that breeding like with like (which intuitively will be more related) is a good strategy. As the animal breeders describe it, “It's line breeding when it works. It's inbreeding when it doesn't work.” In plant breeding, we also do it to establish uniformity by releasing pureline inbreds as varieties, and somewhat ironically, using them as parents for uniform hybrids.
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