Autosomnal DNA: Ethnic Composition
Autosomal DNA testing
http://www.ncbi.nlm.nih.gov/snp - enter number portion only in genographic 2.0 it lists them like rs6891223
Integrated Maps (Hint: click on 'Chr Pos' or 'Contig Pos' column value to see variation in NCBI sequence viewer)
Genealogical DNA test
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From Wikipedia, the free encyclopedia
For a non-technical introduction to genetics in general, see Introduction to genetics.
A genealogical DNA test looks at a person's genetic code at specific locations. Results give information about genealogy or personal ancestry. Generally, 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. They do not determine specific genetic diseases or disorders (see possible exceptions inMedical information below). They are intended only to give genealogical information.
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Autosomal DNA testing for genetic genealogy purposes is provided by the following four companies: 23andMe, AncestryDNA, Family Tree DNA and the Genographic Project.
Comparison Chart
Contents [hide]
This autosomal DNA testing comparison chart has been compiled by ISOGG member Tim Janzen. The chart is provided for informational purposes only. Additions made upon ISOGG member request. Please submit additions, corrections/updates to
This is Part 4 of a multi-part series, The Autosomal Me.
Part 1 was “The Autosomal Me – Unraveling Minority Admixture” and Part 2 was “The Autosomal Me – The Ancestors Speak.” Part 1 discussed the technique we are going to use to unravel minority ancestry, and why it works. Part 2 gave an example of the power of fragmented chromosomal mapping and the raw beauty of the results. Part 3, “The Autosomal Me – Who Am I?,” discussed how to use our pedigree charts to gauge expected results and how autosomal results are grouped into population buckets. We also named this technique, Minority Admixture Mapping, or MAP for short.
In this segment, Part 4, let’s take a look at what the testing company autosomal results look like. The results are presented in timeline order, with the oldest results first and the latest, and presumably most accurate results, last.
23andMe Version 1
23andMe was the first company to offer this type of testing affordably. They initially only offered 3 population groups, and one inferred that Asian was actually Native American. Of course, that wasn’t a valid assumption for everyone, but it was the best that could be done under the circumstances. This was my ethnicity results display at 23andMe until December 2012 went their updated version was released.
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.
I particularly like these results because the X chromosome is included, and seeing Native on the X chromosome, which has a unique inheritance path is a very important piece of data.
Family Tree DNA Version 1
Family Tree DNA’s first version of their Family Finder product produced results stating that I am 100% European, split between western and northern, shown below (minus the map.)
DeCode Genetics
DeCode Genetics initially offered autosomal tests for ancestry. Unfortunately, under the pressure of financial issues, they stepped away from the genetic genealogy marketspace and have since been sold.
Their test showed the following ethnic breakdown, picking up both my Native and African heritage:
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 inHaplogroup 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[edit source | editbeta]
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.
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.
What gets tested[edit source | editbeta]
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. Some ethnic population matching products use them. The preferred choice for both genealogy and ethnic population matching is microarray chips that use hundreds of thousands of autosomal SNPs.
STRs[edit source | editbeta]
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[edit source | editbeta]
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[edit source | editbeta]
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[edit source | editbeta]
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[edit source | editbeta]
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[edit source | editbeta]
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[edit source | editbeta]
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.
A direct maternal ancestor can be traced using mtDNA. MtDNA is passed down by the mother unchanged, to all children. A perfect match is 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 geneticsstudies. See the rest of this article.
What gets tested[edit source | editbeta]
Region
Differences from CRS
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.
Hospital Corpsman 1st Class uses a swab to take a DNA sample from a Fireman aboard USS Iwo Jima (LHD 7)
HVR1
111T,223T,259T,290T,319A,362C
HVR2
Not Tested
More extensive tests will also sequence Hyper Variable Region 2 (HVR2). HVR2 nucleotides are numbered 00001-00576.[6]
My current results from Family Tree DNA’s updated software are shown below.
Mother’s original results are shown above and her most recent results are shown below. Her results shifted within Europe and her margin of error doubled.
Family Tree DNA Updated 2012 Version
My mother was deceased before chip based autosomal testing was available, but I ordered the Family Finder test for her as soon as it was available. Thankfully her DNA was stored at Family Tree DNA and was still viable.
Although 23andMe does not provide participants with the start and stop locations, through alternative means, meaning a very smart friend, Rebekah Canada, who is a Java programmer, start and stop locations can be discerned.
CeCe Moore documented Rebekah’s technique for those who will be following along with their own results through this process.
In a future segment of this series, we’ll look at alternative ways to discern Native segments. Thanks to Rebekah’s technique, I can tell you that 23andMe shows my Native segments as follows:
Chromosome 1 – 165,658,091 to 175,711,116
Chromosome 2 – 86,316,174 to103,145,426
23andMe also provides a Neanderthal percentage. What fun!!!
The speculative level below shows the Native back to .5% but adjusts the European regions significantly.
The conservative estimate, below, shows less Native at .2%.
A second view is available which paints the chromosomes. A split view is also available if one of your parents has been tested at 23andMe as well. That is not an option for me.
It’s also interesting to note that my Native American on chromosome 2 is larger than my mother’s which may well reflect Native heritage on my father’s side. Ironically, the oral history of Native ancestry was on my father’s side, not my mothers.
Doug’s analysis has been updated several times over the years and these results are the most current. The vendors have made upgrades too. In 2012, both 23andMe and Family Tree DNA underwent upgrades to their ethnicity software and the Genographic Project version 2.0 test was released.
23andMe 2012 Updated Version
The new 23andMe software offers different confidence levels.
The standard estimate, or confidence level, shows that I have about .5% Native American. This is consistent with Dr. McDonald’s findings.
Doug indicates that the Native American is found at about the .5% level. Interestingly, on my mother’s graphs and charts (below), the Native segments are nearly identical, but my first grey South Asian segment on my X is Mideast on her chart.
The second graph maps these results on my chromosomes. The American, bright green, is found on chromosomes 1 and 2, and the X chromosome shows South Asian.
Dr. Doug McDonald
Doug McDonald, a retired physical chemistry professor, compiles contributed raw data and compares the raw data locations with both reference populations and the contributor results. This is not a commercial endeavor but a private research project which has been ongoing for years. His analysis of my raw data results from 23andMe and Family Tree DNA showed that they are primarily European. His first analysis was without Middle Eastern populations and the results showed European except for a total of about 3% East Asian, Oceana and American. However, in a second run including the Pakistan and Middle Eastern populations, the results now showed 88% European, about 1% Oceanic and American and the balance Middle Eastern and Pakistani.
A small amount of Middle Eastern heritage is not unexpected since I do have confirmed Turkish ancestors.
Dr. McDonald indicated that this was slightly more, 1-2%, than most Europeans, and that I was generally planted firmly in the middle of the “English” area in his data. His results showed no African.
Standard deviation (statistical noise) is about 1%. He can achieve these low deviation numbers by using such a large number of markers (536,904 to be exact)[1] for his comparison. I am grateful to Dr. McDonald for his contribution, not only to me, but to this field.
The graph below shows that my primary ancestry falls in the English/French region.
Region
Differences from CRS
Further information: Genetic history of indigenous peoples of the Americas
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 anyfederally 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 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. These tests may be useful foradoptees to discover Native American ancestry.
United States - African ancestry[edit source | editbeta]
Y-DNA and mtDNA testing may be able to determine with which peoples in present-day African country 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.[citation needed]African Americans 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[edit source | editbeta]
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 groups in the Upper South were descended from mixed-race people who were free in colonial Virginia and descended from 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[edit source | editbeta]
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. 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 J1and 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[edit source | editbeta]
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.
SNP testing may enable mostly European individuals to determine to which Sub-European population they belong:
Northern European subgroup (NOR) - mostly Northern and Southwestern European
Southeastern European (Mediterranean) subgroup (MED) - mostly Southeastern Europeans (Greeks, Albanians or Turks)
Middle Eastern subgroup (MIDEAS) - mostly Middle Eastern
South Asian subgroup (SA) - mostly South Asian from the Indian sub-continent (i.e. Indian)
Hindu testing[edit source | editbeta]
The 49 established gotras are clans or families whose members trace their descent to a common ancestor, usually a sageof ancient times. The gotra proclaims a person's identity and a "gotra-pravara" is required to be presented at Hinduceremonies. 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 forHindu 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.
Main article: Genetic genealogy
Genealogical DNA tests have become popular due to the ease of testing at home and their 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. But, they are limited by restrictions on lines which may be studied. The civil records are always only as accurate as the individuals who provided or wrote the information.
The aforementioned 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]
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.[citation needed]
Some users have recommended that there be government or other regulation of ancestry testing to ensure more standardization.[23]
Though genealogical DNA test results generally 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][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.[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.
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.
Main article: List of genetic genealogy topics
Family name (Patrilineal surname)
Matriname (Matrilineal surname)
^ AMNH > Our genetic identity Retrieved on 21 Mars, 2009
^ Balding, D.J. et al., eds. (2001). Handbook of Statistical Genetics, New York: Wiley
^ for example: M. Pickford, "Paradise lost: Mitochondrial eve refuted", SpringerLink, July 2006
^ "mtDNA regions". Phylotree.org. Retrieved 2011-06-15.
^ "mtDNA HVR1 region". Phylotree.org. Retrieved 2011-06-15.
^ "mtDNA HVR2 region". Phylotree.org. Retrieved 2011-06-15.
^ "DNA Tests prove that the body found under a parking lot belongs to King Richard III; but was he truly a "hunchback?"".
^ "Y-DNA matches". Smgf.org. Retrieved 2011-06-15.
^ "Here is one such case, see the heading "A success story quote"". Freepages.genealogy.rootsweb.ancestry.com. Retrieved 2011-06-15.
^ "Extending Family Trees with DNA Testing". Dna-testing-adviser.com. Retrieved 2011-06-15.
^ ftdna.com (kept uptodate). http://www.familytreedna.com/faq/answers/default.aspx?faqid=9#961 "FAQ: What do the DYS ... STR names mean?" Retrieved 2012-01-13.
^ "Ybase statistics". Ybase.org. 19 April 2011. Retrieved 2011-06-15.
^ a b 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.
^ "mtDNA matches". Smgf.org. Retrieved 2011-06-15.
^ a b Sykes, Bryan (2001). The Seven Daughters of Eve. W. W. Norton. ISBN 0-393-02018_5, pp. 291-92. Sykes discusses the difficulty in genealogically tracing a maternal lineage, due to the lack of matrilineal surnames (or matrinames).
^ Bolnick, DA et al. The Science and Business of Genetic Ancestry Testing. Science: Vol 318, 19 October 2007
^ Frudakis, T. The Legitimacy of Genetic Ancestry Tests. Science: Vol 319, 22 February 2008
^ "African Ancestry". African Ancestry. Retrieved 2011-06-15.
^ "Patriclan: Trace Your Paternal Ancestry". African Ancestry. Retrieved 2011-06-15.
^ Paul Heinegg, Free African Americans of Virginia, North Carolina, South Carolina, Maryland and Delaware[1], accessed 15 February 2008
^ Paul Heinegg, Free African Americans of Virginia, North Carolina, South Carolina, Maryland and Delaware, accessed 15 February 2008
^ 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.
^ Lee et al., "The Illusive Gold Standard in Genetic Ancestry Testing", Science 3, July 2009: 38-39
^ "Mitochondrial DNA inherited variants are associated with successful aging and longevity in humans". FASEB J. 13 (12): 1532–6. September 1999. PMID 10463944.
^ "Genetic And Rare Disease Information Center (GARD)". Genome.gov. 22 March 2011. Retrieved 2011-06-15.
Anne Hart; Anne Hart M a (April 2004). How to Interpret Family History and Ancestry DNA Test Results for Beginners. iUniverse.ISBN 978-0-595-31684-7.
Megan Smolenyak; Ann Turner (12 October 2004). Trace your roots with DNA: using genetic tests to explore your family tree. Rodale. ISBN 978-1-59486-006-5.
Chris Pomery; Steve Jones (1 October 2004). DNA and family history: how genetic testing can advance your genealogical research. Dundurn Press Ltd. ISBN 978-1-55002-536-1.
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
Foundations and research projects
The National Geographic Genographic Project
Sorenson Molecular Genealogy Foundation A wholly owned subsidiary of Sorenson
STR converters
Information and Maps on Y-DNA haplogroups
External
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.
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.
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.
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 matrilinealsurnames (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.
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' validityand 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.
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[edit source | editbeta]
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:
Before choosing a test, it is important for an individual to check the number of markers that will be tested. For example, theGenographic 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[edit source | editbeta]
Haplogroups are large groups of haplotypes that can be used to define genetic populations and are often geographically oriented.
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]
Further information: Y-chromosome haplogroups by populations
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.
Y-DNA tests generally 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.
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[edit source | editbeta]
mtDNA testing was used by University of Leicester archaeologists to verify the skeletal remains of King Richard III, found in September 2012.[7]
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[edit source | editbeta]
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[edit source | editbeta]
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 which have proved 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 but 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[edit source | editbeta]
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.
Haplogroup[edit source | editbeta]
Most results include a prediction of mtDNA Haplogroup.
Haplotype[edit source | editbeta]
Understanding test results[edit source | editbeta]
United States - Native American ancestry[edit source | editbeta]
United States[edit source | editbeta]
HVR1
111T,223T,259T,290T,319A,362C
HVR2
073G,146C,153G
Strand 1 differs from strand 2 at a single base pair location (a C → T polymorphism).
National Geographic Genographic 2.0
I was very surprised to see my National Geographic results. They were very unexpected, in particular the high percentages of Mediterranean and Southwest Asian, totaling 54%.
It made more sense when I read the information. It’s true, reading is fundamental.
These results are, in essence, more anthropological in nature.
Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.
These are somewhat different than the 23andMe results, although if you add the Neanderthal and Denisovan values together, the resultant 2.2% is very close to 23andMe’s 2.5%.
Ancestry.com
In 2012, Ancestry introduced an autosomal DNA test as well. What it provides is very limited, with limited tools, but it does provide percentages of ethnicity in addition to matches. Recently, Ancestry announced that the percentages may change over time. They have been severely beaten within the genetic genealogy community for quality issues with this product, including percentages of ethnicity that are highly erroneous. Their stated time reference is 500 years ago.
Recently this new page was added before you can see your detailed results.
Ancestry shows my heritage as only British and Scandinavian.
Ironically, Ancestry has mapped the birth locations of my ancestors in Europe on the map above, based on my family tree submitted. Interesting that Germany doesn’t show in Ancestry’s ethnicity list but many of my family lines originated in Germany and Holland, and none in Scandinavia.
Testing Provider Summary
Where do we stand now?
A summary of the various test results is shown below compared to my pedigree analysis.
Test Results Chart
I have included Dr. McDonald’s analysis here, not because he’s a testing provider in the sense of the testing companies, but because his offering was available in this timeframe, and because he worked with Family Tree to develop their Population Finder code.
You can see that the results are relatively consistent between testing companies. There is certainly no question about majority ancestry, but the minority admixture which hovers someplace near 1%, give or take 5% in either direction, is much less consistent and not always reported. If I were to have tested with only one company and taken the results as gospel, I could certainly have been left believing that I had no Native or African admixture. For many people, it’s this small amount of minority admixture that they are seeking. So in answer to the question of which testing company is “best,” the answer is, if you’re looking for trace amounts of anything, the compendium of all the testing companies (minus Ancestry) would provide the best set of results. We will be using the match information as well in the next sections, so certainly nothing has been “wasted” testing with multiple companies, again, except Ancestry. I am hopeful that Ancestry will in the future release our raw data (which they have promised to do) in a useable format, fix their misleading ethnicity results and add chromosome painting tools so that we can fully utilize our data.
In Part 5 of the series, we’ll take a look at third party tools and how they can continue to refine and add to our knowledge of our admixture.
1. Genealogy-DNA Rootsweb posting by Doug McDonald on 7-26-09 and personal correspondence.
2. 71.5% western European, 28.4% Northeastern European
3. Inferred that Asian is actually Native in an American with no history of Asian ancestry.
4. No category, inferred.
5. 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European
6. 54.6% Northern European, .3% Southern European, 43% Nonspecific European
7. 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European
8. 75.18% West Europe (French and Orcadian), 24.82 Europe (Romanian, Russian, Tuscan and Finnish). Note that my mother’s results are almost identical except the Finnish is missing from hers.
9. 43% North Europe and 36% Mediterranean
10. 80% British, 12% Scandinavian
This entry was posted in 23andMe, Admixture, Ancestry.com, Archaic Humans, Autosomal, Denisova,DNA Testing Companies, Ethnicity, Family Tree DNA, Genographic Project, Native American,Neanderthal, Tools and tagged autosomalme by robertajestes. Bookmark the permalink.
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23 THOUGHTS ON “THE AUTOSOMAL ME – TESTING COMPANY RESULTS”
Linda on February 24, 2013 at 5:21 pm said:
Thanks Roberta, It is very in-depth and I can’t say I understand it very well. I have to absorb it all. I am still waiting for the 23andME results. Thanks again for all your effort to help me understand.
Brownie MacKie on February 24, 2013 at 6:59 pm said:
Got my Geno 2 results from Nat’l Geographic. I wish I was a clear on it all as you are. Thanks.
Israel P. on February 24, 2013 at 7:02 pm said:
I think the only way I will ever get this is if I sat with someone in a small group for a few days and have it explained in person.
A.M. McPHERSON on February 25, 2013 at 12:30 am said:
When one gets tested in this same manner, do they shows these charts and graphs when they return with the results? How much is the test? How long does it take to get the results?
on February 25, 2013 at 12:49 am said:
Yes, the charts are shown on your personal page at 23andMe, Family Tree DNA and Ancestry. The McDonald reports are from him privately. DeCodeMe doesn’t sell this test any longer. Family Tree DNA also includes chromosome browsing, a tool that I did now show here that compares results of matches against each other and paints your chromosomes where you match. Thye test at 23andMe is $99. The test at Family Tree DNA is $289. I recommend that you take the test at 23andMe, then download your results and then you can upload them to Family Tree DNA for $89 and you’ll get the benefit of being in two data bases for a total of $188, which is less than the one $289 test. There is a link to both of those companies on the sidebar of myblog. I don’t recommend Ancestry unless you’ve already tested with the other two companies.
Paul on February 25, 2013 at 5:27 am said:
Are you disappointed that the Geno 2.0 did not pick up Native American? From what is advertised, I would think the Geno 2.0 would have the latest, best technology. It appears that Doug McDonald may have the most accurate ethnicity test available. Am I missing something? I did purchase a Geno 2.0 test but have not received the results yet.
on February 25, 2013 at 5:49 am said:
Yes, I was disappointed. I’m sure it’s mixed in with the Asian, but I was hopeful Geno 2.0 would be able to sort it out.
on February 25, 2013 at 7:39 am said:
I’m thinking that the business of selling kits may be impeding the science of DNA study. We must demand from these companies that their science be first and foremost. I don’t want to keep buying tests. Let’s get it right!
Sally
on April 10, 2013 at 5:43 am said:
Hi — I read on the Genographic site that they don’t list anything less than 2%, so that’s part of the problem.
Karla on February 25, 2013 at 5:20 pm said:
I’ve enjoyed your informative posts while awaiting results on my mother’s FTDNA tests. We’ve now got the autosomal results–the matches are all in the distant realm with no common surnames–so I’m very much looking forward to learning more about how I can analyze these matches. Apart from matches with Norwegian ancestry (my mother is half Norwegian), most of the matches are puzzling, and I haven’t been able to download the raw data yet to use elsewhere, which is frustrating (we want to identify her grandfathers, especially the non-Norwegian one).
Anyway, thanks and keep those how-to-analyze posts coming!
Paulette Kelly-Porter on April 28, 2013 at 11:59 pm said:
Thanks , this has giving me some idea, of what I’am looking at. I am from S.W.VA. .5 native,.2 SSA,98 Ep,with the 23 and me test.
Richard on May 31, 2013 at 2:32 pm said:
I notice that even tho Geno shows you as first choice British, you are closest to the Second choice, German. I think you have 14 numerical differences on the Brit, and only 4 on the German. I have the same situation on My Brit and Romanian… I am much closer to the Romanian ( I am British). I asked Geno about this twice, and I have no response. They did ask me for my password… I sent that in… no response.
A closest match should be a closest match ? Perhaps they flip a coin, or look at our surnames.
Anthony on June 3, 2013 at 3:28 pm said:
I’m still not sure sure that for people of African descent,just about all of whom get less than 2% East Asian and Native American results,there is as much certainty in saying they are real as they are in saying “0.2%” is real for someone of majority European descent. Even if Dr. Doug Mcdonald tell a person of African descent that “0.4% Native American” is “likely real”, I’d still doubt it. I still don’t believe that even with Dr. Mcdonald,there is an adequate enough population reference sampling for west Africans. Yoruba and Mandinka just isn’t quite enough,especially for people of west African descent who are much more of a blending of several different west African ethnicities . I believe that if Dr. Mcdonald and testing companies get more adequate population reference sampling for west Africans , these “0.4%”s and “1.1%” results will disappear and future test takers of African descent will not see them. Just like on the Blair Underwood episode of “Who Do You Think You Are? where he did a special and “only for him” version of the then unreleased Ancestrydna from Ancestry.com. he got a detailed African breakdown and his race results were straight African and European.There were no tiny “0.2%” or “1.3% East Asian & Native American” results.