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Old September 11th, 2012, 02:09 PM
kittiesandbirds kittiesandbirds is offline
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Phenotype and Genotype

http://www.nature.com/hdy/journal/v1...dy200977a.html


In the article Wolf of a different Color, published by Nature Magazine they discuss weather or not the black color of some wolves originated from wolf-dog hybridizing. Although the article is very interesting I am more interested in their use of the notion of phenotype.

They state that in conservation herds of North American Bison some of the ancestry is from domestic cattle. The percentage is low, they speak of 1% of autosomal ancestry. They later go on to say that this does not show up in the phenotype of these animals.

So what is phenotype? http://www.thefreedictionary.com/phenotype

How does it differ from genotype?http://www.thefreedictionary.com/genotype

I guess the expression you can't judge a book by it's cover goes for living organisms as well.

http://www.smgf.org/education/animations/autosomal.jspx

Last edited by kittiesandbirds; September 11th, 2012 at 02:41 PM.
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Old September 11th, 2012, 09:44 PM
Digston Digston is offline
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Genotype is DNA based. Say you have a cat with autosomal heterozygous alleles (Mm) that is the cats genotype.
Phenotype is the observable effect or outcome of that pairing. So in this case, Mn was the genotype, the phenotype is the cat is a manx(tailess). Where as a genotype of mm would cause the cat to have the phenotype of a tailed cat.

So in your Bison example; there is evidence of domesticated cattle in the genotype(DNA) but there is no evidence of that unless you actually look at the genetics.

Does that make sense?
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Old September 12th, 2012, 06:54 AM
kittiesandbirds kittiesandbirds is offline
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Quote:
Originally Posted by Digston View Post
Genotype is DNA based. Say you have a cat with autosomal heterozygous alleles (Mm) that is the cats genotype.
Phenotype is the observable effect or outcome of that pairing. So in this case, Mn was the genotype, the phenotype is the cat is a manx(tailess). Where as a genotype of mm would cause the cat to have the phenotype of a tailed cat.

So in your Bison example; there is evidence of domesticated cattle in the genotype(DNA) but there is no evidence of that unless you actually look at the genetics.

Does that make sense?
Well said thank you.

I guess then you enjoy a little microbiology from time to time, at least your response seems to indicate this.

Now mitochondrial DNA is another story all together and I have left out the DNA on the Y chromosome that we can identify certain traits of paternity by.
I am interested in this because many articles that I have read in the last year about authorities finding dead animals and identifying them as belonging to a group of wolves were deemed very costly. They seemed to look at all three types of DNA from my understanding.

Of course I had the unfortunate experience of trying to explain mitochondrial DNA to someone who ended up laughing and telling me that cells did not breath. Our french expression "respiration cellulaire" had thrown her for a loop. It takes specialists to translate scientific texts. I did do translation for a while but had a really big book to look up all the terms in (on loan from my local university). I thank you for coming in and helping me put this into words.

Yet on many forums (did not see the subject here) people said identification of an animal as part wolf was impossible. Maybe it is presently impossible for your ordinary citizen. I wish a group like Nature would explain this or a project like the Human genome project would exist for wolves. My understanding is that it is possible but costly and three tests need to be done to look for markers. However I am unaware how far the mapping of the genome of the wolf has been completed and am looking for info on this subject.

If you have a good understanding of the other types of DNA I'll let you explain you seem to do it quite well. Since my stroke I am wary of being called on the wrong word ect.


Found this and decided to add the link. I remember reading that for some reason doggy DNA had something very specific about it that permitted us to create so many breeds so rapidly. I was trying to find what this was called again. Then I ran into this article and looks like the version of the Human Genome Project for dogs is not such a bad idea after all.
http://askabiologist.asu.edu/plosable/dna-dogs


http://www.plosbiology.org/article/i...l.pbio.1000451 Article speaks of how the phenotype of a dog is influenced by few quantitative trait loci.

With so few quantitative trait loci implicated in the phenotype of a dog it becomes easily manipulated through human selection in just a few generations.

Last edited by kittiesandbirds; September 12th, 2012 at 08:28 AM.
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Old September 12th, 2012, 10:35 AM
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hazelrunpack hazelrunpack is offline
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Interesting articles, kittiesandbirds. Dog breeds come about when breeders create bottlenecks and set a genotype for the breed--in other words, they select a phenotype as their standard and through the process of line-breeding, they 'set' the genotype responsible for that phenotype. Only the combinations of genes that result in the desired phenotype are preserved in that breed--some forms of the genes (alleles) are lost in the process while other alleles are 'set' (always present) for that breed. This makes affected areas of the DNA relatively easy to spot. So the DNA of dogs is a very good tool for geneticists to explore which regions of DNA are most instrumental in affecting the appearance of the breeds.

Any animal with a social structure suitable for domestication and bred to 'standard' shows a similar affect. Selective breeding will create bottlenecks and 'set' part of the genotype for each breed of that animal created.

So it's not something specific to canine DNA that allows for easier selective breeding; it's just that having bred them to a particular phenotype for years, the differences among the breeds' genotypes can tell us a lot about what genes are responsible for those phenotypic characteristics. The genetic subsets are fairly well established and offer a toolbox for geneticists to tease out gene function.

Dogs and wolves still share a lot of genes, though. And since wolves have been bred by natural selection, not the hand of man, their gene pool is likely more 'complete' than what remains in dogs. That being said, though, wolves and dogs in general share an enormous number of genes--way more than just those controlling phenotype--and that can make it difficult to tease out whether a dog has wolf in its recent ancestry.

Have you seen any of the work on cheetahs, kittiesandbirds? Fascinating stuff. I gather that at some point there was a severe bottleneck that makes all living cheetahs essentially identical. Their unique phenotype is the result--unlike any other living cats.
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Old September 12th, 2012, 11:20 AM
kittiesandbirds kittiesandbirds is offline
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Originally Posted by hazelrunpack View Post
Interesting articles, kittiesandbirds. Dog breeds come about when breeders create bottlenecks and set a genotype for the breed--in other words, they select a phenotype as their standard and through the process of line-breeding, they 'set' the genotype responsible for that phenotype. Only the combinations of genes that result in the desired phenotype are preserved in that breed--some forms of the genes (alleles) are lost in the process while other alleles are 'set' (always present) for that breed. This makes affected areas of the DNA relatively easy to spot. So the DNA of dogs is a very good tool for geneticists to explore which regions of DNA are most instrumental in affecting the appearance of the breeds.

Any animal with a social structure suitable for domestication and bred to 'standard' shows a similar affect. Selective breeding will create bottlenecks and 'set' part of the genotype for each breed of that animal created.

So it's not something specific to canine DNA that allows for easier selective breeding; it's just that having bred them to a particular phenotype for years, the differences among the breeds' genotypes can tell us a lot about what genes are responsible for those phenotypic characteristics. The genetic subsets are fairly well established and offer a toolbox for geneticists to tease out gene function.

Dogs and wolves still share a lot of genes, though. And since wolves have been bred by natural selection, not the hand of man, their gene pool is likely more 'complete' than what remains in dogs. That being said, though, wolves and dogs in general share an enormous number of genes--way more than just those controlling phenotype--and that can make it difficult to tease out whether a dog has wolf in its recent ancestry.

Have you seen any of the work on cheetahs, kittiesandbirds? Fascinating stuff. I gather that at some point there was a severe bottleneck that makes all living cheetahs essentially identical. Their unique phenotype is the result--unlike any other living cats.
Very interesting. I remember an article which I am still looking for that stated that there was something very specific and unique to dog DNA. It is not in Nature or Scientific American as far as I can tell.

I buy many magazines and have too many but have been looking for what that specific thing about their DNA is I guess I should keep looking. It bothers me to forget these things.

I don't know much about cheetahs but I will look this up on the Nature site.

It always upsets me when I find an article in my magazines months later and not when I am looking for it. I may be confused about what exactly this specificity does.

I wonder how the scientists know which parts of the DNA have an earlier origin in the animal. Many articles I read seem to indicate that they can differentiate between newer and older segments. Obviously they can't use carbon dating, lol.

Also since the DNA from the mitochondria came from the mother and the DNA in the Y chromosome can help establish certain things about paternity. I was told they are helpful in determining weather or not the dog had some wolf origin. I know that dead animals on the roadside were identified as belonging to certain populations of wolves from markers those groups possess. I guess in years to come more will be published on this subject. As you can see from one of the links mapping of dogs genome and wolf is becoming more interesting to certain groups. I would just like to see some really good article about it. I don't think Nature or Scientific American (which are good at vulgarization) has made an article about this.

Since some articles make the pretense that introduction of domesticated genes into wild populations is detrimental, although it's a controversial idea, I think more gene mapping of wolves should be done. It may be underway as we speak. I continue to search to find how they identify with certitude these roadside carcasses as belonging to these wolf populations. So far the articles I read throughout the years spoke of these tests being done in Universities it does not seem to be something the general public has access to.
I want to take the time to find a link as an example: http://www.timberwolfinformation.org/?p=9305

http://www.thetelegram.com/News/Loca...Newfoundland/1 This article is interesting because we see that originally the University did not possess a bank of DNA to compare with.
Through the years I have seen articles like this or others where they say "The university of ... has determined the carcas was of a ...wolf" I guess for lack of a better article I will just post this one. You may come across some better ones than me though. I have seen many throughout the years, unfortunately after a stroke short term memory is one of the first things to suffer in my opinion, or it may be the subsequent epilepsy.

In humans they say they are now able to give you an idea of where your ancestors were throughout history.It's not a precise thing like your great grandfather lived here...yet they do seem to know that some segments are "older". Again this is very vulgarized, my first language is french. At any rate DNA is a very interesting thing.

They are learning more and more about it, they used to speak of junk DNA for so many years and it became accepted in a widespread way till researchers came up with new ideas. I have many many old articles that disclose everything about junk DNA, I guess now they are junk. http://www.guardian.co.uk/science/20...unk-dna-encode

Last edited by kittiesandbirds; September 12th, 2012 at 11:40 AM.
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Old September 12th, 2012, 02:53 PM
kittiesandbirds kittiesandbirds is offline
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Well the reading was very informative and saddening.


Nature has an excellent article on the cheetah titled The Cheetah in Genetic Peril.

If you are not subscribed to Nature or Scientific American but are curious about the point brought up earlier I found another link that briefly describes the issue.

http://animals.howstuffworks.com/end...tah-info10.htm

http://www.cheetah.org/?nd=genetic_diversity

Thanks hazelrunpack for telling me about this problem. I heard about concerns of this nature with animals like wolves many many years ago, the talk of loss of genetic diversity. I never heard about the cheetahs.
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Old September 13th, 2012, 09:10 AM
kittiesandbirds kittiesandbirds is offline
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More interesting things about DNA.



http://www.genetics.org/content/151/...e2=tf_ipsecsha

*Common to the origin and development of many breeds is a founder event involving only a few dogs and, thereafter, reproductive dominance by popular sires that conform most closely to the breed standard. ...resulting in the loss of genetic diversity within breeds and allele frequency divergence among them."
Ostrander, Elaine A. and Wayne, Robert K. "The canine genome” Genome Research. Retrieved from http://genome.cshlp.org/content/15/12/1706.long#ref-23


This is interesting and evident (the founder event being a serval bred with a domestic cat) when reading about the newest breeds of cats like the Savannah (which I know very little about) where the first generation males can be sterile, in some cases. The breed seems not clearly defined as one standard but more by standards for F1 and the following generations (from what I have quickly gleaned). It is interesting to note how quickly the size variations and appearance can change. NOTE: What I am speaking of as being evident here is the founder event. I know very little about Savannah cats. It seems that as the subsequent generations are said to be smaller that in this case the founder event is repeated at times when certain results are desired (hybridism: serval and domestic cat), this is not what happens in breeds that are established usually. I also read about later generation males that are fertile being used to produce offspring.

Feel free to explain the Savannah and the different generations if you have knowledge on this subject.




http://genome.cshlp.org/content/15/12/1706.long

Last edited by kittiesandbirds; September 13th, 2012 at 10:36 AM.
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Old September 13th, 2012, 06:32 PM
Digston Digston is offline
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The only reason I knew the answer to you first question is because we just covered it in my Genetics class.
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Old September 14th, 2012, 09:15 AM
kittiesandbirds kittiesandbirds is offline
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Well thanks for your assistance in explaining it.
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Old September 15th, 2012, 01:06 AM
Digston Digston is offline
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LOL, I got all excited that I knew the answer! All I could think was, "Yes!! Genetics has paid off!!"
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Old September 15th, 2012, 07:46 AM
kittiesandbirds kittiesandbirds is offline
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LOL, I got all excited that I knew the answer! All I could think was, "Yes!! Genetics has paid off!!"
My daughter did this in her Microbiology class a long time ago (the DNA is an artist one). Hidden in the drawing are notions of the subject. There is also a painting she did inspired by a photograph superimposed in the background by computer. She coined this term back then at least that is the first time I heard anyone say this. It's online on a website (Her drawing) but she was saying this since high school. Yes, genetics does pay off. DNA is an artist.
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Last edited by kittiesandbirds; September 15th, 2012 at 10:39 AM.
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Old September 15th, 2012, 12:20 PM
kittiesandbirds kittiesandbirds is offline
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Whole genome sequencing

Just wanted to add that the type of test that takes into account the mitochondrial DNA is known as whole genome sequencing.
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Old September 15th, 2012, 12:39 PM
Digston Digston is offline
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Your daughter is quite talented!
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Old September 15th, 2012, 01:13 PM
kittiesandbirds kittiesandbirds is offline
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Your daughter is quite talented!
Thank you. The portrait was in the office of the high school principal for quite some time. The story behind the pic is funny.

My daughter actually works as a substitute teacher there from time to time now that is how she got it back. The principal has passed away and they offered the drawing to her as a souvenir.

They were learning about the Camera Lucida, I hope I spelled that right. The teacher offered two methods for doing the drawing. Either by a machine he had which projected the image or with squares. She taped the papers together and made it giant and started drawing with a lifted hand. He told her in no uncertain conditions that if she wasted her time and didn't have time to finish she would get zero. He told her what she was doing was impossible. She became his favorite student and the drawing was exposed for years.

My father could do this and my brother. I did this till I had a stroke and then my pictures would go off to one side if I didn't take many breaks to re-visualize the drawing. My first drawing post stroke looked like an image of Tracy Chapman in a circus mirror, lol.

I have no idea weather this is learned or genetic. Although she had no previous training she may have learned through some sort of passive observation.

She is doing acrylics now and adding lots of color to my life. I guess DNA is an artist.
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