# Why does my simulation not support the idea that inbreeding is bad?

After reading this post, I wrote some code to simulate inbreeding.

We have a population of $N$ creatures. Each creature has two genes, which come in two forms: recessive (a) and dominant (A). The creatures' initial genomes are random. At each stage, the following happens, in order:

1. Each creature with the recessive phenotype (aa) dies with probability $p_R$.
2. Each creature with the dominant phenotype (AA, aA, or Aa) dies with probability $p_D<p_R$.
3. Each creature then decides to have children with probability $q$. Each creature that decides to have children chooses a mate (see below) and has three children with that mate.

I wrote two different kinds of creature, incest-averse and incest-seking. Each time I ran the simulation, the population consisted of either all incest-averse or all invest-seeking creatures.

1. An incest-averse creature chooses a mate randomly and uniformly from the set of its non-siblings.
2. An incest-seeking creature chooses a mate randomly and uniformly from the set of its siblings. If it has no siblings, it just randomly picks anybody.

In practice, since each union produces 3 children, the incest-seeking creatures almost never fail to have siblings after a few generations.

What I found was that whichever type of creature I used, the results were the same: the frequency of the aa genotype plummeted to almost zero. I used the parameters $N=100$, $p_R=0.1$ $p_D=0.05$ $q=0.022$.

Presumably my model is in some way too simple. What am I not taking into account?

Source code

• Your question title does not really fit your post. Your simulations do show that inbreeding is bad since the recessive genotype frequency drops to very low non-zero values in your inbreeding scenario, which is expected under high dominance coefficients. What does not fit your expectations is your null model: the outcome of the non-inbreeding scenario. The main problem seems to be that there is no differential fitness effect for recessive genotypes: if all recessive genotypes have such a strong negative fitness effect, you do not have power to separate your two models. – AlexDeLarge Apr 26 '17 at 14:36
• @AlexDeLarge From the reddit post I linked to, my interpretation was that reducing the frequency of aa is what we want (since that phenotype is less fit). In that case, what do we actually expect to happen under non-inbreeding, and why is it a "good" thing? – Jack M Apr 26 '17 at 14:43
• I notice your simulation doesn't actually compare the spread of phenotypes of "incest-seeking" and "incest-avoiding", you just prescribe one or the other. What your simulation shows is that deleterious phenotypes tend to go extinct, which is what we would expect, incest or no incest (if anything it might happen faster with incest because the deleterious allele is less likely to "hide behind" the non-deleterious one; see: en.wikipedia.org/wiki/Genetic_purging). I think the question is, what does "incest is bad" mean to you and how did you expect this simulation to show it? – Oosaka Apr 26 '17 at 14:50
• Given your setting you expect to have low frequency of recessive homozygotes even without inbreeding. But in reality, recessive homozygous genotypes do not need to be deleterious, in fact only a small fraction is. Accordingly, given that recessive deleterious alleles are very rare and most often found in healthy heterozygous carriers, they are rarely combined by chance. The problem with your simulation is that it does not capture that inbreeding, due to excess homozyogotes, strongly increases that probability as you penalise every homozygous recessive genotype. – AlexDeLarge Apr 26 '17 at 14:59
• @RozennKeribin I was trying to understand why inbreeding is considered "bad", genetically. From the reddit post I linked, I thought the idea was that with inbreeding, deleterious alleles go extinct less quickly, although in retrospect that doesn't make much sense. If that's a mistake, then "Why is inbreeding bad?" should be taken to be part of the question. – Jack M Apr 26 '17 at 15:39