I have a bit of input if you don’t mind! I’ve answered questions similar to this before, so if you want some good reads about Pokémon Gender/Sex/Reproduction you can check out Salazzle, this theory, Marill, or these two asks.
Biological sex is just as complicated in the animal kingdom as you would expect it to be. The chromosomes that determine human sex are paired in XX and XY, whereas other animals may have WZ or ZZ, and some even have more than two, forming XXXX or XXYY or WXYZ.
However, you brought up a good point that gave me a new idea though: the Pokémon Stadium 2 “Gender unknown Egg Group”. Genderless pokémon do have an egg group: Bronzong is in the “Mineral” egg group and Starmie is in the “Water 3″ egg group for example. All pokémon, of course, hatch from eggs. This includes genderless pokémon, so if they hatch from eggs, why can’t they lay them themselves? To answer this, let’s do a quick crash course about what egg-reproduction looks like via chickens.
Hens lay an egg about once a day: it’s essentially the chicken equivalent of a menstrual period. Unless the egg is fertilized before the hen lays it, however, it will never hatch (unless the organism is parthenogenetic like Salazzle, which genderless pokémon are not). The egg yolk is formed in the ovaries, much like with human reproduction. It then travels along the oviduct: this is the stage where it gets fertilized by a rooster’s sperm, if it can. It then builds up the layers of the egg around the yolk, such as the extra protein, the membrane, and finally the shell. Then the egg exits the chicken and is officially laid.
The simple answer to this question would be that genderless pokémon like Metagross never get to the first step. They can’t produce eggs. Ditto can, and so perhaps Genderless pokémon can fertilize the eggs, which is how they can ultimately reproduce. In this sense, genderless pokémon would effectively be entirely male. Entirely female species can still reproduce (as shown with Salazzle), but male pokémon would be down on their luck.
The more complicated answer lies with a mule: A mule, of course, is a cross breed between a donkey and a horse. A child typically inherits half of its chromosomes from each parent. A horse has 64 chromosomes, and a donkey has 62. (Humans have 46 for reference). The horse parent contributes 32 chromosomes to the child, and the donkey parents contributes 31. This means that the mule has a total of 63 chromosomes. This is an odd number: which is generally considered a problem because chromosomes need to match up in pairs. An odd number of chromosomes in humans causes Down syndrome. For a mule, the chromosomes can’t match up at all: they can’t find any similar enough to themselves to form a pair. While horses and donkey genes are similar enough to reproduce, the chromosomes are too different to pair up. Instead of having an even-number of chromosome pairs, a mule effectively has 63 individual chromosomes. Because of this, a mule is incapable producing eggs or sperm. It is the difference between mitosis and meiosis: creating an identical copy of DNA versus creating a half-copy of DNA. Mitosis mule cells can do: meiosis is where the problem lies.
((As a side note, egg groups in pokémon are likely split based on number of chromosomes! Something with 46 chromosomes like a human might be in the “Human-like” egg group, where something with 64 chromosomes like a horse could be in the “Field” egg group with Ponyta and Mudsdale.))
Let’s bring this back to genderless pokémon. They can reproduce, so they’re not exactly like mules, but hopefully you get the idea. Genderless pokémon possibly have an odd number of chromosomes, so it is impossible to divide that in half to breed with their own species. But they can breed with ditto, which basically means that Ditto blurs the line between mitosis and meiosis, possibly using a different method of reproduction altogether. Something about Ditto enables the genderless pokémon’s chromosomes to find matched pairs and be able to reproduce.
Of course, this almost certainly differs from pokémon to pokémon, but hopefully you get the general idea.
Genderless pokémon have an odd number of chromosomes, which makes them unable to reproduce with members of their own species.
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