Daughters of Princess Mary Kittamaquund

Daughters book cover

Recently Shawn and Lois Potter utilized the Minority Admixture Mapping technique I developed, utilized and described in the series “The Autosomal Me” to establish that the mother of John Red Bank Payne was Native American.  Shawn and Lois were so encouraged after that positive experience that they set forth to document another Native ancestor.

They produced this report as a beautiful and fully sourced booklet which they have very graciously given permission to reproduce in part here.

Daughters of Princess Mary Kittamaquund

Every student of American history has heard about Pocahontas—the young Indian princess who struggled to establish peace between the Powhatan Indians and Virginia colonists, married Englishman John Rolfe, and left descendants through her son Thomas Rolfe.  But, few have heard about Mary Kittamaquund—another young Indian princess who likewise promoted peace between the Piscataway Indians and Maryland colonists, married Englishman Giles Brent, and, as revealed by archival research combined with DNA analysis, left descendants through her daughters.  Both women lived heroic yet brief lives; and both should be remembered for their devotion to their people in an age of momentous danger and change.  The following sketch introduces Princess Mary Kittamaquund and her daughters.

Mary Kittamaquund, daughter of the Tayac (Paramount Chief) of the Piscataway Indians, was born in Maryland probably about 1631.[i]  Her father ruled over as many as 7,000 people between the Potomac and Patuxent Rivers.[ii]  Following about six months of dialogue and study with Jesuit Missionary Father Andrew White, Mary’s father converted to Christianity and was baptized on July 5, 1640.[iii]  Soon after February 15, 1640/1, Mary too was baptized, and her father sent her to the English settlement called St Mary’s City, near the mouth of the Potomac River, to be educated by Governor Leonard Calvert and his sister-in-law, Margaret Brent.[iv]

Mary married Giles Brent, brother of Margaret Brent, before January 9, 1644/5.[v]  A band of Parliamentarians led by Richard Ingle and William Claiborne attacked St Mary’s City on February 14, 1644/5, and carried Giles Brent, Father Andrew White, and others in chains to England.  Upon his arrival in London, Giles brought suit against his captors and returned to Maryland before June 19, 1647.[vi]  Mary and Giles moved to present day Aquia, Stafford County, Virginia, after November 8, 1648, and before August 20, 1651.[vii]  Mary died probably after April 18, 1654, and before September 4, 1655.[viii]  Giles Brent died in Middlesex County, Virginia, on September 2, 1679.[ix]

Scholars disagree about the number of children born to Mary Kittamaquund and Giles Brent.  Some list only three children named in the 1663 and 1671 wills of sister and brother Margaret and Giles Brent.[x]  Margaret appointed her brother Giles “and his children Giles Brent, Mary Brent, and Richard Brent” executors of her estate.[xi]  Giles left bequests to his son Giles Brent and daughter Mary Fitzherbert.[xii]  Other historians, such as Dr. Lois Green Carr, Maryland Historian at the Maryland State Archives, on the basis of information gleaned from provincial court records, probate records, and quitrent rolls, identify six children of Mary and Giles, including Katherine Brent (who married Richard Marsham), Giles Brent (who married his cousin Mary Brent), Mary Brent (who married John Fitzherbert), Richard Brent (who died after December 26, 1663), Henry Brent (who died young), and Margaret Brent (who also died young).[xiii]

Some researchers further believe daughter Mary Brent divorced John Fitzherbert before April 26, 1672, and married second Charles Beaven.  This belief is supported by (1) a reference to the divorce of Mary and John in a letter of this date from Charles Calvert to his father, (2) a statement regarding “my brother iñ Richard Marsham” in the June 20, 1698 will of Charles Beaven, (3) the appointment of “my well beloved Richard Marsham” by Mary Beaven to be executor of her 1712 will, and (4) other circumstances demonstrating kinship ties between these families.[xiv]  Still others refuse to accept this relationship without further evidence, lamenting the loss of contemporary records which has “confused researchers for a hundred years.”[xv]

Recent DNA analysis, however, reveals six descendants of Katherine and Richard Marsham and three descendants of Mary and Charles Beaven, representing six separate lineages, inherited at least sixteen matching segments of Native American DNA on chromosomes 2, 3, 4, 5, 6, 7, 8, 13, 15, 16, 20, and 22.  Figure 1 shows the relationships between these descendants; and Figures 2-17 illustrate the sixteen matching Native American chromosomal segments (see Figures 18-33 for additional images of these segments produced by four independent admixture tools; and also see http://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/ for information about Minority Admixture Mapping).  These matching chromosomal segments point to a common Native American ancestor, who, because other possibilities can be eliminated, must have been the mother of Katherine and Mary.[xvi]  Considering this DNA evidence in light of contemporary records, it now seems certain Mary Kittamaquund and Giles Brent were the parents of Katherine, wife of Richard Marsham, and Mary, wife first of John Fitzherbert and second of Charles Beaven.

Genealogical Summary

Katherine Brent was born probably in Aquia, Stafford County, Virginia, say about 1650.  She may have served an unknown period of indentured service to Thomas Brooke, perhaps following the death of her mother, before she married Richard Marsham perhaps before December 26, 1663, and certainly before March 11, 1664/5.[xvii]  Richard immigrated to Maryland in 1658, where he served three-years of indentured service to John Horne for his transatlantic voyage.[xviii]  Katherine died in Calvert County, Maryland, before October 26, 1670.[xix]  Richard married second Anne Calvert, widow first of Baker Brooke Sr., and second of Henry Brent, after April 30, 1695, and before February, 1696.[xx]  Richard died in Prince George’s County, Maryland, between April 14 and 22, 1713.[xxi]  Katherine and Richard were the parents of the following children:

1. Sarah Marsham was born in Calvert County, Maryland, say about 1667, married first Basil Waring say about 1685, married second William Barton after December 29, 1688, married third James Haddock after April 19, 1703, and died in Charles County, Maryland, after January 8, 1733.[xxii]

2.  Katherine Marsham was born in Calvert County, Maryland, say about 1669, married first her future step-brother Baker Brooke Jr. say about 1689, married second Samuel Queen after May 27, 1698, and died in St Mary’s County after March 18, 1712, and before April 14, 1713.[xxiii]

Mary Brent was born probably in Aquia, Stafford County, Virginia, say about 1654.[xxiv]  She married first John Fitzherbert before 1671.[xxv]  Mary and John divorced before April 26, 1672.[xxvi]  Mary married second Charles Beaven say about 1674.  Charles died in Prince George’s County, Maryland, between June 20, 1698, and June 21, 1699.[xxvii]  Mary died in Prince George’s County between April 28, 1712, and June 13, 1713.[xxviii]  Mary and Charles were the parents of the following children:

1. Richard Beaven was born in Calvert County, Maryland, say about 1676, married Jane Blanford before June 11, 1703, and died in Prince Georges County, Maryland, before August 9, 1744.[xxix]

2.  Sarah Beaven was born in Calvert County, Maryland, say about 1678, married Thomas Blanford on June 20, 1698, and died in Prince Georges County, Maryland, after August 7, 1749.[xxx]

3.  Margaret Beaven was born in Calvert County, Maryland, say about 1680, and died in Prince George’s County, Maryland, between April 28, 1712, and June 13, 1713.

4. Elizabeth Beaven was born in Calvert County, Maryland, say about 1682, married John Boone about 1708, and died in Prince Georges County, Maryland, before October 30, 1725.

5. Katherine Beaven was born in Calvert County, Maryland, say about 1684, married Henry Culver about 1711, and died in Prince Georges County, Maryland, before December 20, 1762.[xxxi]

6. Charles Beaven was born in Calvert County, Maryland, say about 1686, married Mary Finch about 1712, and died in Prince Georges County, Maryland, on December 16, 1761.[xxxii]

Daughters pedigree

Following this lineage information, Shawn and Lois included a chromosome by chromosome analysis of the various individuals who tested.  I am including only one example, below.

Daughters DNA

Following the many pages of genetic comparison information, Shawn and Lois included quite a bit for their readers about the Piscataway History and Culture.  After all, DNA without genealogy and history is impersonal science.  Included were early drawings and paintings of Native people and villages, an account of the people by Father Andrew White in 1635 as well as anonymous documents from 1639 and 1640.  Their food, language and vocabulary were discussed as well with historical events being presented in timeline format.

Piscataway Timeline

1550           Piscataway Tayac governed c. 7,000 people between Potomac and Patuxent Rivers

1608           John Smith explored the Potomac River; Piscataway welcomed him with kindness

1622           Powhatan Indians attacked at least 31 Virginia settlements along the James River

1623           Virginia colonists attacked Moyaone, killing many and burning houses and corn

1634           Piscataway Tayac Wannas permitted Leonard Calvert to establish St Mary’s City

1640           Piscataway Tayac Kittamaquund was baptized by Jesuit Father Andrew White

1644           Wahocasso succeeded as Tayac, who was succeeded by Uttapoingassenem in 1658, who was succeeded by Wannasapapin in 1662, who was succeeded by Nattowasso (son of Wahocasso—breaking the tradition of matrilineal succession) in 1663

1666           Facing increasing encroachments by European settlers, the Piscataway petitioned the Maryland council, saying: “We can flee no further.  Let us know where to live, and how to be secured for the future from the hogs and cattle.”

1695           Maryland Governor Francis Nicholson “advised the council to find a way of depriving Indians beyond Mattawoman Creek of their lands, in order to ‘occasion a greater quantity of Tobacco to be made.'”

1697           Piscataway Tayac Ochotomaquath and about 400 others fled to northern Virginia; then they allied with the Iroquois in 1701 and moved to Pennsylvania.

1699           Maryland colonists estimated Piscataway military strength at 80-90 warriors

Although many Piscataway left Maryland by the end of the 17th century in the face of encroaching European settlements, others remained on their homeland, intermarrying with Europeans and Africans, while preserving their cultural traditions.  In 1996, an advisory committee appointed by the Maryland Historical Trust voted unanimously to recommend state recognition of the Piscataway Indian Nation, citing genealogical, linguistic, cultural, and political continuity between the earliest Piscataway people and their modern descendants.  On January 9, 2012, Maryland Governor Martin O’Malley issued two executive orders, granting official state recognition to the Piscataway Indian Nation (about 100 members), and the Piscataway Conoy Tribe—consisting of the Piscataway Conoy Confederacy and Subtribes (about 3,500 members), and the Cedarville Band of Piscataway (about 500 members).

St Mary's City 1634 Indian Village

This drawing of St Mary’s City in 1634 by Cary Carson from the Maryland State Archives Map Collection shows the Native people living outside the city fortifications.

This 262 page book is a wonderful combination of genealogy, genetics and history, and does exactly what genetic genealogy is supposed to do.  It enables us to document and better understand our ancestors, and in this case, to prove they were indeed, Native American.  Shawn and Lois would welcome inquiries about the book or the family lines included and you can contact them at shpxlcp@comcast.net.

               [i] Most scholars estimate her year of birth as 1634, because an unidentified Catholic missionary made the following statement about her.  “On the 15th of February we came to Pascatoe, not without the great gratulation and joy of the inhabitants, who indeed seem well inclined to receive the christian faith.  So that not long after, the king brought his daughter, seven years old, (whom he loves with great affection,) to be educated among the English at St. Mary’s; and when she shall well understand the christian mysteries, to be washed in the sacred font of baptism.”  See “Extracts from Different Letters of Missionaries, from the Year 1635, to the Year 1638,” in E.A. Dalrymple, ed., Relatio Itineris in Marylandiam.  Declaratio Coloniae Domini Baronis de Baltimoro. Excerpta ex Diversis Litteris Missionariorum ab Anno 1635, ad Annum 1638, Narrative of a Voyage to Maryland, by Father Andrew White, S.J.  An Account of the Colony of the Lord Baron Baltimore.  Extracts from Different Letters of Missionaries, from the Year 1635 to the Year 1677 (Baltimore: Maryland Historical Society, 1874), 76.  But, the circumstances of Mary’s life suggest she was born a few years earlier.  So, we suspect the author of this letter underestimated her age.

               [ii] Father Andrew White, “Annual Letter of the English Province of the Society of Jesus, 1639,” in Clayton Colman Hall, ed., Narratives of Early Maryland, 1633-1684 (New York: Barnes & Noble, Inc., 1910), 126.

               [iii] Ibid.

               [iv] Ibid., 131.

               [v] John Lewger to Governor Leonard Calvert, January 9, 1644/5, in Proceedings of the Council of Maryland, 1636-1667, Vol 3, pp. 162-163 (original pages 186-187), Archives of Maryland Online.  “To the horle Governor.  Sir  I doe signify unto you that Mr Giles Brent hath delivered unto me 2. petitions nerewth sent unto you; and I desire you by vertue of the Law in that behalfe, that you wilbe pleased to give him a competent security for his indemnification in the possession of the lands at Kent, mentioned in one of the said petitions, & for iustification of his title in them, according to the said petition, dated 7. January instant: & likewise to satisfy unto him 5700l tob & cask, demanded in the other petition for damage of non pformance of a covenant to his wife Mary touching certaine cattell; or els to shew cause why you refuse to doe either; and to appoint some time when the Counsell shall attend you for it, betweene this & Monday next.  So humbly take leave to rest  Yor servant  S. Johns. 9th Jan: 1644 John Lewger.”  See also Margaret Brent, “Account of the Estate of Governor Leonard Calvert,” June 6, 1648, in Judicial and Testamentary Business of the Provincial Court, 1637-1650, Vol. 4, pp. 388-389 (original pages 159-160).  “By payd to Mrs. Mary Brent Kittamagund 0748.”

               [vi] For information about the arrest and transport of Giles Brent to London during Richard Ingle’s Rebellion, see “Richard Ingle in Maryland” in Maryland Historical Magazine, Vol. 1(1906), 125-140.  For the terminus ad quem (limit to which—latest possible date) Giles Brent returned to Maryland, see Maryland State Archives, Judicial and Testamentary Business of the Provincial Court, 1637-1650, Vol. 4:312-313.  “June 19th This day came Margaret Brent Gent, & desyred the testimony of the prnt Gouernor Mr Tho: Greene concerning the last will & Testamt of the late Gouernor Leonard Calvert Esqr And the sd Gouernor did authorize Giles Brent Esqr one of his Lops Counsell to administer an oath unto him the sd Gouernr concerning the foresd busines.  The sd Gouernor Tho: Greene Esqr answered uppon oath concerning the last will & Testamt of Leo: Calvert Esqr aforesd That the sd Leo: Calvert, lying uppon his death bed, some 6 howres before his death, being in prfect memory, directing his speech to Mrs Margarett Brent sayd in pnce of him the sd Mr Greene & some others I make you my sole Exequutrix, Take all, & pay all.  After wch words hee the sd Leon: Calvert desyred every one to depart the roome & was some space in priuate conference wth Mrs Marg: Brent aforesd Afterwards the Mr Greene comeing into the roome againe, he heard the sd Mr L: Calvert appoint certaine Legacies in manner following.  Viz I doe giue my warring cloaths to James Linsay, & Richard William my servants, specifying his coath suite to Rich. Willan & his black suite to James Linsey. & his waring Linnen to be diuided betweene them.  Aliso I giue a mare Colt to my God sonne Leon: Greene.  Allso hee did desyre tht his exequutrix should giue the first mare Colt tht should fall this yeare, (& if non fall in this yeare, then the first tht shall hereafter fall) unto Mrs Temperance Pippett of Virginea.  And further he deposeth not.  Recognit Teste mc Willm Bretton Clk.”

               [vii] The terminus a quo (limit from which—earliest possible date) for the relocation of Giles Brent from Maryland to Virginia is the date Giles Brent appeared in court at St. Mary’s on November 8, 1648, requesting compensation for destruction of his property on the Isle of Kent by anti-Papists.  See Archives of Maryland, November 8, 1648, Liber A, Folio 205.  The terminus ad quem (limit to which—latest possible date) Giles Brent removed from Maryland to Virginia is the date Giles Brent patented Marlborough in Potomac Neck, Virginia, on August 20, 1651.  See entry from Mercer Land Book cited by W.B. Chilton, ed., “The Brent Family,” The Virginia Magazine of History and Biography, Vol. 16, No. 1 (Jul., 1908), 96-97.

               [viii] Virginia Magazine XVI, 211.  On April 17, 1654, Giles conveyed his personal estate in Virginia and Maryland to his sister Mary, in trust to educate his children and allow maintenance to his wife Mary.  See also Lurene Rose Bivin in “Brent-Marsham-Beaven-Blandford Article: A Closer Look,” Maryland Genealogical Society Bulletin, Vol. 37, No. 3, 328-334.  “In the grant to John Harrison (dated 4 September 1655), he refers to his “sister” as Mrs. Frances Harrison (Nugent, p. 319).”  Giles may have been engaged to marry his second wife, Frances Whitgreaves, widow of Jeremiah Harrison, on this date, because John Harrison made a provision for Giles.

               [ix] W.B. Chilton, ed., “The Brent Family,” The Virginia Magazine of History and Biography, Vol. 16, No. 2 (Oct., 1908), 212.  “‘Register of Christ Church, Middlesex County, Virginia.  Collo Giles Brent of Potomac departed this life 2d of September 1679 and was buried in the Great Church Yard ye next day following.'”

               [x] For example, see Douglas Richardson, Magna Carta Ancestry: A Study in Colonial and Medieval Families (Baltimore: Genealogical Publishing Co., Inc., 2005), 129.  “They had two sons, [Col.] Giles and Richard, and one daughter, Mary (wife of [Capt.] John Fitzherbert).”  See also, Robert W. Barnes, British Roots of Maryland Families (Baltimore: Genealogical Publishing Co., Inc., 1999), 73-74.

               [xi] W.B. Chilton, Vol. 16, No. 1 (Jul., 1908), 98-99.  “The Will of Margaret Brent.  In the name of God Amen.  I Margaret Brent of Peace in the County of Westmoreland in Virginia considering the casualtys of human life do therefore make this my last Will and Testament as followeth my soul I do bequeath to the mercies of my Savior Jesus Christ and my worldly estate to be disposed of by my Executors as followeth to my nephew George Brent I give all my rights to take up land in Maryland except those already assigned to my cousin James Clifton to my niece Clifton I give a cow and to my neece Elizabeth Brent I give a heifer; to Ann Vandan I give a cow calf; to my neece Mary Brent daughter of my Brother Giles Brent I give all my silver spoons which are six; to my nephew Richard Brent son of my brother Giles Brent I give my patent of lands at the Falls of Rappahanock River also my lease of Kent Fort Mannor in Maryland saving yet power to his Father my brother Giles Brent that if he shall like to do so he may sell said lease and satisfye to his son other where as he shall think fitt in lands good or money and in case of my said nephew Richard Brents death under age and without heirs of his body lawfully begotten his legacy thereto to go to his brother Giles Brent or his sister Mary Brent or to the heirs of my brother Giles Brent or otherwise as my said brother shall dispose it by his Deed or last Will to my brother Giles Brent and to his heirs forever I give all my lands goods and chattles and all my estate real and personal and all that is or may be due to me in England Virginia Maryland or elsewhere still excepting the before disposed of in this my last will and Testament and I do appoint him my said Brother Giles Brent and his children Giles Brent Mary Brent and Richard Brent or such of them as are living at the time of my death the Executors of this my last Will and Testament.  In witness whereof I have hereunto set my hand and seal this 26th day of December, Anno Domini, 1663.”

               [xii] W.B. Chilton, Vol. 16, No. 1 (Jul., 1908), 98.  “The Will of Giles Brent.  In the Name of God Amen.  I Giles Brent of the Retirement in Stafford County in Virginia Esquire contemplating the uncertainty of my time of death do ordain this my last Will and Testament in manner and form following my body to the earth and my Soul I bequeath to the mercy of my Savior Christ all my worldly estate I appoint to my Exectors to be disposed of as followeth to my daughter Mary Fitzherbert I give five ewes and a ram to my son and heir Giles Brent and to the heirs of his body lawfully begotten I give for ever all my lands rights unto lands and reversions of lands any ways due to me in either England Virginia or Maryland and for want of such heirs then unto mine own right heirs and for want of such then to the right heirs of my Honored Father Richard Brent, Esquire, deceased Antiently Lord of the mannors of Admington and Lark Stoke in the County of Gloucestershire in England after my debts paid I give all my goods moveable or immoveable whatsoever to be disposed of as followeth three thousand pounds of good tobacco with cask to be given by them my Executors unto pious use where and to whom they shall see fitt for which doing and how and to whom given I Will that to none else but God they shall be accountable.  I also Will that to Mr. Edward Sanders they give four ewes and a ram and to John Howard four ewes and a ram.  Executors of this my last Will and Testament I appoint my son Giles Brent and my Brother Richard Brent and my Brother William Brent both in England and as Attorneys in their Executorship untill my said Brothers shall otherwise order and I do appoint Mr. Edward Sanders and John Howard above mentioned both of Stafford County to be and to act and it is my Will that after my debts and my Legacies paid my said Executors stand possessed of all my goods and personal estate to the sole use of my son Giles Brent then to be delivered into his sole dispose when it shall please God that he hath arrived to the age of one and twenty years.  In witness unto this my within written last Will and Testament I have hereunto set my hand and seal this last day of August, Anno Domini, 1671.”

               [xiii] Image SC4040-0166-1, Dr. Lois Green Carr’s Biographical Files of 17th and 18th Century Marylanders, Maryland State Archives, http://msa.maryland.gov/megafile/msa/speccol/sc4000/sc4040/000001/000166/html/sc4040-0166-1.html.  Note: Dr. Carr lists the children in the following order: Mary, Giles, Richard, Katherine, Henry, Margaret.

               [xiv] See excerpt from Charles Calvert to Cecilius Calvert, April 26, 1672, in William Hand Browne, ed., Proceedings of the Council of Mayland: 1671-1682 (Baltimore: Maryland Historical Society, 1896), xiv.  “Major Fitzherbert’s brother who maryed the Indian Brent, has civilly parted with her, and (as I suppose) will never care to bed with her more; soe that your Lordship needs not to feare any ill consequence from that match, butt what has already happened to the poore man, who unadvisedly threw himself away upon her in hopes of a great portion which now is come to little.”  See also Will of Charles Beaven, signed June 20, 1698, proved June 21, 1699, Prerogative Court (Wills) Vol. 2, pp. 182-183, Liber 6, Folios 285-286.  See also Will of Mary Beaven, signed April 18, 1712, proved June 13, 1713, Prerogative Court (Wills) Vol. 3, p. 240, Liber 13, Folio 513.  See also Maryland Land Patents, BB#37:374.  On March 15, 1696/7, Richard Marsham transferred 600 acre grant called The Hickory Thickett to Charles Beaven by assignment.

               [xv] Lurene Rose Bivin in “Brent-Marsham-Beaven-Blandford Article: A Closer Look,” Maryland Genealogical Society Bulletin, Vol. 37, No. 3, 328-334.

               [xvi] Four potential scenarios explain this matching DNA considered together with Charles Beaven’s reference to Richard Marsham as “my brother iñ Richard Marsham.”  The first scenario is Richard Marsham and Charles Beaven were brothers.  This scenario almost certainly is not true because Richard Marsham and Charles Beaven had different last names and the written reference by Charles Beaven to Richard Marsham as “my brother iñ” appears to have been a standard contraction of “my brother-in-law.”  The second scenario is Richard Marsham and Mary, wife of Charles Beaven, were brother and sister.  This scenario almost certainly is not true because Mary referred to Richard Marsham as “my well beloved Richard Marsham.”  If Richard Marsham and Mary had been brother and sister, Mary surely would have referred to Richard as her brother.  The third scenario is Charles Beaven and Katherine, wife of Richard Marsham, were brother and sister.  This scenario almost certainly is not true because their descendants inherited matching segments of Native American DNA.  Charles Beaven immigrated from England to Maryland in 1666 (Skordas, Liber 9, folio 455), so he surely did not inherit Native American DNA from his parents.  The fourth and most compelling scenario is Katherine, wife of Richard Marsham, and Mary, wife of Charles Beaven, were sisters, and they also were daughters of a parent with Native American ancestry.  This scenario is consistent with other indications that Katherine and Mary were daughters of Mary Kittamaquund and Giles Brent.

               [xvii] Maryland Colonial Land Records, Liber 7, Folio 582, 583, Maryland State Archives.  “March xith 1664.  Came David Bowens and demands land for these rights following John Barnes, Clement Barnes, Margaret Whitthe, Martha Garbett, Catherine Marsham by Assign and Francis Street by Assign as follows–Know all to whom these presents may concern, that I Katherine Marsham doe assigne all my Right and Title of a Right due to mee the said Katherine for fifty acres of land unto David Bowing as witness my hand this Eleventh of March One Thousand six hundred sixty foure.  Katherine Marsham (her K mark).  Witness Richard Marsham, Robert Turner.  Know all men by these presents to whom this may concern that I Francis Streete doe assigne all my Right and Title of a right due to mee the said Francis Streete for fifty acres of Land unto David Bowing as witness my hand this Eleventh of March One Thousand six hundred sixty four.  Francis Streete.  Witness Richard Marsham, Robert Turner.”  See also Maryland Colonial Land Records, Liber 12, Folio 512, Maryland State Archives.  “May 11th 1670.  Came Richard Marsham of Calvert County and proved right to fifty acres of land it being due to him for the time of service of Katherine his wife performed to Major Thomas Brooke, Warrant then issued in the name of the said Richard Marsham for fifty acres of land it being due to him for the causio oraem above.  Certified the 11th of August next.”  Note: Even though these two documents indicate Katherine was due a total of 100 acres, the first 50 acres for an unstated cause and the second 50 acres for service to Thomas Brooke, neither record says Katherine was transported to Maryland, and both records may result from fraudulent claims.  If these records reflect legitimate claims, they do not say or prove Katherine was transported to Maryland, since some claims were granted for people who were born in Maryland.  For example, a patent for 1,644 acres was granted to Mary Brent on November 17, 1652, for the transportation of 33 persons, including “Mrs. Mary Brent, wife to Capt. Brent.”  See Nugent, pp. 266-267.  This Mrs. Mary Brent was Mary Kittamaquund, wife of Giles Brent, who certainly was born in Maryland.  Furthermore, according to Abbott Emerson Smith (“The Indentured Servant and Land Speculation in Seventeenth Century Maryland,” in The American Historical Review, Vol. 40, p. 467), “A great many of the warrants which were granted were for rights proved by the wife of a freedman.  It is not unlikely that some persons managed to get freedom dues in land, although they had never been in indentured service.”  Finally, if Katherine did serve a term of indenture, her service may have resulted from the death of her mother at a time when she was old enough to begin providing for her own maintenance.  It was not unusual during this era for children of deceased well-to-do colonists to serve a term of indenture.

               [xviii] See Maryland Colonial Land Records, Liber 4, Folio 4, Maryland State Archives.  “May the 7th 1659.  John Home demands Land for the transportation of himself and his Servants, Richard Marsham & John Edmondson, in 1658.”  See also Maryland Colonial Land Records, Liber 5, Folio 295, Maryland State Archives.  “Know all men that I Richard Marsham do give and make over to Thomas Pagett my right as is due to me as being a Servant, and now being free in Roberto McJohn Hearen as witness my hand the 16th of September 1661.  Richard Marsham.  Wit: Robert Coberthwail, Michael Coreuly.”

               [xix] See Maryland Colonial Land Records, Liber 12, Folio 512, Maryland State Archives, as cited above.  “May 11th 1670.  Came Richard Marsham of Calvert County and proved right to fifty acres of land it being due to him for the time of service of Katherine his wife performed to Major Thomas Brooke, Warrant then issued in the name of the said Richard Marsham for fifty acres of land it being due to him for the causio oraem above.  Certified the 11th of August next.”  See also Maryland Colonial Land Records, October 26, 1670, Liber 14, Folio 228.  “Patent for 50 acres in St. Mary’s County, originally Calvert County, to Richard Marsham, tract called St. Katherine’s.”  Note: This patent establishes the terminus ad quem (limit to which—latest possible date) for Katherine’s death, because Richard would be unlikely to name this property Saint Katherine’s unless Katherine had died.

               [xx] The terminus a quo (limit from which—earliest possible date) for Richard’s marriage to Anne Calvert is established by the date of a Prerogative Court record concerning the estate of Henry Brent naming Anne Brent executrix.  See Prerogative Court Records, April 30, 1695, Liber 13A, folio 291, Maryland State Archives.  The terminus ad quem (limit to which—latest possible date) for Richard’s marriage to Anne Calvert is the date they were named as husband and wife on a probate record.  See Provincial Court Judgments, February Court 1696, Liber P. L. #3, Folios 556-557, Maryland State Archives.  Richard Marsham with Ann Marsham, administrator of Henry Brent, against Thomas Collier.

               [xxi] Will of Richard Marsham, signed April 14, 1713, probated April 22, 1713, Maryland Prerogative Court (Wills), Liber xiii, Folio 514-520, Maryland State Archives.

               [xxii] The approximate year of Sarah’s marriage to Basil Waring is estimated from the year of Basil’s death preceded by four years to account for the births of two children.  See Will of Basil Waring, signed December 8, 1688, probated December 29, 1688, Maryland Calendar of Wills, Vol. 2, p. 50, and Liber 6, Folio 66.  Basil named his wife Sarah and sons Marsham and Basil.  The terminus a quo (limit from which—earliest possible date) for Sarah’s marriage to William Barton is determined by the probate date of the will of her first husband Basil Waring.  See Will of Basil Waring, signed December 8, 1688, probated December 29, 1688, Maryland Calendar of Wills, Vol. 2, p. 50, and Liber 6, Folio 66.  The terminus a quo (limit from which—earliest possible date) for Sarah’s death is determined by her deed to Robert Mackhorn.  See Deed from Sarah Haddock to Robert Mackhorn, signed January 8, 1733, recorded March 18, 1733/4, Charles County Land Rcords: 1733-1743, Book O #2, page 28.  “Sarah Haddock, widow, of Prince George’s County, formerly wife of William Barton, late of Charles County, Gent., deceased, to Robert Mackhorn of Charles County, planter.  William Barton by his will, divised to his son-in-law, Basil Waring, 300 acres, being part of this tract of land called Hadlow, lying in Charles County, and the rest of Hadlow to his wife, being now the aforementioned Sarah Haddock.  Now this deed witnesses that sd. Sarah Haddock, for 4500 lbs tobacco, has sold to said Robert the rest of Hadlow, lying in Charles County, bounded by Thos. Gerard, the division line made by sd. Sarah Haddock and Basil Waring.  Signed Sarah Haddock.  Wit. Jas. Haddock Waring, Henry Keen.”

               [xxiii] The approximate year of Katherine’s marriage to Baker Brook is estimated from the year of Baker’s death preceded by eight years to account for the births of four children.  See Will of Baker Book, signed February 5, 1698, probated May 27, 1698, Maryland Calendar of Wills, Vol. 2, p. 142, and Liber 6, Folio 83.  Baker named his wife Katherine and four children Baker, Leonard, Richard, and Ann.  The terminus ad quem (limit to which—latest possible date) for Katherine’s marriage to Samuel Queen is determined by the probate date of the will of her first husband Baker Brooke.  See Will of Baker Book, signed February 5, 1698, probated May 27, 1698, Maryland Calendar of Wills, Vol. 2, p. 142, Liber 6, Folio 83.  The terminus a quo (limit from which—earliest possible date) for Katherine’s death is determined by the date her husband’s will was probated.  See Will of Samuel Queen, signed January 10, 1711, probated March 18, 1712, Maryland Prerogative Court (Wills), Vol. 3, p. 222, Liber 13, Folio 389, Maryland State Archives.  The terminus ad quem (limit to which—latest possible date) for Katherine’s death is determined by the date of the will of her father, Richard Marsham, which provides for her children but does not mention her.  See Will of Richard Marsham, signed April 14, 1713, probated April 22, 1713, Maryland Prerogative Court (Wills), Liber 13, Folios 514-520, Maryland State Archives.

               [xxiv] On April 5, 1673, Giles Brent Jr., son of Col. Giles Brent and Mary Kittamaquund, deeded 500 acres, which he had inherited from his father, to his uncle George Brent of Woodstock, Stafford County, Virginia, stating he had reached the age of 21—a condition set in his father’s will for his ability to take possession of the land.  This suggests Giles Brent Jr. was born about 1652.  See W.B. Chilton, Vol. 16, No. 1 (Jul., 1908), 99-100.

               [xxv] Will of Giles Brent, signed August 31, 1671, in W.B. Chilton, Vol. 16, No. 1 (Jul., 1908), 98.

               [xxvi] See excerpt from Charles Calvert to Cecilius Calvert, April 26, 1672, in William Hand Browne, ed., Proceedings of the Council of Mayland: 1671-1682 (Baltimore: Maryland Historical Society, 1896), xiv.  “Major Fitzherbert’s brother who maryed the Indian Brent, has civilly parted with her, and (as I suppose) will never care to bed with her more; soe that your Lordship needs not to feare any ill consequence from that match, butt what has already happened to the poore man, who unadvisedly threw himself away upon her in hopes of a great portion which now is come to little.”

               [xxvii] Will of Charles Beaven, signed January 20, 1698/9, proven June 2, 1699, Prince Georges County Wills, Liber 6, folios 285-286,  Maryland State Archives.

               [xxviii] Will of Mary Beavan, signed April 28, 1712, proven June 13, 1713, Prince Georges County Wills, Liber 13, folio 513, Maryland State Archives.

               [xxix] Will of Richard Bevan Sr., signed February 27, 1738/9, proven May 21, 1739, Maryland Calendar of Wills, Vol. 8, p. 789, Liber 22, folio 58, Maryland State Archives.  For the terminus ad quem (limit to which—latest possible date) of Richard’s marriage to Jane Blandford, see Administration of the Will of William Bayly, June 11, 1703, Liber 24, folio 16a, Prince Georges County, MD.  “Executrix, Mrs. Jane Beven, wife of Richard Beven.”

               [xxx] Will of Thomas Blandford, signed June 17, 1749, proven August 7, 1749, Maryland Calendar of Wills, Maryland State Archives.  Thomas named his wife Sarah executrix.

               [xxxi] Will of Catherine Culver, signed October 6, 1762, proven December 20, 1762, Maryland Calendar of Wills, Vol. 31, pp. 890-891, Maryland State Archives.

               [xxxii] Charles Beaven signed a deposition in 1728, claiming to be 42 years of age.

The Autosomal Me – Summary and PDF File

“The Autosomal Me” is a 9 part series published between February 6, 2013 and May 31, 2013 on the blog, www.dna-explained.com.  I’ve been asked to do a couple of things.  First, to put together a document that has all of the links in one place, and second, to create a pdf file of the compiled articles for download.

The second part turned out to be easier than I anticipated.  One of my readers also saw that request and put together the pdf file, which I’ve uploaded to my website at www.dnaexplain.com and is now available (free) with lots of other good things under the Publications tab.  Very big hat tip to John for doing this.  Thank you so much!

Here’s the list of articles from first to last with their links:

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 two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.

Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments” took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

Part 8, “The Autosomal Me – Extracting Data Segments and Clustering,” we  extract all of the Native and Blended Asian segments in all 22 chromosomes, but only used chromosomes 1 and 2 for illustration purposes.  We then clustered the resulting data to look for trends, grouping clusters by either the Strong Native criteria or the Blended Asian criteria.

The final segment, Part 9, “The Autosomal Me – The Holy Grail – Identifying Native Genealogy Lines,” utilized all of the chromosomal information we’ve gathered in the earlier steps.  We apply that information to our matches and determine which of our lines are the most likely to have Native Ancestry.  This, of course, fulfills the goal of using DNA information to identify small amounts of minority admixture.

In summary, this series has been quite interesting and indeed, it did achieve the goals initially set forth.  However, it was very manually intensive and took far longer than anticipated, partly due to circumstances beyond my control, like software updates and vendor changes.  A second reason that it took longer than expected was due to the sheer amount of work involved in the various steps, particularly steps 8 and 9.  In addition, because Minority Admixture Mapping (MAP) is developmental, I had to try several different approaches to determine which one, or ones, worked best.  Despite the immense amount of work, I would describe this approach certainly as useful and successful.  In fact, I don’t know how else I would have ever eliminated some genealogical lines as candidates for Native heritage and focused on others without the combination of MAP’s new techniques combined with both old and new tools provided by others.

Having said that, I would suggest that this technique, because of the intensive manual effort required, is only for the very committed genetic genealogist – the warrior, so to speak.  It also will not work well with only a few matches.  I would suggest that you would need at least 200 or 300 matches, preferably more, which is typical of someone with colonial American heritage.  If that is you, and you are desperate to find your minority admixed lines….then this type of project may be for you.  Please thoroughly read all 9 articles before beginning.

Many of the techniques in the various steps can be utilized individually, without completing the entire MAP process.  For example, comparing vendor and third party results, using the GedMatch admixture tools and the chromosome comparisons for percentages of ethnicity all provide useful information in their own right, outside of the full MAP process.

Bon voyage on your journey of discovery to find “The Autosomal You”!  Your ancestors are the pot of gold at the end of that rainbow.

The Autosomal Me – The Holy Grail – Identifying Native Genealogy Lines

holy grail

Sangreal – the Holy Grail.  We are finally here, Part 9 and the final article in our series.  The entire purpose of The Autosomal Me series has been to use our DNA and the clues it holds to identify minority admixture, in this case, Native American, and by identifying those Native segments, and building chromosomal clusters, to identify the family lines that contributed that Native admixture.  Articles 1-8 in the series set the stage, explained the process and walked us through the preparatory steps.  In this last article, we apply all of the ingredients, fasten the lid, shake and see what we come up with.  Let’s take a minute and look at the steps that got us to this point.

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 two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.

Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments” took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

Part 8, “The Autosomal Me – Extracting Data Segments and Clustering,” we  extract all of the Native and Blended Asian segments in all 22 chromosomes, but only used chromosomes 1 and 2 for illustration purposes.  We then clustered the resulting data to look for trends, grouping clusters by either the Strong Native criteria or the Blended Asian criteria.

In this final segment, Part 9, we will be applying the chromosomal information we’ve gathered to our matches and determine which of our lines are the most likely to have Native Ancestry.  This, of course, has been the goal all along.  So, drum roll…..here we go.

In Part 8, we ended by entering the start and stop locations of both Strong Native and Blended Asian clusters into a table to facilitate easy data entry into the chromosome match spreadsheet downloaded from either 23andMe or Family Tree DNA.  If you downloaded it previously, you might want to download it again if you haven’t modified it, or download new matches since you last downloaded the spreadsheet and add them to the master copy.

My goal is to determine which matches and clusters indicate Native ancestry, and how to correlate those matches to lineage.  In other words, which family lines in my family were Native or carry Native heritage someplace.

The good news is that my mother’s line has proven Native heritage, so we can use her line as proof of concept.  My father’s family has so many unidentified wives, marginalized families and family secrets that the Native line could be almost any of them, or all of them!  Let’s see how that tree shakes out.

Finding Matches

So let’s look at a quick example of how this would work.  Let’s say I have a match, John, on chromosome 4 in an area where my mother has no Native admixture, but I do.  Therefore, since John does not match my mother, then the match came from my father and if we can identify other people who also match both John and I in that same region on that chromosome, they too have Native ancestry.  Let’s say that we all also share a common ancestor.  It stands to reason at that point, that the common ancestor between us indicates the Native line, because we all match on the Native segment and have the same ancestor.  Obviously, this would help immensely in identifying Native families and at least giving pointers in which direction to look.  This is a “best case’ example.  Some situations, especially where both parents contribute Native heritage to the same chromosome, won’t be this straightforward.

Based on our findings, the maximum range and minimum (least common denominator or “In Common” range is as follows for the strongest Native segments on chromosomes 1 and 2.

  Chromosome 1 Chromosome 2
Largest   Range 162,500,000   – 180,000,000 79,000,000   – 105,000,000
Smallest   Range 165,658,091   – 171,000,000 90,000,000   – 103,145,425

At GedMatch

At GedMatch, I used a comparison tool to see who matched me on chromosome 1.  Only 2 people outside of immediate family members matched, and both from Family Tree DNA.  Both matched me on the critical Native segments between about 165-180mg.  I was excited.  I went to Family Tree DNA and checked to see if these two people also matched my mother, which would confirm the Native connection, but neither did, indicating of course that these two people matched me on my father’s side.  That too is valuable information, but it didn’t help identify any common Native heritage with my mother on chromosome 1.  It did, however, eliminate them as possibilities which is valuable information as well.


I used a new tool, DNAGedcom, compliments of Rob Warthen who has created a website, DNA Tools, at www.dnagedcom.com.  This wonderful tool allows you to download all of your autosomal matches at Family Tree DNA and 23andMe along with their chromosomal segment matches.  Since my mother’s DNA has only been tested at Family Tree DNA, I’m limiting the download to those results for now, because what I need is to find the people who match both she and I on the critical segments of chromosome 1 or 2.

Working with the Download Spreadsheet

It was disappointing to discover that my mother and I had no common matches that fell into this range on chromosome 1, but chromosome 2 was another matter.  Please note that I have redacted match surnames for privacy.

step 9 table 1

The spreadsheet above shows the comparison of my matches (pink) and Mother’s (white).  The Native segment of chromosome 2 where I match Mother is shaded mustard.  I shaded the chromosome segments that fell into the “common match” range in green.  Of those matches, there is only one person who matches both Mother and I, Emma.  The next step, of course, is to contact Emma and see if we can discover our common ancestor, because whoever it is, that is the Native line.  As you might imagine, I am chomping at the bit.

There are no segments of chromosome 2 that are unquestionably isolated to my father’s line.

Kicking it up a Notch

Are you wondering about now how something that started out looking so simple got so complex?  Well, I am too, you’re not alone.  But we’ve come this far, so let’s go that final leg in this journey.  My mom always used to say there was no point in doing something at all if you weren’t going to do it right.  Sigh….OK Mom.

The easiest way to facilitate a chromosome by chromosome comparison with all of your matches and your Strong Native and Blended Asian segments is to enter all of these segment groups into the match spreadsheet.  If you’re groaning and your eyes glaze over right after you do one big ole eye roll, I understand.

But let’s take a look at how this helps us.

On the excerpt from my spreadsheet below, for a segment of chromosome 5, I have labeled the people and how they match to me.  The ones labeled “Mom” in the last column are labeled that way because these people match both Mom and I.  The ones labeled “Dad” are labeled that way because I know that person is related on my father’s side.

Using the information from the tables created in Step 8, I entered the beginning and end of all matching segment clusters into my spreadsheet.  You can see these entries on lines 7, 8, 22, 23 and 24.  You then proceed to colorize your matches based on the entry for either Mom or Dad – in other words the blue row or the purple row, line 7, 22 or 24.  In this example, actually, line 5 Rex, based on the coloration, should have been half blue and half purple, but we’ll discuss his case in a minute.

The you can then sort either by match name or by chromosome to view data in both ways.  Let’s look at an example of how this works.


  • White Rows:  Mother’s matches.  When Mother and I both match an individual, you’ll see the same matches for me in pink.  This double match indicates that the match is to Mother’s side and not Father’s side.
  • Pink Rows:  My matches.
  • Purple “Mom” labels in last column:  The individual matches both me and Mom.  This is a genetic match.
  • Teal “Dad” labels in last column: Genealogically proven to be from my father’s side.  This is a genealogical, not a genetic label, since I don’t have Dad’s DNA and can only infer these genetically when they don’t also match Mother.
  • Dark Pink Rows labeled “Me Amerind Only” are Strong Native or Blended Asian segments from Chromosome Table that I have entered.  My segments must come from one of my parents, so I’ve either colored them purple, if the match is someone who matches Mother and I both, or teal, if they don’t match both Mom and I, so by inference they come from my father’s line.
  • Dark Purple Rows labeled “Mom Amerind Only” are Mom’s segments from the Chromosome Table.
  • Dark Teal Rows labeled “Dad Amerind Only” are inferred segments belonging to my father based on the fact that Mother and I don’t share them.

Inferred Relationships

This is a good place to talk for just a minute about inferred relationships in this context.  Inference gets somewhat tenuous or weak.  The inferred matches on my father’s side began with the Native segments in the admix tools.  Some inferences are very strong, where Mother has no Native at all in that region.  For example, Mom has European and I have Native American.  No question, this had to come from my father.  But other cases are much less straightforward.

In many cases, categorization may be the issue.  Mom has West Asian for example and I have Siberian or Beringian.  Is this a categorization issue or is this a real genetic difference, meaning that my Siberian/Beringian is actually Native and came from my father’s side?

Other cases of confusion arise from segment misreads, etc.  I’ve actually intentionally included a situation like this below, so we can discuss it.  Like all things, some amount of common sense has to enter the picture, and known relationships will also weigh heavily in the equation.  How known family members match on other chromosome segments is important too.  Do you see a pattern or is this match a one-time occurrence?  Patterns are important.

Keep in mind that these entries only reflect STRONG Asian or Native signals, not all signals.  So even if Mother doesn’t have a strong signal, it doesn’t mean that she doesn’t have ANY signal in that region.  In some cases, start and stop segments for Mom and Dad overlapped due to very long segments on some matches.  In this case, we have to rely on the fact that we do have Mother’s actual DNA and assume that if they aren’t also a match to Mother, that what we are seeing is actually Dad’s lines, although this may not in actuality always be true.  Why?  Because we are dealing with segments below the matching threshold limit at both Family Tree DNA and 23andMe, and both of my parents carry Native heritage.  We can also have crossed a transitional boundary where the DNA that is being matched switches from Mom’s side to Dad’s side.

Ugh, you say, now that’s getting messy.  Yes, it is, and it has complicated this process immensely.

The Nitty-Gritty Data Itself

step 9 table 2

Taking a look at this portion of chromosome 5, we have lots going on in this cluster.  Most segments will just be boring pink and white (meaning no Native), but this segment is very busy.  Mom and I match on a small segment from 52,000,000 to 53,000,000.  Indeed, this is a very short segment when compared to the entire chromosome, but it is strongly Native.  We both also match Rex, our known cousin.  I’ve noted him with yellow in the table. Please note that Mom’s white matches are never shaded.  I am focused on determining where my own segments originate, so coloring Mother’s too was only confusing.  Yes, I did try it.

You can see that Mother actually shares all or any part of her segment with only me and Rex.  This simplifies matters, actually.  However, also note that I carry a larger segment in this region than does Mother, so either we have a categorization issue, a misread, or my father also contributed.  So, a conundrum.  This very probably implies that my father also carried Native DNA in this region.

Let’s see what Rex’s DNA looks like on this same segment of chromosome 5, from 52-53 using Eurogenes.  In the graph below, my chromosome is the top bar, Rex’s the middle and the bottom bar shows common DNA with the black nonmatching.  Yellow is Native American, red is South Asian, putty is Siberian, lime green is Mediterranean, teal is North Europe, orange is Caucus.

Step 9 item 3

This same comparison is shown to Mother’s DNA (top row) below.

step 9 item 4

It’s interesting that while Mother doesn’t have a lot of yellow (Native), she does have it throughout the same segment where Rex’s occurs, from about 52 through 53.5.

Does this actually point to a Native ancestor in the common line between Rex, Mom and I, which is the Swiss/German Johann Michael Miller line which does include an unidentified wife stateside, or does this simply indicate a common ancient population long ago in Asia?  It’s hard to say and is deserving of more research.  I feel that it is most likely Native because of the actual yellow, Native segment. If this was an Asian/European artifact, it would be much less likely to carry the actual yellow segment.

Is Rex also genealogically related to my father?  As I’ve worked through this process with all of my chromosomes and matches, I’ve really come to question if one of my father’s dead ends is also an ancestral line of my mother’s.

The key to making sense of these results is clusters.

Clusters vs Singleton Outliers

The work we’ve already done, especially in Step 8, clusters the actual DNA matching segments.  We’ve now entered that information into the spreadsheet and colored the segments of those who match.  What’s next?

The key is to look for people with clusters.  Many matches will have one segment, of say, 10 that match, colored.  Unless this is part of a large chromosome cluster, it’s probably simply an outlier.  Part of a large chromosome cluster would be like the large Strong Native segments on chromosome 1 or 2, for example.  How do we tell if this is a valid match or just an outlier?

Sort the spreadsheet by match name.  Take a look at all of the segments.

The example we’ll use is that of my cousin, Rex.  If you recall, he matches both me and Mother, is a known first cousin twice removed to me, (genetically equal to a second cousin), and is descended from the Miller line.

In this example, I also colored Mother’s segments because I wanted to see which segments that I did not receive from her were also Native. You can see that there are many segments where we all match and several of those are Native.  These also match to other Miller descendants as well, so are strongly indicative of a Native connection someplace in our common line.

If we were only to see one Native segment, we would simply disregard this as an outlier situation.  But that’s not the case.  We see a cluster of matches on various segments, we match other cousins from the same line on these segments, and reverting back to the original comparison admixture tools verifies these matches are Native for Rex, Mom and me.

step 9 item 5

Hmmmm…..what is Dad’s blue segment color doing in there?  Remember I said that we are only dealing with strong match segments?  Well, Mom didn’t have a strong segment at that location and so we inferred that Dad did.  But we know positively that this match does come from Mother’s side.  I also mentioned that I’ve come to wonder if my Mom and Dad share a common line.  It’s the Miller line that’s in question.  One of Johann Michael Miller’s children, Lodowick, moved from Pennsylvania to Augusta County, Virginia in the 1700s and his line became Appalachian, winding up in many of the same counties as my father’s family.  I’m going to treat this as simply an anomaly for now, but it actually could be, in this case, an small indication that these lines might be related.  It also might be a weak “Mom” match, or irrelevant.  I see other “double entries” like this in other Miller cousins as well.

What is the pink row on chromosome 12?  When I grouped the Strong Native and Asian Clusters, sometimes I had a strong grouping, and Mom had some.  The way I determined Dad’s inferred share was to subtract what Mom had in those segments from mine.  In a few cases, Mom didn’t have enough segments to be considered a cluster but she had enough to prevent Dad from being considered a cluster either, so those are simply pink, me with no segment coloring for Mom or Dad.

Let’s say I carry Strong Native/Mixed Asian at the following 8 locations:

10, 12, 14, 16, 18, 20, 22, 24

This meets the criteria for 8 of 15 ethno-geographic locations (in the admix tools) within a 2.5 cM distance of each other, so this cluster would be included in the Mixed Asian for me.  It could also be a Strong Native cluster if it was found in 3 of 4 individual tools.  Regardless of how, it has been included.

Let’s now say that Mom carries Native/Mixed Asian at 10, 12 and 14, but not elsewhere in this cluster.

Mom’s 3 does not qualify her for the 8/15 and it only leaves Dad with 5 inferred segments, which disqualifies him too.  So in this case, my cluster would be listed, but not attributable directly to either parent.

What this really says is that both of my parents carry some Native/Blended Asian on this segment and we have to use other tools to extrapolate anything further.  The logic steps are the same as for Dad’s blue segment.  We’re going to treat that as an outlier.  If I really need to know, I can go back to the actual admixture tools and see whether Mom or Dad really match me strongly on which segments and how we compare to Rex as well.  In this case, it’s obvious that this is a match to my Mother’s side, so I’m leaving well enough alone.

Let’s see what the matches reveal.


Referring back to the Nitty Gritty Data spreadsheet, Mom’s match to Phyllis on row 15 confirms an Acadian line.  This is the known line of Mother’s Native ancestry.  This makes sense and they match on Native segments on several other chromosomes as well.  In fact, many of my and Mother’s matches have Acadian ancestry.

My match to row 19, Joy, is a known cousin on my father’s side with common Campbell ancestry.  This line is short however, because our common ancestor, believed to be Charles Campbell died before 1825 in Hawkins County, TN.  He was probably born before 1750, given that his sons were born about 1770 and 1772.  Joy and I descend from those 2 sons.  Charles wife and parents are unknown, as is his wife.

My match to row 20, inferred through my father’s side, is to a Sizemore, a line with genetically proven Native ancestry.  Of course, this needs more research, but it may be a large hint.  I also match with several other people who carry Sizemore ancestors.  This line appears to have originated near the NC/VA border.

I wanted to mention rows 4 and 17.  Using our rules for the spreadsheet, if I match someone and they don’t also match Mother on this segment, I have inferred them to be through my father.  These are two instances that this is probably incorrect.  I do match these people through Mother, but Mother didn’t carry a strong signal on this segment, so it automatically became inferred to Dad.  Remember, I’m only recording the Strong Native or the Blended Asian segments, not all segments.  However, I left the inferred teal so that you can see what kinds of judgment calls you’ll have to make.  This also illustrates that while Mom’s genetic matches are solid, Dad’s inferred matches are less so and sometimes require interpretation.  The proper thing to do in this instance would be to refer back to the original admixture tools themselves for clarification.

Let’s see what that shows.

step 9 item 6

Using HarrappaWorld, the most pronounced segment is at about 52.  Teal is American.  You can see that Mother has only a very small trace between 53 and 54, almost negligible.  Mother’s admixture at location 52 is two segments of purple, brown and cinnamon which translate to Southwest Asian (lt purple), Mediterranean (dk purple), Caucasian (brown) and Balock (cinnamon), from Pakistan.

Checking Dodecad shows pretty much the same thing, except Mother’s background there is South Asian, which could be the same thing as Caucus and Pakistan, just different categorizations.

In this case, it looks like the admixture is not a categorization issue, but likely did come from my father.  Each segment will really be a case by case call, with only the strongest segments across all tools being the most reliable.

It’s times like this that we have to remember that we have two halves of each chromosome and they carry vastly different information from each of our parents.  Determining which is which is not always easy.  If in doubt, disregard that segment.

Raw Numbers

So, what, really did I figure out after all of this?

First, let’s look at some numbers.

I was working with a total of 292 people who had at least one chromosomal segment that matched me with a Strong Native or Blended Asian segment.  Of those, 59 also matched Mom’s DNA.  Of those, 18 had segments that matched only Mom.  This means that some of them had segments that also matched my father.  Keep in mind, again, that we are only using “strong matches” which involves inferring Dad’s segments and that referring back to the original tools can always clarify the situation.  There seems to be some specific areas that are hotspots for Native ancestry where it appears that both of my parents passed Native ancestry to me.

Many of my and my mother’s 59 matches have Acadian ancestry which is not surprising as the Acadians intermarried heavily with the Native population as well as within their own ethnic group.

Several also have Miller Ancestry.  My Miller ancestor is Johann Michael Miller (1692-1771) who immigrated in the colonial period and settled on the Pennsylvania frontier.  His son, Philip Jacob Miller’s (1726-1799) wife was a woman named Magdalena whose last name has been rumored for years to be Rochette, but no trace of a Rochette family has ever been found in the county where they lived, region or Brethren church history…and it’s not for lack of looking.  Several matches point to Native Ancestry in this line.  This also begs the question of whether this is really Native or whether it is really the Asian heritage of the German people.  Further analysis, referring back to the admixture tools, suggests that this is actually Native. It’s also interesting that absolutely none of Mother’s other German or Dutch lines show this type of ancestry.

There is no suggestion of Native ancestry in any of her other lines.  Mother’s results are relatively clean.  Dad’s are anything but.

Dad’s Messy Matches

My father’s side of the family, however, is another story.

I have 233 matches that don’t also match my mother.  There can be some technical issues related to no-calls and such, but by and large, those would not represent many.  So we need to accept that most of my matches are from my Father’s side originating in colonial America.  This line is much “messier” than my mother’s, genealogically speaking.

Of those 233 matches, only 25 can be definitely assigned to my father.  By definitely assigned, I mean the people are my cousins or there is an absolutely solid genealogical match, not a distant match.  Why am I not counting distant matches in this total?  We all know by virtue of the AncestryDNA saga that just because we match family lines and DNA does NOT mean that the DNA match is the genealogical line we think it is.  If you would like to read all about this, please refer to the details in CeCe Moore’s blog where she discussed this phenomenon.  The relevant discussion begins just after the third photo in this article where she shows that 3 of 10 matches at Ancestry where they “identify” the common DNA ancestor are incorrect.  Of course, they never SAY that the common ancestor is the DNA match, but it’s surely inferred by the DNA match and the “leaf” connecting these 2 people to a common ancestor.  It’s only evident to someone who has tested at least one parent and is savvy enough to realize that the individual whose ancestor on Mom’s side that they have highlighted, isn’t a match to Mom too.  Oops.  Mega-oops!!!

However, because we are dealing in our project, on Dad’s side, with inferences, we’re treading on some of the same ground.  Also, because we are dealing with only “strong clustered” segments, not all Native or Asian segments and because it appears that my parents both have Native ancestry.  To make matters worse, they may both have Algonquian, Iroquoian or both.

I have also discovered during this process that several of my matches are actually related to both of my parents.  I told you this got complex.

Of the people who don’t match Mother, 32 of them have chromosomal matches only to my father, so those would be considered reliable matches, as would the closest ones of the 25 that can be identified genealogically as matching Dad.  Many of these 25 are cousins I specifically asked to test, and those people’s results have been indispensable in this process.

In fact, it’s through my close circle of cousins that we have been able to eliminate several lines as having Native ancestry, because it doesn’t’ show as strong and they don’t have it either.

Many of these lines group together when looking at a specific chromosome.  There is line after line and cousin after cousin with highlighted data.

Dad’s Native Ancestors

So what has this told me?  This information strongly suggests that the following lines on my father’s side carry Native heritage.  Note the word “carry.”  All we can say at this point is that it’s in the soup – and we can utilize current matches at our testing company and at GedMatch, genealogy research and future matches to further narrow the branches of the tree.  Many of these families are intermarried and I have tried to group them by marriage group.  Obviously, eventually, their descendants all intermarried because they are all my ancestors on my father’s side.  But multiple matches to other people who carry the Native markers but aren’t related to my other lines are what define these as lines carrying Native heritage someplace.

  • Campbell – Hawkins County, Tn around 1800, missing wife and parents, married into the Dodson family
  • Dodson – Hawkins County, Tn, Virginia – written record of Lazarus Dodson camping with the Cherokee – missing wife, married into the Campbell and Estes family
  • Claxton/Clarkson – Russell Co., Va, Claiborne and Hancock Co., Tn – In NC associated with the known Native Hatcher family.  Possibly a son-in-law.  Missing family entirely.
  • Cook – Russell Co., Va. – daughter married Claxton/Clarkson – missing wives
  • Harrold, Harrell, Herrell – Hancock Co., Tn., Wilkes Co., NC – missing wives
  • McDowell – Hancock Co. Tn, Wilkes Co., NC, Augusta Co., Va – married into the Harrell family, missing wife
  • McNeil, McNiel – Wilkes Co., NC – missing wives, married into the Vannoy family
  • Vannoy – Wilkes County – some wives unaccounted for pre-1800
  • Crumley – Greene County, Tn., Lee Co., Va. – oral history of Native wife, married into the Vannoy family
  • Brown – Greene County, Tn, Montgomery Co., Va – married into the Crumley family, missing wives

While this looks like a long list, the list of families that don’t have any Native ancestry represented is much longer and effectively serves to eliminate all of those lines.  While I don’t have “THE” answer, I certainly know where to focus my research.  Maybe there isn’t the one answer.  Maybe there are multiple answers, in multiple lines.

The Take Away

Is this complex?  Yes!  Is it a lot of work?  You bet it is!  Is everything cast in concrete?  Never!  You can see that by the differences we’ve found in data interpretation, not to mention issues like no-calls (areas that for some reason in the test don’t read) and cross overs where your inheritance switches from your mom’s side to your dad’s side.  Is there any other way to do this?  No, not if your minority admixture is down in that weedy area around 1%.

Is it worth it?  You’ll have to decide.  It guess it depends on how desperately you want to know.

Part of the reason this is difficult is because we are missing tools in critical locations.  It’s an intensively laborious manual process.  In essence, using various tools, one has to figure out the locations of the Native and Asian chromosome segments and then use that information to infer Native matches by a double match (genetic match at DNA company plus match with Strong Native/Blended Asian segment) with the right parent.  It becomes even more complex if neither parent is available for testing, but it is doable although I would think the reliability could drop dramatically.

Tidbits and Trivia

I’ve picked up a number of little interesting tidbits during this process.  These may or may not be helpful to you.  Just kind of file them away until needed:)

  • Matches at testing companies come and go….and sometimes just go.  At Family Tree DNA, I have some matches that must be trembling on the threshold that come and go periodically.  Now you see them, now you don’t.  I lost matches moving from the Affy chip to the Illumina chip and lost additional matches between Build 36 and 37.  Some reappeared, some haven’t.
  • The start and stop boundaries changed for some matches between build 36 and build 37.  I did not go back and readjust, as most of these, in the larger scheme of things, were minor.  Just understand that you are looking for  patterns here that indicate Native heritage, not exact measurements.  This process is a tool, and unfortunately, not a magic wand:)
  • The centromere locations change between builds.  If you have matches near or crossing the middle of the chromosome, called the centromere, there may be breaks in that region.  I enter the centromere start and stop locations in my spreadsheet so that if I notice something odd going on in that region, the centromere addresses are right there to alert me that I’m dealing with that “odd” region.  You can find the centromere addresses in the FAQ at Family Tree DNA for their current build.
  • At 23andMe, when you reach the magic 1000 matches threshold, you start losing matches and the matching criteria is elevated so that you can stay under 1000 matches.  For people with colonial American or Jewish heritage, in other words those with high numbers of matches, this is a problem.
  • Watch for matches that are related to both sides of your family.  If your family lived in colonial America, you’re going to have a lot of matches and many are probably related to each other in ways you aren’t aware of.
  • If your parents are related to each other, this process might simply be too complex and intertwined to provide enough granular data to be useful.
  • Endogamous groups are impossible to sort through as to where, meaning which ancestor, the DNA came from.  This is because the original group founders’ DNA is just getting passed around and around, with little or no new DNA being introduced.  The effect of this on downstream generations relative to genetic genealogy is that matches appear to be more closely related than they are because of the amount of matching DNA they carry.  For my Brethren and my Acadian groups of people, I just list them by the group name, since, as the saying goes, “if you’re related to one Acadian, you’re related to all Acadians.”
  • If you’re going to follow this procedure, save one spreadsheet copy with the Strong Native only and then a second one with both the Strong Native and Blended Asian.  I’m undecided truthfully whether the Mixed Asian adds enough resolution for the extra work it generates.
  • When in question, refer back to the original tools.  The answer will always be found there.
  • Unfortunately, tools change.  You may want to take screen shots.  During this process, FTDNA went from build 36 to 37, match thresholds changed, 23andMe introduced a new user interface (which I find much less intuitive) and GedMatch has made significant changes.  The net-net of this is when you decide to undertake this project, commit to it and do it, start to finish.  Doing this little by little makes you vulnerable to changes that may make your data incompatible midstream – and you may not even realize it.
  • This entire process is intensively manual.  My spreadsheet is over 5500 rows long.  I won’t be doing it again…although I will update my spreadsheet with new matches from time to time.  The hard work is already done.
  • This same technique applies to any minority ancestry, not just Native, although that’s what I’ve been hunting for and one of the most common inquiries I receive.
  • I am hopeful that in the not too distant future many of these steps and processes will be automated by the group of bright developers that contribute to GedMatch or via other tools like DNAGedcom. HINT – HINT!!!

I would like to follow this same process to identify the source of my African heritage, but I’m thinking I’ll wait for the tools to become automated.  The great irony is that it’s very likely in the same lines as my Native ancestors.

If You Want to Test

What does it take to do this for yourself using the tools we have today, as discussed?

If your parents are living, the best gift you can give yourself is to test them, now, while you still can.  My mother has been gone for several years, but her DNA archived at Family Tree DNA was still viable.  This is not always the case.  I was fortunate.  Her DNA is one of the best gifts she gave me.  Not just by inheritance, but by having hers tested.  I thank her every single day, for both!  I could not have written this article without her DNA results.  The gift that keeps on giving.

If you don’t have a parent to test, you can test several other family members who will provide some information, but clearly won’t carry the same amounts of common DNA with you as your parents.  These would include your aunts and uncles, your parents’ siblings and what I’ve referred to as your close cousin circle.  Attempt to test at least someone from each line.  Yes, it gets expensive, but as one of my cousins said, as she took her third or 4th DNA test.  “It’s only money.  This is about family.”

You can also test your own siblings as well to obtain more information that you can use to match up to your family lines. Remember, you only receive half of your parents DNA, and your siblings will received some DNA from your parents that you didn’t.

I don’t have any other siblings to test, but I have tested cousins from several lines which have proven invaluable when trying to discern the sources of certain segments. For example, one of these Native segments fell on a common segment with my cousin Joy.  Therefore, I know it’s from the Campbell line, and because I have the Campbell paternal Y-DNA which is European, I know immediately the Native admixture would have had to be from a wife.

Much of this puzzle is deductive, but we now have the tools, albeit manual, to do this type of work that was previously impossible.  I am somewhat disappointed that I can’t pinpoint the exact family lines, yet, but hopefully as more people test and more matches provide genealogical information, this will improve.

If you want to play in this arena, you need to test at either Family Tree DNA, 23andMe, or both.  Right now, the most cost effective way to achieve this is to purchase a $99 kit from 23andMe, test there, then download your results from 23andMe and upload them to Family Tree DNA for $99.  That way, you are fishing in both pools.  Be aware that less than half of the people who test at either company download results to GedMatch, so your primary match locations are with the testing companies.  GedMatch is auxiliary, but critical for this analysis.  And the newest tool, DNAGedcom is a Godsend.

Also note that transferring your result to Family Tree DNA is NOT the same thing as actually testing there.  Why does this matter?  If you want a future test at Family Tree DNA, who is the premiere genetic genealogy testing company, offering the most variety and “deepest” commercial tests, they archive your DNA for 25 years, but if you transfer results, they don’t have your DNA to archive, so no future products can be ordered.  All I can say is thank Heavens Mom’s DNA was there.

Ancestry.com doesn’t provide any tools such as the chromosome browser or even the basic information of matching segments.  All you get is a little leaf that says you’re related, but the questions of which segment or how are not answerable today at Ancestry and as CeCe’s experience proved, its unreliable.  It’s  possible that you share the same surnames and ancestor, but your genetic connection is not through that family line.  Without tools, there is no way to tell.  Ancestry released raw data files a few weeks ago and very recently, GedMatch has implemented the ability to upload them so that Ancestry participants can now utilize the additional tools at GedMatch.

Although this has been an extraordinarily long and detailed process, I can’t tell you how happy I am to have developed this new technique to add to my toolbox.  My Native and African ancestors have been most elusive.  There are no records, they didn’t write and probably didn’t even speak English, certainly not initially.  The only clues to their existence, prior to DNA, were scant references and family lore.  The only prayer of actually identifying them is though these small segments of our DNA – yep – down in the weeds.  Are there false starts perhaps, and challenges and maybe a few snakes down there?  Yes, for sure, but so is the DNA of your ancestors.

Happy gardening and rooting around in the weeds.  Just think of it as searching for the very best buried treasure!  It’s down there, just waiting to be found.  Keep digging!

I hope you’ve enjoyed this series and that it leads you to your own personal genealogical treasure trove!

treasure chest

The Autosomal Me – Extracting Data Segments and Clustering

This is Part 8 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 two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.  In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7, “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments”, took a deeper dive and focused on the two chromosomes with proven Native heritage and began by comparing those chromosome segments using the 4 GedMatch admixture tools.

In this segment, Part 8, we’ll be extracting all of the Native and Blended Asian segments on all 22 chromosomes, but I’ll only be using chromosomes 1 and 2 for illustration purposes.  We will then be clustering the resulting data to look for trends.  If you’re following along and using this methodology, you’ll be extracting the Native segment start and stop locations from all 22 chromosomes.

I apologize in advance for the length of this article, but there was just no good place to break it into pieces.

So, let’s get started.  As a reminder, we are using the admixture tools at www.gedmatch.com.

I experimented with several types of extractions to see which ones best reflected the results found by both 23andMe and Dr. McDonald and confirmed by the start and stop segments in the highly Native segments of chromosomes 1 and 2 in Part 7 of this series.  We verified that all 4 tools accurately reflected and corroborated the segments listed as Native, so now we’re going to apply that same methodology to the rest of our chromosomal data.

Initially, I tried to use the information from chromosomes 1 and 2 to extract the Native chromosomes using only the “best” tool, but when I looked at all 4 tools, I quickly realized that there was no single “best” choice.  A couple of crucial points came to light.

  • Some of the geographic colors are almost impossible to tell apart.
  • None of the tools are universally best.
  • When looking at all 4 tools, generally a “best 3 out of 4” approach allowed for one of the tools to be wrong, to perhaps reference a slightly different data base that called the segment differently or for the colors to be indistinguishable.  In other words, if three called a segment Native and one did not, it’s Native and conversely, if less than 3 call it Native, in this comparison, it’s not.

Unfortunately, this created an awful lot of work.  This is probably the best example of where automation tools could and would make a huge difference in this process.

I did two separate extracts.  The first one is what I refer to as the “Strong Native” extract and the second is the “Blended Asian.”  In part, I did these separately as a check and balance to be sure that my first extraction was accurate.

In the first extract, I selected only one category, the one best fitted to “Native American” for each tool.  I used the following categories for each admixture tool:

  • MDLP – Amerind
  • Eurogenes – North Amerindian
  • Dodecad – NE Asian
  • Harrappaworld – American

I completed this process for every chromosome, but I’m only showing the first two chromosomes in this article.

By way of example, using the first tool, MDLP, North Amerind looks black, but is actually very dark grey.  It is, fortunately, distinctive.

On the chromosome painting below, my results for the first part of chromosome 1 are shown in the first band, and mother’s for the same segment are shown as the second band.  The bottom band represents common segments and the black is non-matching segments, meaning those I obtained from my father.  Sometimes this third band can help you determine what you are really seeing in terms of colors and blending, but it’s not always useful.  In this case, trying to spot a small amount of dark gray against black is almost impossible, so not terribly helpful.  But if you were looking for red, that would be another story.  As you move through this process, remember, it’s not exact and utilizing best 3 of 4 will help you recover from any major errors.

You can see that my grey segments show up from about 12-13 and then again at about 14.5.  Sometimes it’s difficult to know how to count something.  For example, my Native at 14.5 – it’s actually more like 14.25 -14.5, but I chose not to divide further than half mb segments.  As long as you are consistent in whatever methodology you select, it will work out.

step 8 - 1

Please note that when reading these charts, that the small hash mark is the indicator for the measure.  In other words, the small hash mark above 10M means that is the 10M location.  It’s obvious here, but on some charts, the hash mark and the location legend look to be 1-off.  Again, as long as you’re consistent, it really doesn’t matter.

Mother’s Native segments are more pronounced and obvious.  They range from about 8-14.  Using the actual tools, you would record this and then continue scrolling to the right until you reach the end of the chromosome.  On chromosomes 1 and 2, I found the strong Native segments for the four admixture tools, as shown below.

The boxed numbers show the areas that were found “in common” between 23andMe, Dr. McDonald and the admixture tools, as determined in Part 7 of this series.  Highlighted segments show segments where at least 3 of 4 admixture tools reported Native heritage.  As you can see, there were clearly additional Native segments not reported by 23andme and Dr. McDonald.

Strong Native Chromosomal Detail Table

step 8 - 2

step 8 - 3

Because we have both my and mother’s results, we can infer my father’s contribution.  Clearly, some of his will wind up being some amount of “noise” and some IBS segments, but not all, by any means, and this is the only way to get a “read” on Dad.  This is one form of phasing data.  Phasing refers to various methodologies of figuring out which DNA comes from what source, meaning which parental line.

While the strongest Native segments are the ones individually most likely to indicate Native American ancestry, that really isn’t the whole story.  I discovered that many of these Native segments are actually embedded in other segments that are indicative of Native heritage too.  In other words, it’s not a line in the sand, yes or no, but more of a sliding scale.

On the chromosome painting below, this one using Eurogenes, with my results shown above and mother’s below, you can see two excellent examples.  Regions relevant to Native ancestry include:

  • Red – South Asian
  • Brown – Southwest Asian
  • Yellow – North Amerindian and      Arctic
  • Putty – Siberian
  • Emerald – East Asian

You can see that while mine is almost universally yellow, or Native, with a little Siberian (putty) mixed in for good measure between 169-170, a hint of East Asian (emerald) plus a little Asian (red), mother’s isn’t.  In fact, hers is a mixture of Native American and South Asian (red), with more red than yellow,  Siberian (putty) and a large segment of East Asian (emerald green).

step 8 - 4A

While her yellow Native segments alone would be staggered across this entire segment in 7 different pieces, when taken together as a whole, the “blended Asian” segment reaches entirely across the screen with the exception of 1 mb between 161.5-162.5, roughly.

The following Blended Asian Chromosomal Detail Table shows all of the blended Asian segments using all four of the admixture tools for chromosomes 1 and 2.

It’s clear that these regions are not solely “Native American” but reach back in time genetically into Asia, particularly Northeast Asia.

Again, the boxed numbers show the “in common” segments between all tools and the yellow highlighted segments are common between at least three of the four admixture tools.

Please note that there were some issues distinguishing colors, as follows:

  • For the MDLP comparison, Mesoamerican and Paleo Siberian are both putty colored and indistinguishable on the chart.  Also, the apple green for Arctic Amerind is very similar to the Austronesian.
  • When using Dodecad, Southeast Asian (light green) and South Asian (apple green) are nearly impossible to distinguish from each other on the graphs.
  • When using HarappaWorld, the apple green for Siberian was very similar to the light forest green for Papua New Guinea and was very difficult to distinguish.  The South Asian putty appears often with the other Native markers, and I considered including this group, but it too was difficult to distinguish from other regions so in the end, I opted not to include this category.
  • If you are colorblind – get help as this is impossible otherwise.

Blended Asian Chromosomal Detail Table

On the blended Asian Chromosome Detail Table, I added yellow highlighting where the same segments show in other Asian geographies that showed in the Strong Native table.  In each column, the Strong Native category is the last one at the bottom of the list.

The blue highlighting shows other common segments found that were not included in the Strong Native segments.  For a Strong Native yellow segment to be highlighted, it had to be present in 3 of 4 tools, or 75%.  In the Blended Asian group, there are a total of 15 categories between the 4 admixture tools, so for a segment to be shaded blue, it must be found in at least 8 of the categories, so just over half.  There are many segments that are found in several categories across the tools.  For example, segment 192-193 on chromosome 1 is found five times.  This isn’t to say you should discount this segment, only that it isn’t one of the strongest, most universal.  Surprisingly, there really weren’t too many that were close to the cutoff.  Several, but not a majority, were in the 4 or 5 range, only one was at 7.

step 8 - 4

 step 8 - 5

step 8 - 6

 step 8 - 7

  step 8 - 8step 8 - 9

 step 8 - 10

 Step 8 - 11

step 8 - 12


The third step in data extraction is to look at all of the data together.  In this step, we are removing the geographic boundaries of Siberian, N. Amerindian, etc. and combining all of our data.  I have only combined the data within columns, not between columns, so we can get a feel for which tool or tools performed best or maybe not so well.  Each chromosome in each column has its data ordered numerically, and yes, this is a manual cut and paste process.  Sorry.  I warned you, this is an very manually intensive process.

After I put each column in numerical order, I arranged them so that the numbers were approximately in a line, or a row, with each other.  For example, in the first group below, you can clearly see that the first cluster of results is found using all 4 tools.  When looked at individually, only the blue results were noted as common (at least 8 of 15 for blue), but when viewed as a cluster, you can see between the tools that the cluster itself runs from about 7.5, with a small break from 8-9, and then to about 14.5.  As you would expect the beginning and end points of the cluster trail off and are not uniform between tools, but the main part of the cluster is found in all the tools.  This introduces the question of how to measure a cluster.  In this case, there is a clean break using all tools between 8 and 9, but that is only 1 mb, rather difficult to measure accurately.  You could record this as two distinct clusters but since it’s very closely adjacent the rest of the cluster, I’m inclined to include this as one large cluster and use the starting and ending segments for the cluster as a whole, in other words, the cluster runs from 7.5 through 14.5.  The alternate, or more conservative methodology would be to use the “in common” numbers, but in this case, that would be only 10-11.5 and I think you would miss a great deal of useful data.  So, for clusters, I’m recording the full extent of the cluster.  In some cases, you may need to exercise a judgment call.

Let’s look at the second group of numbers, beginning with 18.5 in Harrappaworld.  This grouping runs though about 28.  Eurogenes found some blended Asian between 27-28.5 as well in two of the geographies, but over all, of the 15 tools, we don’t see much.  This could be a result of a number of things.  I could have had problems with the colors, there may be only a very small amount and it may be categorized as something else with the other tools.  I would not consider this a cluster, and using our best 3 or 4 methodology eliminates this cluster from consideration.  This also holds true for 43-43.5.

However, the next cluster, from 55.5 to 58 is found in the Strong Native comparison, indicated by the yellow highlighting and is found using all 4 tools.  This is definitely a cluster.

step 8 - 13

step 8 - 14

step 8 - 15

step 8 - 16

step 8 - 17

step 8 - 18

step 8 - 19

Step 8 - 20

step 8 - 21

step 8 - 22

step 8 - 23

step 8 - 24

I’ve synthesized the cluster information into a list.  From the clusters above, I’ve created a list that I will be using in the next segment for data input into my spreadsheet of matches.  The blended segments below that include Strong Native segments are shown with yellow.

step 8 - 25

Using the GedMatch admixture applications, we’ve isolated the strongest Native and the Blended Asian segments and clusters in preparation for identifying specific Native family lines within our group of matches.

This process shows that, for the most part, the Strong Native segments picked up the strongest signals, about half of the segments that will be useful in determining Native admixture, although it does miss some.

When we use the clustering technique to view our results across all the admixture tools, we see a somewhat different picture emerge, adding several Blended Asian clusters.

In Part 9 of this series, we will use the highlighted Strong Native segments and the Blended Asian clusters, both of which suggest Native chromosomal “hotspots” to begin our comparison to our genetic matches for genealogical relevance.  In other words, using this information, we will determine which genealogical lines carry Native ancestry.

Part 9 may be somewhat delayed.  The good news is that Family Tree DNA is finishing work on their Build 36 to Build 37 conversion.  The bad news is that it fell right in the middle of writing this series.  When they finish Build 37, I’ll finish Part 9 of this series.  In the mean time, you can be extracting your minority segments using the tools and techniques that we have covered in Parts 1-8.

The Autosomal Me – Start, Stop, Go – Identifying Native Chromosome Segments

This is Part 7 of a multi-part series.

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 two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.  In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In Part 6, “The Autosomal Me – DNA Analysis – Splitting Up” we began the analysis part of the data we’ve been gathering.   We looked at how to determine whether minority admixture on specific chromosomes came from which parent.

Part 7 – “The Autosomal Me – Start, Stop, Go – Identifying Native Chromosomal Segments”, takes a deeper dive and focusing on the two chromosomes with proven Native heritage, begins by comparing those chromosome segments using the 4 GedMatch admixture tools.  In addition, we’ll be extracting Native segment chromosomal start and stop addresses that we’ll be using in a future segment.

Using Doug McDonald’s tool and the 23andMe results, we can begin with the following two Native segments, one each on chromosome 1 and 2.  These will be our reference points, because according to both sources, these are the largest and most pronounced Native segments, the strongest indicators, so they will be our best yardsticks.

  Chromosome 1 Chromosome 2

165,658,091 to 175,711,116

86,316,174 to 103,145,426


165,000,000 to 180,000,000

90,000,000 to 105,000,000

On all of these admixture graphs, my results are shown first, then mother’s, then the comparison between the two where the colored regions show common ancestry and the black shows nonmatching segments – in other words those contributed by my father.

Please note that Native contribution in this analysis is being evaluated by a combination of geographies.  In some cases, one individual will show as “Native” meaning in the case of MDLP “North Amerindian” and the parent (or child) will show as something similar, like “Actic,” “South American” or “MesoAmerican.”  In order to normalize this, I have combined all of the geographies that are Native indicators.


On the MDLP graph below, the legend indicates that these 4 regions are relevant to Native ancestry.

  • Army green – Mesoamerican
  • Lime Green – Arctic
  • Emerald – South American Indian
  • Grey – North Amerindian

Chromosome 1 – Native Segment

On the graph below, you can see that mother has more grey than I do from about 162-165, but then I have some grey that she does not at about 170.

step 7

A detailed analysis of the segment of chromosome 1 between 158-173 shows the following admixture:

On my results, the putty green, MesoAmerican, is scattered between about 158 and 173, in three segments.  The putty green in my mother’s segments are from 159-160.5 and then 167-170.5.  Therefore, my father, by inference has a segment from about 162-165 and from about 170.5 to 173.

My teal, North Siberian, ranges from 162-163 and from 168-171.  My mother carries no teal in these segments, so this is inferred to be contributed from my father.

My dark grey, North Amerind, ranged from 162-165.5 and then from 168-169.5.  My mother’s range is from 161-165.5.  Therefore my grey segment at 168-169.5 is either recognized as MesoAmerican or Arctic Amerind in my mother.

Chromosome 2 – Native Segment

step 7 - 1

Chromosome 2 is quite interesting.  You can see that on my chromosome, the North Siberian begins at about 80.  Mom has none at that location.  My North Amerind begins at about 95 and extends to 105, where Mom’s begins in the same location but then transitions to a large segment of MesoAmerican which I do not carry.  I do have MesoAmerican, but mine begins about where hers ends and extends to about 105.  Mom’s North Amerind ends about 101, while mine continues to about 105.  She looks to have trace amounts beginning about 105 and extending through 115.


The next graph shows the same chromosomes using Eurogenes.  Regions relevant to Native ancestry include:

  • Red – South Asian
  • Brown – Southwest Asian
  • Yellow – North Amerindian and Arctic
  • Putty – Siberian
  • Emerald – East Asian

Chromosome 1 – Native Segment

step 7 - 2

The difference between my chromosome 1 and my mother’s in this region is quite pronounced.  My mother’s is drenched in beautiful red South Asian, while I have absolutely none.  Some of the area where I have North Amerindian shows as South Asian on hers, but in other areas, there is no correlation.  It is expected of course, that there are areas where she has some ancestry and I have none, due to the fact that I only inherit half of her DNA, but she has a significant segment of East Asian between 163 and 164, and I look to have received only a very small portion.  The same is true of her Siberian segments at 163-164, but then I have Siberian that she does not at 169-170 and she has some that I don’t at 160-161.5.  Some of this difference can likely be explained, especially between the yellow North Amerindian and the red South Asian by slight differences in the DNA read and how it is categorized, but in other cases, the difference is real.  Looking at mother’s red segments from about 166.5 to about 168 and then looking at my corresponding region, you can see that I have nothing that hints at Native.  In that region, I clearly inherited from my father as well as my mother’s North European.

Chromosome 2 – Native Segment

step 7 - 3

As different as our chromosomes 1 were, one wouldn’t expect chromosome 2 to be so similar.  In the graph, I included my large South Asian segment surrounding 80, where Mom has a trace, although that is beyond the area indicated as Native by 23andMe and Doug McDonald.  In the range of interest, beginning at about 80, we find nothing until about 94 where mother and I both have North Amerindian segments that stretch through about 105.  Mom’s goes slightly further than mine, to about 105.5.  It’s interesting to note that in part of this region, on either side of 101, her Siberian and my North Amerindian are the same shape at the same location, so obviously the same DNA is being read and categorized as two different regions, probably due to my father’s admixture.


On the Dodecad graph of the Native segment, you can see the Native colors are in shades of green.

  • Putty – West Asian
  • Yellow-green – South Asian
  • Emerald – Northeast Asian
  • Light Green – Southeast Asian

To use Dodecad in an equivalent manner as the rest of the tools, it looks like Northeast Asian is the closest we would get to Native American since that is where Native Americans lived just prior to crossing Beringia, so the greens should probably be evaluated as a group.  As can be seen on chromosome 1, they do clump together.  Even though West Asian is also found with this group, it seems to be outside the range, so I am not including it in the evaluation.

Chromosome 1 – Native Segment

You can see another example here of one segment being called South Asian in Mom’s and Northeast Asian in mine at about 170mb.

step 7-4

The Native, or in this case, Northeast Asian/Southeast Asian begins at about 162.5 where Mom’s and mine are very similar.  However, we diverge at about 164.5 where Mom begins with large segments of South Asian.  I have a little bit, but not much.  Beginning about 168, I have a large Northeast Asian segment, but she shows with South Asian there, although the segments are not exact.

Chromosome 2 – Native Segment

step 7 - 5

Chromsome 2 is quite simple using Dodecad.  Only two of the three groups appear.  Southeast Asian is absent, South Asian is present only in trace amounts except for one small area between 79.5 and 80 on my chromosome.  As expected, Northeast Asia is more prominent.  Mother has a few areas that I don’t, which is to be expected.


Last, we have HarrappaWorld.  American and Beringian are the Native American categories here.  Regions relevant to Native American heritage would be:

  • Teal – American
  • Periwinkle – Beringian
  • Lime Green – Siberia
  • Emerald – Northeast Asia

Chromosome 1 – Native Segment

You can see both Beringian and American embedded again at about location 169.  In mine, this entire block reads as American.

step 7 - 6

There is one large chunk of Northeast Asian showing for both results, but part of that region of my chromosome, between 163-164 shows as American instead of Northeast Asian.  The Beringian is scattered through the American, which I would expect.  The American runs either strongly or weakly through this entire segment from 163 to 175 in mine or to 179 in mother’s.  Surprisingly there is no Siberian at all.  I would have expected to see Siberian before Northeast Asian.

Chromosome 2 – Native Segment

step 7 - 7

Where on chromosome 1, we saw no Siberian, on chromosome 2, we find Siberian instead of Northeast Asian.  I have no Beringian, but mother has 4 segments.  Three of her 4 segments are embedded with American segments.  Two may simply be categorized differently in my results, but two, I did not inherit.

Analysis Discussion

What have we learned?

When we are dealing with small amounts of minority admixture, they may or may not be able to be picked up directly by the testing companies.  Of course, part of this has to do with their thresholds for what is “real” and reportable, and what isn’t.  Aside from that, lack of identification of minority admixture probably has to do with which segments were inherited and their size, if they have been isolated and identified as Native by population geneticists, and the robustness of the data base sources the data is being compared against.

We can also see how difficult it is to sort through threshold matches, meaning what is Native, Asian, central Asian, etc.  Many of these differences are probably not actually differences between groups, but similarities with slight categorization differences.  Of course, it’s those differences we seek to identify our ancestral heritage.  Combining similar geographies may help reveal relationships masked my reporting and categorization differences.

Given that multiple sources have indicated Native ancestry, and on the same two chromosomes, I have no doubt that it exists.  Had any doubt remained, the exercises creating the MDLP Chromosome Map Table and reviewing the segments on chromosome 1 between 160 and 180mb would have removed any residual concerns.

The following table shows the results for the Native segments of chromosomes 1 and 2 beginning with the 23andMe and McDonald results, and adding the start and stop segments from each of the 4 admixture tools we used.

  Chromosome 1 Chromosome 2

165,658,091 to 175,711,116

86,316,174 to 103,145,426


165,000,000 to 180,000,000

90,000,000 to 105,000,000


162,000,000 to 173,000,000

80,000,000 to 105,000,000


162,500,000 to 171,500,000

79,000,000 to 105,000,000


162,500,000 to 171,000,000

79,500,000 to 105,000,000


163,000,000 to 180,000,000

79,000,000 to 104,000,000

In Common

165,658,091 to 171,000,000

90,000,000 to 103,145,426

Although the start and end (or stop) segments vary a bit, all resources above confirm that the region on chromosome 1 between 165,658,091 and 171,000,000 is Native and on chromosome 2, between 90,000,000 and 103,145,426.  Those are the areas “in common” between all resources, which is shown in the last table entry.

The concept of “in common” is important, because while any one resource may report something differently, or not at all, when all or most of the resources report something the same way, it is less likely to be a fluke or reporting issue, and is much more likely to be real.  We’ll be using this methodology throughout the rest of the articles in “The Autosomal Me” series.

In the next segment, Part 8, we’ll be extracting the actual start and stop addresses of the Native only segments, referred to as the “Strong Native” method, and the combined Native indicator segments, referred to as the “Blended Asian” method and looking at how we can use those results.

The Autosomal Me – DNA Analysis – Splitting Up

DNA Analysis purchased 1-24-2013This is Part 6 of a multi-part series.

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 two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.  In Part 5, “The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools,” we looked at 5 different third party tools and what they can tell us about our minority admixture that is not reported by the major testing companies because the segments are too small and fragmented.

In this segment, Part 6, “DNA Analysis – Splitting Up” we’re going to focus on specific aspects of those tools and begin our analysis of our minority ancestry.

Analysis.  Sounds like I’m climbing on the shrink’s couch.  But I’m not, I’m saving all my dollars for DNA kits!  Besides, I don’t want to stop!  This analysis, we’ll do by putting several pieces of data together and sorting the wheat from the chaff.  And yes, we’ll be splitting up…well…splitting our DNA up into pieces contributed by our father and mother.

Let’s start with looking at the DNA segments that mother and I share that are Native.

According to Doug McDonald, we have significant Native matches on chromosomes 1 and 2, with third party tools confirm that finding.  Unfortunately, the only company where Mom’s DNA resides is Family Tree DNA whose test did not reveal the Native ancestry.  23andMe did confirm Native segments in my DNA in those locations.

I’ve used several third party tools at GedMatch to see where Mom and I both have Native heritage, where she has it and I don’t, and equally as important, where I have it and she doesn’t?  What is that so important?  Simple, it means my father had Native heritage too, and tells me on which chromosomes his Native DNA is located  This could, when matching people in the future, on particular segments, help to isolate who our common Native ancestor was, or at least which line.  That is the ultimate goal we are working towards with this entire process.

In this case, to identify my father’s Native lines, if Mom and I neither or both have Native markers at a particular chromosome location, the values are irrelevant, because the Native lineage came from mother.  I did notice in a few cases that I had more than mother, and of course, in that situation, it means that my father contributed some too, or my mother had a misread in that region or a categorization issue exists.  For that reason, I am looking for patterns, not single instances.  We’ll discuss using patterns in a future segment.

Using the MDLP chromosome mapping tool, as MDLP appears to be the most comprehensive, I created a spreadsheet using my results as a base.  I then added mother’s values in the spaces where I had no values, and then I highlighted my results in the locations where mother had no value.  The essence of this is that the red, bold, underscore values mean Mom had a Native result here, but I didn’t receive it.  A yellow highlighted cell means I got the entire amount from my father, because my mother has no percentage showing.  In other cases, of course, it’s possible that both mother and father contributed Native ancestry on some adjacent chromosome segments.  The MDLP mapping tool with my additions is shown below for chromosomes one through eight.  Chromosomes 9-22 are similar, but the chart is too big to display as a whole.  This provides an example of how to do this analysis with your own results.

MDLP Chromosome Map Table

The results were very interesting.

My two primary regions, North-East-Europe and Atlantic-Mediterranean-Neolithic, were represented on every chromosome for both my mother and myself.  No surprises there.  The other regions would be considered minority admixture.

In 2 categories, North-European-Mesolithic and East Siberian, only my father contributed genetic material on some chromosomes and there were no chromosomes where my mother alone contributed.

In 1 category, Melanesia, only my mother contributed genetic material on some chromosomes and there were no chromosomes where my father alone contributed.

In all other categories, both parents contributed on some chromosomes where the other didn’t.  This is important, because it will allow me to associate a match with a particular segment of a chromosome on a particular parent’s side with Native ancestry.

In the minority categories for Native American, Mesoamerican, Arctic-Amerind, South America Amerind and North Amerind, grouped together, both parents contributed on some chromosomes where the other didn’t, and in two categories, on 3 chromosomes, I carry more than my mother, indicating an additional contribution from my father.

This is a repeated occurrence, with Native ancestry for my parents and I combined showing on a total of 42 chromosome locations across 4 geographic/ethnic categories, and in at least three cases, both parents contributed.

In the African categories, South African, Sub-Saharan and Pygmy, I had contributions from both parents on a combined total of 18 chromosome segments.  The African admixture, in total, was less than the Native, and they are assuredly below 5% combined.  If they were present at higher levels, I wouldn’t need to go through these genetic gyrations to prove or disprove the heritage and which parent contributed, because it would be evident in the testing results of all companies.

In our next segment, Step 7, we will be further scrutinizing Chromosomes 1 and 2 for additional information about Native heritage and assigning specific Native segments that I carry on various chromosomes  to either my mother or father’s lineage.

The Autosomal Me – Rooting Around in the Weeds Using Third Party Tools

This is Part 5 of a series.

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 two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.  Part 3, “The Autosomal Me – Who Am I?,” reviewed using our pedigree charts to gauge expected results and how autosomal results are put into population buckets.  Part 4, “The Autosomal Me – Testing Company Results,” shows what to expect from all of the major testing companies, past and present, along with Dr. Doug McDonald’s analysis.

In this segment, Part 5, we’re going to look at various third party tools and what they can do for our search for minority admixture.  We will use the download files from either 23andMe and Family Tree DNA and utilize third party tools to analyze the raw data.  We’ll see how third party developers put those puzzle pieces together, if the results are consistent and what they tell us.

The Weeds

When dealing with testing companies, particularly any individual source (as opposed to multiple testing company results, as I have done), minority admixture, especially less than 1% may not be successfully recognized.  One percent equates to between 6 and 7 generations or about to the 1800 threshold in time.  However the history of both African and Native admixture in colonial America goes back another 200 years to the Jamestown era.

The social history in the US means that there are many people looking for this admixed heritage as long ago as 1609 when Jamestown was established and the first European/Native marriages took place (although there were “blonde Indians” reported by Jamestown settlers).  In round numbers, that’s about 400 years or between 13 and 16 generations.  Of course, a minority ancestor drops below the 1% threshold between 7 and 8 generations (with the first generation being the person tested) and by the time you get to the 12th generation, you’re at .048%.  At this level, Bennett Greenspan says we’re “rooting around in the weeds,” and he’s right.

However, rooting around in the weeds for those dreaded IBS (Identical by State) segments in genealogy is exactly what we need when looking for small amounts of minority admixture.  What’s an IBS segment you ask?  It’s a segment that is typically too small to be counted as an IBD, or identical by descent, segment.  IBS means that you’re from a common population if you match someone with a very small segment, not necessarily that you share a common ancestor within the past several generations.  But how to you tell if a small segment is IBS or IBD?

There is no absolute line in the sand, but often segments smaller than 7cM (centimorgans) or 700 SNPS (some say 5cM and 500 SNPs) fall into the IBS category.  This has caused some researchers to discard all segments of this size because they can’t tell the difference.  That’s unfortunate, because clearly some of these segments are IBD and the IBS segments can be useful too.

When looking for minority admixture in two people, both of them having these small segments in the same location can provide meaningful information, and can confirm minority heritage.  Said another way, if two people have less than 1% Native heritage, both share a common ancestor, and both carry part of their “less than 1%” on the same segment….one might say it’s not likely to be coincidence.  Identifying the common segments of your common ancestor can lead to identifying the specific family line those segments came from, especially if you match others as well.  This is in essence what Minority Admixture Mapping, or MAP, does.  It uses these techniques to look for patterns in these small fragmented pieces that, when taken together, indicate minority heritage.  Having said that, some IBS segments will indeed, be simply that, because you share the same base population, but some will be IBD, or more current in time.  With the MAP technique, we’re sorting through ways to utilize these small segments, whether they are IBS or IBD.

Using the tools, MDLP, Eurogenes, Dodecad and HarrappaWorld at GedMatch allows us to “root around in the weeds,” to quote Bennett, and find those all-important small IBS/IBD segments that connect us to a particular ethnicity and ultimately, to other relatives who carry these same segments in the same locations.

In general, using these this type of DNA is called BGA, or Biogeographical Ancestry where we use SNPs of autosomal DNA called AIMs, Ancestry Informative Markers.  A SNP is a Single Nucleotide Polymorphism, or a mutation that happened in one specific location on a gene.  AIMs are generally SNPs, not clusters of markers, found at different frequencies in different populations.  We combine all we know about them scientifically with information about population frequencies and then draw inferences about where our ancestors came from based on that information.  So a SNP that is useful in determining ancestry is called an AIM.

These SNPs, or AIMs, are the foundation for these BGA tools that we will be using to sort through small segments of minority admixture.  So this is a building block process.  Scientists identify SNPs found in different populations at different frequencies and identify them as such, then scientists and genetic genealogists create BGA tools that use and combine SNPs/AIMs to suggest populations and ethnicities for those who carry them.  Using these tools, majority ancestry is easy to discern.  We’re going to use those tools to look at groups of SNPs/AIMs clustered in small, fragmented IBS or IBD segments to do Minority Admixture Mapping (MAP) to confirm our minority admixture and to identify our minority admixed lines, families and perhaps even (in time) our original minority ancestor.

I bet you thought I couldn’t fit all of those acronyms in one paragraph, but I did:)  It is a bit like alphabet soup, but when you understand that this is a building process, it’s much easier to grasp as a whole.

Having at least one parents DNA makes this process much easier, because you can immediately tell if your other parent, by inferrence or process of elimination, has contributed any of the minority ancestry, or if it’s all on one side of the tree.  Of course, that’s assuming your parents aren’t related to each other.  There’s a test for that too at GedMatch.  If you don’t have one parent available, you can “make do” with aunts, uncles and cousins, but it’s a much more tedious process.

Third Party Tools

To use any of these BGA tools, you’ll need to download your results from either 23andMe, Family Tree DNA or National Geographic.  Currently at GedMatch, the only supported formats are 23andMe or Family Tree DNA, because the National Geographic test is so new.  I used my Family Finder (Illumina Build 36) raw data file.

To download your results from 23andMe, sign on to your account, then click on this link and it will take you to the area to download your results.


Save the file and do not open it as the act of opening it sometimes causes corruption and you will have a hard time uploading the file.  If the upload fails, download a new copy and start over.  If you have an older copy on your computer, it’s always a good idea to use a fresh copy to incorporate any changes made by the vendor since your last file download.

To download your results from Family Tree DNA, sign on to your personal page, click on the Family Finder tab and then on “Download Raw Data.”  As I write this, Family Tree DNA is in the midst of a conversion from Build 36 to Build 37 for their autosomal files (in order to facilitate the integration of 23andMe results), so you may need to be a bit patient while this process completes.  Files may not be available for download at some points.  You certainly don’t want to mix comparisons, meaning using one build 36 and one build 37 file for comparison.

If you’re following this process yourself with your own data, please read all the way through this posting before starting your own processing.

Now, let’s look at the third party tools.

Stanford University

This tool is available at Stanford University.  Scientists have collaborated to provide this service and I think it’s quite interesting.  This tool is not compatible with any browser except Chrome and it requires a download of your autosomal data in a .txt file.  If it can’t load your file, the loading task simply never completes.  For me, that meant it wasn’t a .txt file I was trying to load.


Load your file and choose Ancestry, then Paintings, then Hap Map 3 (experimental), then Paint my Chromosomes.

weeds 1

Their legend, above, translates to the regions, below.

ASW – African ancestry in Southwest USA

CHD – Chinese in Metropolitan Denver, Colorado

GIH – Gujarati Indians in Houston, Texas

LWK – Luhya in Webuye, Kenya

MEX – Mexican Ancestry in Los Angeles

TSI – Toscani in Italia


Unfortunately, this isn’t terribly useful.  Hap Map 3 utilizes additional regions, including Utah, but this tool doesn’t seem to be mapping them, so my closest match region is Italy, which is midleading since none of my family was from Italy.  Hap Map 2 is also an option which does include the Utah population, but it’s not as up to date otherwise as Hap Map 3.

David Pike has figured out how to tweak these settings some.  You can read about it at this link:  https://www.23andme.com/you/community/thread/8062/.  David’s posting on June 20th shows what he did.  However, compared to the other tools available, I find this a poor choice and did not spend a lot of time trying to work with it.

However, a second feature that they provide is fun.

Stanford provides a Neanderthal tool that’s a little different than the Nat Geo or 23andMe ones.  Click on Explore, Neanderthal, Look Up Exercise.  Then enter your primary ethnicity and click on Look Up Exercise again.

Of a possible 84 Neanderthal alleles, I have 9, partially displayed below.



www.Gedmatch.com is a complimentary (voluntary contribution) site created by two genetic genealogists that includes several autosomal analysis tools.  One of the areas of this site is “Admix Tools.”  On that page one finds several private or proprietary tools, some written by genetic genealogists, some by researchers, and all free.  Let’s take a look at each one and their results.  If you want to see any of the results more closely than the photos here allow, you can run each of the comparisons using kit F6656 (mine) as the first kit and kit F9141 (my mother) as the second kit.

Each of these tools offers the same functionality, as follows.

weeds 4

We will be utilizing 4 of these functions for each tool.

  • Admixture Proportions
  • Admixture Proportions by Chromosome
  • Chromosome Painting
  • Paint Differences between 2 kits, 1 chromosome

We select from the tools as follows:

weeds 5

Let’s take a look at what the tools provide.

MDLP World 22

The MDLP software is sponsored by two genetic genealogists.  You can read more about the project at http://magnusducatus.blogspot.com/ and http://magnusducatus.blogspot.com/2012/09/behind-curtains-mdlp-world-22-showcase.html.

weeds 6

MDLP shows several populations.  I was interested to see if my mother also shared the African percentage.  Interestingly, mother does have a South African segment, but it’s .12, so less than mine.  Therefore, I would have obtained part of my African heritage from my father.  She also has three different categories of Native American heritage, compared to my one.  She carried a total of 1.92% and I carry .58%.  Otherwise, our results are very similar.

weeds 7

The next feature is ethnicity mapping by chromosome.  While the display is too large to see well it’s interesting to note that indeed, both Native American and African were detected on several chromosomes, not just on chromosomes 1 and 2 as reported by 23andMe and Dr. McDonald.  Note that DeCode Genetics showed “East Asian” admixture on several chromosomes.

weeds 8

Here’s a portion of the above chart that you can actually see.  The highlighted blue regions are your major ethnic regions.

weeds 9

Another feature is chromosome painting, shown below.  This shows the first part of my chromosomes 1 and 2 painted by ethnic/regional breakdown.  The legend for each tool is different and above their graph.

weeds 10

weeds 11

These tools also provide the ability to compare one chromosome between two people.  On the graph below, my chromosome 1 is on the top, and my mother’s is second, with the third band being our common painting.  The black represents non-shared regions, meaning those contributed to me by my father.  Unfortunately, North American Native American is dark grey, sometimes difficult to distinguish from black.

weeds 12

The graph below shows that while I do share a large piece of Chromosome 1’s Native region (about 160-180mb) with my mother, there are also segments, 169-170 for example, where I have Native genes that she does not, indicating Native heritage in this location from my father’s side.

weeds 13

Eurogenes K9

Eurogenes was created by another genetic genealogist.  You can read more about it at http://bga101.blogspot.com.au/2012/04/eurogenes-admixture-utilities-at.html.

weeds 14

Eurogenes calls me primarily North European with .67 Native American and no African in the percentages above, but below, on the individual chromosomes, some African does show, although not on as many chromosomes as MDLP.

weeds 15

In the charts above and below, you can see that Eurogenes detected small amounts of African along with Native American.

weeds 16

weeds 17

Notice that at about 10mb on chromosome 1, on the graph below in the top band, that the North American Indian (yellow) and the South Asian (red) are imbedded with each other.  These appear again together at the beginning of chromosome 2, shown as the second band.  This hints at how and why it’s sometimes so difficult to determine and filter Native American from Asian.  There is no line in the sand, there is a continuum between populations, the only differentiator being 10,000 to 15,000 years spent apart in which time, they, hopefully, developed enough differentiating mutations that we can tell them apart.

weeds 18

On the chart below, the top band shows the chromosome painting of my chromosome, and the second band shows the chromosome 1 Native American segment (about 160-180 mb) of my mother with the third band showing both matching and non-matching regions, painted black.  Looking at the segment of chromosome 1, in the graph below, characerized as Native, we can see in mine, top row, that this is categorized as Native American (yellow), but some of the same regions below, in Moms are categorized as South Asian (red), causing a technical non-match, when in reality, It’s likely a categorization issue, not a genetic mismatch.  In future analysis, we’ll be using two methods of comparison, one called “Strong Native” that only matches Native to Native and another, the “Blended Asian” method that allows for grouping of similar ancestral types that together likely indicate a Native heritage.

weeds 19

Dodecad V3

Dodecad was created by an anthropologist.  You can read more about it at http://dodecad.blogspot.com/ and http://dodecad.blogspot.com/2011/06/design-of-dodecad-v3.html.

weeds 20

Dodecad, unfortunately, does not subdivide into Native American, so the Native will show here as some form of Asian.  Northwest Africa shows in the percentages above, but more detailed African heritage shows in the chromosome detail below in regions not shown above.

weeds 21

weeds 22

weeds 23

weeds 24

Above, my chromosome painting for the first part of chromosomes 1 and 2.

Below, the comparison showing the Native segments from about 160-180mb.   My Native segment (top) compared to mother’s (middle) with the comparison of the two on the bottom for chromosome 1.

weeds 25


HarappaWorld divides results into fewer population groups and is focused on Asia.  You can read more about it at http://www.harappadna.org/2012/05/diy-harappaworld/.

weeds 26

In HarrappaWorld, Beringian and American appear to be equivalent to Native American.  Like Dodecad and Eurogenes, African does not show in the total percentages, but does on the individual chromosome analysis, although in smaller percentages with this application.

weeds 27

weeds 28

weeds 29

Chromosome painting of my chromosomes 1 and 2 are shown below.

weeds 30

The graphs below show the Native region comparison of chromosome 1 between me, top row, mother, middle row, and the third graph showing the common areas, with black representing areas where there is no match.

weeds 31

For each of these tools and their results, we’ll do further analysis in a future segment of this series.

Tools Summary

Now that we’ve looked at these individual tools,  and building on the Test Results Chart created in Parts 3 and 4, let’s compare and see what information these tools add.

Test Results Chart Including Third Party Tools

Test/Company European Asian Native African Unknown
Pedigree Analysis






Testing Companies
Family Tree   DNA – Original










deCodeme –   X





Dr.   McDonald





23andMe –   Original






23andMe –   2012 – Standard






23andMe –   2012 – Conservative






23andMe –   2012 – Speculative






Family Tree   DNA – 2012


Geno 2.0












Third Party Tools
























Of the various chromosomes, the breakdown is as follows. Dodecad does not break the categories in a comparable fashion to these other 3 tools, so their results are omitted in the following chart.  Please note that how geographies are categorized can make a significant difference.

Minority by Chromosome Chart

Tool/Chr MDLP Native Eurogenes Native Harrappa Native MDLP African Eurogenes African Harrappa African
1 Y Y Y N N N
2 Y Y Y Y Y N
3 N N N Y Y N
4 Y N Y N N N
5 N N N N N N
6 Y Y Y Y N N
7 N N Y N N N
8 Y Y Y Y N Y
9 Y N N Y N N
10 Y N N Y N N
11 Y N Y Y N N
12 Y N Y N N N
13 Y N Y N N N
14 Y Y Y Y N N
15 Y N N N N Y
16 Y Y Y Y N N
17 Y Y Y N N N
18 N N N N N N
19 Y Y Y Y N N
20 Y Y Y Y N N
21 Y N Y N N N
22 N N N Y Y N

From these various tools, it’s obvious that I do have some Native admixture, probably about 1%, and it’s from both parents.  I also have some African, but it looks to be an even smaller proportion that Native American.

Join me for Part 6 of this series, where we look at how to analyze and use this information.

[1] 71.5% western European, 28.4% Northeastern European

[2] Inferred that Asian is actually Native in an American with no history of Asian ancestry.

[3] No category, inferred.

[4] 78.6% Northern European, 1.8% Southern European, 18.7% Nonspecific European

[5] 54.6% Northern European, .3% Southern European, 43% Nonspecific European

[6] 91.7% Northern European, 3% Southern European, 3.3% Nonspecific European

[7] 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.

[8] 43% North Europe and 36% Mediterranean

[9] 80% British, 12% Scandinavian

The Autosomal Me – Testing Company Results

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.

Autosomal test 1

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:

autosomal test 2

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.)

autosomal test 3

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.

autosomal test 4

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.

autosomal test 5

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.

autosomal test 6

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.

autosomal test 7

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.

autosomal test 8

The conservative estimate, below, shows less Native at .2%.

autosomal test 9

The speculative level below shows the Native back to .5% but adjusts the European regions significantly.

autosomal test 10

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!!!

autosomal test 11

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.

autosomal test 12

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.

autosomal test 13

My current results from Family Tree DNA’s updated software are shown below.

 autosomal test 14

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%.

autosomal test 15

It made more sense when I read the information.  It’s true, reading is fundamental.

autosomal test 16

These results are, in essence, more anthropological in nature.

autosomal test 17

autosomal test 18

Of course, one of the fun parts of the Genographic results are the Neanderthal and Denisovan percentages.

autosomal test 19

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%.


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.

autosomal test 20

Ancestry shows my heritage as only British and Scandinavian.

autosomal test 21

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

autosomal test 22

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

The Autosomal Me – Who Am I?

This is Part 3 of a multi-part series.

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 two gave an example of the power of fragmented chromosomal mapping and the beauty of the results.

This series focuses on answering the questions of identity through autosomal testing, in particular, for minority ancestry.  By minority, I mean any small, elusive amount of any type of ancestry you are seeking to discover in your heritage.  In my case, that’s both Native American and African.

This segment, Part 3, focuses on using pedigree charts to gauge expected results, how autosomal ethnic groups are determined and how fragmented minority admixture mapping is different from other techniques.  This leads us into Part 4 which shows the various results from different testing companies and how they differ.

Part 5 features third party analysis tools and Part 6 begins the analyses of the data that parts 3, 4 and 5 provide.

Let’s hope that with all of this information, we can answer at least part of the question: Who am I?  I was reminded on Christmas day, that I still don’t have the answer to that question.  On Christmas afternoon, our family saw Les Miz, again.  Nothing reduces me to tears as quickly.  In Les Miz, Jean ValJean certainly knew who he was……24601.


His assurance of who he was reminded me that I still don’t’ know.  Who am I really?  I don’t have the conviction that Colm Wilkinson sings with.  And let’s face it, I don’t have his voice either, but I still want to answer that burning question.  Surely there must be better tools today.  I resolved to reevaluate what we can do with current technology and tools.  Hence, this series.

A lot of who I am has to do with who my ancestors were, where they lived, what they did, choices they made.  Did they fight in the American or French Revolution?  On which side?  Were they Native?  Were they African?  Were they slaves?  So, who were they?

One of the reasons I began with genetic genealogy more than a decade ago was to confirm or disprove the persistent family history of Native American heritage that I had been unable to resolve using only traditional genealogy tools.  I have made inroads with that, in unexpected ways and places, because of and in addition to genetic genealogy.  Genetic genealogy and traditional genealogy go hand in hand.

It’s difficult tracking down each line to perform mitochondrial or Yline DNA tests.  Sometimes, it’s beyond difficult and it’s impossible.  Lines die out, people refuse to test or you simply can’t find the right people.  We need other tools.

Enter autosomal genetics. From the beginning, early in genetic genealogy, we had the CODIS type forensic and paternity type tests.  I reviewed the results of those early tests relative to my pedigree chart in a paper I wrote, “Revealing American Indian and Minority Heritage UsingY-line, Mitochondrial, Autosomal and X-ChromosomalTesting Data Combined with Pedigree Analysis,” published in JoGG in the Fall 2010 Issue.  We’ve come a long way since then.

In that article, I dissected my pedigree chart to determine how much of different types of ancestry I carried and how that compared with the testing that had been performed at that time.

Using the end of line ancestors pedigree analysis method described in the paper, which determines the percentage of ethnicity that each end-of-line ancestor contributed to me, my origins totals were as follows:

Geographic Origin Chart

Geographic origin chart

(1) The ethnic heritage of several lines could probably be inferred by surname or ethnicity of marriage partner.  However, I have avoided the temptation to make inferences within the United States, as the Native or African ancestry may well lie with one of these ancestors.  These are in fact the perfect candidates and to eliminate them from consideration by inferring origins would be a disservice.

In broader categories, and combining those that are similar, we find:

geographic origin summary

This is a useful exercize, not just for minority admixture, but to help evaluate the results you receive from the various testing companies.  For example, you might notice that there is no Scandinavian showing in my pedigree chart, which makes Ancestry’s 80% British and 12% Scandinavian suspect right off the bat.  It also makes results as high as 25% Native American reported in one of the earlier tests impossible.  This pedigree analysis tool helps you understand what is reasonable to expect in terms of ethnicity breakdown.

Now that we know what the majority ancestry looks like and any minority ancestry that we are aware of, let’s take a look at the various types of autosomal testing available.

Tests and Population Markers

In the paper, I reviewed the older results from companies using either CODIS or proprietary markers.  These low resolution tests are out of date now (although many are still being sold) and have been replaced by the much more thorough wide spectrum tests using chip based technology, allowing hundreds of thousands of DNA locations to be tested and evaluated.  Of course, the word evaluated is the loose cannon in that sentence, because the quality of the evaluation is key here.  And the evaluation is dependent upon accurate and widespread data bases to compare DNA results against to determine which populations have higher and lower frequencies of specific alleles (markers) occurring in their populations.

For example, let’s compare a population in Siberia that shows 100% of a specific marker value, let’s say a value of 10 at marker location ZZZ.  Now let’s compare that result to a population from Africa at that same marker location, but with a value never found in Siberia, let’s say a value of 7.  Each of thousands of markers are evaluated this way, creating patterns.  Now, you have a tester who doesn’t know where their ancestors are from, whose results at marker location ZZZ have a value of 10.  Would you say they are more likely to have ancestry in Siberia or Africa?

This participant’s marker results for ZZZ go in the “very strongly Siberia” bucket.  Of course, other markers they carry might indicate Africa, or Europe, or elsewhere, because we are a Heinz 57 mix of all of our ancestors.  But this is, in essence, how our ethnicity is determined by autosomal DNA testing.  Needless to say, you can be a lot more accurate with thousands of markers than with the 15 or 21 CODIS markers, or even the 300+ in some of the proprietary tests.

BGA Testing

Using autosomal results to determine ethnicity is called BGA testing, or Biogeographical Ancestry testing.  It has been used for years to determine percentages of ethnicity.  So, how is what I’m doing different and what makes it unique and new to genetic genealogy?

1. Traditional BGA testing deals in percentages of ethnicity, meaning generally 1% or more.  Small amounts are difficult to track in the best of circumstances.  When dealing with small amounts of admixture, not all tests will be able to identify the minority ethnicity in question.  We’re using these tests, plus additional BGA chromosomal painting tools combined with some spreadsheet comparison techniques to cross that 1% threshold.

2.  The prevailing winds in this industry have been that anything smaller than 1% was undetectable, and that any amount of admixture less than 7cM, 5cM or 3.5cM (depending on the source) was usless.  While this is relatively accurate (but not always) when determining a genealogical relationship within the past few generations, it’s not true when looking beyond the accepted 6 to 7 generation threshold where the 1% ethnicity issue comes into play.  At that point, we know we can’t identify the minority ancestor genealogically, so we have to identify them by their membership in a minority population group.  I am using a variety of tools and techniques to reach across that threshold.

3.  Instead of using these various tools to try to establish a genealogical relationship with another tester (such as we share a common great-grandfather), I am using these tools to attempt to identify which line or lines carry minority admixture.  If you already know who in your family tree contributes that admixture, you don’t need this technique.  If you are looking to confirm minority admixture below 1%, searching for the minority admixture contributing line, or trying to figure out which of your known ancestors contributed minority admixture, then this technique is for you.

Typically these tools have been used to track segments from known ancestors, like a Jewish grandmother, for example.  These segments are large and evident.  That’s not the case with small amounts of minority admixture.  Using several BGA tools together helps to eliminate the possibility of one tool picking up on these small segments and another one missing it.  We are bringing all of the resources from various camps together to bear on the situation.  This is the ultimate form of recycling, using the shreds that were left on the cutting room floor and deemed to be usless when in actuality, they are diamonds in the rough.  We’re reassembling them and looking at them from a different perspective.  It’s a new kind of quilting!

A New Name

As I’ve worked through this process, it seems that Minority Admixture Mapping best suits what we are doing, so MAP it is.  It makes sense and you can say it.

I still want to know who I am, so in Part 4, we begin our data analysis by looking at the autosomal ethnicity results of the various testing companies and how they compare.

The Autosomal Me – The Ancestors Speak

This is Part 2 in the series, “The Autosomal Me.”  Part 1 was “The Autosomal Me – UnRaveling Minority Admixture.”

Every Sunday, I write something called a Sunday Story.  I’ve done this for years.  I send them to my kids and I delude myself into thinking they read them.  I’m really writing them for my grandkids someday and hopefully, some as yet unborn descendants I’ll have that will care about finding out about the life and times of their a-few-greats grandmother who lived along with the dinosaurs in the last half of the 1900s and first half of the 2000s.  I know, I’m optimistic.

I decided that perhaps I would share this weeks Sunday story with all of you.  This way, I know that at least someone will read it.  Actually, aside from my husband, it’s my daughter-in-law who comments the most often.  So welcome to my Sunday Story!  You are all honorary cousins!


I know that a great deal of what I do with genetics is lost on my friends and family members.  That’s OK, because it’s very specialized.  However, I wanted to take a little bit of time to share with you an aspect of the genetics I work with that I think is very beautiful in both a literal and a spiritual way.

The point of genetic genealogy, of course, is to learn about our ancestors, who they were and our connection to them.  There are various ways to do this, but most of the time it’s through various matches to other people who share a common ancestor either recently or perhaps further back in time.

Of course, therein lies the rub – how long ago are two people related and who was their common ancestor?  Some people who carry minority ancestry are at a distinct disadvantage, because the testing that provides matches and ethnicity generally relies on amounts in excess of 1%, which equates to about 6 or 7 generations.  While many of us know that we carry minority ancestry, we would be hard pressed to say that our “pure” Native (or other minority) ancestor fell into that 6 or 7 generation bracket.  Six or 7 generations equates to about 150-175 years before our birth, or about 1775-1800 for most of us.  By then, many Native people were already admixed and many already lived outside of a traditional tribal unit.  Some people carry Native heritage from multiple lines, but since it comes from multiple ancestors, it too is often quite fragmented, so it doesn’t really improve the situation much unless some of those fragments happen to fall together to make larger segments.

Therefore, we are looking for very small amounts of admixture that often don’t show on traditional tests, or if they do, it’s in miniscule amounts.

Enter chromosome painting.

Without going in to boring detail, I’ve recently been working with a new methodology of identifying these fragmented and very small segments.  I am using several chromosome painting tools.  I’ll be blogging soon enough about how all of this is done, but I just wanted to share with you a couple of beautiful pieces of DNA, through which our ancestors are speaking, and we can see them, in a manner of speaking.

On the graph below, which is my chromosome painting of one a small part of one of my chromosomes on the top, and my mother’s showing the exact same segment on the bottom, the various types of ethnicity are colored, or painted.  You can see that both of us have a primary ethnicity of North European, shown by the teal.

ancestors speak

The grid shows location 120 on the chromosome.  Think of this number as a house number on a street.  It’s numbered so we can keep track of where we are on the chromosome.  For genealogy purposes, the smallest segment normally considered as relevant is 7 mb or marker segments long.  Each tick mark equals one segment or address, so a segment 7 mb long would be from 120-127 which takes you right over to the legend.  As you can see, the primary ethnicity has no problem reaching way beyond the contiguous 7 threshold, but the minority ethnicity would not be counted because it’s too small.

However, by the very definition of what minority ancestry is, these small segments are not only present, providing critical information, they are essential in our search and very informative.  Let’s see what they are saying to us.

First, let’s talk for a minute about ancestry.  There is no line in the sand very often between populations.  There are generally only degrees of difference.  So in the case of Native American, which is yellow on this chart, we also expect to see it “drift back in time” by being found in conjunction with Siberian (putty), South Asian (red) and East Asian (emerald green).  Native Americans were not dropped from alien spaceships, they evolved over time from these other Asian populations, so we would expect to see some of their genetics in Native American people.

So let’s take a look at what we do actually see in the DNA.

The first brightly colored segment in the top band is mine.  It includes Native American (yellow), South Asian (red), a big chunk of East Asian (emerald Green), a little bit from the Caucus (ginger) which is the Middle East area, and a piece of West African (light green).

There are two messages from the ancestors in this piece of DNA.  First, this segment absolutely, positively does NOT come from mother.  We can see this clearly because she has nothing but North European (teal) in that section of her DNA.  So, this little gem came from Dad.

The second piece of information is that the ancestor who provided this DNA to Dad was very likely admixed, Native and African.

Of course, if you’re thinking ahead at this point, you’ll be asking, “Which one of your Dad’s other relatives has this same segment?” because, yes, that’s exactly how we will tell which of his lines contributed the Native ancestry.  But you’re getting ahead of the story, and well, that is a story for another time.  This story today, is about the direct messages of the ancestors and the beauty of our DNA itself.

Let’s look at the next segment of minority DNA.  It starts about location 123.  Mom’s is much more pronounced than mine and much richer.  This tells us that I didn’t receive much of Mom’s.  Instead I received mostly North European (teal), along with some East Asian (emerald).

Mom has almost a perfect Native segment here.  By perfect, I mean we find a progression from Native back through time through all 4 categories I would expect to find.  I consider this entire segment “Native” because it indicates Native heritage.  You can see the emerald green (East Asian), putty (Siberian), red (South Asian) and yellow (North American Indian and Arctic) nestled together with no other minority ancestry in close proximity.  This means it’s not part of a different kind of Asian segment.  Remember, part of Europe was settled by the Mongol Hordes and the Huns, so we do see Asian and western Asian DNA in Europe, along with DNA from the Caucus, but we don’t see isolated segments like this, with just eastern Asian DNA and Native American.  So this little beauty is the perfect Native indicator, positively, even though it is only about 4 segments long.

Now take a look at my DNA in that same region in the top row.  It’s kind of hard to see the emerald green against the teal, but I only inherited the East Asian (emerald) segments from Mom.  Of note, however, is that I also have an East Asian (green) segment that Mom doesn’t have.  My East Asian starts about 122 where hers doesn’t begin until 123.  So good old Dad contributed a bit here as well.  Again, we know this because Mom only has North European at that segment.

And now of course for the kicker.  Your DNA looks this same way.  How boringly teal it is, or how beautifully rainbow multi-colored depends on how much minority ancestry you have, from how many different lines, and which of your parents you received it from.

I hope you can see why I’m so excited to be developing this new technique to work with highly fragmented DNA to find our ancestors.  They are there, they have a voice, and they are speaking to us.  All we have to do is figure out how to listen.

I am simply in awe of the beauty of this technique, literally as well as figuratively.  While I certainly understand and appreciate logically that matching other people means we’re related, there is something awe-inspiring and tangible about being able to see the painted graphs and view the layers of ancestry nestled together, life forces reaching through time, protecting that DNA with its precious message for us over many generations.  All this time, just waiting for us to be able to understand the most personal message from our ancestors, delivered, from them, in our genes, to each of us.  This is the voice of our ancestors.