#even though the difference on a majority of genes wouldn't be any greater than the difference between some genes on skydancer vs other wing

[here-there-were-dragons]

judging by the "fixes" they've applied to fern and i'm fairly sure also to a few other genes, they likely intend to flatten and generic-ify EVERY gene that does anything interesting with especially the top feathers portion of the wings. :/

[o-craven-canto]

Increasing complexity in evolution

Over the history of life there have been many occasions in which new complex systems developed from earlier, simpler ones, leading to explosion in diversity as the new system fills niches that it can exploit better than the old. Some examples are the formation of the first prokaryotic cells from looser collections of genes and membranes, the origin of eukaryotic cells from prokaryotic ancestors, the development of sexual reproduction, the origin of multicellular animals and plants, and the appearance of animal colonies or societies and of complex symbiotic relations.

There are two main types of such complexity transitions, which can be labelled "egalitarian" and "fraternal".

Egalitarian transitions involve the union and cooperation of entities with different origins and abilities. Examples are the combination of self-replicating genes into the coherent genomes of the earliest cells; bacteria and archaea coming together to form eukaryotic cells with mitochondria and sometimes chloroplasts; the origin of societies with non-kin members; mutualist symbiosis between different species, as in lichens; and possibly the union of partners in sexual reproduction.

The defining trait of an egalitarian transition is that the different units are genetically diverse, and therefore must all reproduce on their own: if they didn't all pass on their genes, they wouldn't stay part of the relationship. Even today, in our cells, mitochondria replicate independently of the nucleus. That also means the different units are in competition with each other.

Sure, in the long term cooperation may be best for all: the main driver of egalitarian transitions is cooperation between elements with different "skills", such as the photosynthesis of algae and the talent for nutrient mining of fungi in lichens. But evolution doesn't really do "long term". If an element can replicate itself more by mooching off the others, the mooching variant will become more numerous than the self-effacing variant.

Therefore, the way these transitions occur is by enforcing mutual dependence, for example by enclosure and by synchronized reproduction. When proto-genes were first enclosed by proto-membranes to form proto-cells, they were all in the same boat: any cheater mutant would quickly destroy itself by destroying its own sustainance. Parasites often become beneficial symbionts when they cannot easily jump to a new host, and viruses may become less deadly over time.

The interdependence can be enforced further by exchanging genes: mitochondria and chloroplasts turned over many essential genes to the nucleus of their host cell, and though they can reproduce on their own, they cannot survive for long. Also, mitochondria are only ever passed by the mother's eggs, not by the father's sperm, preventing the zygote from becoming a battleground (in algae, mitochondria always come from one parent, and chloroplasts from the other).

When all goes well, the result of an egalitarian transition is a cell or a society, or a small ecosystem built from cooperating interdependent parts that function as a whole.

In fraternal transitions, in contrast, the units all share the same origin and nature. Examples are the evolution of clonal colonies (e.g. of trees or coral polyps), eusocial colonies (think ants, bees, or naked mole rats), and the origin of animals, plants, and fungi with multicellular bodies. The main benefit here is not complementary skills, but economy of scale: when mole rats dig for tubers, they gain more by sharing the rare but abundant finds than by each digging on their own (and going hungry most of the time).

One major difference from the other type is that all the members of the greater unit are genetically identical, or nearly so: therefore, they do not all need to reproduce (from the POV of my genes, it makes no difference at all whether I or my identical twin have children: any gene I have, they will pass on just as well). Indeed, the disposability of most elements is a selling point of this kind of transition.

But you know who cannot say the same? Cheater mutants -- cancer, if you will. Any cancerous mutation, by virtue of being new, cannot count on being transmitted by other units, and benefits from replicating itself on expense of other genes. The uniform terrain will give it plenty of fertile soil.

An excellent way to put a stop to that is to limit reproduction to few units: think of the egg and sperm cells of animals, or ant queens. First of all, these segregated reproductive units can be kept in conditions that favor a low mutation rate, for example slow metabolism and protection from light. Most importantly, they put a bottleneck through which all mutations must pass: if a cancerous mutation occurs in (say) digestive tissue, that's regrettable, but it won't be passed down to the offspring; but if it happens in the germinal line, well, the new offspring will be entirely composed of cancerous cells, and the bad mutation once again destroys itself. Reproductive segregation resets genetic uniformity in each generation.

Genetic uniformity does not mean morphological or functional uniformity: thanks to contextual gene activation, the cells in your brain, bones, liver, and heart all have the exact same genes, but very different structures and functions. When all goes well, fraternal transitions may end with the constituent units specializing for different functions, taking on some of the advantage of the egalitarian transition, while still keeping genetic diversity as low as possible.

And that's how you go from bacteria to humanity, more or less.