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.