Words & DNA

TERMINOLOGY

When we get our results or even beforehand, if we join groups and read the pages at testing sites, we encounter new terminology that quickly makes us feel really dumb! Fear not – it will all become clear with time. Here are some common questions and answers to get you started. Then you can proceed to some articles and find/join groups and projects that will help you along :)

What is CRS? When you get your results, the numbers plus letter (like 16223T or 73G ) shows what is different from the CRS – Cambridge Reference Standard (now the revised CRS — rCRS). All results are compared to this and the differences are noted. Basically it refers to one person who was tested in 1981 and then those mtDNA results have been used as the "normal" or standard ever since. While the differences are sometimes referred to as ‘mutations’, they are not in the true sense. The CRS is merely a reference sequence sample and not a record of the earliest human mtDNA.
Links:
Human Mitochondrial DNA Revised Cambridge Reference Sequence
Reanalysis of the Cambridge Reference Sequence

HVR

What is HVR1 and 2? HVR means ‘hyper variable region.’ HVR1 locations are numbered 16001-16568. This first part will define your haplogroup (usually) and you will have many matches at this level. If you are going to test, then do the Plus test at the very least, which includes HVR2 locations that are numbered 001-574. Some testing facilities test to 574 and include this in the HVR2 results. (and some do not) More on that in Choosing A Testing Facility.

The HRV1 and HVR2 are ‘control regions’ that contain no personal information because they are not part of the ‘coding region.’ Additionally, they have the fastest rate of mutation as compared to other regions of mtDNA and that makes it invaluable for tracking populations. Bases 16001-16568 covers HVR1 16,024 to 16365. This corresponds to FTDNA’s basic MtDNA test. Bases 1 to 400 covers HVR2 73-340 in your report. Bases 401 to 576 covers HVR3 438-576. FTDNA includes this section in their HVR2 results which is their mtDNA Plus test.
Links:
DNA Heritage mtDNA graphic courtesy of DNA Heritage

What Are Haplogroups? A haplogroup is an ethnically distinct lineage as traced through mitochondrial DNA. It is said that simple HVR1 results can identify the group you belong to. To an extent this is true – but that’s not the whole story. To correctly determine haplogroup, parts of the coding region must be looked at. The HVR1 & 2 results come from the non-coding region and as such, can only act as pointers to the most likely haplogroup. Real confirmation comes from the Coding Region. See Haplotype / Haplogroup definitions below.

Haplotype – /hap•lo•type/ – A set of numbers or letters obtained from the DNA test of an individual. A set of alleles for genetic markers (aset of gene or genetic marker DNA sequences) inherited as a unit. A contraction of the phrase "haploid genotype". Different combinations of polymorphisms at a set of polymorphic sites are known as haplotypes.

The term haplotype is commonly used term in Genetic Genealogy for the series of DYS STR numbers which are the alleles of the test results of a set of genetic markers of a Y chromosome paternal line DNA test. The test results of the maternal line mtDNA test is also a haplotype and is expressed as a set of alphanumeric alleles.

Note: Y-DNA haplotypes are not unique to an individual but are Y chromosome DNA signatures carried by all related males who share a direct paternal line common male ancestor. Likewise mtDNA haplotypes are not unique to an individual but are mitochondrial DNA signatures carried by all individuals who share a direct maternal line common female ancestor. Compare to Haplogroup and CODIS. See STR, Genotype, Y-DNA Haplotype, mtDNA Haplotype, and Atlantic Modal Haplotype.

Haplogroup – /hap•lo•group/ - A group of similar patterned and related descendant haplotypes which share a common ancestor defined by a unique event polymorphism (a one-time SNP mutation) at a specific locus in their DNA sequence, i.e., a UEP. Haplogroup branches are assigned alphanumeric designators by geneticists. These alphanumeric haplogroup branch names are diagrammed in tree format on a chart to link human beings together to form a Phylogenetic Tree.

There is a Phylogenetic Tree for the male lines of descent and one for the female lines of descent. For example for the male line mode of genetic marker inheritance, the Y chromosome, R1b1 is the Y chromosome haplogroup branch alphanumeric label given to those who test positive at the UEP SNP locus P25, i.e., P25+ means you are part of the Y chromosome haplogroup sub-branch named R1b1 and your Y chromosome would be located on that part of the YCC Phylogenetic Tree. R1b1 would be a smaller branch of R1b. R1b would be a smaller branch of R1. And R1 would be a smaller branch of the major branch R. For the female line mode of genetic marker inheritance, the mtDNA molecule, H1 is a common alphanumeric haplogroup sub-branch for the major H haplogroup branch for the maternal line mtDNA molecule Phylogenetic Tree.

Different sets of alpha-numeric designators are given to male Y-DNA haplogroup branches and female mtDNA haplogroup branches. A commonly occurring paternal line Y chromosome major haplogroup branch found in males tested today is the alphanumeric R1b, which is found in high frequency in Western Europe males and direct male line descendants of European males from that area. A commonly occurring maternal line mtDNA major haplogroup branch found in people tested today is the letter H and is found in high frequency in Western Europe and direct maternal line descendants of European descendants from the area.

The major maternal line mtDNA haplogroup branches have been even further personalized by Dr. Brian Sykes in his book, "The Seven Daughters of Eve." Since the mtDNA haplogroup branches represent common maternal lines, he gave the haplogroups female names which correspond with the first letter of those major mtDNA haplogroup branches. He also made up a little story about each of these seven female ancestors in his book to try to describe their life and times 10′s of thousands of years ago when he surmises they lived in various parts of what is now Europe.

Haplogroups are mainly used for anthropological research and deep ancestry research for time frames long prior to the adoption of surnames. We’re talking 10′s of thousands of years ago when these haplogroups became defined. Knowledge of one’s haplogroup, while interesting, does not typically provide much assistance to the genealogist other then pointing to a large geographic area of the world where that haplogroup is found in high frequency. For traditional genealogical research, haplotypes are more important than haplogroups. While the definitive test to determine your haplogroup is a SNP test, many times your haplogroup can be estimated with a reasonable confidence level based on your haplotype test result data. There is quite a bit of dialog online about estimating and knowing one’s haplogroup. But as I said, knowing one’s haplogroup is of very limited use to traditional genealogical research which is typically focused on the last several hundred years.

DNA EXPLAINED

 

DNANucleotides are the building blocks of DNA. The definition of DNA is: A nucleic acid that carries the genetic information in the cell and is capable of self-replication and synthesis of RNA. DNA consists of two long chains of nucleotides twisted into a double helix and joined by hydrogen bonds between the complementary bases adenine and thymine or cytosine and guanine (the A,T,C,G you see in your results). And more simply — The sequence of nucleotides determines individual hereditary characteristics. There are 4 different nucleotides : * dATP : deoxyadenosine triphosphat * e dGTP : deoxyguanosine triphosphate * dTTP : deoxythymidine triphosphate * dCTP : deoxycytidine triphosphate These are also know an (AKA) dNTPs (deoxynucleoside triphosphates). A nucleotide is made of three major parts : a nitrogen base, a sugar molecule and a triphosphate. Only the nitrogen base is different in the 4 nucleotides.

DNA

DNA is formed by coupling the nucleotides between the phosphate group from a nucleotide (which is positioned on the 5th C-atom of the sugar molecule) with the hydroxyl on the 3rd C-atom on the sugar molecule of the previous nucleotide. To accomplish this, a diphosphate molecule is split off (and releases energy). This means that new nucleotides are always added on the 3′ side of the chain.

DNA2

above two images courtesy of Andy Vierstraete at Avierstr