20 November 2008

DNA -- A Foreign Language

Most people who attend a DNA lecture for the first time walk away with more questions than they may have had before the presentation. That definitely sounds as if understanding DNA is greatly difficult or the presenter cannot deliver the information in an understandable form. In truth, understanding how DNA testing works and how it benefits genealogy is very simple once you learn the language.

If you have taken a foreign language you know that repetition is one of the best ways to retain the knowledge. You also know that you cannot learn a great deal in one session. These are true of understanding Genetic Genealogy, the use of DNA Testing to aid traditional genealogical research.

SO…how do you push this new language into your brain?

Like learning a new language, you must understand some new words. Although there are hundreds of terms associated with DNA, the average person only needs to know a few basic ones.

1. Y-chromosome DNA (Y-dna) – The sex chromosome which determines that a person is male. Men have both their father’s Y-chromosome and their mother’s X chromosome. Women have an X chromosome from their father and one from their mother. The Y-chromosome has passed from father to son virtually unchanged since mankind began. This is why we can test a living male and determine the DNA signature of his all male line (top line of a pedigree chart) back to the beginning. These tests are referred to as Ydna tests. There are several levels of Ydna tests and each designates the number of markers which are tested. For example, Family Tree DNA tests 12, 25, 37, and 67 markers on the Y-chromosome.

2. Mitochondrial DNA (mtDNA) – The mitochondria is outside the nucleus of a cell. It contains 16,568 base pairs. The part of the mitochondria that is tested for genealogy purposes is the non-coding/control region, meaning it rarely changes or mutates. This is the part that is used as a check to make sure the copy process worked. It does have a function. Most people test the parts are called the Hyper Variable Region 1 and 2 (HVR1 and HVR2). Testing the full sequence includes HVR1, HVR2, and the coding region. This is the only definitive mtDNA test. It is scary though because it may reveal medical information. One medical problem that comes from a bad mtDNA mutation is LHON. You can read about LHON here:

Both males and females have mitochondria. Only the females can pass it to the next generation, however. That is to say, a mother gives all her children her mitochondrial DNA, but only the daughters can pass it to the next generation. For this reason we can test the mtDNA of a living person and determine the DNA signature of his or her all female line (bottom line on a pedigree chart) back to the beginning. Tests for the mitochondrial are often called mtDNA tests and can either involve the HVR1 or both the HVR1 and HVR2 and are numbered as follows:

Region: Positions
Hyper Variable Region 2: 00001-00574
Coding Region: 00575-16000
Hyper Variable Region 1: 16001-16569
mtDNA forms a circle so 00001 comes after 16569.
(This chart courtesy of Rebekah C.)

3. Autosomal DNA (atDNA) – The 44 non-sex chromosomes. These chromosomes recombine or mix together differently (re-code) with every conception. This is why you look like a sibling or other relative, but not exactly, unless you are identical twins. This part of the DNA is not useful for genealogy, but very useful in determining paternity or sibling relationships. The atDNA also contains your health issues…at least those known currently by scientists.

4. Allele – The term used for the result of a tested marker. In Ydna, the number for the specific marker is the allele (Ex: DYS 393 has a 13). In mtDNA the marker results is the chemical bases. (Ex: 156G)

5. Haplotype – a set of allele values (i.e., the result of a DNA test) for a group of markers. This is your DNA signature. If the test was a Ydna test, then the set of values are a series of numbers, one each for each marker tested. If the test was an mtDNA test, then the results is show with a letter of one of the chemical bases. Only the mutations that occur when the mtDNA is compared to the Cambridge Reference System are designated.

6. Haplogroup – a group of similarly patterned Haplotypes which share a common ancestor as defined by a unique event polymorphism (one type mutation) at a specific locus (location). It is a tester’s twig on the World Family Tree (Phylogenetic Tree). Haplogroup names are a series of letters and numbers, starting with a letter. For example: R1b1b2. This is a Y-dna haplogroup and each letter and number indicates a smaller branch. That is, R is the branch of the World Family Tree and the one following the R is the subset under that R branch. This means there is an R2 as well. Then the next letter, b, is a subset of R1. This means there is an R1a, also.

There are haplogroups for mtDNA which are designed the same way. For example: U5a1a. This means the U branch on the World Family Tree and the twig from it is 5. Therefore, there is a U1 twig, a U2 twig, etc.

NOTE: Do not compare the haplogroups for Ydna with mtDNA…they were developed separately. They are apples and oranges.

7. Phylogenetic Tree – The pedigree chart for every man or every woman in the world…The World Family Tree. Just like genealogists have a pedigree chart, all of mankind and womankind each has a pedigree chart. The chart cannot use surnames as surnames were created after DNA groups were determined; therefore, a series of letters and numbers are used. Geneticists have been able to determine the order of development of these branches and twigs on this tree. Groups on the Phylogentic Tree have "names" such as: R1b2, I2b, K2.

8. DNA Chemical Bases – DNA is made up of four chemical bases: Adenine, Cystosine, Guanine, and Thymine. These are abbreviated A, C, G, and T. They are always in pairs, and they always pair the same way. A pairs with T and C pairs with G.

9. Mutation – a change in any marker. Mutations in the autosomal markers could result in situations damaging to the species, but mutations in the non-coding region do no harm. The markers tested for genealogy are in the non-coding region and include the HVR1 and HVR2 for the mtDNA and specific markers of the Ydna.

10. STR – Short Tandem Repeat. A short pattern of the four chemical bases repeated in tandem (next to each other). The number of times this sequence is repeated determines the allele (result) of the marker. For example: GATAGATAGATA is a pattern repeated three times. Thus the marker result (allele) would be 3. Markers are known to repeat their patterns more times than three, however. Each marker has a range in which it repeats. That is, DYS 393 is known to repeat its pattern from 9-17 times, so the result of that marker in a tested person could be any number from 9-17.

11. SNP (pronounced “snip”) – Single Nucleotide Polymorphism. This is a mutation (change) in the marker of a nucleotide. Nucleotides are unique markers in the genome. For example the chemical basis G (Guanine) may change to a T (Thymine). This is done only once in this nucleotide, and these changes determine what haplogroup a person is. There is no harm to the species with this change. SNPs have unique names, such as M207 or P224. The test is either positive or negative for the particular SNP, and this helps determine where a tester is on the Phylogenetic Tree. A person can have a SNP test to determine the detailed twig on their haplogroup branch. That is, testing various SNPs helps determine if you are a U5 or a U5a1a. The more SNPs tested, the more detailed the haplogroup will be.

12. DYS (DNA Y-chromosome Segment) – a locus (location) on the Y-chromosome. Examples of the names for the markers for the Ydna, include DYS 393; DYS CDYa; and DYS 464c.

13. Cambridge Reference System (CRS) – The first sequence completed for the human mtDNA and is now been corrected or revised and is called the Revised Cambridge Reference System. Everyone uses the acronym CRS, however. The sequence contains 16,568 base pairs and was recorded at Cambridge, England, hence the name. All mtDNA results are compared to the CRS, and only the differences from that comparison are recorded as the test result. You can see the entire sequence by using the link listed below. Marker result for mtDNA gives the number of the marker (from 1 to 16,568) and then the letter of the chemical bases that mutated). For example: 15326G

14. DNA Project – An established group of tested people. DNA Projects include those with a specific surname and its variant spellings for males. For both male and females there are haplogroup projects, geographical projects, and ethnic projects. Not every testing company offers this variety of projects, so investigate the various companies and what they offer before testing.

The benefits from these projects do vary. For a surname project a male can determine if they do descend along their all male line with this surname. Sometimes one finds there was a Non-Parental Event (adoption, illegitimate birth, name change, etc.) For the geographical projects, you may find close relationships to a geographic location which could help direct you in your genealogy research. For haplogroup projects your haplotype (DNA signature) can help those interested in the migration patterns of our most ancient ancestors understand more.
With ethnic groups, a collection of haplotypes also provides more data to further the understanding of various cultural groups. Often project managers analyze the data and develop hypotheses which helps further the study of DNA and how it can help genealogy.

Besides reading the above definitions, Google the terms on the Internet to find variations which will help you better understand as you can view different ways the term is explained.

Once you learn some vocabulary of a foreign language you are ready to form phrases and sentences. The same is true of Genetic Genealogy. Using the above terms, the following sentences are true, and you only need to complete the statement with the above word that fits correctly. Can you answer them without looking at the above list or the answers below?

1. What are the three types of DNA which can be tested?

2. What are the four types of DNA Projects?

3. What is the collective result of a DNA test called besides a DNA signature?

4. What is your twig on the Phylogenetic tree is called?

5. Males can test their all male lines (the top line of their pedigree charts) with which test?

6. Females and males can test their all female line (bottom line bottom line of their pedigree chart) with which test?

7. Which test is least useful test for genealogy, but the best test for paternity?

8. What is the result of testing a specific DNA marker is called?

9. What determines the number (ex: the 25 for DYS 447) in the result of a marker tested for Ydna?

10. What is CRS?

11. What is DYS mean and which test has them?

12. What is a mutation?

13. What is the Phylogenetic Tree?

14. What is the difference between coding (recombining) and non-coding markers? Which are used for genealogy?

Lastly, you are ready to begin reading more about Genetic Genealogy. You can refer to the articles on this blog; however, there are many online tutorials and books which can help you. Remember to treat them like a reference book and not the “Great American Novel.” Mark in the books if you own them. Print out what you want from the online tutorials. Review the information from time to time to keep your new foreign language readily available.

A list of recommended books and online tutorials can be found in the archives of this blog for February 2007, but they are repeated here for your convenience.

Charles Kerchner's Webpage
This is a wonderful tutorial and array of information on Genetic Genealogy, including book recommendation.

Family Tree DNA Tutorial
This contains a large variety of information on testing. Click on SITE MAP at the bottom of the page to better locate desired information.

Megan Smolenyak Smolenyak's website with many resources. It also lists surname projects from several testing companies.

Dave Dorsey's Website
This site shows how DNA you take your DNA sample for testing

Revised Cambridge Reference Sequence
This is the 16,568 markers for mitochondrial DNA (mtDNA)

Family of Women
The site has many mtDNAHaplogroup projects and information on them.

Cyndi’s List for DNA
Various links to a wide range of DNA sources

World Families Network
Many wonderful resources

International Society of Genetic Genealogist (ISOGG)
Email list of Newbies -- anyone interested in Genetic Genealogy can join and ask any question on the email list.
Email list for Administrators with many links and files to help them.
(Join ISOGG today. There is no cost. Tell them you learned of it from Emily's Blog.)

1. Ydna, mtDNA and atDNA
2. Surname, Geographical, Ethnic, and Haplogroup
3. Haplotype
4. Haplogroup
5. Ydna
6. mtDNA
7. atDNA
8. allele
9. STRs…the number of times a short pattern of checmical basis repeats itself
10. Cambridge Reference System – the first testing of the entire mitochondria.
11. DNA Y-chromosome Segment. Ydna
12. any change in a marker
13. The World Family Tree
14. Coding markers recombine with every conception while non-coding markers remain virtually the same over time. Non-coding is best for genealogy as you want consistency over time.

©Aulicino, Nov 2008

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