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how flowers spread

I am not 100% sure on this. The guides I've read all subtly conflict, and I haven't read any code, so this is based on intuition from playing the game and also being a programmer for over 20 years. I believe the algorithm is as follows.

For every flower on your island:

  1. If it isn't fully-grown, grow by one stage.
  2. If it hasn't been watered, give up and move on to the next flower.
  3. Roll reproduction chance (see below). If it fails, give up and move on to the next flower.
  4. Mark this flower as “inactive”.
  5. Make a list of all the neighboring empty cells (up to 8). If there aren't any, give up and move on to the next flower.
  6. Pick one of those cells at random. This is the “target cell” and where a new flower will go.
  7. Make a list of active flowers of our same species that neighbor the target cell (up to 7, because we're a neighbor and we're already inactive).
  8. If there aren't any, put an exact duplicate of this flower into the target cell.
  9. Otherwise, pick one at random; this will be our breeding partner. Mark it as inactive as well, combine our genes at random, and put our offspring into the target cell.

A flower's reproduction chance starts out at 5%, but can be increased two ways.

Every flower keeps track of how many nights have passed that it had been watered but did not reproduce, even if it wasn't fully grown. (This is the devs' way of smoothing out the RNG — repeated failures increase the chance of success.) Starting from night 4, every night increases the reproduction chance by 5%, up to a maximum increase of 85%, or a total maximum of 90%. (In other words, 5% × mid(n - 3, 0, 17).) The counter resets to zero when the flower reproduces, or when it's dug up. The nights don't need to be consecutive.

There's also a bonus for every visitor (a human player from another island on another Switch) who waters a flower. Sources vary, but generally agree that it's around 15% per visitor, up to a maximum of five visitors. This bonus is reset overnight or when the flower is dug up.

Numbers come courtesy of aeter.

some takeaways from that

If my understanding is correct, then the following are true.

In an arrangement like yellow rose red rose yellow rose, it's possible for the two yellow roses to breed — each one has a 2 in 7 chance of targeting a tile adjacent to the red rose, and then a 1 in 2 chance of picking the other yellow rose as the other parent.

Cloning produces new flowers twice as fast as breeding. Breeding rolls once, produces one child, and marks two flowers inactive; but cloning rolls once, produces one child, and marks only one flower inactive.

Flowerbeds are very sensitive to layout; if a flower wants to reproduce but all its possible neighbors have already bred with someone else, it'll clone instead.

how genes work

If you forget everything from 9th grade biology class (then I hope you're not on Twitter telling people how chromosomes work), here's a recap:

Flowers have 4 genes: red, yellow, white, and... "brightness", I guess. The first three are a rough measure of how much of that color is in the flower, and the fourth is a goofy thing only used by roses that controls how much impact the red gene has.

Each gene is represented by two alleles, essentially either "on" or "off". Traditionally, a capital letter is used for "on" and a lowercase for "off", so the red gene might either be RR, Rr, or rr. (rR is the same as Rr, since order doesn't matter.)

When two flowers breed, they each donate one random allele from each gene to the child. So if the parents are RR and rr, the child can only ever be Rr. If the parents are RR and Rr, the child has equal chances of being RR or Rr. If the parents are both Rr, the child could be any of RR (25%), rr (25%), or Rr (50%, because it could happen two ways).

The full set of alleles a flower has is called its genotype, and each flower species has its own table of what genotypes correspond to which colors, or phenotypes. That table is below.

The variation and "memory" of ancestors' genes can lead to a lot of surprises, like colors resurfacing after many generations, which adds a lot of fun to the game! But you're just here so you can crank out one of each color, so, feel free to use the tabs above to find out how to do that.

all phenotypes

Each flower's tab also has an "exploded" Punnett square at the bottom.

Sorry, this table is slightly broken at the moment and I'm too tired to fix it.