How DNA Genealogy Works
Let us first discuss briefly the science behind the project. The Y-chromosome looks like a fuzzy lowercase “y” with small strands of DNA material looking like hairs sticking out from the arms of the “y”. Only males have Y-chromosomes, thus, unlike the remaining chromosomes which are mixed in each generation, each male inherits his “y” only from his father. Each “hair” of DNA on the Y-chromosome always occurs at the same place so that locations (called short tandem repeat or STR markers) can be numbered just like street signs. When you see the extensive charts of numbers such as 13-24-14-10 that means that at the first listed location the STR was 13 units long of repeating DNA; the second location was 24 units long, etc. There is no magic order in which STR data is presented; we use the Family Tree DNA (www.familytreedna.com) order convention for the first 111 numbers (markers) because Family Tree DNA has been our primary lab for STR testing since 2003.
The significance of the numbers is very simple: the larger the fraction of them that match between two people, the more closely the two people are related.
As the genetic structure of the Y-chromosome is being replicated, slippages or mutations occur. By definition mutations are random and can happen once each generation or once in a thousand generations. Thus, all of our answers are based on probabilities rather than fixed mechanical calculations.
Persons are also identified by "Haplogroups" like R1a-L176 (called by FTDNA R-L176) or I-M223. The mutations that define Haplogroups change much more slowly than the ones that define Haplotypes, but there are far more possible places a mutation can happen (over 10 million). It used to be said that people in different haplogroups cannot be related in the last 2000 years. This is still true for the part before the dash, but in some cases the overall Haplogroup can have originated recently, for example, R1a-CLD12 originated in the year 1352 with the birth of Ranald mac Donald, 1st of Clanranald and Glengarry.
The mutations on the Y-chromosome do not identify us as blonde, brunette, redhead, tall, short, thin, stocky, swarthy or fair, smart or dull. There is no first or last prize for having the most or fewest mutations from a single common signature.
You have probably read about "genetic testing" or "genetic counseling" for various diseases. The parts of the Y chromosome tested for genealogy purposes are not related to any disease. However, one marker, DYS464, is very rarely related to male infertility. If you already have children, this of course cannot be a worry to you. In any case, the probability of this being detected is extremely small.
For an optional longer discussion of the DNA science here on this web site, which explains lots more of the jargon, go to Doug's Intro pages. There are other many studies and websites which provide excellent discussions of the scientific issues behind the studies. You can click on a link to each of those studies by clicking on National Geographic Society (very slick but superficial) or the International Society of Genetic Genealogy. Questions may be addressed to the Genealogy-DNA discussion board at rootsweb.com, which is populated by many very knowledgeable but often opinionated people, or the forums at familytreedna.com.