Getting a handle on genetics.

[Gregg]

Dear Rich, Kathy, Serpwidgets, et al....

Morning Tea time: and I'm in front of my computer, again. Faced with a day full of work, but I choose instead to get a grip on this issue of genetics. Anything to postpone the inevitable.

I am aware of the myriad problems my approach might have when actually applied to the nature of genes and genetic influences/variables/trips/falls/attractions/and so forth; but all I'm after is a clearer understanding of this "1 in 4, 27 in 64, 3 in 16" sort of thing.

I'm using as my example two snakes I got from Kathy recently: 1.1 Normals, het. for amel/lav/motley. Right, triple hets. We're going to be up in the $64,000.00 question area.

According to Mick's CPP, I should get .... Well, you know.

So, what I did was cut out 64, 1/2" x 3/4" pieces of paper and made sure that I had 27 marked N; 9 others were marked L; 9 more were marked A, and 9 more were marked Mot. 3 pieces of paper were marked L/mot; 3 more were marked A/Lav, and 3 more were marked A/Mot. Lastly, 1 piece of paper was marked A/Lav/Mot. I then put all of these little bits of paper into a box with a lid. (I'm sure the world of genetic scrambling is far more vast and complicated, but for my purposes, my gene scrambler was 4-7/8" square and 2-1/2" deep cardboard lavender bath soap box with a lid.)

Okay, all the paper bits are in the box. I shake. Open the lid and draw out a piece without looking. It's an A--for amelanistic. Now, I put that piece of paper back into the box. Shake. Draw. This time I get Mot. I put that piece back into the box. (My understanding is that what is drawn never leaves the realm of possibilities, right?)

I repeat this proceedure six more times--a total of 8 draws in all.
Why 8? It's based on the assumption that I have had the perfect clutch of 16 eggs. However, for various reasons, half have died before three months have passed--I don't know; I've never had a snake that laid eggs, so I couldn't tell you how close I am to real Life. I did this "experiement" twice--too much work to do besides this, but hey....

Here are my results.

1st Run:

1) A
2) Mot
3) N
4) Mot
5) N
6) L/Mot
7) Mot
8) A

2nd Run:

1) A
2) N
3) A/Lav
4) L
5) N
6) A/Mot
7) Mot
8) Mot

Now, my question to you all is this: Am I way off base with this approach? Or am I close to understanding the 27/64, 1/4, 3/16 genetic possibility statements I see?

 

[Kat]

Sounds like you're getting a good idea of how these things work. The draw of what genes show up is random. The odds that an individual snake will have a specific combination of genes are what the progeny predictor outputs.

Even if the odds say that statistically you should get 50% of some morph, the odds of you getting exactly 50% of some morph are slim. All statistics are are averages. Too many people see the numbers and figure that they're guaranteed those ratios.

Your slips of paper in the hat are far more realistic to the way it happens than most people's conceptions. Of course, there are always other things which can influence outcomes... like linked traits. Linked traits can skew the odds in favor or against certain outcomes. IIRC Serpwidgets had the whole linked-trait explaination written up at some point or another... I could try to explain it, but odds are I'd forget something in the process. Plus I'm a tad lazy and don't want to type out the big huge explaination. Hopefully he has it saved somewhere and can repost it.

But to answer your question, yes... you have a better grasp on the predictability issue with the method you're using.

 

[Gregg]

Talk about having no life!

I guess the only computer game I play more than Solitaire is Mick's CPP. After so long, however, one gets bored even with this game, so I came up with the paper idea to pass the time. I was really curious if I was right on or not. My mind is analog, not digital. The paper approach helps me see genetics in a 3D verses virtual-reality mode. Thank you very much, Kat, for letting me know that I'm on the right track.

Now, back to my shaker.

"Come on Seven, Daddy needs a new pair of shoes!"

 

[Serpwidgets]

Linkage explanation...

Remember, animals have a number of chromosomes. In corns it's somthing like 18 pairs. Linkage happens when two genes (for different traits) are close enough on the same chromosome. What happens is when sperm and egg are being produced (a form of cell division called meiosis) is that the chromosomes are actually cut into pieces.

Take half a deck of cards and line up the spades from Ace through King. Beside that, do the same with the Hearts. This is the two copies of chromosome 1 in the father, for example. Each card is one locus on the chromosome.

Remember, each parent passes down only one of these two copies. When the father passes down a copy of "chromosome 1" it is not always going to be all spades or all hearts. Instead, you could slice up the chromosomes (in the same place on both of them, in meiosis this is called a "crossover") say at the sixes, and then switch them to make two mixed-color chromosomes.

So, if for example the amel gene is on chromosome 1 where the threes are, and the anery gene is on chromosome 1 where the fives are, and assuming that there's an average of one crossover on chromosome 1 per sperm cell being produced... how likely is any offspring from that animal to inherit a 3 and 5 of different colors? What you'll notice is that there are only two places (out of 12) where the chromosome can be cut that would separate those two and end up with differently-colored threes and fives.

The farther apart you move those two traits, the more likely they will be inherited independently.

This means that traits can be strongly linked or weakly linked or not linked, or anywhere in between. It also means (because a chromosome has a lot more slots in it) that two traits that are very strongly linked might in almost every instance act the same way as a simple trait.

So here's the fun question to keep you busy a little longer, hehe...

If amel and anery, for example, are linked, and those two loci inherit together 75% of the time: (In other words, only 25% of the time is that chromosome split up between those two cards)

What kind of results would you expect from breeding an anery to an amel, and then breeding those F1s together?

What kind of results will you expect from breeding a snow to a normal, and then breeding these F1s together?

(Those of you who know, don't give away the answers.)

 

[carol]

Hey Gregg, if you are going to go along with the soap box thing. what you need to do is this:
You need three separate boxes, one for lav, one for mot, and one for amel.
In each box put 2 normal genes and 2 morph genes belonging to that "box". You see each parent can put out two possibilities for each morph, morphed or normal.
After you have your boxes set up, draw TWO pieces of paper from each box, (one gene from each parent)
So for every "test hatchling" you would have to peices of paper from each box.
Then you can figure out what you have.
For instance, one drawing can get you a
NA, LL, NM
Lavendar het amel and motley
or
AA, NN, MM,
amel motley,
the possibilities are very vast with triple hets.
If you want to get even more complicated you could make a box for each morph for each parent, which would be more accurate, but I think in this case it works out the same. I'll have to think about that....AFTER I run the kid to school. lol

Ok, yes in this case it works out the same but you will need separate boxes for each morph of each parent if you are factoring in a trait that only one parent is displaying. For example if you bred an anery het mot to an amel het mot, you'd have six boxes.
For anery one box would have 2 An's one box would have two NN(normal)
Same for amel
And two motley boxes each with one N and one M.

Serpwidgets card trick is a lot easier, but I know once I start a project and start ripping up paper, it would bug me to no end to drop it with out making it work.
So between everyone who replies, hopefully you'll find one that speaks your language and you can understand.

 

[Gregg]

Re: Linkage explanation...

OUCH! I swore, when I left Graduate school, that I wasn't going to think this hard any more. Dad-gum you Serpwidgets, now I'm going to have to take an aspirin. (joking)

So here's the fun question to keep you busy a little longer, hehe...

If amel and anery, for example, are linked, and those two loci inherit together 75% of the time: (In other words, only 25% of the time is that chromosome split up between those two cards)

What kind of results would you expect from breeding an anery to an amel, and then breeding those F1s together?

What kind of results will you expect from breeding a snow to a normal, and then breeding these F1s together?

(Those of you who know, don't give away the answers.)

My guess would be: that the F1's from the first pairing and the F1's from the second pairing might be similar in their make-up of morph types, but not neccessarily identical. That is to say, most will be normal, het for snow; some will be simply normal; some will be anerythristic, or anerythristic/het. amelanistic; some will be amelanistic, or amelanistic/het. anerythristic; some will be normal/het. anerythristic, or normal/het. amelanistic; and you'll get the odd snow.

However, my point is this: all this is still a statistical probability, not a statistical actuality. I imagine that, within this statistical probability, the actual make-up of individual baby snake types one ends up with in a deli-dish is basically up to chance--like the wings of the butterfly that changes the weather.

I'll go back to my soap box to demonstrate.

F1's, 100% Heterozygous for Snow, according to Mick's CPP calculations, would theoretically produce: 4/16 normals, het for snow; 2/16 anerythristics, het for amel.; 2/16 amelanistics, het for anery; 2/16 normals, het for anery; 2/16 normals, het for amel; 1/16 would be a snow; 1/16 would be anerythristic; 1/16 would be amelanistic; and 1/16 would be normal.

That totals up to 16 pieces of paper I'll have to mark. Again, I'm going to assume that, for some reason, I only ended up with eight baby snakes out of sixteen eggs to raise to adults; so I'll only draw from the box eight times. Into the box they go. Shake-a-shake-a-shake, shake your booty! Draw one out: it's a Normal! Put that back into the box. Put the lid back on. Shake, shake--Shake-n-Bake; and I helped. Draw another out--Remember don't look! Anery, het for amel. Put that back into the box. To shorten this paragraph, here are my results:

1) Normal
2) Anery, het amel
3) Normal, het snow
4) Normal, het amel
5) Normal, het snow
6) Normal, het amel
7) Snow (Dang, what are the odds?)
8) Normal, het anery

If I were to do this again, I would be willing to bet that my list would be different. For my first clutch of eggs, then, I only got one snow. If I was wanting a snow, then I'd count myself as being lucky. The rest of the clutch I'll have to sale off somewhere, or go broke raising them.

 

[Gregg]

Hey Carol,

I'm going to have to think about your suggestion a little more in order to figure out if my mind is following you.

Brain over-load...

Must rest...

Does not compute...

Danger, Will Robinson!

 

[carol]

LOL, No doubt. I think I am going to post a sticker to my computer that says "do not operate with out consuming coffee". I just reread and saw that what you did was write down all the possibilties from the predictor and then draw. That is pretty much how it goes. As usual, I am on a different page/planet. I thought you were asking something else than you really were. Too much Jack D last night. At least it's Friday.

 

[Gregg]

Carol,

that Jack-in-the-Black'll give yo'r head a crack.

A long, long time ago, in seems like a past life ago, I hiked up Mt. Le Conte in the Great Smoky Mountains, along with a group of friends. We celebrated our successful ascent with champain and Jack-in-the-Black. I had brought along some Wild Turkey and Yukon Jack as well. At an elevation of around 9,000 feet this stuff hits pretty hard. I remember climbing into the top bunk that night, but when I woke up in the morning, I was underneath the cabin--in the dirt--looking up at the floor. Oooooh, and I hurt all over. I had a hell of a time trying to find a way out from underneath there. I must have found a small hole in the floor and fell through on my way to the out-house.



I hate admitting this, but mental exercises sometimes cause me to stare blankly into the distance for long periods of time--only to find myself waking with a, "Say what?" I guess I've got too many dead brain cells from all that Unrighteous living.

 

[Serpwidgets]

Re: Re: Linkage explanation...

If amel and anery, for example, are linked, and those two loci inherit together 75% of the time: (In other words, only 25% of the time is that chromosome split up between those two cards)

If they both inherit together, this will end up skewing the results. I'll show you.

What kind of results would you expect from breeding an anery to an amel, and then breeding those F1s together?

Let's put the Amel and Anery slots at the Fives and Sevens on our chromosomes. We only need to deal with this one chromosome since the other ones don't affect our outcomes here.

Given that, the Amel is going to have one pair of chromosomes, both of which will have a red five and a black seven.

The Anery will have a black five and a red seven on both.

So, make your "double het" offspring and you end up with all of them looking the same: they have one chromosome with a red seven and another chromosome with a red five.

Now, you are going to breed two of these double hets together. Remember that each one can only pass down one of its chromosomes. If you are unable to split the chromosomes at all, then you will never be able to get any snows. Notice that each offspring could either inherit two red sevens, two red fives, or one red seven and one red five.

The odds say: 25% amels, 25% Anerys, 50% double hets.

But, fortunately for us, 25% of the time the chromosomes would split somewhere between the fives and the sevens, creating a new pair of chromosomes that is two reds paired with no reds. At that point, you are then able to pass down two reds to the offspring from that parent.

However, in order for an offspring to be a snow, it would have to have that happen in both parents. So the odds of that are 1 in 4 X 1 in 4, or 1 in 16. And that doesn't guarantee a snow, it just means that there's a 1 in 16 chance of using this other altered set of chromosomes to even TRY for a snow!

Once you've beaten these odds, you also have to get both of the "two red" chromosomes into the same offspring. Since there's an equal chance of getting the "no reds" from either parent, you then have a 1 in 4 chance of getting the desired snow outcome.

The total of that 1/16th of the clutch will be: 25% snow, 50% double het, 25% normal (not het at all)

In the end, from that pairing and with that much linking between the traits, you'd only get one snow out of 64!

And we didn't even cover the other cases where only one parent had a relevant crossover... that would be where a two red and two black is in one parent, and the other parent still has a pair of "one red one black" chromosomes.

What kind of results will you expect from breeding a snow to a normal, and then breeding these F1s together?

The important difference here is that the skewing of the odds will be on the other side. Your F1s would inherit a double red from one parent, and a double black from the other. In order to get a snow, all you have to do is get two double reds together.

Remember, each parent has a 1 in 4 chance of a crossover, so we have 3 in 16 cases where one has a crossover, another 3 in 16 where the other does, and another 1 in 16 where both had a crossover.

So, 9/16ths of the time, you will have the standard pairing of double red, double black in each parent. You probably know by now that the odds in these instances of inheriting the desired stuff from both parents is 1 in 4.

In the end, this pairing would produce snow at a rate of 1 in 4 times 9 in 16, for a total of 9 out of 64, or a little more than 1 in 8.

Also notice that you will have a hard time producing any amels or anerys in this clutch.

Oh, and yes these are statistical probabilities. That's always a given when doing this stuff, so I seldom mention it because it's like saying "these are cornsnakes" hehe.

And what I'm curious about and haven't workd out is if you add everything up in the linkage-affected outcomes is that there is a sort of "conservation of odds" going on. When you combine all of the odds together from both types of pairings, do you end up with the same thing you would get if there was no linkage at all? I haven't sat down and gone through the whole thing, but I think you'd even end up with an overall total of 66% het for any offspring that isn't expressing a trait. hehehe

 

[Serpwidgets]

Oh and if you want to do the boxes again...

The thing you were doing before was making 64 pieces of paper based on the progeny predictor's final outcomes. You were picking offspring.

Another way to do it (because I'm lazy and it's easier to write out) is you can make the possible eggs and sperm and pick those out of the boxes. It also uses less paper, hehe. In the case of the triple het thing, you'd only need 8 pieces of pacer instead of 64.

If you want to do this with the crossover thing, here's how you could do it with breeding the F1s of the Anery X Amel in the above thingy:

Make two boxes, in the standard box, put two pieces of paper:

Amel/Normal
Normal/Anery

In the "crossover" box, put two pieces of paper:

Normal/Normal
Amel/Anery

(Or put any number in each box, half of each possibility)

Then flip two coins. If you (25%) get both heads, pick one piece of paper from the crossover box. If you get anything else (75%)pick from the standard box. (Or instead of the coins use a box with 4 pieces of paper, only one of which says "crossover" on it.)

Do this once for each parent, picking the piece of paper and writing down the results and then putting the paper back before picking for the other parent.

If you get two pieces that say amel, that's an amel. Same for anery. Only one piece of paper saying amel (or anery) is a het for that trait. None is a non-het that is not expressing that trait.

If you want to flip the original pairing to be snow X normal, just switch the contents between the crossover box and the standard box.

 

[Gregg]

"If you want to flip the original pairing to be snow X normal, just switch the contents between the crossover box and the standard box."

As I regain consciousness, I think:

Or...

I could say, "Instruction Book? I don't need no stinkin' Instruction Book!"

Or...

I could just say "F-It" and go outside and have a cigarrette--Even though I'm a non-smoker.

Or...

I'm sorry, but all that information is way above my desire to learn.

...................................................................................................


WOW! Now I remember why I didn't go the BS route in college. Imagine me being in front of you on my knees, bowing up and down with my hands out-stretched, saying, "I'm not worthy!"
When it comes to genetics: You Da Man, Serpwidgets--You da Man! I didn't follow a thing you said after, "Let's put the Amel and Anery slots at the Fives and Sevens on our chromosomes." Whew! It all went black after that. Please, don't get me wrong--I think that what you said is very valuable--It's just sort of wasted on me.

I love science. I loved science all through school. Nevertheless, when it came down to actually being a scientist, I chose the path of a Social Scientist, not that of a Pure Scientist. This genetics stuff is all more of a brain strain than what I'd like to admit. However, on behalf of all those who are interested in the ins and outs of genetics, I thank you for going to all the time and trouble of explaining it to me.

In a couple of years, I think I'll just stick the two snakes together and see what shakes out in the end. It's not that important for me to know the probable out-come of a clutch before it happens.


I really do apologize for any negative vibes this might be sending. I intend none.

Stay Cool Serp, you Rock!

 

[Susan]

Lady Luck does play a part...

An example...I bred a normal zigzag het snow to a snow non-patterned...the results...

Out of only 5 surviving eggs hatched:
1 Normal zigzag
3 Snow zigzag
1 Snow non-patterned

Now THAT'S beating the odds!!

 

[Gregg]

WOW, Susan!

You lucky Dog! How do you feel about going to Reno with me? It sounds like you'd be winner at the craps table.

Way to go!