A (lengthy) article on BP Gentics

I wanted to share a rather lengthy article I've written on genetics, specific to ball pythons.

http://ballpython.110mb.com/wiki/index.php/Genetics

I have posted this for a couple of reasons. First, I would appreciate any feedback on the article itself, and second (and perhaps more important) is that the article is released under an opensource license.

What that means, is you can use it on your own site!

A few notes:
If you want to use it, please check the following page:
http://ballpython.110mb.com/wiki/ind...rights:Summary

This will give you the (rather minimal) requirements to use the article. Secondly (and most important) the photos of the snakes themselves are not released under the above license. All the photos are copyrighted, and permission was granted for their use. The graphics, diagrams and other information are released under Public Domain... meaning you can use them in any fashion you want.

As long as you fullfill the obligations listed in the Copyright link above, you are free to use the content, no permission neccesary :).

Again, I would love to receive feedback on the article, especially any errors.

Very nice presentation and thorough!

Without any formal genetics training since high school I do have a few questions.

I've gathered that there have been several competing genetics notations coming from different fields. Is that still the case or is this an agreed upon standard? I see where you used the color coding to distinguish the normal for albino allele “N” from the normal for clown allele “N”. Do you have anything against using the notation where the same letter is used for both variants at a locus of an interesting mutation like “C” for normal for clown and “c” for the clown variant and similarly “A” for normal for albino and “a” for albino? I know this isn’t perfect either and will get more complex as we identify situations with more than 2 possible variants at a locus (like the Platy complex). I’m also unclear how to handle the capitalization in cases of co-dominance. I’m just thinking the common “N” is confusing and color coding might not always be available to keep it straight.

Also, are you aware of any homozygous spiders?

Hi there!

Thanks so much for sharing, since this is a field that combines both my professional abilities and personal interests, I'll review it as if it were one of my student's if you don't mind. If you do... you probably shouldn't read any further! As I'm sure this is something you want read by wider circles, I'll comment on both the writing and the content:

This article seems to be a cross between a well-considered structure and off the top of your head writing. If you truly intend for this article to be a reference you will have to correct the errors, be more specific with your definitions, and prepare the content with more academic rigor. I do like the structure, and you have a firm foundation for the type of writing you wish to produce. Your grammar is better than most people's, though there are typos throughout to correct. Your use of the vocabulary makes me think a good review of a genetic textbook would be a good investment of time. Excellent diagrams and pictures, and while your writing is awkward at times, it isn't too flowery to distract from the information presented. You will want to flesh out certain parts though, as it is unclear, even from the given structure what information will be presented and why. It is a bit too scattered to be considered a wiki just on vertebrate/eukaryotic genetics, and not robust enough to be a wiki on ball python morphs.

Here are some specifics:

"The wide variety of Ball Python morphs available today are possible through genetic mutations. A key to successful breeding is understanding genetics at its very core."
-The first sentence is awkwardly written, and you need a transition into the second sentence. As it stands now they shouldn't be in the same paragraph.

"This article intends to be a de facto reference for explanations of genetic mutations among Ball Pythons."
-That is an uncommon use of 'de facto' and doesn't fit well with the article.
-Awkwardly worded again... article, reference, explanation all a little redundant.

-If you use quotation marks, cite the reference.

"a single gene is [the] fundamental unit of heredity. The act of procreation distributes these genes to the parents' [or parent's] offspring. By receiving the genes from two parents, it widens the gene pool, and allows offspring to [ob]tain unique genetic characteristics from each parent (second parent is redundant)."
-As an introduction for beginners you'll want to indicate new vocabulary with bold or italics and not use them as if they are part of a layman's vernacular.
-In general, the fundamentals of genetics and sexual reproduction have been widely written about. Emulating the style of published literature isn't plagiarism.

"We are already aware that chromosomes come in pairs, and as such, so do genes."
-Are we aware of this already?
-Also, if you think alleles only come in pairs, there is a significant limitation in your knowledge that if addressed will help with the short-comings of the genetic information presented here.

"We can put a number of pots and pans at each of these heating elements, however, each pot and pan has unique characteristics. In this example, the pots and pans are genes and the frying pan and sauce pan are different variations of it, or the alleles."
-Very interesting analogy, is it yours? It works.

"when discussing specific genetics of an individual morph."
-You might want to define morph to give the article a better flow and make it more informative.

"Is is extremely likely that there is a pigment gene, and the "Albino gene" is simply an allele that prevents the creation of melanin."
-What is your source for the "pigment" gene?
-For this to be a truly informative and useful article, you will probably want to investigate the different types of pigment produced by the wild-type, and discuss whether it is a disrupted gene, a disrupted promoter, or an upstream/downstream component of a genetic system that leads to phenotypic expression.

"and aside from that, we simply don't know how many genes are being affected by each charactAristic."
-Simply, because all morphs that have been identified as "genetic" through linebreeding and outcrossing, we know nearly all traits to be simple recessive, simple dominant, or co-dominant... meaning the number of genes involved in yielding any "base" morph is 1.

"a single gene is being mutated in any given morph."
-improper tense, a gene mutation arises, and if in a sex cell is passed onto progeny. All in the past.

"Earlier in the article, we learned that Ball Pythons are diploid..."
-this is the first time you've used "diploid".

"However, where these chromosomes can differ [is] in the alleles they carry."
-Most spellcheckers will detect sentence fragments....
-Also, chromosomes may also differ because of imprinting, meaning the chromosome from the mother can behave differently than the same chromosome from the father.

"During the fertilization process, the offspring retain two cells from the sire and dame"
-retain is "to keep", obtain is "to get".
-this is an inaccurate description of the fertilization process. Two haploid cells join, and their nuclei fuse. Not two cells are obtained...

"its offspring have the potential to [inherit] one of two alleles"

"any given offspring has a 50% chance of inheriting either one of the alleles."
-there's a 100% chance of inheriting either one
-there's a 50% chance of inheriting one over the other, odds is a difficult concept.

"Typically, when referencing specific morphs the morph name alone implies the animal is homozygous. Although, this depends on the allele's phenotype."
-This is the atypical case. Usually it is only a recessive morph that's name is synonymous with homozygous, with pseudo-exceptions like Leucistic.
-alleles cannot have phenotypes, alleles make up a genotype, which gives rise to a phenotype.

"A phenotype is one or more visible characteristic[s] of an organism, caused by a specific allele."
-this is an uncommon definition, that probably won't gain acceptance from an educated audience. The last clause is causing you problems.

"A recessive allele, causes a phenotype that is only visible in the homozygous form. An Albino, for example, is a simple recessive trait."
-Traits are recessive, meaning the allele in question does not have a visible effect unless the 'normal' allele's influence is removed. You'll want to careful when using the term "recessive allele" though this is probably more of a pet peeve.
-generally, "An Albino" would refer to an amelanistic individual, not a trait.

"is prefixed before the morph's heterozygous name"

"A dominant allele, causes a phenotype that is visible in both the heterozygous and homozygous form."
-this definition does not distinguish between dominant and co-dominant. Since you're so intent on using your own definitions for things, incorporate the fact that the homozygous and heterozygous forms are visibly indistinct.

"the only way to prove it is through breeding it to a normal."
-Since all spiders in captivity are descended from one animal (unless this is an urban legend), it will be very easy to tell if a Spider could be homogzygous by its pedigree which would be readily known.
-As well, simple non-specific genetic tests that do not rely on sequence knowledge could determine the zygosity of the 'Spider' locus.

"When more than a single allele is being impacted,"
-impacted by what?
-the rest of this section is some of your better writing.

"an organism with 10, 25, or 100 genetic mutations would make for a very long conversation."
-funny

"A heterozygous Albino may be written as "Na" the capital "N" showing the allele, and the lowercase "a" indicated the Albino allele."
-Randy is absolutely correct on notation. You do not complicate genetic notation by using different letters for the same trait!
-First define your gene, then your notation and give an example:
Trait - Albinism
Gene - Melanin-production protein 1
N - wildtype allele
n - albino allele
A male albino ball python would have the genotype: aaXY

"Regardless of the letters used, just remember if both letters are uppercase, the animal is normal"
-this isn't correct either.
-a 'normal' animal's Pastel locus would be pp, and a Super Pastel: PP

"if both are [of the same] case, it's a homozygote."

"Determining the possible offspring for a dame and offspring"
-what does this mean?

Good work on the Punnett Square, you'll want to fix your notation.

"When breeding a normal ball python to a heterozygous Albino, the results are 50% NN and 50% Na"
-Wrong again!
NN x Na (your notation) yields 25% Na, not 50%.
-You were thinking of breeding NN x aa.

"It is drastically important..."
-unconventional/incorrect use of 'drastically'
-awkward wording of this paragraph.

Coloration of the Punnett Square is quite impossible with "paper and pencil", and needless. I would suggest reworking this suggestion.


Hope this helps!

Wow! People pay a lot of money for that kind of review! That's awesome!!

Great stuff!! That post above us is proably the longest one I have ever seen!:eek:

yeah, I have some skills :P Unfortunately, the university doesn't pay well enough for them!

Like I said, it's something I'm passionate about... and the more articles or pages out there that someone can show a loved one, a friend, a child, etc to educate them and share their passion and knowledge, the better!

The section titled Gene/Allele confusion is very confusing.

"we simply don't know how many genes are being affected by each characteristic"


Not really sure what you mean here.
First of all in traditional genetics genes influence traits, not the other way around.

We know that traditional albinism is caused by one gene. There are other forms of albinism caused by different gene loci. They are usually called something different like lavender albino or caramel albino etc.

It is possible that two different traditional-looking albinos of separate lineages are mutants of different gene loci. But you could easily distinguish these two possibilities by using the recessive complementation test.

If they were slightly different mutations of the same gene-->A1 (a1a1) x A2 (a2a2)-à a1a2 (all Albinos)


If the mutations were of separate gene---> A1 (a1a1 A2A2) x (A1A1 x a2a2)à A1a1A2a2 (A normal looking animal that would be heterozygous for both albino genes)

Furthermore, when a base morph is discovered initially. You can determine whether that particular genetic aberration is caused by one or two genes. For example, let’s say you find a white looking snake. You breed your snow to a normal looking bp (the F1 generation). All offspring in the F1 generation are normal looking. At this point, your putative genetic aberration is either non-genetic, a one gene-recessive, or possibly a multi-gene recessive. You can begin to distinguish among the possibilities by crossing two of the F1 offspring. If after years of nice large clutches you find ~25% of the offspring to be white while ~75% are normal, you’ve found a one gene recessive trait.


Now let’s say you get different results from your F1 x F1 cross. Your amazed that in your first clutch you get a normal looking offspring, albino offspring, and axanthic offspring. Furthermore, after patiently waiting for your F1 parents to be ready to breed again you repeat the cross. This time you get 1 white snake almost identical to the original founding parent. After decades of work and recording keeping you find that you get ~56%(9/16) normals, ~18% albinos (3/16), ~18% (3/16), and 6% (1/16) white looking snakes. This is the classic two gene or dihybrid ratio of 9:3:3:1.

Now the second scenario was made up, but it was based off of the designer morph snow. This is exactly the kind of thing that would happen if you found a snow in the wild and wanted to prove it genetic!

While your unlikely to find a snow or two gene aberrant in the wild, the scenario illustrates that you can distinguish a trait that is caused by one gene from a trait that is caused by two or more genes using classic Mendelian analysis.

One gene recessive-->3:1 phenotypic ratio

Two gene recessive--->9:3:3:1 phenotypic ratio

Wow, this is great! I never expected to receive such a response and I can't be happier with the results. Thank you VERY much for the review Dread, I never expected a professional review to this degree and I was certainly hoping someone much more experience would give it a once over.

A few comments:

Randy and Dread are right on with the Punnett Square. I used different letters and colors to indicate why a double recessive animal would have two "normal" alleles, but in doing so probably created more problems than solutions, since it breaks from tradition.

Mendel, what I was referring to were dependent mutations, but perhaps I should have made that more clear. For example, there seems to be a serious genetic influence in Clowns, that can be bred to reduce the pattern of the side stripes. This to me suggests that there is a second gene at work, dependent on the Clown allele.

Perhaps I am wrong on that, and if so it should be corrected. Again, thank you all for the awesome posts!

I like to thank all you guys Jhall, Dread and Mendel for the crash course in genetics. I know how thw basics of co-dom, dom and recessive works but you guys have really opened a whole new dimension to me on the nuts and bolts of what puts it all together. I saw the thread this morning but didn't have the time to read it but just finished and I'm glad I did. REALLY informative! Thanks! :sunny:

Having trouble posting......not sure why.