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APPENDIX 2:
"Haplogroups" are, in a sense, genetic fingerprints that characterize a group of people. For example, Ireland has several regions in which there are groups of ancient families who have lived in their same region for generations, and in which the Y-DNA of male members from their regional group is genetically distinct from the Y-DNA of men living in other regions. These genetically-defined, local populations are known as "Y-DNA haplogroups". There are also "MT-DNA haplogroups", but these are based on mitochondrial DNA intead of chromosomal DNA. The "haplo" prefix in the above cases refers to a single chromosome, as in the Y-chromosome that only men carry. It can also refer to the mitochondrial DNA that we all carry, irregardless of gender. By contrast, "diplo" refers to a pair of chromosomes, as in the diploid chromosomes that are examined in an autosomal DNA analysis, where one of the chromosomes is passed on from a father to his child, and the other chromosome comes from the child's mother. 
Men contain within the DNA molecule of their Y chromosome thousands of basic, functional units that are called genes. These functional units can also be characterized as groups of "DNA markers" that are inherited as single unit from one parent. Some genes determine physical traits, such as eye color, whereas other genes may control body functions. However, many genes are thought to be just "filler" that does nothing at all. Alleles are variations or alterations of genes, such as the different genes/alleles that control eye color, and which result from the presence of inherited mutations. In other words, alleles are alterations/mutations that evolved over the generations from an original gene. Although the mutations that transform genes into alleles are infrequent, and therefore rare, they account for much of human diversity. Also, because the mutations that create alleles are subsequently passed down from parent to child over the generations, they form a genetic record that we can use to characterize our ancestry. "Haplotypes" and "Haplogroups" are related terms that are easily confused with each other. A haplotype is a group of DNA markers on an individual chromosome that are inherited as single unit, and tend to be inherited as a single group by people sharing the same ancestry. Although most of these groups of DNA markers are "genetic filler" that do nothing, they are completely analogous to the genes and alleles that control traits, such as male baldness. Haplogroups differ from haplotypes in that they are larger, more inclusive units, which contain haplotypes that share a common ancestral mutation. For example, a haplogroup not only includes the given parent haplotype that defines the group, but also all the downstream haplotypes (i.e., genetic children) that evolved from that parent haplotype over the centuries. A haplogroup is in essence a genetic nation that includes all the haplotype communtities within that nation. Mutations not only transform genes into alleles, but they also change one haplotype into another. Thus, the presence or absence of certain mutations form the basis by which different haplotypes and haplogroups are identified. These mutations are known as "single nucleotide polymorphisms", or "SNPs". Another way of looking at SNPs is to consider them as locations on a DNA molecule where the composition has changed. In other words, an SNP is where a mutation has taken place. A DNA molecule is shown on the right, and it is made up of building blocks called nucleotides, of which there are four - Adenine, Thymine, Cytosine and Guanine. Each nucelotide is joined to another to form a "base pair", and the simplest way to create a mutation, and thereby also create an SNP, is to simply remove one of the "base pairs" from the DNA molecule. Thus, identifying the SNPs in a sequence of DNA is how we identify haplotypes, in order to ultimately characterize haplogroups. The ultimate grandparent haplotype is L1085, also known as "Y-DNA Adam", which evolved perhaps 140,000 to 300,000 years ago, and is thought to be the original upstream haplotype from which all subsequent downstream Y-DNA haplotypes diverged from over the millenia. Furthermore, every human on this planet, so far as we know, is a member of the L1085 Haplogroup, and descends from "Y-DNA Adam". Haplogroups also represent branches on a "Y-DNA genetic tree". The so-called "Y-chromosomal Adam", who is the common ancestor of all men alive today, sits at position A0 at the top of this tree. Then branching down from him are the haplogroups of all living men. Because members of a haplogroup share a common ancestor, the haplogroup branches on this tree are also clades and subclades, where a clade is a major branch, and subclades are minor branches below clades. Branching down from Y-DNA Adam is the R1b branch (Major Haplogroup M343), which is the clade that most people in Europe belong to. Then branching down from M343 is the M269 Haplogroup, which is the R1b subclade that is most common in western Europe. Continuing down from M269 is the L21 Haplogroup, beneath which are various Irish and Scottish haplogroups (L21 subclades), some of which we discuss more fully under "Celtic Haplotypes of Ireland". The maps below show the major haplogroups found in Europe today, and the most common subclades of the R1b Haplogroup. The "Y-DNA Terminal Haplotype" is the youngest-known haplotype (mutation) that is known for a given man. In other words, it is the lowest-known position for that individual on their Y-DNA ancestral tree. It obivously is dependant on the amount of detail you can expect from a given DNA analysis, and generally the more you pay for an analysis, the more detail you can expect. Thus, the only way to know for certain what the ultimate Y-DNA terminal haplotype is for someone, is to sequence their entire Y chromosome, which might entail considerable cost. This means that the terminal haplogroup you get from a DNA analysis by 23andMe or Living DNA will likely change if you do a more expensive Big Y-700 analysis from Family Tree DNA.
Maps of Major Haplogroup Distribtions in Europe
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A Short Introduction to Y-DNA Haplogroups 
