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If you need help with inheritance math, after the djed part gets squared away, let me know. Whether or not it winds up drawing upon "genetics" proper. There's actually a lot more than dominant and recessive out there to use as models, and I'm fairly well-steeped in this stuff for RL reasons.
You do raise a good point with trying to stay away from hard genetics and more fluid genetics. Let me rephrase my thoughts with less math in mind:
6-armed with 6-armed = 100% 6-armed I agree with this.
6-armed with 4-armed = 70% 6-armed and 30% 4-armed I do not agree with this because it naturally increases the purity (without needing a specific genetic program). Something like 40% 6-armed and 60% 4-armed would provide that feeling that the purity is declining. Or even 30% 6-armed and 70% 4-armed.
4-armed with 4-armed = 85% 4-armed and 15% 6-armed This could be viable because there may be hidden genes/djed within the 4-armed Eyphs.
Benshira with Eypharian Only half or less than half of their offspring should be able to be Eypharian. Otherwise we run into the same problem as earlier with the intensive spreading of their genes/race.
Human/Other with Eypharian No offspring should be Eypharian (based on the lore of mixed-races).
And I just saw your post Sedge. That could be really insightful. I'm mostly basing my knowledge from things I've seen in real life with regards to dominant/recessive genes and what I've learned about them. I know that there are other means but I'm not as well versed in them. If you do that in real life, then that would be awesome to hear about.
Still my above thoughts are in regards to creating a 'purity' driven artificial selection. Because if there is no genetic 'problem' then the society wouldn't have tried to come up with a 'solution'.
Last edited by Sayana on March 7th, 2015, 6:36 pm, edited 1 time in total.
You guys are too fast! I didn't realize you'd posted, and was jsut editing my last post -
Ok, after consulting the gods/STs, it was previously decided that DNA works exactly the same, I just went a little too far off into my own world here. I'll be rewriting the necessary sections above (after my chicken's done), which actually isn't as much as I was afraid it'd be.
Have a moment? Maybe drop by and leave a peer review?
Ok, I looked back and I think I found why I went off the tracks. If the six-armed gene is recessive and comes from a single person, Royet, then how would the gene even propagate? His own children would have only had one recessive gene each, and only if they started doing some serious inbreeding would anyone have been able to reproduce it.
The only idea I can think of is that Royet started blessing children/grandchildren/great-grandchildren to magically have both genes to grow the six arms. There was some discussion on Eyphs stealing a lost discipline of magic, which could have resulted in all gods, including Royet taking off, leaving the Eyphs to try and generate the six armed feature on their own. Thoughts?
Sedge and Sayana both, I would deeply appreciate experienced input on genetics here. I have not thought of this stuff beyond casual conversation in near 15 years, so I'm trying to catch up.
Have a moment? Maybe drop by and leave a peer review?
Not meaning to cheat or find the easy way out, but maybe since Royet was an Alvina his genes were particularly strong. So maybe for the first few generations the Eypharian gene was more dominant than the 2-armed gene, and eventually as the generations went along it faded.
Also, in real life if you want to breed a unique recessive trait (going back to my brother and him breeding snakes), one good way is to have a male mate with as many females to spread the gene (it doesn't show up visibly but it is spread). Then you can breed the offspring together to get 25% likelihood of visibly seeing that gene. Could there have been a couple of male Eyphs early on who just really got around?
I'd say it's a complex genetics problem, not a Mendelian genetics problem. I can think of a couple likely models, with incomplete penetrance or multiple loci or both, that aren't too complex. I have to address a stack of other things now, but I'll work on this this evening. Unless you guys come up with something you like sooner.
Wow, but this took a lesser age to write. I hope it does what you need!
I'm going to approach this from a somewhat different paradigm, so I'm including some background information. Some of this will be familiar to you both, but I also want it to be fairly transparent for anyone following along, so I'm explaining from nearly square one. Plus I'm bringing more terminology to the discussion, and that requires definitions. I'll put that stuff in spoilers for sake of readability.
Complex Genetics 201:
Genes and Alleles :
Although people frequently refer to genes as 1:1 determiners of traits, i.e. "the gene for blue eyes", that's not really accurate. For one thing, every member of a species has basically the same genes; if they didn't, there would be more reproductive incompatibility, akin to what is seen with large cat crosses (e.g. ligers) or horses and donkeys (mules/hinnies). You can think of the genome as one of those MadLibs paragraphs, with slots where you fill in key words; those slots would be like genes. The words that go in those slots are then something like alleles, variations of a gene, although the range of variation in alleles is much smaller than the possible variation in words. This also means that a gene may have more than two versions.
I'm presuming that most races on Mizahar have more or less the same "slots", because we don't have hybrid infertility. We just get mixed bloods with normal fertility, except in a few cases where the biology is even more weird (female Dhani, male Symenestra, Akalak and Konti) or there's no compatibility to begin with (Jamoura, Charoda, Pycon). So it's more correct to talk about the "four-armed allele" or "six-armed allele" than either as a distinct gene, and these are the terms I will be using.
When it comes to interactions of alleles, "dominant" and "recessive" are shorthand terms which describe the visibility -- the penetrance -- of the phenotype, not the mechanism by how it occurs. Generally, specific alleles can be classified as having normal function, loss of function, or gain of function. Loss of function means that allele is not able to do something it normally would. Albinism, for example, is a loss of function in melanin production. Typically, loss of function alleles are "recessive", because in a heterozygote (one variant copy, one normal copy), the normal copy is sufficient to do what's needed. Gain of function means either that the allele does something new, or it does more of what it normally does. Gain of function alleles are usually "dominant", because that one copy of the variant allele will go right on ahead and do its new thing.
Patterning, Modifiers, and Penetrance :
As I said above, genes don't really code for specific traits, except in a few cases. This is especially true for genes which control the development and form of the body. Most of these genes define and lay down patterns, instructions which other molecular machinery interprets and eventually builds into the final structures. For example, basically the same genes underlie the design of fish fins and human fingers/wrists, but the expression and interpretation of those instructions is radically different. Many developmental aberrations can be ascribed to changes in patterning, particularly the number of repeats. Polydactyly is a case in point, where the patterning machinery essentially lays down more stripes than it's supposed to, and the developed person comes out with extra fingers or toes.
Genes which influence the expression or interpretation of other genes are referred to as "modifiers". On the molecular biology level, development is basically one gigantic mare's nest of modifiers -- and, truth be told, so is most of the rest of the genome. This leads to many traits having "incomplete penetrance" and being a major headache for geneticists. Incomplete penetrance means that one may have a variant allele which should dictate a certain phenotype, but for whatever reason, that phenotype is not evident. It may be partially expressed, or there may be no sign of it at all. In most cases, we simply don't know enough about how that gene and that allele interact with the rest of the molecular machinery to pin down what modifiers are affecting its penetrance. But depending on a phenotype's penetrance, even something which is a "dominant" trait may not actually be expressed 100% of the time.
I will not really be involving incomplete penetrance in my model, for sake of simplicity on our parts. But as far as the Eypharian race's IC studies go, if even a modicum of incomplete penetrance is actually involved, then every now and again a cross won't come out as they expect. They could potentially be chasing the exact mechanisms for decades even with the equivalent of modern RL understanding and technological capabilities. Without those, there will always be mysteries for them to chase.
Population Genetics :
There are two elements of population genetics which I think also come into play here. One is the idea of genetic drift and fixation (i.e. everybody has the same allele). My understanding from what you've already posted is that the Benshira split off pre-Valterrian, and I presume they survived in separate communities underground. During that time, you have a population bottleneck -- a sharp reduction in the number of breeding adults -- and the opportunity to say that certain alleles became fixed in either population. This applies equally to recessive and dominant phenotypes, because it has to do with chance.
Also, I will be employing the Hardy-Weinberg Law, as the quickest and easiest way to handle population genetics. In order to say how frequently a cross might occur in the population, we need to be able to say how abundant the alleles involved are across the entire group. Hardy-Weinberg assumes no mutation, migration, or natural selection, which are all valid enough. It also assumes random mating, i.e. nothing special dictates who paris up. Obviously this is not true in the case of the Eypharian program, but it's the only way we can start to calculate allele frequencies. And we really don't need to be exact, we just need to be able to assign something, so this is good enough.
The Hardy-Weinberg equation is this: 1 = p^2 + 2pq + q^2.
Here, p and q are the population frequencies of two alleles in the same gene. Genotype pp occurs in p^2 percent of the population; genotype pq occurs in 2pq percent of the population; and genotype qq occurs in q^2 percent of the population. Using this, we can assign population allele frequencies, determine how common each genotype is among Eypharians, and calculate how often a given cross occurs. This then lets us estimate the phenotypes of Eypharian children for any given pairing of parental phenotypes.
All right. With the background out of the way, let's get down to actual modeling.
Let's assume that there's some developmental 'pattern' gene involved in defining shoulders. Everyone in the world has the same allele for this gene, which says don't repeat; in essence, make two shoulders. Then Royet comes along and introduces a new allele, which is a gain of function that says do repeat: make more shoulders. The repeating allele is R, because we can call a gain of function allele "dominant", and the non-repeating allele is r.
The interpretation of the pattern, however, depends on a second gene, a modifier. This is another gene where every race has the same allele, except the proto-Eypharians, who have some natural variation. Before Royet, this natural variation didn't matter. With the repeat instruction that Royet introduced, however, this gene now has the opportunity to modify: it controls how many times the shoulder pattern is repeated. This gene has three possible alleles, At which is 1 instance, or two arms; A which is 2 instances, or four arms; and a, which is 3 instances, or six arms. At is effectively dominant to all others, while A is dominant to a.
This gives us the following possible combinations:
rr ____
two arms
R_ At__
two arms
R_ A__
four arms
R_ aa
six arms
With regards to Royet and Eypha, since all of the A-variant alleles occured naturally in proto-Eypharians, we can assume Eypha had the aa genotype. Obviously, Royet did as well. So their cross is RR aa x rr aa, from which all children are Rr aa, six-armed. After that point, because the children are all heterozygous for R, the grandchildren and further generations have only at best a 50% chance of being six-armed. It depends further on the A-variant genotypes of their spouses, but we can legitimately have a higher than otherwise expected rate of six-armed descendants, and also a nontrivial chance of getting six-armed children from a four-armed parent even some ways down the tree.
The assumption then is that Eypharians selected for R, which wound up fixed in their race. They also lost At because they selected equally strongly against it. So all modern Eypharians are RR AA, RR Aa, or RR aa.
Benshira are a little more muddy under this model, because while R is dominant for its gene, its effect can be masked by At at the other gene. But we can assume that genetic drift comes into play with the Valterrian, and the modern population is essentially rr AtAt, with perhaps the rare individual harboring either A or a if we so desire. Because r is fixed in their population, there is no way for a multi-armed child to be arise from Benshira stock without an Eypharian parent introducing the R allele. If At is also fixed among Benshira, then there's no way at all unless Eypharian alleles for both genes filter into the population anew. That could for all practical purposes be never. In essence, the odds of this happening are open to our decree.
That leaves the question of Eypharian population proportions, and how common children of different phenotypes are. Here we just have to assign some allele frequencies for the population. If I say that A has 60% frequency and a has 40% frequency, then genotype frequencies by the Hardy-Weinberg equation are:
four-armed AA
0.6 ^ 2
36%
four-armed Aa
2 * 0.6 * 0.4
48%
six-armed aa
0.4 ^ 2
16%
If those don't suit, feel free to change the allele proportions and recalculate until you find something that you like.
For now, given the above, I'm just going to round and say that half of four-armed Eypharians are AA and half are Aa. They're close enough to equal, especially since we're already fudging on things like random mating to even use this math.
Given that assumption, for a four-armed x four-armed cross, the chances of genotype pairings are: 33% AA x AA, 33% AA x Aa, 33% Aa x Aa. There's only one cross that can give a six-armed child (aa), and that outcome has a 25% chance of occurring. So the overall odds of getting a six-armed child out of two four-armed parents are 33% * 25% = basically 8%.
For a four-armed x six-armed cross, the chances of genotype pairings are: 50% AA x aa, 50% Aa x aa. Only one cross could produce a six-armed child (aa), and that outcome has a 50% chance of occurring. So the overall odds of getting a six-armed child out of a mixed pairing are 50% * 50% = 25%.
Six-armed Eypharians are RR aa, so they will always breed true with one another. Unless you want to throw in a chance for sports due to incomplete penetrance, which can be any arbitrary odds you please.
Again, these are at the population level and assuming random mating, so the odds may be higher for individual pairings -- if the Eypharians running the program are correct in their deductions.
Whoot Sedge! That was a lot of writing and explaining but there was a lot of good stuff there. It also makes sense why the Eypharians would quickly take over genetically (at the beginning) but then later start to have issues with breeding pure.
I have one question and one potential issue.
Question: Would two Eypharians ever have the misfortune of having a Benshira as an offspring? By the looks of it, I don't think it's possible and we might not want it to be possible either.
Potential issue: For other races that have had no reason to breed the "At" gene to be pure, what happens if they have offspring with an Eypharian? Would the "A" and "aa" genes that are likely spread fairly evenly result in mixed race offspring having 4 and 6 arms? Currently the lore states that Eyph + humanoid offspring only have 2 arms.
I really think you did a great write-up and I'd love to work with the model you have going.
Would two Eypharians ever have the misfortune of having a Benshira as an offspring?
Modern Eypharians, no, because of allele fixation at the R gene and the deficit of At in the population.
Historically, yes. For example, an Rr x Rr cross, if it occurred, would have 25% chance of an rr child, who would be two-armed. If one is rr, the A gene could technically be anything, and it wouldn't matter at the phenotype level. I went back and fixed that in the summary table.
For other races that have had no reason to breed the "At" gene to be pure, what happens if they have offspring with an Eypharian? Would the "A" and "a" genes that are likely spread fairly evenly result in mixed race offspring having 4 and 6 arms? Currently the lore states that Eyph + humanoid offspring only have 2 arms.
The alleles are not spread evenly. A and a existed only in the proto-Eypharian population. Every other race in Mizahar is uniformly At. This was chosen for consistency with the Mixed Blood lore.
by Sayana on March 7th, 2015, 6:27 pm 
