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How can a highly advanced sub-luminal galactic empire minimise the effects of speciation?

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The Humern Empire (no relation) spans the galaxy, using a variety of methods to move from place to place and planet to planet.

One thing all of their modes of transport share is that they are not faster than light, and as such they have large temporal dilation effects associated with them. The most advanced form of transport, the Tube network, only takes five minutes to move a traveler (from the point of view of the traveler) what may be decades of travel at light speed.

One of the issues with this is that multiple generations may be born, live and die in the time it takes someone from the other side of the Empire to visit, which raises the possibility that different sections of the Empire will become incapable of interbreeding, essentially splitting off into different species of Humern.

The Empire is a very effective governing body, comprising many levels of civil servants in order to keep the Empire cohesive: their populace remains loyal to the Empire and rebellion is practically unthinkable. They have access to very advanced technologies, but they cannot breach the speed limit of the universe no matter how hard they try.

Given that it may take hundreds of thousands of years (from the point of view of the galaxy) for a representative of the Empire (or even a message) to get from one side of the Empire to the other, how can they account for and minimise the effects of speciation in their populace?

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This post was sourced from https://worldbuilding.stackexchange.com/q/94227. It is licensed under CC BY-SA 3.0.

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One possible solution, is that your species have abandoned sexual reproduction entirely in favour of reproducing clonally. They are all derived from a database of genomes that were at some point in the past deemed to be the most satisfactory, and since then new individuals have been gestated in artificial wombs using only these chosen genomes.

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