28
Feb
10

Discovering African Ancestry Through DNA Testing (1/3)

Every Black History Month, many Americans and Canadians of African descent are confronted with one simple question – why do we need a Black History Month? After all, there’s no month dedicated to white history or gay history. The black history tradition dates back to 1926 and was founded by American historian Carter G Woodson, who sought to preserve and propagate knowledge of the artifacts and publications about the contributions of African-Americans to American life. The holiday was originally called “Negro History Week” and later expanded to a month-long celebration.

Of course this all took place before the rise of mass media, the internet and, most importantly, the legal rights that allow blacks in the United States to control their own destiny. Now in the digital age, discovering black history is as easy as visiting Wikipedia or scouring for an old copy of Encyclopedia Africana. So, why are so many black people still deeply attached to a concentrated celebration of widely-available information?

Part of the answer may be that assorted factoids about George Washington Carver and Harriet Tubman are the most intimate history many blacks have – due in part to slavery and the destructive breeding practices learned from that era. History within individual families can be hard to follow, with available information starting after the slave ship landed on American soil. The very label “African-American” implies a lack of knowledge about actual ethnic identity – a Somali has a considerably different culture and history than a member of the Ashanti tribe. Comparatively, the term European-American is rare except when in use by white nationalists. The majority of white Americans will refer to their heritage by nation – Irish-American, German-American, etc – and celebrate the specific contributions of those ethnic groups to American culture.

Fortunately, African-Americans no longer need to rely entirely on historical records to determine their ancestry. Specifically, DNA Ancestry testing has become tremendously popular over the past few years by promising to discover long-lost African history through genetically linking users to pre-defined samples of African ethnic groups. Some services, like Ancestry.com and DNA Consultants, offer comprehensive testing while other services like African Ancestry concentrate specifically on African heritage.

But what benefit can be gained from such services and how believable are the results? I’ve spent the better part of a year overseeing tests for myself and others as well as doing some research into the benefits and limitations of DNA testing. A summary of DNA Testing as well as my own experience will be spread over three blog posts. Readers are encouraged to submit their own experiences with DNA testing.

What can a DNA Test Tell you?

Present DNA ancestry testing is based on scientific findings that all present-day human beings can be traced back approximately 150,000 years to common ancestors in East Africa. Various waves of early humans migrated from Africa to different parts of the globe and their DNA mutated in tiny increments. These natural mutations, known as single-nucleotide polymorphisms (SNP’s for short) occurred randomly every few thousand years and were passed down from generation to generation. While these mutations are complex and there can be many different sequences (also known as Haplotypes), mutations are generally quite similar for early humans that migrated to the same part of the world around the same. Haplotypes are thus clustered into haplogroups, which are understood to have a common ancestor. There are separate male (Y-Chromosome) and female (X-Chromosome) haplogroups which are distributed geographically.

Y-DNA Haplogroups

Three types of DNA tests can be used to determine ancestry:
mtDNA – Short for mitochondrial DNA, mtDNA is carried by both males and females. However, mtDNA is passed exclusively from mother to child, meaning an mtDNA test can only determine your mother’s contribution to your genetic makeup. Since this relationship is true all the way up your family line, mtDNA ancestry tests can determine the origin of your mother’s mother’s … mother. Because mtDNA is only inherited from mothers, it does not change (or mutate) significantly over time (due to the slow-changing nature of SNP’s). This slow rate of mutation allows scientists to determine the long term origin (also known as “Deep Ancestry”) of your maternal line.
yDNA – Y-Chromosomes works in a similar manner to mtDNA, except that they are only passed from father to son. Thus, only males have yDNA tests. Females wishing to discover their deep paternal lineage must have a paternal male relative take the test (e.g. father, brother).
(side note: human females obtain X-Chromosomes from both mother and father; thus, “X Chromosome” cannot be used interchangeably with mtDNA in this instance)

Autosomal – Every human has 22 pairs of autosomal chromosomes. There are equal copies of the autosomal chromosomes in males and females, allowing genetic identification based on the heritage of both parents. However, autosomal DNA is not “deep”, as the 22 pairs are inherited randomly from parents (for a given pair, one chromosome comes from each parent; each parent can pass 1 of 2 chromosomes, meaning 4 possible configurations per pair). No two people -except for identical twins- have the exact same autosomal DNA, which contrasts with the direct inheritance of yDNA and mtDNA.

What can’t a DNA Test tell you?

So with all of this technology, it should be easy to figure out where you originally set up shop before the transatlantic trip, right? Not quite. Apart from the fact that an overwhelming percentage blacks in the western hemisphere are of mixed heritage, the current testing methods have noteworthy limitations

  1. yDNA and mtDNA tests are single-line. This means that they measure straight inheritance via mother or father only. Thus, one cannot use mtDNA to test whether a mother’s father is part-native because the mother’s mtDNA comes exclusively from her mother. Similarly, yDNA only provides information on a line of fathers. Thus, even combining mtDNA and yDNA tests will not allow a person to determine their entire ancestry.
  2. Autosomal DNA can only reliably measure back to the grandparent generation. Typically, autosomal DNA used in paternity testing, crime scene investigation and other situations where either exact identity or close family relationship needs to be established.
  3. Autosomal DNA cannot determine what percentage of each ethnic group is in a person’s total makeup

Ergo, it may not be possible to tell whether you are a direct decedent of the Zulus unless either your mother’s mother’s … mother or father’s father’s … father happens to belong to that ethnic group. If you are so lucky it will still not possible to determine just how “Zulu” you are.

Discovering your Ancestry through Genebase

There are many different websites and offline services offering DNA testing as a way to discover heritage. Being Canadian and somewhat concerned about how foreign governments might use a DNA sample, I chose the Vancouver-based Genebase (note: many Americans also use this service).

Genebase offers mtDNA and yDNA test kits of varying comprehensiveness (and prices) for ancestral discovery. The initial tests are STR (short tandem repeat) tests that can be used to predict haplogroups. Additional SNP tests can be ordered to confirm haplogroup, and most recently Genebase has added subclade tests for further confirmations.

For example, a male users interested in his paternal ancestry could order the Advanced Paternal Ancestry Package (Y-DNA 44 Marker Test). After the test predicts that he belongs to the J haplogroup, he could confirm this by upgrading with a Y-DNA DNA haplogroup Backbone SNP Test. If the client wants more detail he could choose to order the Y-DNA J Subclade SNP Test and use the results to determine the probable region form which his earliest haplogroup member originated.

Apart from haplogroup identification, Genebase offers two other useful ancestry tools for incoming DNA samples -

DNA Reunion – yDNA and mtDNA STR markers can be compared to all the other users in the DNA database. The software ranks user matches according to number of overlapping markets to be compared between two users and the genetic distance (calculated by number of markers that have different values). For the example above, the user might upgrade from a 44 marker test to a 67 marker test, since having a larger pool of markers to test will improve the probability of finding matches. Using the search preferences, he can direct DNA Reunion to return a list of users who have a maximum genetic distance of 1 (ie only 1 marker different) out of a minimum 18 overlapping markers. The results might show that the majority of users matching this criteria reside in Egypt, suggesting (though not proving) that user’s deep ancestral roots may lie in that region.

Indigenous DNA – Similar to DNA Reunion, except DNA samples are compared to indigenous (and some non-indigenous) groups from around the world. The software makes STR comparisons over several different journals using a selectable number of marker matches. Again, the results do not strictly prove ancestry but are an excellent aid for determining probability.

Autosomal test kits are also available and are used in DNA Reunion – however Genebase only uses autosomal DNA to match near family relations to others users in the database. This contrasts to many other ancestry services which use autosomal DNA to predic ethnic identity.  Still, autosomal testing could be used for cheap, legal paternal testing.

At one time DNA kits used to be available in Best Buy but these days it seems the only way to get a kit is to order directly from the Genebase website. The kit is mailed to the user’s home with a return envelope, small swab brushes and full instructions on how to collect a buccal swab. Once the sample is returned, processing takes place over the next few weeks and the results are uploaded to a website. The user can then view the results and start using the tools described above.

Continue to Part 2


1 Response to “Discovering African Ancestry Through DNA Testing (1/3)”


  1. 1 john quirindongo Apr 14th, 2011 at 10:26 am

    As I understand it, the yDNA and mtDNA are ancient 9,000 yr old while
    autosome gives more recent 200 yr updates (See four % distribution here)
    DNA results
    Family finder
    Quirindongo MDKO-1740 (all) Peñuelas PR Percentage Autosome
    1.- John Henry Self- b.1933 NYC 22 Autosome 100%
    2.-Carmelo Father-b.1888-1968 Peñuelas PR 50% ½ of 22 Autosome
    3.-Monserrate Grandparent-b.1858-1921 Peñuelas PR 25% ¼ of 22 Autosome
    4.-Alejandro 1st Great Grandparent-b.1841-1893 12.5% 1/8 of.22 Autosome
    5.-Eugenio 2nd Great Grandparent -b.1820 6.2% 1/16 of 22 Autosome
    6.-Pedro 3rd Great Grandparent- b.1760 3.1% 1/32 of 22 Autosome
    7.-Juan Nicholas 4th Great Grandparent-b.1740? 1.6% 1/64 of 22 Autosome
    Arroyo MDKO-1733 (all) Peñuelas PR Percentage Autosome
    1.- John Henry Self- b.1933 NYC 22 Autosome 100%
    2.-Carmelo Father- b.1888-1968 Peñuelas PR 50% ½ of 22 Autosome
    3.-Carmen Arroyo Grandparent-b.1861-1953 Peñuelas PR 25% ¼ of 22 Autosome
    4.-Rita Maria Torres 1st Great Grandparent-b.1845 12.5% 1/8 of.22 Autosome
    5.-Claudina Santiago 2nd Great Grandparent-b.1825 6.2% 1/16 of 22 Autosome
    6.-Catalina Cortés 3rd Great Grandparent-b.1768 3.1% 1/32 of 22 Autosome
    7.-Juana deTorres 4th Great Grandparent-b.1733 1.6% 1/64 of 22 Autosome
    Cortés MDKO-1849 (all) Peñuelas PR Percentage Autosome
    1.- John Henry Self- b.1933 NYC 22 Autosome 100%
    2.-Sara Arroyo Mother- b.1910-2004 Peñuelas PR 50% ½ of 22 Autosome
    3.-Juan Arroyo Grandparent-yDNA-b.1887-1942 25% ¼ of 22 Autosome
    4.-Isaias Cortés 1st Great Grandparent-b.1862-1919 12.5% 1/8 of.22 Autosome
    5.-Francisco Cortés 2nd Great Grandparent-b.1849-13 y.o. 6.2% 1/16 of 22 Autosome
    -6 not known 3rd Great Grandparent 3.1% 1/32 of 22 Autosome
    -7 not known 4th Great Grandparent 1.6% 1/64 of 22 Autosome
    Cadiz MDKO-1885 (all) Peñuelas PR Percentage Autosome
    1.- John Henry Self- b.1933 NYC 22 Autosome 100%
    2.-Sara Arroyo Mother- 1910-2004 Peñuelas PR 50% ½ of 22 Autosome
    3.-Angela Cadiz Grandparent-b.1885 Peñuelas PR 25% ¼ of 22 Autosome
    -4 Velazquez 1st Great Grandparent Peñuelas PR 12.5% 1/8 of.22 Autosome
    -5 not known 2nd Great Grandparent 6.2% 1/16 of 22 Autosome
    -6 not known 3rd Great Grandparent 3.1% 1/32 of 22 Autosome
    -7 not known 4th Great Grandparent 1.6% 1/64 of 22 Autosome

    ///////////////////////////////////////////////////////////////////////////////////////////////////

    ////////////////////////

    FTDNA POPULATION FINDER Beta
    John Henry FIRST RUN
    Continent (Subcontinent) Population Percentage Adjustment
    1.) Europe (Western European) Spanish 68.50% ±0.10% (-13.74%)
    2.) Native American (Central American) Maya 18.79% ±0.01% (-2.25%)
    3.) Africa (West African) Mandenka? Yoruba 12.71% ±0.10% (-4.35%)
    ///////////////////////////////////////////////////////////////////////////////////

    ******UPDATED 4/8/2011**********

    Continent (Subcontinent) Population Percentage Margin of Error
    1.) Europe Finnish, French, Orcadian, Spanish 54.76% ±2.83%
    2.) Native American Colombian, Maya 16.54% ±1.19%
    3.) Africa Mandenka, Yoruba 8.36% ±1.09%
    4.) Middle East (North African) Mozabite 20.33% ±4.58%

    ////////////////////////////////////////////////////////////////////////////////////////
    POPULATION FINDER Beta

    Sister
    Nancy Marie
    FIRST RUN

    Continent (Subcontinent) Population Percentage Margin of Error
    1.) Europe (Northeast European) Finnish 43.59% ±0.56%
    2.) Native American Maya 15.01% ±0.85%
    3.) Middle East (North African) Mozabite 41.40% ±0.29%
    /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

    I believe that because all of my ancestry are NOT listed in the FTDNA Autosomal SNP reference database that DEFAULT ethnicities were inserted. Amazingly Irish and Dutch are not any listed referenced categories that apply to me and according to oral and documented history seem correct.

    1.) Finnish appears listed on top first above Russian, only 2 choices in “Europe (Northeast European)” with Finnish the top being default, only 2 choices.
    2.) Maya appears listed on top first above the very small population Arizona Pima, only 2 choices.
    3.) Mozabite appears listed last in the small North Africa list category. Amazingly Irish and Dutch are not any listed referenced categories that apply to me and seem correct.

    If my sister had not also submitted to Family Finder and Population Finder previously and was found dissimilar, we would not have asked for a 2nd run when my results of Population Finder first came back. The discrepancy and complaint changed the results of my “Population Finder” alone considerably. My sister’s “Population Finder” was untouched.

    A new corrected category “Middle East (North African)” appears for me on the 2nd run taking small Percentage from all three others. First FTDNA says I am 68.50% Europe (Western European) Spanish then it was updated and lowered to 54.76% (-13.74) and Europe (Northeast European) Finnish, French and Orcadian were added to Spanish. My sister was Northeast European, Finnish 43.59%, an obvious and glaring mistake.

    Conclusion: multiple beta flaws in small FTDNA reference database for Population Finder and also the “margin of error” ± is always wrong if you consider the 1st run and adjustments (above) made after the 2nd run. Finnish seems misdiagnosed and a grave beta unfamiliar territory error.

    In my 1st run, the “Middle East” 20.33% and Finnish were not found. In my sister’s 1st run “Africa (West African)” 8.36% was omitted or too small to register.

    I believe Autosome can distinguish general areas such as European but not specific ones such as Europe (Northeast European) Finnish and French. In my case Finnish is out of the question especially since Autosome is relegated mostly to RECENT history.

    The big question is: y didn’t FTDNA include the Dutch and Irish yDNA that were developed by FTDNA (kit 41475 and kit 35383) that are admittedly very small amounts but reliably proven true since the 1953 Francis Crick discovery of DNA and later discoveries of the dominant yDNA and mtDNA. My 1600AD oral history era odyssey does appear in history books and are corroborated by my family oral history as unusual immigrants to PR. Both my sister’s (kit 192134) and my FTDNA Autosomal SNP Population Finder report results altho’ majority European were not included in any other proven values of yDNA and mtDNA results are not included in the final results. Finnish ancestry appears and FTDNA insists it’s there and they have found it but I deem it faulty especially in my sister’s lone high percentage 43.59% along with my other sundry supposedly “recent” heritage European ethnicities in the Autosomal SNP Population Finder report. If they are “recent” European heritage ethnicities they especially Finnish should appear in my oral history.

    FTDNA doesn’t answer my sister’s repeated requests for a 2nd run adjustment.

    In the very recent past… “Autosomal DNA can only reliably measure back to the grandparent generation. Typically, Autosomal DNA used in paternity testing, crime scene investigation and other situations where either exact identity or close family relationship needs to be established. Autosomal DNA cannot determine what percentage of each ethnic group is in a person’s total makeup” … “As stated, current DNA technology can’t reliably identify any ancestry that is not patrilineal, matrilineal or within the last couple of generations. It is almost certainly not possible to calculate ethnic percentages as some websites advertise… autosomal testing could be used for cheap, legal paternal testing.”
    Re: http://www.cynicsunlimited.com/2010/02/28/discovering-african-ancestry-through-dna-testing-12/

    Excellent but slightly flawed “first step” Biogeographical matches presentation analyzed “in depth” http://salabencher.blogspot.com/2010/11/biogeographical-ancestry.html

    EURO-DNA-CALC altho’ concerned with Europe-only will be tried in the future when I have time to decipher their instructions.
    //////////////////////////////////////////////////////////////////////////////////////////////////////////

    Family finder RESULTS:
    John Henry and sister Nancy Marie results seem correct
    2,447.35 cM (centimorgan) shared chromosomes of:
    3,300.00 cM total
    123.19 matching longest blocks

    No unknown cousins found
    Closest “non-cousin” Candy Torres
    112.94 cM shared chromosomes and sister
    93.11 cM shared chromosomes
    24.11 matching longest blocks and sister
    23.45 matching longest blocks

Leave a Reply

 



Further Research

Twitter

Archives

Categories