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I came up with anthropoidal creature that has several subspecies, let's call them red, green & blue, that can interbreed with each other. My problem in this setting is that:

  1. I don't want any ugly hybrids,
  2. I don't want any of the subspecies to disappear due to interbreeding

So this is what my proposal how should their reproductive system work:

Each individual contains chromosomes that are shared for all the colors e.g. 80, plus certain amount of chromosomes unique to each color e.g. 20. Males produce sperm which contains half of the genetic material, just as humans do in this case the sperm would contain 50 chromosomes of which 40 are shared & 10 are unique for each color.

When couple of same color (red & red, green & green, blue & blue) have a child it works the same way as in humans. The child could either be male or female, will have the same color as its parents, and has 50% DNA from its mother and 50% DNA from its father.

However when a couple of different colors (red & green, red & blue, green & blue) has a child, the mother reproductive system only uses the shared chromosomes of the specie from the father's sperm, while the chromosomes with different color are discarded and mother's own chromosomes are used instead. So in that case the child will be always be a female, will have same color as its mother, and will have 60% DNA from its mother and 40% DNA from its father.

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    $\begingroup$ Is it out of the question to just suggest a mule-like genetic system? Horses and donkeys can inter-breed, but their result (the mule) cannot. Simple way to allow inter-breeding but ensuring the preservation of the initial stock. $\endgroup$ – GrinningX Oct 12 '16 at 18:24
  • $\begingroup$ @GrinningX I would prefer a fertile offspring, but it's a good start if I can't think of anything better. $\endgroup$ – Platypus Oct 12 '16 at 18:25
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    $\begingroup$ Could you be thinking of hybridogenesis? $\endgroup$ – Anonymous Oct 12 '16 at 18:44
  • $\begingroup$ You are implying a DNA system identical to humans? Also with mitochondria? And you are saying ALL the color comes from one parent? If "color" is the subspecies, in the case I just described, they can't disappear, unless the proportion of one gender is much higher than the other, AND the mating patterns are such that persons of that gender are less desirable partners in a subspecies that will gradually disappear. How do you define "ugly" ? $\endgroup$ – WGroleau Oct 15 '16 at 2:36
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    $\begingroup$ Check whether I understood: Children of a mixed marrriage are always female and the same color as the motherr? If that's the case, then as long as there are fertile females of every color that males of any color are willing to mate witth, then no color will die out. $\endgroup$ – WGroleau Oct 15 '16 at 5:19
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The simplest way to achieve the desired result is through the Mitochondrial DNA. Humans and most other eukaryotes contain a smaller, secondary genome outside of their nuclei in another organelle called the Mitochondrion. This mitochondrial genome is very useful for our purposes because it is only inherited from the mother through the egg.

If you imagine three significantly different mitochondrial genomes: red, green, and blue you will arrive at precisely your desired scenario. There is only one set of mitochondrial DNA per organism so there can be no hybrids. In any cross-population procreation only the mitochondria of the mother is passed on meaning all of a female's offspring will have identical mitochondrial genomes regardless of the genotype of the father.

Edit: To address the plausibility of the mitochondrial genome influencing phenotypic traits.

It is certainly plausible that mitochondrial DNA could encode phenotypic traits like skin color, but perhaps unlikely. The mitochondrial genome in humans is ~30,000 nucleotides in length and contains 37 genes. This means compared to the nuclear genome it is ~1/100000 the size and contains ~1/5000 of the genes. The chance of any given trait being encoded by the mitochondrial genome is thus somewhat small, but those 37 genes (most of which aren't actually proteins, but rather encode RNAs) do have functions. There are many disorders caused by mutations in the mitochondrial DNA.

I don't know of any phenotypic traits encoded by the mitochondrial DNA but currently we are much better at finding disease alleles than we are at finding the loci that govern more complex traits like skin, or hair, or eye color. This means there may be phenotypic traits encoded in the mitochondrial DNA that we don't know of, or there may not be, but I would argue that either way it's certainly plausible that the genes transcribed in the mitochondrial DNA could influence such features.

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  • $\begingroup$ Is it plausible for Mitochondrial DNA to affect external traits like skin color, how good is your eyesight, etc? $\endgroup$ – Platypus Oct 12 '16 at 20:27
  • $\begingroup$ Is it plausible to assume a species completely unrelated to anything on the real earth would have mitochondria? $\endgroup$ – WGroleau Oct 15 '16 at 2:37
  • $\begingroup$ @WGroleau Mitochondria and their genomes are found throughout Eukarya meaning virtually every multicellular organism has them. They also aren't unique in being organelles with their own genome as chloroplasts in plants also have separate genomes. That said, were there to be an anthropoidal species with no relation to Earthly biology without mitochondria you could substitute the mitochondrial genome with the Y chromosome in my answer. The only difference would be the type of the offspring would be the type of the father instead of the mother. $\endgroup$ – Mike Nichols Oct 15 '16 at 3:22
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Hybridogenesis

There is no system like this on Earth. The closest is hybridogenesis, where one parent is a sexual parasite on the other to produce hybrid offspring which only pass down the parasite chromosomes. Species that engage in hybridogenesis are dependent on it to reproduce and consist of only one sex.

Mendelian alleles

If your goal is to have subspecies with traits which cannot be watered down through interbreeding, then an alternative is that subspecies is determined by a single gene.

Let's call the resulting alleles Cᴿ, Cᴳ and Cᴮ. These genes are recessive or dominant, so there are only three possible phenotypes of red, green or blue. Let's assume the dominance pattern is a circular B>R>G>B. The possible genotypes (and phenotypes) are CᴿCᴿ (red), CᴳCᴳ (green), CᴮCᴮ (blue), CᴿCᴳ (red), CᴿCᴮ (blue), and CᴳCᴮ (green).

If the allele is located on the X- or Z-chromosome or its equivalent, then heterozygous (XY, ZW) offspring (who have only one allele) will be the same color as the parent who contributed the X- or Z-chromosome. (Males are XY or ZZ, females are XX or ZW.)

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  • $\begingroup$ Hybridogenesis looks like it's what I want, if the parasite mother has a child, how much DNA will parasite daughter have from the father? $\endgroup$ – Platypus Oct 12 '16 at 19:21
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    $\begingroup$ @Platypus: the offspring will have 50% as usual. However, the offspring will produce gametes using only its mother's chromosomes. This has the same disadvantages as asexual reproduction, hence the reliance on the father $\endgroup$ – Anonymous Oct 12 '16 at 19:24
  • $\begingroup$ Thanks but that's not what I want. On the other hand the other approach is very elegant, but I want my subspecies to be quite different, doubt that single gene would do the job. $\endgroup$ – Platypus Oct 12 '16 at 19:30
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    $\begingroup$ @Platypus: Not necessarily. It could be a regulatory gene that tells a set of other genes to activate, like flipping a master switch. Or you could increase the number of regulatory genes to Cᴿ¹, Cᴳ¹, Cᴮ¹, Cᴿ², Cᴳ², Cᴮ², and so on. $\endgroup$ – Anonymous Oct 12 '16 at 19:36
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Apologies if this has been said... The premise is that a mixed marriage has only daughters in which color comes solely from the mother. Therefore

  1. Doesn't matter where it comes from in a non-mixed.
  2. There can never be mixed color females
  3. If mixed matings happen at all, females will outnumber males
  4. If mixed marriages are common, females will greatly outnumber males and the overall population will slowly decrease. (But it will stabilize probably at some lower limit.)
  5. If one "color" is more desirable for some social reason, that color will increase in population and the others decrease because those females will have more mates.
  6. If gestation is of significant length, polygamy will likely be the norm due to the females being so numerous.
  7. There will be no mixed males, since they all come from non-mixed unions.

Whether or not there are mitochondria doesn't matter; there will be some biological explanation for the premise (first paragraph) but the story can probably be told without revealing how the genetics actually work.

Seems to me it would be rather easy to program a simulation, but I can't afford the time to do it. I shouldn't even be typing this, but it's an interesting problem and I'm quite tempted. :-)

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  • $\begingroup$ I don't understand reasoning behind 4, could you explain? 5 I'm quite sure blondes are more desirable in our world, but I don't see them increasing in population. $\endgroup$ – Platypus Oct 15 '16 at 20:20
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    $\begingroup$ Blondes in our world don't have only blonde daughters. Each mixed mating in your world will produce a daughter or nothing. Each same-color mating will produce a son or a daughter or nothing. So the next generation has more females than males. Now, if blue and green for some reason think red is more desirable, red women and men will mate more often and thus the red women will increase in number faster than the others. $\endgroup$ – WGroleau Oct 15 '16 at 20:41
  • $\begingroup$ You're right about blondes. But I don't think that ratio of colors will change, if B&G men prefer R women R women will produce more Red women , but Blue & Green women will produce B&G since they have to mate with R men, there would be more women but ratio will stay. Beside preventing one color to breed their number will stay. But it could happen that one color males could disappear, if they prefer mating with other colors, which is part of my story :). Actually all but one color males disappeared before the written history, and nobody knows why. $\endgroup$ – Platypus Oct 15 '16 at 20:57
  • $\begingroup$ There's no mixed color anything, daughter from RF & RM is completely equal to daughter from RF & BM or RF & GM. The child of mixed couple is always female. $\endgroup$ – Platypus Oct 15 '16 at 21:04
  • $\begingroup$ Yeah, I'm still getting details wrong. I had it closer to correct the first time. $\endgroup$ – WGroleau Oct 15 '16 at 22:12

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