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Author Topic: Creature color genetics experimentation  (Read 10196 times)

DeKaFu

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Creature color genetics experimentation
« on: June 10, 2016, 08:06:04 pm »

Alright, so...
I was recently working on a personal mod to improve coat colors and patterns in dogs and cats, and found myself with some questions about how genetics are handled in DF. After much searching on the forum and elsewhere, I wasn't able to turn up much information. There has been some experimentation looking at attributes and body size, but very little about how hair or skin color is handled. Possibly because it's completely useless outside of flavor, but I think it's fun. :P

Anyway, to remedy this I decided to embark on some experimentation myself.
(I'm putting this here because animal breeding pertains to Fort mode, but it can be moved if people think it is better suited to DF General or Modding.)

So, here is what Toady has said about color genetics:

Quote from: Toady One, DF Talk #8
  Then all of the colours, like eye colours, hair colour, I think that uses a dominant/recessive thing now where you pass on two copies and then it picks probably the colour with the lowest index; maybe there's an alphabetic bias right now on which genes are dominant, or it might be the first you listed, it could be the first one you list in the raws that's the dominant gene.

…It kind of sounds like not even Toady's entirely sure on the details, but that gives us a good place to start from. With that in mind...

GOALS:

1. See if genetic inheritance of tissue layer/body part coloration actually happens.
This seems like a given, but you can never assume everything is working as stated in Dwarf Fortress. It's not impossible that the features on animal offspring are generated randomly or taken from an existing population somehow.

2. Verify whether or not creatures actually carry two different copies of a gene.
In which case the dominant copy would be expressed, and the recessive one would be hidden. Before I looked into it, I was under the impression that DF probably used a very simple system where it just picked either the color of the mother or father at random to pass on. According to that quote, it might be more complicated. Let's find out!

3. Check whether color dominance is based on the order of options listed in the creature's raw file, or the order in the color raw file (which would make it alphabetical).
Just because the quote was a little ambiguous. For most vanilla creatures, it comes out about the same because the options are listed alphabetically in the creature raws. But it's useful information for anyone who wants to modify things!

EXPERIMENTAL SETUP

For greater control and consistency, I created a custom creature to do my testing with:
Spoiler: Here is the raw file (click to show/hide)
It's a modified mongoose that can be brought on embark and always gives birth to 10 babies at a time. Its body parts and tissues are all default, I only changed the color options and descriptive names. Name starts with z for easy access on huge lists.

It has three features that come in different colors:

Fur that comes in white, ivory, or cream.
Stripes that come in red, sky blue, purple, or black.
Eyes that are usually black, but have a rare 1:10 chance of being golden yellow.

Assuming the non-alphabetical model is correct, the order of dominance should be:

Fur: WHITE > IVORY > CREAM
Stripes: RED > SKY BLUE > PURPLE > BLACK
Eyes: GOLDEN YELLOW > BLACK

I used Arena mode for my testing. If you put a mating pair of creatures on the same team in Arena mode, they will eventually breed and produce babies. The only catch is that all the babies are born on separate teams from the parents and each other, so un-pausing results in an instant bloodbath. No second generation testing, sadly.

Testing was done by setting the game to pause when it announced an animal giving birth. I opened up five instances of the game in Arena mode, and in each one placed one male and one female Zangoose in the enclosed central ring. Then I went and had lunch. When I came back, the games had paused and I was able to open up the unit lists and record the color-features of all of the offspring. One of the five pairs decided not to play ball on the romance game (c'est la vie), but the other four worked out perfectly.

RESULTS

Posting these as code tables to keep the formatting. I hope they're readable enough.

Code: [Select]
Pair #1
M/F | Fur Stripes Eyes
--------------------------------------------------------------
Father M ivory sky-blue black
Mother F ivory red black
--------------------------------------------------------------
Pups:

#1 F ivory sky-blue black
#2 F ivory sky-blue black
#3 F cream sky-blue black
#4 M cream red black
#5 F ivory red black
#6 F ivory red black
#7 F ivory sky-blue black
#8 M ivory sky-blue black
#9 M ivory sky-blue black
#10 M cream sky-blue black

Awesome results right out of the gate!
First of all, we can tell right away these results aren't random. They are definitely inheriting colors from their parents.
After that, the fur color is the main thing to look at here. The next thing we can rule out is the game simply picking a color from mom or dad, because we have two ivory parents producing three cream-colored babies. Based on that, we can assume each parent actually carries two separate copies of each gene and picks one at random to pass to the offspring, so we are indeed looking at some form of Mendelian inheritance here.
Thirdly, in order for the cream coloration to show up in the offspring but not the parents, it would need to be recessive to ivory and therefore hidden in the parents. Which in turn means we can throw out the alphabetical dominance theory because that would require cream (early alphabet) to be dominant to ivory (later alphabet). Yay!

So that's most of my questions answered already, but let's keep going...
In order to see cream from two ivory parents, they would have to both be carrying one copy of the ivory gene and one copy of the cream gene (IC IC). If you plug that into a classic Punnet square, you'd see that it would predict 75% ivory offspring and 25% cream offspring (25% II, 50% IC and 25% CC). Which is… Pretty much exactly what we got. It works!

We can also deduce that the parents have all black-eye genes, which isn't surprising based on how rare golden yellow is.

Code: [Select]
Pair #2
M/F | Fur Stripes Eyes
--------------------------------------------------------------
Father M white purple black
Mother F white red black
--------------------------------------------------------------
Pups:

#1 F white black black
#2 F white black black
#3 F ivory red black
#4 F white black black
#5 F white red black
#6 F white red black
#7 F white purple black
#8 M ivory black black
#9 M white red black
#10 M white red black

So, we've pretty much determined the model, but this is still interesting.
Parents with red stripes and purple stripes produced a mix of red-, purple-, and black-striped babies.  Black stripes are the most recessive possible stripes, which means both parents must be carrying black stripe genes, meaning dad is carrying purple and black (PB) and mom is carrying red and black (RB). That means the Punnet square prediction would be 50% red (RB), 25% black (BB) and 25% purple (PB). It ended up being 50%, 40%, and 10% respectively, but given the sample size that's still pretty close.

Code: [Select]
Pair #3
M/F | Fur Stripes Eyes
--------------------------------------------------------------
Father M white sky-blue golden-yellow
Mother F white purple black
--------------------------------------------------------------
Pups:

#1 F white sky-blue golden-yellow
#2 M white sky-blue golden-yellow
#3 F white sky-blue black
#4 M white sky-blue black
#5 F ivory purple black
#6 M white purple golden-yellow
#7 M white purple black
#8 F white sky-blue black
#9 M white purple black
#10 M white sky-blue black

Yay! Golden-yellow eyes!
Not a lot to say here, really. Dad is carrying one golden-eye and one black eye gene, and mom has two black eyes (ouch). That gives us a predicted ratio of 50% golden and 50% black, which... it's close enough. In terms of the fur, the one ivory girl shows that one of the parents is carrying a hidden ivory gene, and the other has either a hidden ivory or cream. If they had produced a litter containing only the nine white ones, it would've been easy to mistakenly assume they had only white genes. This is why big litters are good for testing!
Code: [Select]
Pair #4
M/F | Fur Stripes Eyes
--------------------------------------------------------------
Father M white red golden-yellow
Mother F ivory sky-blue golden-yellow
--------------------------------------------------------------
Pups:

#1 M white red golden-yellow
#2 M ivory red golden-yellow
#3 M ivory sky-blue black
#4 F white sky-blue golden-yellow
#5 M white red golden-yellow
#6 F white sky-blue golden-yellow
#7 M ivory red golden-yellow
#8 F white sky-blue black
#9 M ivory red golden-yellow
#10 F white red golden-yellow

Last one. I was really surprised to get two golden-eyes in one pair. Doesn't really tell us anything new, though if you had any lingering concerns that baby colors might be chosen randomly based on their rarity in the raws, this 80% golden-eyed litter should put that to rest.

CONCLUSIONS

I might have gotten a little carried away, but after all that I can state pretty definitively that:

YES, DF models a simple form of genetics.

For any given individual creature, for each body part or tissue that can have a range of colors, DF stores two (potentially different) color genes. When you check its description, what you see is the color for the more dominant of the two. Dominance is determined by the order the potential colors are listed in that creature's raw, with the first being most dominant in the last being most recessive. When two creatures breed, it randomly selects one of the two color genes from each parent and passes them to the offspring. This appears to be done separately for each color-defined body part in a given child (that is, hair color is determined entirely separately from skin color, etc.)


It would be awesome if people could do some more testing, especially second-generation testing after figuring out the genes of the parents. I'm not currently equipped to play fortress mode, so that's a bigger project I can't really tackle. I also don't use any third-party programs, but someone who does might be able to look into things more deeply. Anyone is welcome to use my creature or methods and expand on it.
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steel jackal

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Re: Creature color genetics experimentation
« Reply #1 on: June 11, 2016, 12:36:39 pm »

amazing work, its kinda cool that DF is a game where the players know more about it than the guy who actually makes it


one thing though, i get how the red stripes and blue are to be for normal and shiny zangoose, but where does the black stripe come from?
i can figure that purple would be from red and blue mixing, but black seems to be the odd one out
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milo christiansen

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Re: Creature color genetics experimentation
« Reply #2 on: June 11, 2016, 12:39:16 pm »

Clear and well written, good work!

AFAIK it would be possible to do more detailed research by looking at how the genetic information is stored (via DFHack), that could produce some more interesting data to add to your collection.

one thing though, i get how the red stripes and blue are to be for normal and shiny zangoose, but where does the black stripe come from?
i can figure that purple would be from red and blue mixing, but black seems to be the odd one out

The colors are not obtained from mixing, but from gene expression, go read up on genetics and try again.
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steel jackal

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Re: Creature color genetics experimentation
« Reply #3 on: June 11, 2016, 12:49:09 pm »

Clear and well written, good work!

AFAIK it would be possible to do more detailed research by looking at how the genetic information is stored (via DFHack), that could produce some more interesting data to add to your collection.

one thing though, i get how the red stripes and blue are to be for normal and shiny zangoose, but where does the black stripe come from?
i can figure that purple would be from red and blue mixing, but black seems to be the odd one out

The colors are not obtained from mixing, but from gene expression, go read up on genetics and try again.

well ik that, im just saying that i can understand why he chose purple, but not black.

im well aware that there is a gene that says "blue" and one that says "red" and then whichever one is dominant is active, and if either both are dominant or both are recessive then its just random chance which trait shows up.
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PatrikLundell

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Re: Creature color genetics experimentation
« Reply #4 on: June 11, 2016, 05:18:19 pm »

Clear and well written, good work!

AFAIK it would be possible to do more detailed research by looking at how the genetic information is stored (via DFHack), that could produce some more interesting data to add to your collection.

one thing though, i get how the red stripes and blue are to be for normal and shiny zangoose, but where does the black stripe come from?
i can figure that purple would be from red and blue mixing, but black seems to be the odd one out

The colors are not obtained from mixing, but from gene expression, go read up on genetics and try again.
Well, as far as I understand real world genetics use both the dominant/recessive model, as well as the additive one. I think skin color(!) among humans is mainly controlled by 4 genes that follows the additive method, so if both copies of all of them are full dark, you'll get a kid who's as dark as they get, while if all of them are full pale the kid becomes as pale as they get, while the ones with mixtures end up along a scale between these extremes (there aren't just two alleles of these genes, of course, and the strength of the genes on this trait differ as well). As a result, two mixed heritage parents occasionally get kids whose parentage can get challenged because their color differs significantly from both of their "middle of the road" looking parents.
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Dunamisdeos

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Re: Creature color genetics experimentation
« Reply #5 on: June 11, 2016, 06:29:43 pm »

For second-generation testing, couldn't you turn off combat in the arena? I recall there being an option to set everything to friendly or something.
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crazyabe

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Re: Creature color genetics experimentation
« Reply #6 on: June 11, 2016, 06:49:56 pm »

PTW
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DeKaFu

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Re: Creature color genetics experimentation
« Reply #7 on: June 11, 2016, 07:30:11 pm »

For second-generation testing, couldn't you turn off combat in the arena? I recall there being an option to set everything to friendly or something.

I don't think you can turn off combat, but you can adjust the conflict level so that they use the "sparring"-type combat and avoid injuring each other. I've been setting it to "Encounter" and using that as a failsafe to keep parents from killing their offspring if I accidentally unpause.

Also, I discovered today that even if a breeding pair are hostile to each other (that is, independent or on different teams), they WILL breed and give birth even though they've spent their entire existence locked in combat. So second-generation testing should be possible after all.

That said, it looks like DF probably doesn't allow direct inbreeding (sibling-sibling or sibling-parent) so it'll require a lot of micromanagement (and some editing of the arena map) to do it in a controlled fashion. Need to have two breeding pairs that are kept separate until they breed and then somehow kill off all first-generation offspring except a single male and one-or-more females before letting them meet, or else there's no simple way to track the parentage.
 
Anyway, I'm currently looking into what happens when colors are defined separately for males and females. I think the only animals which have that situation in vanilla DF are peacocks (blue males and brown females) and maybe a couple other birds, but they only have one color option for each sex. Once you add more, it's a complete mystery how it works. One of the things I wanted to do when I started was add a calico pattern to cats that could only show up in females, but I had no idea how the system would handle that. So: Science!
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steel jackal

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Re: Creature color genetics experimentation
« Reply #8 on: June 11, 2016, 08:07:49 pm »

For second-generation testing, couldn't you turn off combat in the arena? I recall there being an option to set everything to friendly or something.

I don't think you can turn off combat, but you can adjust the conflict level so that they use the "sparring"-type combat and avoid injuring each other. I've been setting it to "Encounter" and using that as a failsafe to keep parents from killing their offspring if I accidentally unpause.

Also, I discovered today that even if a breeding pair are hostile to each other (that is, independent or on different teams), they WILL breed and give birth even though they've spent their entire existence locked in combat. So second-generation testing should be possible after all.

That said, it looks like DF probably doesn't allow direct inbreeding (sibling-sibling or sibling-parent) so it'll require a lot of micromanagement (and some editing of the arena map) to do it in a controlled fashion. Need to have two breeding pairs that are kept separate until they breed and then somehow kill off all first-generation offspring except a single male and one-or-more females before letting them meet, or else there's no simple way to track the parentage.
 
Anyway, I'm currently looking into what happens when colors are defined separately for males and females. I think the only animals which have that situation in vanilla DF are peacocks (blue males and brown females) and maybe a couple other birds, but they only have one color option for each sex. Once you add more, it's a complete mystery how it works. One of the things I wanted to do when I started was add a calico pattern to cats that could only show up in females, but I had no idea how the system would handle that. So: Science!

would it be possible to use the caste system and give the calico pattern as a caste specific trait?
female dwarves dont have beards, but it can be modded in by altering their caste to have the beard tag, perhaps you could replicate gender specific castes in cats
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BlackBronze

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Re: Creature color genetics experimentation
« Reply #9 on: June 12, 2016, 01:05:54 pm »

This is a great article! I love reading forum pages about the *Science* of DF. They're always the best.  :D

I also always wanted to set up a breeding program in order to the best looking pet, but my forts would always die before I'd reach that point..

speaking of which, what are some animals that have a HUGE variety of fur genes? I've been looking through the raws of many furry animals, and the majority of them just have ONE possible fur and eye color, and about ten possible skin colors.
« Last Edit: June 12, 2016, 03:18:28 pm by BlackBronze »
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DeKaFu

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Re: Creature color genetics experimentation
« Reply #10 on: June 12, 2016, 04:55:12 pm »

Alright, experimentation on sex-linked color genes continues, but in the meantime I figured I would post the setup I've worked out for second-generation testing in the arena. It is straightforward and repeatable, though pretty time-consuming. It could potentially be useful for checking the heritability of stuff like attributes as well.

Setup:

The first thing I did was remove the [SWIMS_INNATE] tag from the creature's raw, for reasons that will become apparent.

The second thing was to slightly edit the arena layout in arena.txt. I added a 3-square-thick moat of water bisecting the circle in the center of the arena. I also have announcements.txt set up to pause the game whenever an animal gives birth, which is important if you want to record the children's stats before they die.


Running the experiment:

Upon starting up arena mode, make sure to set the conflict level to Encounter. This is important to keep everything past the first generation from murdering each other.

You place one breeding pair in the top half, and the second breeding pair in the bottom half of the circle. Make sure they're set to be on the same team!



The moat keeps the two populations from interacting with each other, so they can only breed with the critters on their own side. The next phase is just a waiting game until one of the pairs gives birth. The game pauses, and at this point I record the stats for the parents and offspring. After this, the next task is to kill off both the parents and all but one of the offspring, who we'll use as one of the parents in the second round of breeding.

Luckily, the moat has a handy secondary function!



As soon as you unpause the game, the parents and children instantly begin a sparring free-for-all. Because the conflict level is set to Encounter, their attacks only "lightly tap" the target, but they hop and dodge around like crazy. The end result is that all but one of them very quickly throw themselves into the moat and drown. It only takes a few seconds. No mess, no fuss, just a moat full of dead bodies! And no risk of injury to the survivor!

So this should leave you with one child left on that half of the chamber. You can check its stats and gender and decide whether it's a good candidate. What I did here was to make a save before un-pausing after the parents gives birth, before they started fighting, so that if I didn't like the survivor (or one of the parents survived instead of a child) I could keep reloading until I got one that I liked.

After this you just wait for the breeding pair on the other side of the moat to give birth and repeat the entire process. Make sure the second surviving child is the opposite gender from the first.



After this you're stuck waiting for an in-game year to pass so the children can grow into adults. They can't breed as children, and removing the [CHILD] tag to make them born as adults is a bad idea for reasons I'll get to shortly.

Once you have an adult male and female, the final big step is removing the moat so that they can finally meet and produce your long-awaited third-generation babies. This is accomplished by using k -> l to place magma over each of the 39 water squares of the moat. When you un-pause, the moat will be converted entirely into obsidian floor.



The pair will be locked in eternal touch-tag combat with each other, but that won't stop them from breeding. At this point, it's just a matter of sitting back, waiting, and hoping to hell they aren't gay. :P



Finally, I discovered the hard way today that I was wrong about DF preventing inbreeding.

It turns out that creatures can and will mate and produce offspring with direct siblings.

I had the bright idea of removing the [CHILD] tag from my test creatures so that I wouldn't have to sit around waiting for them to grow up. This led to slightly disappointing results on my first successful third-generation litter when I realized that the female had not mated with the intended male, but instead with one of her brothers during the few seconds before they jumped in the moat. (Her brothers had golden-eye genes and the intended father did not.)

This means that if you set your creatures to be born as adults, when a female gives birth the father could be any one of her male siblings. Without knowing who the father is, you can't really learn anything from the results. Annoying, but that's how it is.


This is a great article! I love reading forum pages about the *Science* of DF. They're always the best.  :D

I also always wanted to set up a breeding program in order to the best looking pet, but my forts would always die before I'd reach that point..

speaking of which, what are some animals that have a HUGE variety of fur genes? I've been looking through the raws of many furry animals, and the majority of them just have ONE possible fur and eye color, and about ten possible skin colors.
The majority of pets and domestic animals in the game have a ton of color variation. A bit too much, IMO (which is why I was modding it ;)). The standard seems to be the same 43 potential hair colors for cats, dogs, horses, mules, donkeys, cows, pigs, goats... practically all the non-bird species you can bring on embark. It's a bit unrealistic, but at least there's a lot of potential variation.
In the case of dogs and cats, each one of their ears, paws, tail, head etc. has its own set of color genes so it's challenging to breed one that's not a bit of a multicolored patchwork mess.
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gentgeen

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Re: Creature color genetics experimentation
« Reply #11 on: June 12, 2016, 05:12:48 pm »

Dogs.
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Dirst

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Re: Creature color genetics experimentation
« Reply #12 on: June 12, 2016, 09:13:56 pm »

Anyway, I'm currently looking into what happens when colors are defined separately for males and females. I think the only animals which have that situation in vanilla DF are peacocks (blue males and brown females) and maybe a couple other birds, but they only have one color option for each sex. Once you add more, it's a complete mystery how it works. One of the things I wanted to do when I started was add a calico pattern to cats that could only show up in females, but I had no idea how the system would handle that. So: Science!
Nice science!

To save you some work, the Appearance Tweaks mod in my signature has gender-specific coloring for the wings of fairies and pixies.  You'll have to remove the vermin tags from them to get them in the arena, but they conveniently have overlapping color choices for the males and females.  This will help determine if there is really one set of genes or two.

The relevant part of the fairy is below (scroll to the right to see the differences):

   [CASTE:FEMALE]
      [FEMALE]
      [MULTIPLE_LITTER_RARE]
      [BABYNAME:fairy baby girl:fairy baby girls]
      [CHILDNAME:fairy girl:fairy girls]
      [SET_TL_GROUP:BY_CATEGORY:WING:CHITIN]
         [TL_COLOR_MODIFIER:SPOTS_WHITE_SILVER:2:SPOTS_WHITE_PERIWINKLE:2:SPOTS_WHITE_PEARL:2:STRIPES_WHITE_SILVER:2:STRIPES_WHITE_PERIWINKLE:2:STRIPES_WHITE_PEARL:2:SPOTS_SILVER_PALE_PINK:1:SPOTS_SILVER_PINK:1:SPOTS_WHITE_PALE_PINK:1:SPOTS_WHITE_PINK:1:STRIPES_SILVER_PALE_PINK:1:STRIPES_SILVER_PINK:1:STRIPES_WHITE_PALE_PINK:1:STRIPES_WHITE_PINK:1:PERIWINKLE:1:PEARL:1:SILVER:1:WHITE:1:PINK:1:PALE_PINK:1]
            [TLCM_NOUN:lacy wings:PLURAL]
   [CASTE:MALE]
      [MALE]
      [BABYNAME:fairy baby boy:fairy baby boys]
      [CHILDNAME:fairy boy:fairy boys]
      [SET_BP_GROUP:BY_TYPE:LOWERBODY][BP_ADD_TYPE:GELDABLE]
      [BODY_DETAIL_PLAN:FACIAL_HAIR_TISSUE_LAYERS]
      [SET_TL_GROUP:BY_CATEGORY:WING:CHITIN]
         [TL_COLOR_MODIFIER:SPOTS_WHITE_SILVER:2:SPOTS_WHITE_PERIWINKLE:2:SPOTS_WHITE_PEARL:2:STRIPES_WHITE_SILVER:2:STRIPES_WHITE_PERIWINKLE:2:STRIPES_WHITE_PEARL:2:SPOTS_SILVER_PALE_BLUE:1:SPOTS_SILVER_LIGHT_BLUE:1:SPOTS_WHITE_PALE_BLUE:1:SPOTS_WHITE_LIGHT_BLUE:1:STRIPES_SILVER_PALE_BLUE:1:STRIPES_SILVER_LIGHT_BLUE:1:STRIPES_WHITE_PALE_BLUE:1:STRIPES_WHITE_LIGHT_BLUE:1:PERIWINKLE:1:PEARL:1:SILVER:1:WHITE:1:LIGHT_BLUE:1:PALE_BLUE:1]
            [TLCM_NOUN:lacy wings:PLURAL]

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Fleeting Frames

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Re: Creature color genetics experimentation
« Reply #13 on: June 12, 2016, 09:21:01 pm »

Your science certainly adds convenience to livestock breeding. Would I be correct to assume that there isn't anything barring parent-child relationships either? (This would be very convenient for things born adults like demons and thus not differentiable at glance - all one would have to do is to ensure one female who met a male once remains in the litter output system.)

PatrikLundell

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Re: Creature color genetics experimentation
« Reply #14 on: June 13, 2016, 03:22:46 am »

Animals have no restrictions on breeding. If you keep a breeder GCS pair and immediately order the offspring to be hauled off to cages you'll nevertheless find the female (caged) offspring giving birth a while later, so the father or a brother have impregnated them virtually immediately.
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