Saturday, January 17, 2015

Decoding Brockle - Trying to Understand How DNA works


This is all Brockle's fault. He has been a confusing puzzle of a dog since the day we met. I have owned several dogs in my life. Our relationship was uncomplicated and easy. Then I met my boy. He is complicated in ways that freak me out a little. He piqued my interest. 

My confused thoughts are written in blue and corrections from brilliant readers will be added in green.

His quirkiness, sense of humor and fierce loyalty caught the eye of others. The guesses at what was in him were wild and varied. It got me studying dogs in a way I'd never considered. 

I started by looking at dog DNA. Yuck. 

This is the kind of stuff I am really bad at. I try to process the information and end up going blind and thinking about horses. My difficulty understanding this kind of thing is the reason I was considered stupid, lazy or both, in school. Since those days of pure hell, I've discovered I can learn if I'm interested enough, and can break things down far enough.

I'm really hoping that those of you who get this more than I do will help me clear up the foggy parts.
Here goes: 

Most of the DNA in a cell is stored in the nucleus, but there is a little tiny bit found in the mitochondria, the mitochondial DNA (MtDNA). Researchers studying dog DNA use mtDNA, to compile complete genomes (a dog's complete set of DNA).






The reason researchers studied mtDNA is because they reproduce asexually, independent of the rest of the cell. Regular DNA comes from both parents and mtDNA comes only from the mother.I had a killer Eureka! moment when I realized even these teeny bits of DNA don't need no man to take care of business.

Sexual reproduction creates rapid genetic change in each generation, since the genes from both parents are mixed. On the flip side, mtDNA can change only by mutation, which happens at around one or two percent every 100,000 years.


That means that mtDNA can be used kind of like an evolutionary clock, or maybe calendar is a better description, and show when and where dogs developed throughout history. 

Wolves and coyotes differ by about six percent in their mtDNA, and, according to fossil evidence, separated from a common ancestor about a million years ago. 

Wolves and dogs differ by about one percent; using the wolf-coyote time scale, this suggests that they parted company about 135,000 years ago.

Recent studies show two groups originally split from the wolf, rather than the single event of domestication originally thought. Domestication began in two separate and distinct populations in East Asia. One group developed from the first domestication and the second group came from specific breeding.(Does "specific breeding" mean humans started screwing around with breeding dogs from the get go, or are we talking about limited gene pools?)

There is a competing study that argues that the domestication of dogs happened between 18,000 and 32,100 years ago...in Europe. It is thought European hunter gatherers had dogs long before humans developed agriculture. I say, whatever, I've got my story and I'm sticking to it.

These two groups interbred and backcrossed (breeding with parents and siblings) Backcrossing is one factor in creating breeds (I think-- this is one of my foggy places), because the common origin makes dogs with similar structures.

Then, the two groups became four. Researchers established four matriarchal lines according to mtDNA differences. The largest line includes the genes of most known breeds. The other three formed later and encompass more specific and unique breeds. 

mtDNA stops being useful at this point. It can only show mutations prior to the creation of the modern breeds.

Aaaand it got more complex.

In order to determine the lineage of actual breeds, science switched to loci research, which is based on the location of genes on chromosomes. 




Loci research detects genetic changes that might have occurred because of genetic drift. From what I understand, genetic drift is the random movement of a gene from one chromosome to another. This genetic bar hopping can cause huge changes in dogs in a very short period of time.

Genetic drifts happen in very small populations and after severe reductions in populations. If there are only five or six dog breeding, then the barhopping commences. The same thing happens if say, all the long eared dogs die off and again when a new population of dogs forms from a small group.

Whisper_the_Wind wrote: 
"Genetic drift is when population gets isolated and either 'concentrates' an allele, or 'eliminates' the allele from the population, not so much the gene moving from chromosome to another (happens much more often in plants). With humans selecting for traits ever since dogs started looking to us (I wonder who was really domesticated), the genetics of dogs may never really get clarified." 
 So..dump my WONDEFUL bar hopping visual and go to a frat house with a drunken hazing party in the basement...or said party is busted and all involved members are thrown out of the fraternity.

It gets even more complicated, but I'll be honest, allele frequency made my head hurt, and I decided I had got the drift, (snort) and could move on.

The differences between these bar hopping genes let researchers distinguish different breeds. Then, they found dog breeds can be clustered by ancestry.

So far, these clusters have been broken down into three groups. All breeds of Asian origin, mastiff type dogs, working type dogs and hunting dogs. 

This is where it gets crazy. At least to me. The scientists built themselves this cool map.

You can find it here: http://www.bu.edu/synapse/files/2011/11/F2.large_.jpg



K=2 (yellow) represent the cluster of Asian dogs
K=3 (green and red) represent the cluster of hunting and herding dogs
K=4(blue) are the cluster of mastiffs.

You can see how they overlap.
I also wonder if the biggest group, the hunting dogs are the breeds contained in the largest mtDNA line. 

According to those crazy loci German Shepherds are actually Mastiffs. The two genetically closest breeds to said GSD are the Newfoundland and the Boston Terrier. Border Collies are hunting dogs and Borzoi are herding dogs.

When I think about it, there is a crazy kind of sense to this. We're talking about Nature. When those European hunter gathers decided to keep herds it was their wooly rhino killing Border Collies they turned to for help hanging on to them. We were the ones reshaping the genetic dynasty  of our dogs. It's what we do best.

While I was choking on all of this info I noticed there is an awful lot of theory being used as fact. The words maybe, thought and might showed up a bunch during my research.

It got me thinking about criticism of the Dog DNA tests. I often read, "I have a little white fluffy dog and his test came back saying he was part Keeshond. Seeing how genetically close some of these breeds are, in spite of the visual differences is giving me something to think about.














16 comments:

EvenSong said...

Yikes! I kinda sorta like this kind of science, but you're makin' my head hurt! (It's been awhile since I DID anything with this sort of science, beyond my dabbling with equine color genetics...)

mugwump said...

I was trying to make it simple enough so I could understand it...I'm hoping some of the science nerds out there would jump in and clarify further. I know you're out there...color people and mustang fans come to mind.

KD said...

Woosh!! The sound of this going over my head. I'll read it a couple more times. I just watched a Nova special which claims that the jump from wolf to dog happened quickly and by their choice kind of. I'm so confused! :)

whisper_the_wind said...

I love genetics (my students hate my horse genetic problem from hell), but I don't fully get dog genetics. Plasticity in the species is great because it allows for all sorts of combinations of alleles/genes to work.

Genetic drift is when population gets isolated and either 'concentrates' an allele, or 'eliminates' the allele from the population, not so much the gene moving from chromosome to another (happens much more often in plants). With humans selecting for traits ever since dogs started looking to us (I wonder who was really domesticated), the genetics of dogs may never really get clarified.

Like Darwin showed with pigeons/doves, there really aren't enough differences that would not have 'dogs' reverting back to the ancestral type given 100 or so years of truly free interbreeding. I have a friend that DNA'd her mutts and the results came back with her 70lb 'lab' mixes having 45% dachshund DNA. Then again...I cannot explain how my Pit/Boxer mix (and I saw the parents) looks like a red merle Basenji with a Pitbull head.

mugwump said...

Oooh, thanks on the alleles clarification Whisper. Concerning the dachshund/Lab dogs...on the dog gene relative chart Rhodesian Ridgebacks are right next to Dachshunds. Could this mean it's easier for them to cross breed into a Ridgeback size? OR could the DNA test mistake Doxie DNA for a closely related breed?

MichelleL said...

Interesting stuff...so when will you get the test back.

Snipe said...

It makes a lot of sense. Dogs are such a plastic species that a wide variety of expressions can be developed into distinctive phenotypes (appearances) or even functions. Their genetics aren't necessarily distinct enough to identify one breed or the other on the genetic level. The genetic chart instead identifies the link between genes and the geographical area where those genes were known to develop into a distinct, recognizable type. This is similar to the four primary ancestors of domestic horses. Modern domesticated horses are all shapes, sizes, and functions, but they descended from four distinct types that originally came from distinct geographic areas.

For instance, the chart says the GSD is related to the mastiff. They were likely derived from a common ancestral group, which is the molossor in that area of the world, if memory serves.

You could also expect to find covergent traits in different populations. Since you're dealing with similar source DNA (wolf or coyote), you could find similar mutations or crop-outs in different geographical areas, even if the populations did not interbreed for centuries.

Hope that makes sense. Genetics are fascinating.

Anonymous said...

Boy howdy, Mugs, you do go whole hog. My hat's off to you! Best quote ever: "even these teeny bits of DNA don't need no man to take care of business." Even students texting in class will remember mtDNA if we teach using that line, lol! Stealing it!

Whisper nailed my train of thought with population isolation. Picture Marco Polo on the spice trade route to the East, accompanied by European dogs. Then, meeting up with Chinese dogs for the first time, European canine nuclear DNA was getting busy. The breeds that are yellow on the DNA chart were introduced into the red and green breeds.

The phrase "backcrossed" (correct me if I'm wrong) is just a synonym of "line-breeding" as used in the TWH world. Everyone knows it's really incest, but that sounds raunchy and somewhat illegal so polite folks call it something else.

Great post!

Amy in Ohio

Shadow Rider said...

Great info! People ten d to forget that are no real "pure' breeds. they were all developed by crossing a type until it because predominant. One breed history that is fascinating is the Irish Wolfhound. That breed is one of the most ancient, and was used in the development off many other breeds. Then when the breed almost became extinct, it was carefully brought back by crossing with those breeds created FROM it. I'm sure the DNA from them would be fascinating. How much ancient DNA is left? By looking at ancient paintings, and looking at the smaller but mostly identical breed, Scottish Deerhounds they are pretty close to the ancient breed.

mugwump said...

Michelle L and Anon/Amy. - A few weeks...plenty of time to bore you guys with all the research I ended up doing. You're going to find out what an obsessive whackadoo I am...

NotAFollower said...

You might also want to try a different brand of DNA test to compare the two. I have heard of people who tried multiple DNA tests out of curiosity and got back different answers.

NotAFollower said...

This got me to thinking about one breed of dogs known for a specific problem: Dalmatians. There's a project to use backcrossing to develop dalmies that don't have the gene that leads to kidney issues. So, first I looked up backcrossing:
http://www.extension.org/pages/32449/backcrossing-backcross-bc-populations-and-backcross-breeding#.VL1Slu85BbI

Then I looked for a topic about Dalmies: http://www.dalmatianheritage.com/about/schaible_research.htm
Go down to the paragraph headed "Dalmatian-type spotting..."

They were successful in developing Dalmies that don't have the kidney issues. Pretty cool.

Anonymous said...

I had the dog DNA test done on my 90 pound mixed breed dog who I was sure was some kind of Rhodesian Ridgeback/Anatolean Shepherd/Mastiff mix. The test results showed his parents were a purebred German Shepherd and a purebred Boxer. I never saw that coming! DNA tests are fascinating. I can hardly wait to see Brockle's results.

MichelleL said...

I find all this stuff fascinating and I have an Ace In The Hole if I get really stumped, my brother is a molecular biologist - no joke - so you can obsess all you like and I will try to keep up.

Anonymous said...

Considering the Ridgeback is a really modern breed (started in the 1800's South African/Rhodesian (now Zimbabwe) kennel club standard was only established in 1921. prior to that there were more brindles and they sometimes had 4 crowns on the ridge. They've got damn near everything in them - bulldog, mastiff, greyhound, terrier, collie, great dane are all breeds I have seen being attributed to the foundation of the breed, so I think any DNA test that says a mixed breed dog is heavily ridgeback (unless it has a ridge) is possibly a bit sketchy.

mugwump said...

Anon - Most of the dog breeds were created around the time breed shows.From my understanding, the DNA of a Ridgeback, or any other breed, will show true for the first couple generations, after that it gets murky.

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