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Some genes are dominant and some are recessive. Dominant genes override recessive genes regardless of which parent it's inherited from. Some genes that simply aren't compatible with each other are altered during fertilization. These altered genes are called mutations. Some are beneficial, some are harmful, but most are benign. Some genes only come from the Mother, which would be the genes for the mitochondria. While some will only come from the father, which would be the genes for the nucleus.
As for X and Y chromosomes. The X chromosome contains a lot of info you need in order to live while the Y chromosome just codes for what makes a being male. If you have a defective gene in your X chromosome and are male, chances are that it's going to present itself. If you're female, it depends on if that gene is dominant. One notable case is the genes for the cones in your eyes. They reside in the X chromosome and sometimes one of those genes has mutated. If you only have the mutated version you may be unable to see some colors. As [email protected] pointed out, this has advantages and disadvantages.
Disclaimer: I'm going by what I remember from high school biology. If I made an error, then please correct me.
EDIT: Corrected my wording in regards to colorblindness.
Yeah. That's a little out of date.
Colorblindness isn't worse vision, just different.
You got more rods for the missing cones, it's not just blank space.
That helps lowlight vision, and the colorblind are also better at differentiating shades of brown.
Like, my dad was colorblind, and he could spot a deer in the woods from like a mile away. To him it was completely obvious and he never got why other people couldn't see the deer.
I didn't mean to imply it was bad. I'll reword my comment.
Also, with 2 x chromosomes it's possible to get an extra set of cone cells and see more colors.
Tetracromacy
Ahh thanks, this is all coming back to me now! Despite being a pretty nerdy student, my biology teachers at school didn't instil much enthusiasm in me for the subject. But the more I learn about it now, the more fascinating I find it.
Do you have any more detail/links about incompatible genes causing mutations?