Originally Posted by Ziphius
What else do they look at? My understanding was that Y chromosome and mitochondrial DNA were the only way to determine ancestry as they are passed on from one generation to the next (ie do not under go recombination).
The best way I can describe it is to draw your family tree for 10 generations, doesn't matter if you don't know the details just draw a template.
At 1 generation you have two ancestors (parents), at 2 you have 4, at 3 you have 8 and for each subsequent generation the number doubles from the previous one (assuming no inbreeding). At 10 generations you have 1,024 ancestors in that generation timeline (for each generation you can use 2^n, n = generation number), add this to all the line above it and you have over 2,000 ancestors going back 10 generations.
Now what Y DNA will look at is the direct male lineage, your father, his father, his fathers father, his fathers fathers father etc and in you tree of over 2,000 ancestors Y DNA will directly link 10 people. Y DNA is useful for trying to trace direct male lineages and from a big picture point of view it might give an idea of population movements.
Now take the Mitochondrial DNA, this looks at direct female ancestry. It takes in your mother, her mother, her mothers mother etc all the way back through the direct female line. In the case of your 10 generation family tree you have now picked up 10 females.
So using just Y DNA and mtDNA you have picked up 20 people out of over 2,000 but yet all these people have contributed to your genetic make up; your grand mother on your fathers side or your grand father on your mothers side etc
The DNA that doensn't get passed down directly like Y & mtDNA is known as autosomnal and comes from the first 22 chromosomes. The technique used to determine shared ancestry with these other people is called Identity by Descent (I think), it looks at what shared genes you have with other people.
Sorry if that is a mouthful but National Geographic used to have a great explanation on their website but it was taken down.