What to bring on a Generation Ship/Fleet

[Varyon]

Still working on my Harpyia setting, and now I need to determine what Earth species the colonists would have brought with them. The colonists were working under the assumption that the initial planet being colonized would have life, but not that it would necessarily be compatible with Earth life, so they needed to bring enough to basically create an Earthlike biome at the destination planet.

As things worked out, it turned out the initial colonized planet, and those they colonized later after working out how to travel through hyperspace, had extremely simplistic organisms, which were rapidly outcompeted and replaced by the life they brought with them. As there won't be any alien plants or critters to deal with, this means I need to determine the flora and fauna the humans brought with them.

The civilization that produced the generation fleet was mostly TL8, with a few superscience technologies (primarily for our purposes, superscience energy capacitors and reaction drives with impossible delta-v's). As part of the plot has the (immortal) survivor of a nuclear incident (which killed everyone else, and cause the fleet to abandon the ship and let it drift away, as it was too irradiated to safely salvage) aboard one of the ships basically creating an "alien" race, I've decided they were advanced in biology, enough to be able to create exowombs/growth tanks. So, some of the animal species wouldn't need to have been brought over and bred aboard the ships, but could instead have been transported as fetuses (or just gametes) in cold storage, to be grown upon arrival.

I'm primarily interested in the animal species, although some ideas of the plants would be useful. I'm assuming that while on board the ship, they probably would have been growing primarily rice and/or maize (probably genetically modified strains that avoid deficiencies), with some other crops (and non-crop but still CO2-recycling plants) for variety. For animals, while cattle are certainly going to be present in the colonies, they take up too much space, so would be grown in exowombs later. So, for meat, there are probably fisheries, chickens (also useful for eggs), pigs, and either sheep or goats (both of which also produce milk, of course), the last depending on which would be more amenable to being raised in the confines of a spaceship. I'd also expect the colonists (and their children, and so forth - it's a 500 year journey) to have pets while en-route for companionship, so a sizable dog and possibly cat population would also make sense. What sort of insects would likely be brought, on purpose or by accident? What about larger stowaway animals - I could see rats and mice being on board (this would also give the cats a more utilitarian role)? Later generation ships, which make the journey in only 100 years, may also bring more exotic animals with them, but I'm mostly interested in what the original fleet would have brought.

Since that's a bit rambling, here's my primary questions. Given the above assumptions (500 year journey, large fleet rather than single ship, exowomb availability, needing to create an Earth-like biome on a planet with an agreeable atmosphere but no real complex lifeforms to compete with or rely on), what flora and fauna would the generation fleet have likely brought with them, and which of these would have been present during the trip over, rather than basically just being in "cold storage?"