Most of us are not geneticists, so here is an attempt at a plain language guide to some of the terms used. Words defined elsewhere in the alphabetical list are given in italics:

• Allele - any of two or more genes that have the same relative position on related chromosomes

• Allele Value - The number of repeats of the short nucleotide sequence in the locus, obtained by adding a fixed offset to the score (see DYS charts)

• AMH - a common haplotype known as 'Atlantic Modal Haplotype' found in surnames along the Atlantic coast in Europe. Defined as R1b, it is further defined by DYS 19, 388, 390, 391, 392 & 393 with repeats 14, 12,  24, 11, 13, & 13 respectively.

• Chromosome - A group of several thousand genes. Humans are defined by 22 pairs of chromosomes plus X & Y. An  X chromosome pair defines a female, while an X & Y pair defines a male (23 pairs in all)

• CRS - Cambridge Reference Series otherwise known as haplotype H for mtDNA (more recently refined to be H2b

• DNA - Deoxyribonucleic Acid; the main constituent of chromosomes - the double helix containing the chemical code that defines who and what we are. The main four chemical bases that make up that code are Adenine, Thymine, Cytosine & Guanine (indicated by their first letter)

• DYS (number) - DNA Y Chromosome unique Segment, also known as microsatellite loci (pronounced "lo-see" In Europe and "lo-si" in the US). The numbering scheme is controlled by the HUGO standards body. These loci are where the genotyping takes place, however caution is advised when comparing results between different labs as full international standards are yet to be established

• Gene - A unit of heredity, capable of replication and mutation, occupying a fixed position on a chromosome, and passed on from parents to offspring during reproduction

• Genetic Distance or GD - The difference in the number of mutations between individual samples

• Haplogroup or Clade - A group of individuals sharing the same haplotype and therefore share a common ancestor. In the case of mtDNA they have motifs such as H, T, U, X, etc., which have been popularized through the use of virtual maternal clan names such as Helena, Tara, Ursula, Xenia, etc. Y-chromosome haplogroups have been given names relating to locations where they commonly occur, such as AMH.  8 Y-chromosome haplogroups in Europe are connected by a defined mutation event. These are defined by DYS & UME. A haplogroup is defined by "slowly" mutating loci (cf. haplotype), so matching or close matching haplotypes belonging to different haplogroups are not closely related genetically

• Haplotype - The results of the Y-chromosome test that can be used for DNA matching. It can be a single or unique set of chromosomes. Haplotypes are described by the number of base repeats (A, C, T or G) at the microsatellite loci (DYS) and in general are defined by "rapidly" mutating loci (cf. haplogroup). The Extended European Haplotype is defined by loci DYS 19, 385 I/II, 389I, 389II, 390, 391, 392, 393, YCAII a/b

• HUGO - Human Gene Nomenclature Committee; a standards body

• HVS-1/HVR-1 - When geneticists test mtDNA, they look at an area where mutations are most likely to occur. Then they compare the result to a standard reference series (CRS) to see which bases are different. One common region to test is Hypervariable Segment 1 (HVS-1) also known as Hypervariable Region 1. HVR-1 starts at base 16,001 and looks at the next 400 or 500 bases. More detailed analysis includes HVS-2. People with an identical HVS-1 panel are currently thought to have a time to MRCA of about 52 generations (median value), whereas an additional match of the HVR-2 panel gives a median number of 28 generations. My direct maternal line only goes back to 1818 and 6 generations

• Mitotype - Deviations or mutations found in mtDNA tested HVS-1 or HVS-2. Compared to the reference series (CRS) my results, as an example, showed the following mutations at bases on HVS-1: 16126C, 16163G, 16186T, 16189C, 16294T & 16519C & on HVS-2: 073G, 152C, 183G, 195C, 263G, 309.1C, 315.1C. This defines my mitotype. The base numbers are often shortened to 126, 163, etc. Larger groups of mitotypes are called haplogroups. mtDNA haplotypes are also referred to as mitotypes. I belong to haplogroup T1a (as defined by Pike), part of "clan Tara", a direct maternal ancestral origin estimated about 17,000 years BP in Tuscany. As T1 has recent origins, there has been relatively little time for mutations (est. 7000-8000 years BP) so a large number of matches will be found all over northern and southern Europe west of the Urals. It is estimated 1% of Europeans have the same, so millions of us have the same mtDNA roots. Frustratingly, most sites that further define T1 are located in mtDNA coding regions not part of commercial sequencing at this time. Currently it is considered that if you match mtDNA (both of HVS-1 & HVS-2), then common maternal-line ancestry probably goes back 350-1,250 years

T1 mt-Haplogroup project

For those part of "clan Helena", my wife's mtDNA (Irish ancestry) is coded with only two mutations 16179T & 16304C (based on the first 400 bases). Helena is the most widespread, with origins about 20,000 years BP in the borders of present day Spain & France. 304C (along with 519C not tested for) defines H5a, with origins 7000-8000 years ago in Central Europe post-Ice Age recolonisation. Alternatively, she is in subclade H1, noting that the mutation at position 179 is rare, and probably happened first. 304 is much more mutable. You can check your mtDNA at Mitosearch

• MLE - Most Likely Estimate when your MRCA appeared (using a 50% probability)

• MRCA - Most Recent Common Ancestor (between two people)

• mtDNA - Mitochondrial DNA. Found in all cells and passed on only by a mother to her offspring, i.e. preserved through the mother-daughter relationship only

• Mutation - It is estimated that a mutation occurs once every 500 generations per loci. (Assuming five generations per century, this would be a mutation every 10,000 years*). This gives geneticists a tool for estimating how far back a common ancestor may have been shared by two individuals. In the case of 12 loci being genotyped, then this would provide a probability of at least one mutation every 40 generations, or 800 years (using the same assumption above). Since a large proportion of the Eurasian population was wiped out in the C14th by the Black Death (up to a third in the period1348-50), then for those of European & Asian origins this should provide a good guide to any common ancestor that survived this pandemic. It was also a time when many modern family names were being established. It should also be noted that a particular mutation, which may define one branch of the family tree, can, in some cases, mutate back! [*some demographic experts suggest an average of 18 years per generation prior to the Industrial Revolution and 22 years per generation since]

• Mutation Rates - Reference Y-STR(67) haplotype mutation rate (ystrHMR67) calculations:
  
  .002 x 67 DYS STR markers = .134 per birth of new generation. (1/.134)=7.5. A new mutation can happen at any time but a 67 marker haplotype using the .002 historical mutation rate indicates it can typically survive unchanged since the generation of the prior mutation event for a bit more than seven generations. Random matches will be minimal, if any. The resolving power of a 67 marker test places the most likely time to recent common ancestor definitely in a time frame of genealogical interest and a time frame when many male lines had already adopted their surnames and written birth records started to be maintained. If you share the same or similar surname and match closely with a 67 marker test you probably share a genealogically relevant most recent common male ancestor even if not known via the traditional evidence. A more recent study by FamilyTreeDNA indicates the average Y-STR marker mutation rate may be more like .004. .002 was based on fewer markers in earlier tests, therefore:

.004 x 37 DYS STR markers = .148 per birth of each new generation. (1/.148) = 6.8 generations from MRCA
.004 x 67 DYS STR markers = .268 per birth of each new generation. (1/.268) = 3.7 generations from MRCA

• Score - The private code used by a lab. Add a fixed offset to the score to get the allele value (see DYS charts)

• SNP - "snips"; Single Nucleotide Polymorphisms. The substitution of one DNA base for another. This are commonly tested for to further define subclades. The following results placed me in the former R1b1b2g (FTDNA 2008nomenclature):

• UEP - Unique Event Polymorphisms used by the YCC. Mutations which presumed have occurred only once in human history because the observed mutation rate is so very low

• UME - Unique (or near-Unique) Mutation Event that can be used to further define a haplogroup. These are diallelic markers notated as SY81, SRY4064, YAP, SRY1532, SRY10831, M13, M9, TAT, M20, SRY+465, 92R7 & M17, as examples. The Basque population is a subclade defined by a mutation at SRY2627. These UMEs are included in the new Y-chromosome tests for genealogy and are part of the new YCC nomenclature. See also SNP.

• YCC - Y-Chromosome Consortium introducing a new and standardised nomenclature for haplotypes.  http://ycc.biosci.arizona.edu/nomenclature_system/frontpage.html
  The nomenclature is based on results of UEPs, including SNPs and indels (insertions or deletions of DNA segments). Note: Genealogical testing is done on other kinds of mutations with a higher mutation rate, whereas population geneticists use the slower rates for the bigger picture.

Caution: It is important to note that this is a developing science and includes assumptions, estimates and statistical probabilities. Exact matches will show a clear, recent MRCA, while one or two differences will indicate common ancestry much further back in time.

Feedback (amendments, suggestions) on technical aspects of this page are welcome!