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Genealogical DNA test

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For a non-technical introduction to genetics in general, see Introduction to genetics.

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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. The most common way to collect a DNA sample, which can be done by either visiting a DNA test clinic or by ordering a home test through an independent DNA test supplier, 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.

Types of tests

There are two major types of genealogical DNA tests, Recent admixture Ancestry (autosomal atDNA and X-chromosome DNA) and Lineal Ancestry (mitochondrial DNA mtDNA and Y-chromosome Y-DNA).[1] Autosomal and X-chromosome tests are for recent ancestry of both males and females, Y-DNA tests a male along his direct paternal line and 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.[2]

Autosomal DNA (atDNA) testing

What gets tested

Autosomal DNA is the 22 pairs of chromosomes that do not contribute to sex.[2] These are inherited exactly equally from both parents and roughly equally from grandparents to about 3x great-grand parents.[3] Inheritance is more random and unequal from more distant ancestors. Generally, a genealogical DNA test might test about 700,000 SNPs (single-nucleotide polymorphisms). Like mtDNA and Y-DNA SNPs, autosomal SNPs are changes at a single point in genetic code. Autosomal DNA recombines each generation.[4] Therefore, the number of markers shared with a specific ancestor decreases by half each generation. Some type of microarray chip is used by the laboratory. Different chips test different SNPs.

STRs

Some genealogical companies offer autosomal STRs (short tandem repeats). These are similar to Y-DNA STRs. The number of STRs offered is limited, and not genealogically useful.

Matching process

The major component of an autosomal DNA test is matching other individuals. If two individuals share more than a certain threshold of DNA, they are considered a match by the testing company. Based on the amount of shared DNA, usually expressed in centiMorgens(cM), their relationship may be predicted. A centiMorgan usually about one million base pairs of DNA (a region where the is a 1% chance of recombination happening within one generation).[5] Due to the random nature of DNA inheritance, the exact relationship cannot be exactly predicted. Depending on the threshold, all 5th cousins and closer should be a match. Whether 6th cousins and further match depends on how DNA has been inherited.

More detailed analysis of matches including the method of triangulation can reveal more precisely how two matches are related genealogically. This area of DNA testing can be the most complex and difficult to understand. Many popular blogs and websites explain these tools for beginners.

Bio-geographical ancestry

Most companies offer a percentage breakdown by ethnicity or region. Generally the world is specified into about 20-25 regions, and the approximate percentage of DNA inherited from each is stated. This is usually done by comparing the frequency of each Autosomal DNA marker tested to many population groups.[2] 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. Earlier ethnicity estimates were often wildly inaccurate, but their accuracies have since improved greatly.

X-chromosome DNA testing

The X-chromosome SNP results are often included in Autosomal DNA tests. Both males and females receive an X-chromosome from their mother, but only females receive a second X-chromosome from their father.[6] The X-chromosome has a special path of inheritance patterns and can be useful in significantly narrowing down possible ancestor lines compared to atDNA - for example an X-chromosome match with a male can only have come from his maternal side.[7] Like autosomal DNA, X-chromosome DNA undergoes random recombination at each generation (except for father to daughter X-chromosomes which are passed down unchanged). There are specialised inheritance charts which describe the possible patterns of X-chromosome DNA inheritance for males and females.[8]

Mitochondrial DNA (mtDNA) testing

The Mitochondrion is a component of a human cell, and contains its own DNA. Mitochondrial DNA usually has 16,569 base pairs (the number can vary slightly depending on addition or deletion mutations)[9] and is much smaller than the human genome DNA which has 3.2 billion base pairs. Mitochondrial DNA is transmitted from mother to child, thus a direct maternal ancestor can be traced using mtDNA. The transmission occurs with relatively rare mutations compared to the genome DNA. A perfect match found to another person's mtDNA test results indicates shared ancestry of possibly between 1 and 50 generations ago.[2] 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,[10] 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]).[11] Test results are usually compared to the mtDNA of the Cambridge Reference Sample (CRS) which is a European in Haplogroup H2a2a.

The two most common mtDNA tests are a sequence of HVR1 and HVR2 and a full sequence of the mitochondria. Some mtDNA tests may only analyze a partial range in these regions. Generally, testing only the HVRs has limited genealogical use so it is increasingly popular and accessible to have a full sequence. The full sequence is still somewhat controversial because the coding region DNA may reveal medical information about the test-taker.[12]

Understanding test results

It is not normal for test results to give a base-by base list of results. Instead, results are normally compared to the CRS, which is the mitochondria of a European who was the first person to have their mtDNA published in 1981 (and revised in 1999).[13] Differences between the CRS and testers of European origin are usually very few, thus it is more convenient than listing one's raw results for each base pair.

Examples

Note that in HVR1, instead of reporting the base pair exactly, for example 16,111, the 16 is often removed to give in this example 111. The Letters refer to one of the 4 bases (A,T,G,C) that make up human DNA.

Region HVR1 HVR2
Differences from CRS 111T,223T,259T,290T,319A,362C 073G,146C,153G

Haplogroups

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.

All humans descend in the direct female line from Mitochondrial Eve, a female who lived probably around 200,000 years ago in Africa. Different branches of her descendants are different haplogroups. Most mtDNA results include a prediction or exact assertion of one's mtDNA Haplogroup. Mitochrondial haplogroups were greatly popularized by the popular book The Seven Daughters of Eve, which explores mitochondrial DNA from a European perspective.

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.[14]

Y chromosome (Y-DNA) testing

Y-chromosome testing is one of the oldest and most powerful DNA tools used for genealogical purposes.[15] The Y-Chromosome is one of the 23rd pair of human chromosomes. Only males have a Y-chromosome, because women have two X chromosomes in their 23rd pair. A man's patrilineal ancestry, or male-line ancestry, can be traced using the DNA on his Y chromosome (Y-DNA), because the Y-chromosome is transmitted father to son nearly unchanged.[15] 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 very close, they are related within a genealogically useful time frame.[16] A surname project is where many individuals whose Y-chromosomes match collaborate to find their common ancestry.

Women who wish to determine their direct paternal DNA ancestry can ask their father, brother, paternal uncle, paternal grandfather, or a paternal uncle's son (their cousin) to take a test for them.

There are two types of DNA testing: STRs and SNPs.[2]

STR markers

Most common is STRs (short tandem repeat). A certain section of DNA is examined for a pattern that repeats (e.g. ATCG). The number of times it repeats is the value of the marker. Typical tests test between 30 and 120 STR markers. STRs mutate fairly frequently. The results of two individuals are then compared to see if there is a match. Close matches may often join a surname project. DNA companies will usually provide information about how closely related two matches are, based on the difference between their results.[17]

Haplotype

Further information: Y-chromosome haplogroups by populations

A Y-DNA haplotype is the numbered results of a genealogical Y-DNA STR 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.[18] For high marker tests the allele frequencies provide a signature for a surname lineage.

Kit Surname Haplo 3
9
3

  		3
9
0

  		1
9


  		3
9
1

  		3
8
5
a

 3
8
5
b

 4
2
6

  		3
8
8

  		4
3
9

  		3
8
9
-
1 		3
9
2

  		3
8
9
-
2 		4
5
8

  		4
5
9
a

 4
5
9
b

 4
5
5

  		4
5
4

  		4
4
7

  		4
3
7

  		4
4
8

  		4
4
9

  		4
6
4
a

 4
6
4
b

 4
6
4
c

 4
6
4
d

11111 Rumpelstiltskin Q 12 23 13 10 16 17 12 12 13 14 14 31 18 8 9 11 11 27 13 19 28 14 14 15 15

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). Testing companies usually provide information on this.

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. 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.

SNP markers and Haplogroups

Strand 1 differs from strand 2 at a single base pair location (a C → T polymorphism).
Dominant Y-chromosome haplogroups in pre-colonial world populations, with possible migrations routes according to the Coastal Migration Model.

A single-nucleotide polymorphism (SNP) is a change to a single nucleotide in a DNA sequence. Typical Y-DNA SNP tests test about 20,000 to 35,000 SNPs.[19] Getting a SNP test allows a much higher resolution than STRs. It can be used to provide additional information about the relationship between two individuals and to confirm haplogroups.

File:Haplogroups europe.png
The most common Y-DNA-haplogroup in different regions in Europe

All human men descend in the paternal line from a single man dubbed Y-chromosomal Adam, who lived probably between 200,000 and 400,000 years ago. A 'family tree' can be drawn showing how men today descend from him. Different branches of this tree are different haplogroups. Most haplogroups can be further subdivided multiple times into sub-clades. Some known sub-clades were founded in the last 1000 years, meaning their timeframe approaches the genealogical era (c.1500 onwards).[20]

New sub-clades of haplogroups may be discovered if an individual tests, especially if they are non-European. Most significant of these new discoveries was in 2013 when the haplogroup A00 was discovered, which required theories about Y-chromosomal Adam to be significantly revised. The haplogroup was discovered when an African-American man tested STRs at FamilyTreeDNA and his results were found to be unusual. SNP testing confirmed that he does not descend patrilineally from the "old" Y-chromosomal Adam and so a much older man became Y-Chromosomal Adam. If enough individuals belong to a newly discovered subclade, the subclade is added to the ISOGG Y-DNA haplogroup Tree, which is the most up-to-date and respected tree of Y-DNA haplogroups.

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.[21] 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.[22] 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

As discussed above, autosomal tests usually report the ethnic proportions of the individual. 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. Geneticist Adam Rutherford has written that these tests "don’t necessarily show your geographical origins in the past. They show with whom you have common ancestry today."[23]

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[24] 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[25] Approximately 58% of African Americans have at least 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.[26]

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.[citation needed] 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

Main article: Melungeon § DNA 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.[27] 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 Native American heritage as well. 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

Native American ancestry

Further information: Genetic history of indigenous peoples of the Americas

The pre-columbian indigenous people of the United States are called "Native Americans" in American English.[28] Autosomal testing, Y-DNA, and mtDNA testing can be conducted to determine the ancestry of Native Americans. 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.[citation needed]

The U.S. government relies on recognized tribal organizations to determine their own membership. Consequently, individuals must apply to their American Indian and Alaska Native tribes directly to establish membership and enrollment. Applicants may wish to find out in advance whether the organization accepts blood tests or DNA tests.[29] They may also wish to contact the American Indian & Alaska Native Genetics Resource Center. [30]

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. Tribes are political constructs, not genetic populations.[citation needed]

The vast majority of Native American individuals belong to one of the five identified mtDNA Haplogroups. Many Americans are now just discovering they have some percentage of Native ancestry.

Cohanim ancestry

Main article: Y-chromosomal Aaron

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. In response to the low resolution of the original 6-marker CMH, the testing company FTDNA released a 12-marker CMH signature that was more specific to the large closely related group of Cohens in Haplogroup J1.

A further academic study published in 2009 examined more STR markers and identified a more sharply defined SNP haplogroup, J1e* (now J1c3, also called J-P58*) for the J1 lineage. The research found "that 46.1% of Kohanim carry Y chromosomes belonging to a single paternal lineage (J-P58*) that likely originated in the Near East well before the dispersal of Jewish groups in the Diaspora. Support for a Near Eastern origin of this lineage comes from its high frequency in our sample of Bedouins, Yemenis (67%), and Jordanians (55%) and its precipitous drop in frequency as one moves away from Saudi Arabia and the Near East (Fig. 4). Moreover, there is a striking contrast between the relatively high frequency of J-58* in Jewish populations (»20%) and Kohanim (»46%) and its vanishingly low frequency in our sample of non-Jewish populations that hosted Jewish diaspora communities outside of the Near East."[31]

Recent phylogenetic research for haplogroup J-M267 placed the "Y-chromosomal Aaron" in a subhaplogroup of J-L862,L147.1 (age estimate 5631-6778yBP yBP): YSC235>PF4847/CTS11741>YSC234>ZS241>ZS227>Z18271 (age estimate 2731yBP).[32]

European testing

Further information: Genetic history of Europe

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.

Popularity

The number of testers has dramatically increased with time. In 2014 and 2015 all three major DNA testing companies (23andMe, Ancestry, and Family Tree DNA) reported to have more than 1 million customers.[33]

According to the ISOGG and other sources, the following atDNA SNP testing customers had these numbers of testers in the database as of 2016. These lists are not exhaustive, but all companies not mentioned on these lists are very small.

Ancestry.com : ~2,500,000
23andMe : ~ 1,200,000
National Geographic : ~230,000
FamilyTreeDNA : ~275,000
Chromo2 (Britains DNA+subsidiaries) : ~20,000

The following companies offered Y-DNA STR tests

FamilytreeDNA : ~590,000 [34]
Genebase Systems
Oxford Ancestors
YSEQ

The following companies offered Y-DNA SNP tests

23andMe: included in atDNA test
National Geographic : included in atDNA test
FamilytreeDNA
Chromo2
Full Genomes Corporation

The following companies offered mtDNA tests [35]

FamilytreeDNA : ~239,000 [34]
23andMe : included in atDNA test
National Geographic : included in atDNA test
Chromo2
Oxford Ancestors
Full Genomes Corporation
Genebase systems

Benefits

Main article: Genetic genealogy

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,[36] while a 111 of 111 marker match gives the same 95% likelihood of the MRCA being within only 5 generations back.[37]

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).[22]

Drawbacks

Common concerns about genealogical DNA testing are cost and privacy issues.[38] Some testing companies[39] retain samples and results for their own use without a privacy agreement with subjects.[40][41] The most common complaint from DNA test customers is the failure of the company to make results understandable to them.[42]

DNA tests do some things well,[clarification needed] but they have limitations.[43][44][45] Testing of the Y-DNA lineage from father to son may reveal complications, due to unusual mutations, secret adoptions, and false paternity (i.e., that the perceived father in a generation is not the father indicated by written birth records).[citation needed] According to some genomics experts,[who?] autosomal tests may have "blind spots,"[46] and a margin of error up to 15%.[clarification needed][citation needed]

Some have recommended government or other regulation of ancestry testing to ensure its performance to an agreed standard.[47]

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.[48][better source needed][unreliable source?]

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.[49] The National Human Genome Research Institute operates the Genetic And Rare Disease Information Center[50] 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.[51] DNA-family tree wall charts are available.

See also

Main article: List of genetic genealogy topics

References

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  3. ^ Bettinger (2016, p. 68)
  4. ^ Bettinger (2016, p. 70)
  5. ^ Bettinger (2016, p. 73)
  6. ^ Bettinger (2016, p. 107)
  7. ^ Bettinger (2016, p. 114)
  8. ^ Bettinger (2016, p. 111)
  9. ^ Bettinger (2016, p. 9)
  10. ^ for example: M. Pickford, "Paradise lost: Mitochondrial eve refuted", SpringerLink, July 2006
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  19. ^ Bettinger (2016, p. 41)
  20. ^ Bettinger (2016, p. 40)
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  36. ^ ftdna.com (kept uptodate). http://www.familytreedna.com/faq/answers/default.aspx?faqid=9#922 "FAQ: ...how should the genetic distance at 37 Y-chromosome STR markers be interpreted?" Retrieved 2012-01-13.
  37. ^ ftdna.com (kept uptodate). http://www.familytreedna.com/faq/answers/default.aspx?faqid=9#925 "FAQ: ...how should the genetic distance at 111 Y-chromosome STR markers be interpreted?" Retrieved 2012-01-13.
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Further reading

Tutorials
Societies
Foundations and research projects
Information and Maps on Y-DNA haplogroups
External
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