Tuesday, May 8, 2018

Mama's Got A Brand New Clade

My 1st Cousin 2x removed Clara Harvey 
This blog is in honor of my cousin Clara Harvey, who turned 95 on April 26, 2018, just one day after National DNA Day. She is truly one of the last Mohicans — one of two surviving first cousins from my maternal grandfather's generation. 

With Mother's Day fast approaching, this is the perfect time to share phenomenal news about matriarch Clara's MATERNAL (mitochondrial-DNA or mtDNA) HAPLOGROUP, and we took it to the "Bank" (more on this later).

I'm also making an urgent appeal to add Cousin Clara's maternal haplogroup to the mtDNA phylogenetic tree so we can present it to her at an upcoming family event. 
I also have a new hypothesis about the source of our Native American ancestry. 

In my recent blog Guide to Building Your Family's Haplotree I revealed that cousin Clara's Maternal Haplogroup was B2, which is exclusively found in Native Americans. Since cousin Clara's mother and my grandfather's mother were full sisters this proved that the direct matrilineal line of my maternal grandfather — and by extension myself — biologically descend from a foremother of Native American descent.

I pray this blog inspires more relatives from my maternal grandfather's branch (Gillette, Hall, Jackson, Shipley, Van Horn, Van Ness, Winkey, Wyckoff) to participate in DNA testing; see my Family History & Genetic Genealogy Book Project. Our cousin Cousin Clara (and her brothers) tested without hesitation and in return unlocked a rich legacy that keeps exceeding all expectations. 


Special thanks to cousin Richard Oakley and genetic experts Claudio BraviJames Lick, and Ian Logan for their invaluable assistance. Read on:


BACKGROUND 
In 2014 cousin Clara Harvey and her son Richard Oakley tested at 23andMe, which includes lower res maternal (and paternal) haplogroup assignments as part of its testing product. That's when we first learned about founding Native American haplogroup B2 in the family. 

However MtDNA Haplogroup B2 has a lot of sub-clades (ie B2a, B2b, B2c), and sub-groups of those sub-clades (ie B2a1, B2b3, B2c1), and subgroups of those subgroups (ie B2a1a, B2b3a, B2c1a) and sub-subgroups of...you get the picture. We were hoping for a more specific B2 assignment in an effort to learn more about our indigenous roots.

Cousin Richard Oakley (he has an exact copy of his mother Clara's mtDNA), decided to take FamilyTreeDNA's Full Mitochondrial Sequence test, which genotypes the entire mtDNA code and provides the most specific terminal haplogroup available, as well as mtDNA genetic relative matching. Richard's FamilyTreeDNA "predicted" Maternal Haplogroup assignment were the same as his 23andMe results = B2.

I then advised cousin Richard to take the National Genographic 2.0 DNA test. At the time 
National Genographic 2.0 (before they switched to the Helix platform) customers could transfer their raw data file to FamilyTreeDNA and in turn receive a "confirmed" terminal Maternal Haplogroup assignment. Interestingly National Genographic 2.0 assigned cousin Richard, B2b3.

However there was a problem: FamilyTreeDNA "confirmed" Richard's mtDNA haplogroup as B2 with no subclade. To investigate the discrepancy, Richard uploaded his FamilyTreeDNA FASTA file to James Lick's MtDNA Haplogroup Analysis program. Here are the results (click to enlarge):





With Richard's James Lick MtDNA Haplogroup Analysis results (above), his best mtDNA haplgroup predictions fit with B2 and B2b3, the latter of which is a sub-group of B2b. That's when I noticed the discrepancy: 

Richard is mismatch for the defining marker for B2b (indicated above in red as marker 6755A  Cousin Richard has 6755G). This means cousin Richard's terminal haplogroup could not be B2b3 if he's negative for the defining mutation of her parent subclade B2b.

I contacted James Lick about the results. He told me that either there was a reversion of the defining mutation (G6755A) for B2b back to its ancestral state (G6755— usually haplogroup mutations are confirmed in their derived state) or it was not B2b3

I reviewed the B2b samples in Roberta Estes's comprehensive database of Native American mtDNA haplogroups here but could not find any B2b's negative for G6775A.

Next I reached out to Argentinian anthropologist and geneticist Dr. Claudio Bravi and asked him our family's mtDNA haplogroup B2 discrepancy. After analyzing cousin Richard and Clara's mtDNA data, here is what Dr. Bravi wrote back to me:
"Hi TL,
No, it is not B2b3 with reversion. Instead, it is a new clade with homoplasic polymorphism at 13708. 13708 is a rather hotspot that appears over and over again in different mtDNA lineages. 
Your cousin´s sequence has an almost perfect match with one  published one from the US, unfortunately without info regarding ethnicity or geographic origin. See below a comparison of these sequences. I only listed the polymorphisms accumulated since the arrival to America: both sequences share the same five mutations and differ at hypervariable 16092. This indicates that they are really very close as seen here. 
A homoplastic polymorphism occurs when defining mutations of two haplogroups are similar but not derived from a common ancestor. In Richard's case, the defining marker for B2b3 would not be derived from its parent B2b — which is 6755A (derived state) whereas Richard has 6755G (ancestral state) in that location — but perhaps another B2 subgroup

This indicates that cousin Richard's terminal mtDNA haplogroup is a new branch of B2  and also positive for the hypervariable 13708. I formerly proposed her be named B2 + 13708...I was wrong. 
  • King Genome's Tip: Claudio Bravi offers a free detailed report of full mito sequence matches from all over the Americas. Note: You MUST have taken a Full Mitochondrial Sequence test at FamilyTreeDNA and be assigned one of the Native American-specific haplogroups A2, B2, C1b, C1c, C1d, C4c, D1, D2, D3 (=D4b1a2a), D4e1c, D4h3a, X2a, or X2g. Please download your FamilyTreeDNA FASTA file and send it to cmbravi@yahoo.com.ar for analysis.
Taking Clara's Maternal Haplogroup to the "Bank" 

To learn more about cousin Clara's rare B2 mtDNA haplogroup; to take the next step of getting her (the B2 subclade) officially named, which is achieved by receipt of a node on the mtDNA phylogenetic tree; to find more mtDNA testers with the same sequence (they could be the source of our indigenous roots), we decided to publish Richard's full mito sequence test on GenBank.

GenBank is the "National Institutes of Health (NIH) genetic sequence database, an annotated collection of all publicly available DNA sequences...GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at the National Center for Biotechnology Information (NCBI)."

GenBank's database is "designed to provide and encourage access within the scientific community to the most up-to-date and comprehensive DNA sequence information." My hope is that geneticists, citizen scientists and researchers will examine our family's rare mtDNA B2 motif and include it in scientific studies, especially those revealing information about her origins. Here's cousin Richard Oakley's official GenBank submission:

 

On April 9, 2018, cousin Clara's full mitochondrial sequence results (via her son Richard Oakley)  was officially published on GenBank. Our family's B2 is now public. 

I also published the following sequences on 
GenBank:
  • My own mtDNA haplogroup L1b1a, MH161386, 09-APR-2018 — a common African haplogroup with major subclades but lacking information for more specific L1b1a assignment. 
  • My cousin Barbara Shipley's mtDNA haplogroup M20, MH161389, 09-APR-2018 —a rare Asian haplogroup representing the first Austronesian female settlers in Madagascar; Barbara is related to me and cousin Clara's side of the family.
  • My cousin Cleo Wilson's mtDNA haplogroup M32cMH208838, 27-APR-2018 —Asian haplogroup found more frequently in Madagascar; Cleo and I share Southeast Asian admixture via a shared Madagascan ancestry, who is also the source of Cleo's mtDNA haplogroup. 
When publishing to GenBank please keep in mind:
  • Your full mitochondrial sequence will be publicly and internationally available; 
  • Your submission is assigned an ID or Ascension number and will referenced by that ID number in any scientific studies and literature. 
  • Submission owners are not credited. Instead the owner of the DNA company or research leader that produced your full mitochondrial sequence test receives the acknowledgment; this is why Bennett Greenspan, president/CEO of FamilyTreeDNA, is listed as "Author" of Richard Oakley's submission.
If you're interested in submitting your Full Mitochondrial Sequence to GenBank please use Ian Logan's GenBank Submission utility.

Cousin Clara's Brand New Native American 'Clade

When I contacted Ian Logan about publishing cousin Clara's rare B2 sequence on GenBank, I asked him to examine her file. Logan confirmed that it was indeed a B2 motif without a sub-group label; in other words a brand new B2 subclade. However instead of focusing on homoplastic polymorphism at 13708 he turned his attention to mutation 
T8736C.

There are only 2 other sequences with the 'B2-T8736C' motif out of the 43,000+ sequences
 in GenBank:

(1) JQ705147 Behar B2 07-APR-2012
A73G    A263G   T310C   G499A   A750G   A827G   A1438G  A2706G  A3547G  A4769G
G4820A  T4977C  C6473T  C7028T  C8281-  C8282-  C8283-  C8284-  C8285-  T8286-
C8287-  T8288-  A8289-  T8736C  A8860G  T9950C  C11177T G11719A G13590A G13708A
C14766T A15326G C15535T T16092C A16182C A16183C T16189C T16217C A16230G T16249C
T16519C

(2) JX669283 (Peru) Tito B2 09-OCT-2013
A73G    G143A   A210G   A263G   309.1C  315.1C  G499A   523.1C  523.2A  523.3C
523.4A  A750G   A827G   A1438G  A2706G  A3547G  A4769G  G4820A  T4977C  T5628C
C6473T  C7028T  C8281-  C8282-  C8283-  C8284-  C8285-  T8286-  C8287-  T8288-
A8289-  T8736C  A8860G  A9242G  T9950C  C11177T G11719A G13590A C14766T A15326G
C15535T A16183- C16186T T16189C T16217C T16519C

The first B2 mtDNA sequence carrying the motif T8736C was from an unidentified person in FamilyTreeDNA's database (possibly African-American), and the second was from Peru.

Further according to Mr. Logan, the mutation T8736C occurs about 20 times on GenBank so it will also make a good subgroup definer for B2
  • King Genome's Decree: Wherefore our family's proposed new mtDNA B2 haplogroup subclade should be named B2-T8736C.
REQUEST To Add B2-T8736C to MtDNA PhyloTree

Now that cousin Clara's full mito sequence is published on GenBank and it has a new proposed name B2-T8736C, our family hopes it can be swiftly added to Phylotree.org.

Phylotree.org a website that "provides a comprehensive phylogenetic tree of mitogenomes showing worldwide human mitochondrial DNA variation, and currently comprising over 5,400 nodes (haplogroups) with their defining mutations." 

However in order for a new haplogroup or sub-clade to be added to Phylotree.org, administrators require (1) at least 3 of the same distinct sequences from 3 unrelated people, and (2) strong defining mutation(s) for that haplogroup or subclade.

The great news our family's B2 mito sequence meets Phylotree.org's criteria and thus makes a solid candidate for addition to Phylotree.org:
  • Our GenBank B2 submission makes the 3rd published distinct sequence of its kind;
  • The mutation T8736C occurs about 20 times on GenBank (in other haplogroups) so it makes a good subgroup definer for B2
Over the past few weeks I've made several attempts to contact Mannis van Oven at Phylotree.org about making a new subgroup/node based on B2-T8736C. I've also reached out to FamilyTreeDNA's MtDNA Haplogroup B2 project administrators. At press time no one reached out to me.

King Genome's Tips: 
  • Take FamilyTreeDNA's Full Mitochondrial Sequence (FMS) test ($199 US; on sale $149 Mother's Day). FamilyTreeDNA's FMS test will provide your most specific haplogroup assignment and is the only major company offering mtDNA relative matching and genealogical haplogroup projects...If you have a Native American mtDNA haplogroup from your FamilyTreeDNA FMS test send your FASTA file to cmbravi@yahoo.com.ar.
  • If you're not so interested in publishing on GenBank then take any of the following DNA tests to learn about your basic maternal haplogroup assignment: 
    • 23andMe ($99 US; on sale $79); or National Genographic 2.0 Helix ($199 US; on sale $69.95); or LivingDNA ($159 US; on sale $99) — each DNA test includes basic maternal haplogroup assignments with its personal genome service. Sales prices thru Mother's Day, May 13, 2018! 
 New Theory About Our Native American Ancestry
From left to right: my great-grandaunt (and Clara Harvey's mother) Jenny Jackson Van Ness; my great-grandaunt Clara Jackson Van Horn; and my great-grandmother Mary Louise Jackson Winkey 
In my recent blog Guide to Building Your Family's Haplotree I revealed that my maternal grandfather's family had the ubiquitous Native American anecdote. According to my grandfather's first cousin Clara Harvey, their maternal grandmother Sophia Shipley, born 1862 in White House, Hunterdon county, New Jersey, actually knew her Native American relatives. 

My 2nd-great-grandmother Sophia Shipley married Claiborne Jackson, who migrated from Louisa Virginia, and together they had 11 childrenthey all would have carried and passed to their children the B2-T8736C motif):
(1) Ida; (2) India; (3) Jenny(4) Nelson; (5) Mabel; (6) Gladys; (7) Clara(8) Leroy;(9) Claiborne Jr; (10) John, and (11) Mary Louise (my great-grandmother)
My own research shows that Sophia Shipley and her ancestors were free people of color with colonial roots in New Jersey. Sophia inherited B2-T8736C from her mother Mary Jane Wyckoff (born 1828 in NJ) and Mary Jane's mother Jane Wyckoff (born 1800 in NJ). They were all either described as "Colored," "Mulatto" or "Black" on most genealogical records.

When I saw photos of my great-grandmother Mary Louise and two her siblings Jenny and Clara (all pictured above; Clara Harvey was named after her aunt Clara), I knew there must be something to the family rumors. Although phenotypes are an unreliable indicator of ethnicity the faces of my ancestresses looked to have Native American and/or Asian influences.

From a historic standpoint the colonial New Jersey hinterland had an African presence (enslaved, indentured, freed and escaped) since the 1600's, and they intermixed with indigenous and European populations. Many came directly from Africa (Guinea Coast and Madagascar) while others arrived after first being seasoned in the Caribbean (Barbados).  

When cousin Clara tested at 23andMe in 2014, not only did she have a Native American maternal haplogroup, her results supported family rumors and New Jersey's history:

As you can see cousin Clara Harvey's total East Asian & Native American is 7.9%. However only 1.3% to 1.5% is Native American. The 6.1% Southeast Asian
the highest amount I've seen in an African-American profileis separate and proven Madagascan ancestry.

When I inquired about our specific Native American connection, cousin Clara and other relatives told me that my 2nd-great-grandmother Sophia Shipley was a Mohawkan Iroquoian-speaking indigenous people of North Americaand what's more there was a photo of her wearing buckskin shoes and holding a peace pipe. 

Although New Jersey was historically inhabited by Algonquin-speaking Lenni Lenape tribes, it would be reasonable to assume we could have Mohawk ancestry because they had long contact with the Lenni Lenape of New Jersey and the Mahican people. 

But I'm still am not satisfied with Mohawk. This is because mtDNA haplogroup B2, one of the founder haplogroups of the Americas, is found most commonly today in southern US (ie North Carolina, Louisiana, Texas); Mexico, and Central & South America. 

B2 has much lower frequency in Northeast USA (see Roberta Estes here). More recently B2 was discovered in an Alaskan ancient genome  (see LiveScience) and its basal sub-clade B2c has been found in Canada and Pennsylvania (see Estes). 

This suggests if our proposed mtDNA haplogroup B2-T8736C is derived from a Mohawk  or Lenni Lenape  ancestress, then it would represent a very ancient Native American B2 lineage. 

Cousin Clara's autosomal DNA results from such 3rd-party websites GEDmatch and DNA.Land below support her Native American ancestry clustering closely to South Amerindian/Amazonian reference populations: 

Since B2 sub-clades are found further south in the Americas, this opened up the possibility that our Native American foremother could have carried B2-T8736C from a southern region where B2 is much more common:
  • Black Caribs were African slaves who mixed with indigenous peoples of places like Barbados, Dominica, St.Vincent and the Grenadines, Trinidad, etc. Since many enslaved Africans were first seasoned in the Caribbean, it is possible for them to have first mixed with Island Caribs before disembarking in New York and New Jersey where one became our ancestress. Island Caribs originally descend from South America where B2 is widespread.
King Genome's New Theory: How 'bout them "Spanish Indians"? 

Based on Cousin Clara's B2-T8736C GenBank matches to a Peruvian [JX669283, Tito, 09-OCT-2013], another unidentified match, and the Kayapo peoples of Brazil [EU095217, Fagundes, 07-MAR-2008], where T8736C was found in a B2i1 sequence, as well as cousin Clara's Native American admixture clustering to Amazonia, it's reasonable to assume our indigenous ancestress may have been from a more southern source.

As it turns out there is another southern Americas sourced possibility where our family's B2-T8736C could've derived, and it has to do with New York and New Jersey's unique history with slavery, black market slave traders, and the obscure fact of European colonial powers enslaving Native Americans.

Some years ago I learned about Veracruz, Mexico, being a slave trading post where Africans were routinely taken to slave markets in the southern US. My African Winkey ancestors from Virginia had arrived there by way of Veracruz. Could some of the enslaved indigenous peoples from Veracruz have been shipped to New Jersey? 

In the late 1600's slavery in New York and New Jersey waned after the English Crown took over from Dutch and the demand for slave labor in the South grew exponentially. As a result New York and New Jersey did not have fully developed slave laws until the first decade of the 18th century. Yet there still was a demand for slaves, especially after Barbadian planters migrated to the area for new economic prospects: 
"Because the [English] Royal African Company, formed as a monopoly in 1664 to supply slaves to the English Colonies, largely ignored New York and New Jersey, colonists obtained most slaves from local adventurers and pirates plying the Madagascar Coast, in single consignments from the West Indies, and directly from Africa." [Hodges, Graham R. "Root & Branch: African Americans in New York and East Jersey, 1613-1863." University of North Carolina Press, 1999.]
New York and New Jersey colonists turned to "local adventurers" and pirates whose slaves were obtained through "illegal" means and who may have come from places other than West Africa. As such colonists enslaved local indigenous peoples and bought those kidnapped from Veracruz and Campeche, Mexico; they were known as Spanish Indians and they practiced Catholicism due to Spain's colonial influence in their homeland. Many runaway ads showed that indigenous people were indeed a part of the region's eclectic slave society:
Eventually a diplomatic dilemma about the legal status of these captive Spanish Indians  forced the English Crown to base slave identity on "race":
"On December 8, 1679, Governor Edmund Andros ruled that enslaving local American Indians was illegal but holding blacks in bondage was permissible....Yet in New York and New Jersey, race was an issue complicated by ethnicity and religion. Despite the governor’s edict, local masters continued to enslave Indians. Andros’s edict also failed to solve the vexing diplomatic problem of kidnapped free Spanish Indians, a dilemma with international implications. Privateers’ sales of Spanish Indians as slaves in New York contradicted English colonial policy....The legal dilemma of Spanish nationals resurfaced in 1687 when the New York Colonial Council ordered that “Christian Indians and children of Christian Parents from Campeche and Vera Cruz” be liberated." [ibid, Hodges]

One of the potential black market slave traders carried a surname common my family, Van Horn. Nicholas van Hoorn (b. circa 1635 in Vlissingen – buried 24 June 1683, in Isla Mujeres) was a Dutch merchant sailor, privateer and pirate. Van Hoorn was engaged in the Dutch merchant service from about 1655 until 1659, often dealing the New York and New Jersey slave market potentially with colonists and relatives with the Van Hoorn surname. 
  • Interestingly Cousin Clara Harvey's namesake maternal aunt married an African-American Van Horn, and we appear have collateral genetic European connections to them too. The town of White House, Hunterdon, New Jersey, where my ancestors lived, was founded by Abraham Van Horne.
After accumulating wealth Van Hoorn bought his own vessel, and afterward he and his bandits became a terror to the commerce of the Dutch Republic and the Spanish Empire.  Van Hoorn was also determined to gain the French part of the Hispaniola Island (Haiti). Eventually Van Hoorn took a commission from Hispaniola's French governor to attack Vera Cruz, a 1683 raid against its port. 

Thus Van Hoorn is likely one of  the kidnappers of the Spanish Indians of Veracruz, transporting them to colonial New York and New Jersey where they were sold off—to potentially become one of my ancestors.

I suspect after the Spanish Indians were freed some of them remained in the New York and New Jersey area mixing with African enslaved, runaway and free people of color communities, as well as local indigenous peoples where they may have been adopted by and taken on the identity of a tribe like the Mohawk.  

Genetically, indigenous people from the Veracruz and Campeche area are of  Mayan extract and today they cluster with both Mesoamerica—often used as its reference sample—and South Amerindians. More importantly one of these Spanish Indians could have been our ancestress bearing the unique MtDNA motif B2-T8736C

OUTRO

I've invested a lot of time into learning more about my maternal grandfather's Native American origins since I discovered his first cousin Clara Harvey carried Native American mtDNA haplogroup B2

After publication of my Guide to Building Your Family's Haplotree I began a quest to find out more information so we published our family's B2 sequence to GenBank. During the course of this process I learned that our family's mtDNA B2 haplogroup has a new name, B2-T8736C

At present my challenge is to get our family's B2 motif officially recognized by included it on Phylotree.org. Since cousin Clara son's GenBank submission marks the 3rd distinct sequence of its kind, and the mutation T8736C occurs about 20 times on GenBank, making it a good subgroup definer for B2, the submission meets the requirements for a new node on Phylotree.org.

I've pontificated potential sources of our Native American matrilineal line—from Mohawks to Spanish Indians—but a dearth in Native American testes generally makes this task insurmountable. This is why it remains crucial for relatives from my maternal grandfather's family to participate in DNA testing.

So far Mannis van Oven of Phylotree.org has not returned my inquiries, and I'm sure he and the other administrators are busy. Yet I will keep trying. Our family simply desires to give our 95-year-old family matriarch Clara Harvey her flowers while she can still smell them.

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1 comment:

  1. What a fabulous,extensive,scholarly,important, and impressively significant work not only in the field of human DNA, but also in an area previously often ignored human history and loving gift not only to your mother, but also to human history. Kudos!

    ReplyDelete