allele: variant of a gene or genetic marker. Each allele is the number of repeats of the short base sequence.

base : the building block of DNA, one of four molecules that link up to make a DNA chain. The four are named adenine, cytosine, guanine, and thymine (A, C, G, T for short).

buccal : pertaining to the cheeks or the mouth cavity in general. Buccal cell samples for analysis can be obtained easily and painlessly by a gentle brushing or scraping of the inside of the mouth.

chromosome :one of the DNA macromolecules found in the cell nucleus. Humans have 46 chromosomes. See also X and Y.

DNA : deoxyribonucleic acid. The chemical constituent of genes and chromosomes. DNA has four different base units, designated A, C, G, and T, which are connected in long double chains, and the sequence of these bases encodes the genetic information.

DYS : DNA Y-chromosome Segment. A label for loci or genetic markers on the Y chromosome. Each marker is designated by a number, according to international conventions. At present, virtually all the DYS designations are given to STR markers (a class often used in genetic genealogy because of their relatively high mutation rate).

gene : a meaningful sub-unit of DNA, encoding a protein.

genome :the entire repertory of nuclear DNA in an organism.

haplogroup :  One way to think about Haplogroups is that a Haplogroup is a branch on the tree of Homo Sapiens and a Haplotype represents the leaves of the tree. All the Haplotypes that belong to a Haplogroup are leaves on the same branch. The Haplogroup database tells you about your deep ancestral origins. A SNP test of the Y Chromosome, which tests deep ancestral Markers, determines the Haplogroup.

The Y Chromosome Consortium has defined 18 major Haplogroups, called A through R, using capital letters. Each of these major Haplogroups, which are also called clades, can have subgroups, which are called subclades. The 18 major groups at the top level, A through R, represent the major divisions of human diversity based on SNPs on the Y chromosome.

haplotype : a set of allele values of many markers measured for one individual and identified as coming just from one parent, particularly markers on the Y chromosome.

locus : (plural: loci) specific site on a DNA chain.

marker : a distinctive sub-unit of DNA, often not part of a gene. Often used interchangeably with locus, but referring to the contents of the site, rather than the site itself.

mutation : An event in which the DNA chain alters. In the case of STR markers, a mutation is almost invariably the gain or loss of one repeat of the basic short sequence (or, rarely, two repeats). Other types of mutations include the substitution of one base for another and the insertion or deletion of a whole segment.

"Mutations are very rare occurrences but necessary to figure out the Most Recent Common Ancestor  (MRCA) of two or more individuals with matching DNA. The Y-Chromosome is passed from father to son and the vast majority of the time the father passes an exact copy of his Y-Chromosome to his son. This means that the markers of the son are identical to those of his father.

However, on rare occasion there is a mutation or change in one of the markers. The change is either an insertion or a deletion. An insertion is when an additional repeat is added to a marker. A deletion is when one of the repeats is deleted. 

Mutations occur at random. This means it is possible for two distant cousins to match exactly on all markers while two brothers might not match exactly. Because of the random nature of mutations we must use statistics and probability to estimate the Time in generations to the Most Recent Common Ancestor (TMRCA).

The actual calculations of TMRCA are mathematically complex and depend on knowing the rate of mutation and the true number of mutations. At this time there is not enough data to accurately determine either of these factors so certain assumptions have to be made. Rate of Mutation = .002. This assumes that any given marker has a .002 chance of mutating with each generation. In other words, we could expect any marker to mutate once in 500 generations. The rate of .002 is considered conservative and is the average of a number of studies. It will result in a TMRCA that is longer than higher mutation rates."

As more markers are tested on our samples more will be revealed as far as finding the generation of where their Most Recent Common Ancestor (MRCA) occurs. Excellent discussions and graphs on the importance of the MRCA can be viewed at  http://www.ftdna.com/faq2.html and http://blairgenealogy.com/dna/dna101.html .

PCR : Polymerase Chain Reaction. A chemical process that replicates a given sample of DNA many times, in imitation of natural replication. The process cycles between two stages: splitting the two strands of DNA apart and then forming new double strands by adding a mixture of the four DNA bases. By adding primers as well, the process can be used to replicate just the one or more DNA segments of interest.

primer : a reagent consisting of a relatively short DNA sequence exactly matching the sequence flanking a marker of interest. A primer needs to be long enough that (in principle) it matches only one spot in the entire human genome, but, in practice, many segments of human DNA appear more than once, through a poorly understood process of duplication. Two primers, one for each end of the desired marker, are used in the PCR amplification step to selectively amplify that marker. The primers are often tagged with a fluorescent dye to help in detecting the amplified DNA segments.

STR : Short Tandem Repeat. Also known as microsatellite. This is a genetic marker consisting of multiple copies of a short sequence of DNA bases (typically three or four). Occasionally, one will mutate by the gain or loss of one repeat.

X : one of the two sex-determining chromosomes, See also Y.

Y : one of the two sex-determining chromosomes. A person with the combination XX is female, while a person with XY is male. The Y chromosome, unlike the others, does not trade DNA with a "partner chromosome," and it therefore passes intact from father to son. This property leads to a minimum of ambiguity in interpreting the results of Y DNA analysis.