Genealogical DNA test

A genealogical DNA test looks at a person's genome at specific locations. Results give information about genealogy or personal ancestry. In general, these tests compare the results of an individual to others from the same lineage or to current and historic ethnic groups. The test results are not meant for medical use, where different types of genetic testing are needed. They do not determine specific genetic diseases or disorders (see possible exceptions in Medical information below). They are intended only to give genealogical information.

Procedure

Hospital Corpsman 1st Class uses a swab to take a DNA sample from a Fireman aboard USS Iwo Jima (LHD 7)

Taking a genealogical DNA test requires the submission of a DNA sample. This is usually a painless process. The most common way to collect a DNA sample is by a cheek-scraping (also known as a buccal swab). Other methods include spit-cups, mouthwash, and chewing gum. After collection, the sample is mailed to a testing lab.

Some laboratories, such as the Human Origins Genotyping Laboratory (HOGL) at the University of Arizona, offer to store DNA samples for ease of future testing. All United States laboratories will destroy the DNA sample upon request by the customer guaranteeing that a sample is not available for further analysis.

Types of tests

There are three types of genealogical DNA tests, autosomal (atDNA), mitochondrial DNA (mtDNA), and Y-Chromosome (Y-DNA). Autosomal tests for all ancestry. Y-DNA tests a male along his direct paternal line. mtDNA tests a man or woman along their direct maternal line.

Any of these tests can be used to some degree for recent genealogy or for ethnic ancestry.

Autosomal DNA (atDNA)

What gets tested

Generally, a genealogical DNA test might use either autosomal STRs or autosomal SNPs. (STR's are Short Tandem Repeats; SNPs are single-nucleotide polymorphisms.) However, testing companies do not currently offer autosomal STRs tests that use enough STR markers for genealogy. The preferred choice for both genealogy and ethnic population matching is microarray chips that use hundreds of thousands of autosomal SNPs.

STRs

Like Y-DNA STRs, autosomal STRs are counts of repeated genetic code. As autosomal DNA recombines each generation, the number of markers shared with a specific ancestor is reduced by half each generation.

SNPs

Like mtDNA and Y-DNA SNPs, autosomal SNPs are changes at a single point in genetic code. Autosomal DNA recombines each generation. Therefore, the number of markers shared with a specific ancestor decreases by half each generation. Most testing companies overcome this by using technologies that include around 700,000 autosomal SNPs.

Matching process

There are currently two types of matching processes used. The first is haploblock matching. This process counts the number and size of matching runs of DNA from one point to another. It then computes the likely number of generations between two people. The second method is biogeographical analysis. This method seeks to match individual SNP values' frequencies in reference populations to match geographic origins.

Genetic distance among relatives

Where the genogram or family tree of individuals is known, it can be used to determine the genetic identity between individuals. It is often described as percentage of genetic identity, referring to the fraction of genome inherited from common ancestors, and not actual genomic identity, which is always approximately 99.9%^[1] identical from one human to another.

One method of calculating this genetic similarity is to do an inbreeding calculation by the path or tabular method and then multiply by 2, because any progeny would have a 1 in 2 risk of actually inheriting the identical alleles from both parents. For instance, a brother/sister relation gives 25% risk for two alleles to be identical by descent.

Biogeographical ancestry

The theory behind using a forensic profile for ancestry tracing is that the alleles' respective frequency of occurrence develops over generations with equal input of the two parents, since for each location we take one value from our mother and one from our father. It thus serves as a window into a person's total ancestral composition.^[2]

As studies from more populations are included, the accuracy of results should improve, leading to a more informative picture of one's ancestry.

SNP based testing

Biogeographical analysis uses scientific methods from population genetics to assign someone to one or more population groups. This is usually done by comparing the frequency of each Autosomal DNA marker tested to many population groups. The reliability of this type of test is dependent on comparative population size, the number of markers tested, the ancestry informative value of the SNPs tested, and the degree of admixture in the person tested.

Early tests used only a few dozen autosomal DNA SNPs. Current tests often, like genealogy purposed tests, use around 700,000 autosomal SNPs.

STR tests

STR analysis measures the frequency of a person's DNA profile within major world regions. This analysis is based on objectively identified world regions and does not depend on any system of presumed biogeographic classifications. As most STR analysis examines markers chosen for their high intra-group variation, the utility of these particular STR markers to access inter-group relationships may be greatly diminished.

Mitochondrial DNA (mtDNA) testing

Map of human migration out of Africa, according to Mitochondrial DNA. The numbers represent thousands of years before present time. The blue line represents the area covered in ice or tundra during the last great ice age. The North Pole is at the center. Africa, the center of the start of the migration, is at the top left and South America is at the far right.

A direct maternal ancestor can be traced using mtDNA. MtDNA is passed down by the mother unchanged, to all children. A perfect match found to another person's mtDNA test results indicates shared recent ancestry. More distant matching to a specific haplogroup or subclade may be linked to a common geographic origin.

Some people cite paternal mtDNA transmission as invalidating mtDNA testing,^[3] but this has not been found problematic in genealogical DNA testing, nor in scholarly population genetics studies.

What gets tested

mtDNA, by current conventions, is divided into three regions. They are the coding region (00577-16023) and two Hyper Variable Regions (HVR1 [16024-16569], and HVR2 [00001-00576]).^[4] All test results are compared to the mtDNA of a European in Haplogroup H2a2a. This early sample is known as the Cambridge Reference Sequence (CRS). A list of single nucleotide polymorphisms (SNPs) is returned. The relatively few "mutations" or "transitions" that are found are then reported simply as differences from the CRS, such as in the examples just below.

The two most common mtDNA tests are a sequence of HVR1 and a sequence of both HVR1 and HVR2. Some mtDNA tests may only analyze a partial range in these regions. Some people are now choosing to have a full sequence performed, to maximize their genealogical help. The full sequence is still somewhat controversial because it may reveal medical information.

Understanding test results

The most basic of mtDNA tests will sequence Hyper Variable Region 1 (HVR1). HVR1 nucleotides are numbered 16024-16569.^[5]

Examples

• Some test reports might omit the "16" (16nnn) prefix from HVR1 results, i.e. 519C and not 16519C.

• More extensive tests will also sequence Hyper Variable Region 2 (HVR2). HVR2 nucleotides are numbered 00001-00576.^[6]

Haplogroup

Most results include a prediction of mtDNA Haplogroup.

If you belong to a Haplogroup that is distantly related to the CRS, then the prediction may be sufficient. Some companies test for specific mutations in the coding region. For large Haplogroups, such as mtDNA Haplogroup H, an extended test is offered to assign a sub-clade.

mtDNA in the news

mtDNA testing was used by University of Leicester archaeologists to verify the skeletal remains of King Richard III, found in September 2012.^[7]

Y chromosome (Y-DNA) testing

Dominant Y-chromosome haplogroups in pre-colonial world populations, with possible migrations routes according to the Coastal Migration Model.

A man's patrilineal ancestry, or male-line ancestry, can be traced using the DNA on his Y chromosome (Y-DNA) through Y-STR testing. This is useful because the Y chromosome passes down almost unchanged from father to son, i.e., the non-recombining and sex-determining regions of the Y chromosome do not change. A man's test results are compared to another man's results to determine the time frame in which the two individuals shared a most recent common ancestor, or MRCA, in their direct patrilineal lines. If their test results are a perfect, or nearly perfect match, they are related within genealogy's time frame.^[8]

Each person can then look at the other's father-line information, typically the names of each patrilineal ancestor and his spouse, together with the dates and places of their marriage and of both spouses' births and deaths. This information table will be referred to again within the mtDNA testing section below as the (matrilineal) "information table". The two matched persons may find a common ancestor or MRCA, as well as whatever information the other already has about their joint patrilineal ancestry prior to the MRCA—which might be a big help to one of them.^[9] Or if not, both keep trying to extend their patrilineal ancestry further back in time. Each may choose to have their test results included in their surname's "Surname DNA project". And each receives the other's contact information if the other chose to allow this. They may correspond, and may work together in the future on joint research.^[10]

Women who wish to determine their direct paternal DNA ancestry can ask their father, brother, paternal uncle, paternal grandfather, or a male cousin who shares a common patrilineal ancestry (the same Y-DNA) to take a test for them.

What gets tested

Y-DNA testing involves looking at the "junk" DNA segment of DNA on the Y chromosome trunk, to look for STRs and SNPs. STRs and SNPs are called DNA markers

STR markers

A Y-chromosome contains sequences of repeating nucleotides known as short tandem repeats (STRs). The number of repetitions varies from one person to another and a particular number of repetitions is known as an allele of the marker. Individual Y-DNA sequences or STRs that have proven useful in genealogical DNA work are called markers, and each has a name, such as DYS393 in the following example. (Names are assigned by the HUGO Gene Nomenclature Committee, and DYS means Y-DNA unique Sequence [or Segment] while 393 is this sequence's unique identification number – its identifier.)^[11] This example states that the allele of Rumpelstiltskin's DYS393 marker is 12, also called the marker's "value". The value 12 means the DYS393 sequence of nucleotides is repeated 12 times—with a DNA sequence of (AGAT)₁₂. STRs are mutations that happen on branches of the Y chromosome trunk. Even though they mutate rarely, they mutate much more than SNPs. From a father to a son 150 thousand STRs mutate out of millions existing STRs on the Y chromosome trunk that is composed of 2 billion blocks stacked as along thread. However for Genetic genealogy purposes only several predetermined STRs (usually the originally assigned 6 STRs in 1997 or up to expanded 76 STRs) are assigned for study and comparison between peoples and nations out of the millions of existing STRs. A match of 50 STRs between two males means they are brothers, the less matches the less relatedness but the compared males have to have same SNP (Y haplogroup or subclade). STRs are used to study Recent genealogy (in the 4000 years before present such as surname studies) while SNPs are used to study old genealogy (mainly more than 4000 years before present to determine genealogy (ancestry of nations such as ancient Greek for example).

SNP markers

Strand 1 differs from strand 2 at a single base pair location (a C → T polymorphism).

A single-nucleotide polymorphism (SNP) is a change to a single nucleotide in a DNA sequence. The relative mutation rate for an SNP is extremely low. This makes them ideal for marking the history of the human genetic tree. SNPs are named with a letter code and a number. The letter indicates the lab or research team that discovered the SNP. The number indicates the order in which it was discovered. For example, M173 is the 173rd SNP documented by the Human Population Genetics Laboratory at Stanford University, which uses the letter M. SNPs are mutations from the original and happen on the blocks of the trunk of the Y chromosome and happen much less frequently than STRs. From father to son hardly one SNP happen on all the Y chromosome trunk. A random SNP happens on average every two to three generations.

Understanding test results

In general, Y-DNA tests examine 10-67 STR markers on the Y chromosome, but over 100 markers are available. STR test results provide the personal haplotype. SNP results indicate the haplogroup.

Haplotype

A Y-DNA haplotype is the numbered results of a genealogical Y-DNA test. Each allele value has a distinctive frequency within a population. For example, at DYS455, the results will show 8, 9, 10, 11 or 12 repeats, with 11 being most common.^[12] For high marker tests the allele frequencies provide a signature for a surname lineage.

The test results are then compared to another project member's results to determine the time frame in which the two people shared a most recent common ancestor (MRCA). If the two tests match perfectly on 111 markers for members with the same surname, there is a 50% probability that the MRCA was fewer than 2 generations ago, 90% probability that it was fewer than 4 generations ago, and 95% probability it was fewer than 5 generations ago.^[13]

Before choosing a test, it is important for an individual to check the number of markers that will be tested. For example, the Genographic Project looks at only 12 markers, while most laboratories and surname projects recommend testing at least 25. The more markers that are tested, the more discriminating and powerful the results will be. A 12-marker STR test is usually not discriminating enough to provide conclusive results for a common surname.

STRs results may also indicate a likely haplogroup, though this can only be confirmed by specifically testing for that Haplogroups' single-nucleotide polymorphisms (SNPs).

Haplogroup

Y-DNA-haplogroups in Europe

Haplogroups are large groups of haplotypes that can be used to define genetic populations and are often geographically oriented.

Y-DNA haplogroups are determined by SNP tests. SNPs are locations on the DNA where one nucleotide has "mutated" or "switched" to a different nucleotide. The nucleotide switch must occur in at least 1% of the population to be considered a useful SNP. If it occurs in less than 1% of the population, it is considered a personal (or private) SNP.

Haplogroup prediction

A person's haplogroup can often be inferred from their haplotype, but can be proven only with a Y-chromosome SNP tests (Y-SNP test). In addition, some companies offer sub-clade tests, such as for Haplogroup G. For example, Haplogroup G has a known modal haplotype:

Few haplotypes will exactly match the modal values for Haplogroup G. One can consult an allele frequency table to determine the likelihood of remaining in Haplogroup G based on the variations observed.

Additional predictions include:

• If DYS426 is 12 and DYS392 is 11, one is probably a member of haplogroup R1a1.
• If DYS426 is 12 and DYS392 is not 11, one is probably a member of haplogroup R1b.
• If DYS426 is 11, one is probably a member of haplogroup G,I, or J.
• If DYS426 is 11 and DYS388 is 12, one is in the known modal haplotype for G shown above.

Audience

The interest in genealogical DNA tests has been linked to both an increase in curiosity about traditional genealogy and to more general personal origins. Those who test for traditional genealogy often utilize a combination of autosomal, mitochondrial, and Y-Chromosome tests. Those with an interest in personal ethnic origins are more likely to use an autosomal test. However, answering specific questions about the ethnic origins of a particular lineage may be best suited to an mtDNA test or a Y-DNA test.

Maternal origin tests

For recent genealogy, exact matching on the mtDNA full sequence is used to confirm a common ancestor on the direct maternal line between two suspected relatives. Because mtDNA mutations are very rare, a nearly perfect match is not usually considered relevant to the most recent 1 to 16 generations.^[14] In cultures lacking matrilineal surnames to pass down, neither relative above is likely to have as many generations of ancestors in their matrilineal information table as in the above patrilineal or Y-DNA case: for further information on this difficulty in traditional genealogy, due to lack of matrilineal surnames (or matrinames), see Matriname.^[15] However, the foundation of testing is still two suspected descendants of one person. This hypothesize and test DNA pattern is the same one used for autosomal DNA and Y-DNA.

Geographic origin tests

European genetic structure (based on Autosomal SNPs) by PCA

Autosomal tests that test the recombining chromosomes are available. These attempt to measure an individual's mixed geographic heritage by identifying particular markers, called ancestry informative markers or AIM, that are associated with populations of specific geographical areas. The tests' validity and reliability have been called into question but they continue to be popular.^[16][17] Anomalous findings most often result from databases too small to associate markers with all the areas where they occur in indigenous populations.

United States

Because of its history of immigration, slavery, and significant indigenous peoples, people of the United States have been interested in using genealogical DNA studies to help them learn more about their ancestry.

United States - Native American ancestry

Autosomal testing, Y-DNA, and mtDNA testing can be conducted to determine Amerindian ancestry. A mitochondrial Haplogroup determination test based on mutations in Hypervariable Region 1 and 2 may establish whether a person's direct female line belongs to one of the canonical Native American Haplogroups, A, B, C, D or X. If one's DNA belonged to one of those groups, the implication would be that he or she is, in whole or part, Native American.

As political entities, tribes have established their own requirements for membership, often based on at least one of a person's ancestors having been included on tribal-specific Native American censuses (or final rolls) prepared during treaty-making, relocation to reservations or apportionment of land in the late 19th century and early 20th century. One example is the Dawes Rolls. In addition, the U.S. government does not consider DNA as admissible evidence for enrollment in any federally recognized tribe or reception of benefits. Tribes are political constructs, not genetic populations.

The vast majority of Native American individuals do belong to one of the five identified mtDNA Haplogroups. Many Americans are now just discovering they have some percentage of Native ancestry. Some attempt to validate their heritage with the goal of gaining admittance into a tribe, but most tribes do not use DNA results in that way. The tests may be useful for adoptees to discover Native American ancestry.

United States - African ancestry

Y-DNA and mtDNA testing may be able to determine with which peoples in present-day Africa a person shares a direct line of part of his or her ancestry, but patterns of historic migration and historical events cloud the tracing of ancestral groups. Testing company African Ancestry^[18] maintains an "African Lineage Database" of African lineages from 30 countries and over 160 ethnic groups. Due to joint long histories in the US, approximately 30% of African American males have a European Y-Chromosome haplogroup^[19] Approximately 58% of African Americans have the equivalent of one great-grandparent (12.5 percent) of European ancestry. Only about 5% have the equivalent of one great-grandparent of Native American ancestry. By the early 19th century, substantial families of Free Persons of Color had been established in the Chesapeake Bay area who were descended from people free during the colonial period; most of those have been documented as descended from white men and African women (servant, slave or free). Over time various groups married more within mixed-race, black or white communities.^[20]

According to authorities like Salas, nearly three-quarters of the ancestors of African Americans taken in slavery came from regions of West Africa. The African-American movement to discover and identify with ancestral tribes has burgeoned since DNA testing became available. Often members of African-American churches take the test as groups. African Americans usually cannot easily trace their ancestry during the years of slavery through surname research, census and property records, and other traditional means. Genealogical DNA testing may provide a tie to regional African heritage.

United States - Melungeon testing

Melungeons are one of numerous multiracial groups in the United States with origins wrapped in myth. The historical research of Paul Heinegg has documented that many of the Melungeon groups in the Upper South were descended from mixed-race people who were free in colonial Virginia and the result of unions between the Europeans and Africans. They moved to the frontiers of Virginia, North Carolina, Kentucky and Tennessee to gain some freedom from the racial barriers of the plantation areas.^[21] Several efforts, including a number of ongoing studies, have examined the genetic makeup of families historically identified as Melungeon. Most results point primarily to a mixture of European and African, which is supported by historical documentation. Some may have a very small amount of Native American lineages (none in one study). Though some companies provide additional Melungeon research materials with Y-DNA and mtDNA tests, any test will allow comparisons with the results of current and past Melungeon DNA studies.

Cohanim ancestry

The Cohanim (or Kohanim) is a patrilineal priestly line of descent in Judaism. According to the Bible, the ancestor of the Cohanim is Aaron, brother of Moses. Many believe that descent from Aaron is verifiable with a Y-DNA test: the first published study in genealogical Y-Chromosome DNA testing found that a significant percentage of Cohens had distinctively similar DNA, rather more so than general Jewish or Middle Eastern populations. These Cohens tended to belong to Haplogroup J, with Y-STR values clustered unusually closely around a haplotype known as the Cohen Modal Haplotype (CMH). This could be consistent with a shared common ancestor, or with the hereditary priesthood having originally been founded from members of a single closely related clan.

Nevertheless, the original studies tested only six Y-STR markers, which is considered a low-resolution test. Such a test does not have the resolution to prove relatedness, nor to estimate reliably the time to a common ancestor. The Cohen Modal Haplotype (CMH), while notably frequent among Cohens, also appears in the general populations of haplogroups J1 and J2 with no particular link to the Cohen ancestry. So while many Cohens have haplotypes close to the CMH, many more of such haplotypes worldwide belong to people with no likely Cohen connection at all. According to researchers (Hammer), it is only the CMH that is found in J1 that is to be attributed to the Aaron lineage, not the CMH in J2. Jews with the CMH in both J1 and J2 cannot all be descended from one man who lived approximately 3,300 years ago, because J1 diverged from J2 10,000 years ago.

Resolution may be increased by the testing of more than six Y-STR markers. For some, this could help to establish relatedness to particular recent Cohen clusters. For many, the testing is unlikely to distinguish definitively shared Cohen ancestry from that of the more general population distribution. So far no published research indicates what extended Y-STR haplotype distributions appear to be characteristic of Cohens.

Although some high-resolution testing has been done, to date the results have not been released.

European testing

For people with European maternal ancestry, mtDNA tests are offered to determine which of eight European maternal "clans" the direct-line maternal ancestor belonged to. This mtDNA haplotype test was popularized in the book The Seven Daughters of Eve.

Hindu testing

The 49 established gotras are clans or families whose members trace their descent to a common ancestor, usually a sage of ancient times. The gotra proclaims a person's identity and a "gotra-pravara" is required to be presented at Hindu ceremonies. People of the same gotra are not allowed to marry.

One company says it can use a 37-marker Y-DNA test to "verify genetic relatedness and historical gotra genealogies for Hindu and Buddhist engagements, marriages and business partnerships." This has not been supported by independent research. Any Y-DNA test can be used to compare results with another person whose gotra is known.

Benefits

Genealogical DNA tests have become popular due to the ease of testing at home and their usefulness in supplementing genealogical research. Genealogical DNA tests allow for an individual to determine with high accuracy whether he or she is related to another person within a certain time frame, or with certainty that he or she is not related. DNA tests are perceived as more scientific, conclusive and expeditious than searching the civil records. However, they are limited by restrictions on lines that may be studied. The civil records are always only as accurate as the individuals having provided or written the information.

Y-DNA testing results are normally stated as probabilities: For example, with the same surname a perfect 37/37 marker test match gives a 95% likelihood of the most recent common ancestor (MRCA) being within 8 generations,^[22] while a 111 of 111 marker match gives the same 95% likelihood of the MRCA being within only 5 generations back.^[13]

As presented above in mtDNA testing, if a perfect match is found, the mtDNA test results can be helpful. In some cases, research according to traditional genealogy methods encounters difficulties due to the lack of regularly recorded matrilineal surname information in many cultures.(see Matrilineal surname).^[15]

Drawbacks

Common concerns about genealogical DNA testing are cost and privacy issues (some testing companies retain samples and results for their own use without a privacy agreement with subjects). The most common complaint from DNA test customers is the failure of the company to make results understandable to them.

DNA tests can do some things well, but there are constraints. Testing of the Y-DNA lineage from father to son may reveal complications, due to unusual mutations, secret adoptions, and false paternity (i.e., the father in one generation is not the father in birth records). According to some genomics experts, autosomal tests may have a margin of error up to 15% and blind spots.

Some users have recommended that there be government or other regulation of ancestry testing to ensure more standardization.^[23]

Medical information

Though genealogical DNA test results in general have no informative medical value and are not intended to determine genetic diseases or disorders, a correlation exists between a lack of DYS464 markers and infertility, and between mtDNA haplogroup H and protection from sepsis. Certain haplogroups have been linked to longevity.^[24]

The testing of full mtDNA sequences is still somewhat controversial as it may reveal medical information. The field of linkage disequilibrium, unequal association of genetic disorders with a certain mitochondrial lineage, is in its infancy, but those mitochondrial mutations that have been linked are searchable in the genome database Mitomap.^[25] The National Human Genome Research Institute operates the Genetic And Rare Disease Information Center^[26] that can assist consumers in identifying an appropriate screening test and help locate a nearby medical center that offers such a test.

DNA in genealogy software

Some genealogy software programs now allow recording DNA marker test results, allowing for tracking of both Y-chromosome and mtDNA tests, and recording results for relatives. DNA-family tree wall charts are available.

See also

References

Further reading

External links

Tutorials

• Tutorial for Y-DNA STR tests (phrased as FAQs)
• Tutorial for Y-DNA SNP tests (also as FAQs)
• Tutorial for mtDNA tests (as FAQs)

Societies

• International Society for Genetic Genealogy

Foundations and research projects

• The National Geographic Genographic Project
• Sorenson Molecular Genealogy Foundation A wholly owned subsidiary of Sorenson

Information and Maps on Y-DNA haplogroups

• Y-haplogroups World Map
• Y-Haplogroups brief descriptions and regional origins
• Y-DNA Ethnographic and Genographic Atlas and Open-Source Data Compilation

External

• A list of DNA testing companies