The main problem with inbreeding is that a child may get the same recessive gene from both parents, turning it active. Recessive genes are genes that may carry a disorder, but are only active if the child gets the same gene from both parents; otherwise, the healthy version will be the active one. With three genetic parents, the child would have to have the recessive gene from all three parents to activate the disorder, and this is far less likely. In a human population, if 1 in 100 has the bad gene, the chance is 1 in 10,000 that the child will get it from both parents - if there are three parents, the chance will be 1 in a million. This vastly reduces the risk of damaging inbreeding. In fact, the prevalence of the bad gene could be as little as 1 in 22 and still carry a lower risk of harm.
There is a caveat to this: Some hereditary disorders, like hemophilia, are tied to the gender-bearing X chromosome. A male child will get hemophilia if he gets a recessive hemophilia-bearing chromosome from his mother - he can't get a good version from his father, since he gets no X chromosome from him. A girl child only gets hemophilia if she get hemophilia-bearing chromosomes from both her mother and her father. If there are three gender-bearing chromosomes (X, Y, and Z) instead of two, the risk may be greater, or smaller, depending on how gender is determined by the genes.
Not there has to be three gender-bearing chromosomes to get three genders. Say you get an X or a Y chromosome from each parent. The possible combinations are XXX, XXY, XYY, and YYY. It may be that the 'pure' combinations XXX and YYY manifest as the same gender, with XXY and XYY being the two remaining genders. The XXX/YYY gender will then be half as common as either of the other two genders. If an X chromosome carries a recessive disorder, the XYY gender will get it if they receive it from any one of their parents. The XXY gender will need to get it from two parents, and the XXX/YYY gender will need to get it from all three parents. If every 100th X chromosome carries the disorder, one in a 100 XYY's wil have it; one in 10.000 XXY's will have it, and 1 in 2 million XXX/YYY's will have it.
Overall, it hence looks like your three-gender species carries far LESS risk of inbreeding problems than our two-gender species. Depending, of course, on how chromosomes (or the equivalent) works to determine gender. and how common gender-based genetic disorders are.
How many generations before it is no longer considered an inbreeding problem? – Trevor – 2019-06-20T17:40:13.590
I believe that the problem was that eventually the small population would start to produce offspring that are not capable of surviving or reproducing – Michael Stachowsky – 2019-06-20T17:45:49.893
Island societies interact with each other a lot more than most people think. Polynesia being a good example. And if your islands are really that far apart (or the oceans that treacherous), how on earth did your species evolve in one place then spread out to near total isolation? OR somehow independently evolve not only into 3 sexes but with similar species on various islands? – Cyn says make Monica whole – 2019-06-22T17:25:51.660