The term Haplogroup and Haplotype are similar and misappropriated in the genetic genealogy community as they have been more strictly defined in biological sciences. So any definition here is subject to criticism depending on your background.

A Haplogroup in genetics is defined as a group of individuals with one or more SNPs that are derived and shared. A member of a haplogroup is positive for change in all the alleles in the haplogroup (that is, all the SNPs are derived). There may be only one SNP to define a haplogroup but often there are tens to hundreds. Often, a primary SNP is designated and used to name the haplogroup. See YCC for more information on naming.

Historically, haplogroups were defined for more ancient, anthropological-defined populations. And they only came into genetic genealogy) to help verify that those with similar ((haplotypes, defined by STR values, were truly in the same haplogroup. But more recently, due to NGS testing, much more extensive maps of known SNPs are being made. As a result, haplogroups are being tracked to the near genealogical time frame within 500 years ago. As a result, haplogroups are now being defined for particular surname lines.

Deeper studies show that the order of when SNPs changed can likely be determined. So multiple haplogroups may be defined where one is a proper subset of the other. A subgroup, or subclade as it is also termed, can then simply be defined as later in time. A benefit is that only the SNPs that are unique to the sub-clade can be used to define that haplogroup; leaving the earlier-in-time changed SNPs (that is, the proper subset of SNPs) to be defined by the earlier haplogroup. This ordering (more properly, a mathematical partial order) of haplogroup definitions is then termed a phylogenetic tree (and is more properly, a mathematical spanning tree with a defined root) When you hear the term haplogroup tree, they are really referring more properly to a phylogenetic tree made up of haplogroups as the nodes (that is, branch points and leaves). But as the informal genetic genealogy community has co-opted the incorrect terminology, we feel compelled to go along here. See YCC for more information on naming.

Generally, haplogroups in humans are only defined for SNPs on the yDNA and mtDNA strands. This because they do not recombine and are stable for thousands of generations (tens of thousands of years). But who knows. As the field of genealogy and genetic anthropology intertwine even more, maybe they can start identifying autosomal and X SNPs as belonging to a haplogroup also.

Major Y DNA Haplogroup Tree Sites

Major Mitochondrial Haplogroup Tree Sites

  • PhyloTree: Tree
  • FamilyTreeDNA: (only available by login to those tested on that site)
  • NGG: (only available by login to those tested on that site) (see Trees for a hint)