Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

[PNGarrison]

http://www.pnas.org/content/early/20...84112.abstract
open access
Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean
Hannes Schroedera,b,1,2, María C. Ávila-Arcosa,c,1, Anna-Sapfo Malaspinasa, G. David Poznikd, Marcela Sandoval-Velascoa, Meredith L. Carpenterc,3, José Víctor Moreno-Mayara, Martin Sikoraa,c, Philip L. F. Johnsone, Morten Erik Allentofta, José Alfredo Samaniegoa, Jay B. Haviserf, Michael W. Deeg, Thomas W. Stafford, Jr.h, Antonio Salasi, Ludovic Orlandoa, Eske Willersleva, Carlos D. Bustamantec, and M. Thomas P. Gilberta,2



Abstract

The transatlantic slave trade resulted in the forced movement of over 12 million Africans to the Americas. Although many coastal shipping points are known, they do not necessarily reflect the slaves’ actual ethnic or geographic origins. We obtained genome-wide data from 17th-century remains of three enslaved individuals who died on the Caribbean island of Saint Martin and use them to identify their genetic origins in Africa, with far greater precision than previously thought possible. The study demonstrates that genomic data can be used to trace the genetic ancestry of long-dead individuals, a finding that has important implications for archeology, especially in cases where historical information is missing.

Abstract
Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

[xyyman]

ancestor of R1b-M269

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Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean - Hannes Schroedera,b,1,2, María C – FEB2015


of three enslaved Africans whose remains were recovered in the Zoutsteeg area of Philipsburg on the Caribbean island of Saint Martin (Materials and Methods). Previous reports (6) suggest that the “Zoutsteeg Three,” as they became known locally, were likely born in Africa as opposed to the New World. But they did not reveal where in Africa they originated. Bayesian analysis of individual calibrated radiocarbon dates suggests that the burials date between A.D. 1660 and


Divergence time of the STM1 Y-chromosome lineage

Upon merging STM1 data with related modern Y-chromosome sequences, we estimated a splittime of roughly 8500 years between the STM1 lineage and the CLOSEST FULLY SEQUENCED Y CHROMOSOMES currently in the literature, a cluster of eleven R1b1c3-V35 sequences reported in a sample of 1204 Sardinians (42). To do so, we estimated the length of time between the STM1- lineage divergence and the emergence of R1b, and then we compared this interval to the age of R1b (Fig. S17).


Francalacci et al. (42) report a cluster of 29 R1b1c-V88 lineages from Sardinia. Though the terminal branch lengths from this study must be viewed with caution due the low-pass sequencing approach, the internal branches had high effective coverage due to the superposition of multiple sequences. …….). Consequently, approximately 103.1 (30 + 51 + 22.1) SNPs accumulated between the emergence of R1b and the time when the STM1 lineage diverged from R1b1c3-V35. Because this study was based on 8.97 Mb of sequence, whereas that of Underhill et al. (37) analyzed 10.35 Mb, we must scale the mutation period by a factor of 1.154. Thus, we estimate that this interval corresponds to 14.5 ky (103.1 SNPs ・ 1.154 ・ 122 years/SNP). Consequently, we conclude that it was approximately 8.5 kya that the Y-chromosome lineage carried by STM1 diverged from that carried by the 11 Sardinians.


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[xyyman]

ancestral R1b-M269- Sardinia?

Interestingly they did not state the Uniparental male marker for the second male.

The other interesting thing is, the STM1 cluster autosomally with Bantus but carry a “ Eurasian” HG lineage. STM2 and STM3 cluster autosomally with non-Bantu even “Eurasian”/Sudanic but the male line was not disclosed.



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Downstream of R1b1c-V88, there are TWO main subgroups in (42). A cluster of 18 individuals represents a lineage we refer to as “R1b1c-V88*,” and the remaining 11 represent R1b1c3-V35, which ISOGG currently labels “R1b1c2.” We observed 7 ancestral alleles amongst 7 R1b1c- V88* sites for which STM1 had data, and we observed 5 derived and 9 ancestral alleles on the R1b1c3-V35 branch. Upon diverging 5/14 of the way down this branch, the STM1 lineage parts company with fully-sequenced Y chromosomes of the current literature. No sequencing data were available for the V35 mutation, but this SNP most likely arose subsequent to the split, as Cruciani et al. (75) observed it just twice in a survey of 5326 Y chromosomes that included more than 1800 individuals from 69 African populations, and both carriers were Italian. This leaves two other known subgroups of R1b1c-V88, those defined by V69 and those that carry the two-base insertion, M18. Unfortunately, no sequencing data were available at either site. Because M18 was only observed in a single Corsican and V69 was present in about one third of the Central African R-V88 lineages, we suggest that STM1 most likely claims affinity to either R-V69 or to another, as yet uncharacterized, branch of the R-V88 subtree

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XYYMAN Comments: So they are not sure where STM1 fits on the R-V88 tree. “European” side or what. Nevertheless, looking at Italian/Sardinia genetic profile all leads to “continuous southerners migration”. Male hg-A is found in Sardinia, isolated Italian villager carry old clades such E1b1 and A. A clear picture is emerging

[xyyman]

So what does the data from the study show? Questions to ask.

1. what were the lineage of the other two male “slaves”
2. were there Sardinians/Italians “slaves” in the caribbean?
3. two of the “slaves’ do NOT cluster autosomally with West Africans
4. The One slave that clustered autosomally with west Africans suprisingly carry R1b.
5. So where does that leave us?

[hazel_ion]

So what does the data from the study show? Questions to ask.

1. what were the lineage of the other two male “slaves”
2. were there Sardinians/Italians “slaves” in the caribbean?
3. two of the “slaves’ do NOT cluster autosomally with West Africans
4. The One slave that clustered autosomally with west Africans suprisingly carry R1b.
5. So where does that leave us?

I have mtDNA L3e2a and that does not show up in this study or any other paper I have read. I have been told to look for "slaves" in my tree and nothing. All females are accounted for and birth records found back to late 1500's England. No one can tell me how I ended up with this or even when. I have read the last mutation dates to about 10,000-12,000 years ago. And that L3 is 70,000 "out of Africa" L3e about 35,000 years ago.

So I have come to the conclusion "no one" knows much about this line and I have a mystery on my hands.

[hazel_ion]

Also I know the mt has shown up in Sicily

[xyyman]

siblings

I assume based on your perplexity on your L3e2a that you are of traceable Italian decent thus your confusion?


Keep in mind that “slaves” is always used to “explain” away the presence of certain lineage IN Europe. You are most likely not of slave decent. What many people don’t get is that there was no border police that patrol between Europe and Africa. Only about 7 miles of water seperates parts of Africa and Europe. In fact Europe land mass can be seen from Africa and Africa land mass can be seen from Europe. There are a few studies, that confirms the presence of mtDNA L1b and other lineage unique to Europe. There are also a few aDNA studies confirming the presence of mtDNA L in Europe during the pre-historical period. Possibly the Helocene Period. What Guido Barbujani and Rosenberg calls genetic drift and purification , Regionalist like to call admixture. My guess is you are NOT admixed but pure Italian. As the study above stated – there is an African version of R-V88 and a European version of R-V88(Sardinia)…separated by about 8000years.

If you are interested I can quote a few recent studies. Eg read the PhD Thesis of Eva Fernandez freely available on the web.

There is also speculation that mtDNA hg-H has also an Helocene origin outside of Europe and I am not talking about the Levant. Achilli and Torroni has been debunked. Works by Kefi et al(2014) confirms that. It is not played up in pop media because it does not conform to popular perceptions and belief. Peoples from the south have always been migrating north.

L3(L3e2a) is a sibling of L3(m/n).

[hazel_ion]

I assume based on your perplexity on your L3e2a that you are of traceable Italian decent thus your confusion?


Keep in mind that “slaves” is always used to “explain” away the presence of certain lineage IN Europe. You are most likely not of slave decent. What many people don’t get is that there was no border police that patrol between Europe and Africa. Only about 7 miles of water seperates parts of Africa and Europe. In fact Europe land mass can be seen from Africa and Africa land mass can be seen from Europe. There are a few studies, that confirms the presence of mtDNA L1b and other lineage unique to Europe. There are also a few aDNA studies confirming the presence of mtDNA L in Europe during the pre-historical period. Possibly the Helocene Period. What Guido Barbujani and Rosenberg calls genetic drift and purification , Regionalist like to call admixture. My guess is you are NOT admixed but pure Italian. As the study above stated – there is an African version of R-V88 and a European version of R-V88(Sardinia)…separated by about 8000years.

If you are interested I can quote a few recent studies. Eg read the PhD Thesis of Eva Fernandez freely available on the web.

There is also speculation that mtDNA hg-H has also an Helocene origin outside of Europe and I am not talking about the Levant. Achilli and Torroni has been debunked. Works by Kefi et al(2014) confirms that. It is not played up in pop media because it does not conform to popular perceptions and belief. Peoples from the south have always been migrating north.

L3(L3e2a) is a sibling of L3(m/n).

I wish I could say I was pure Italian and explain it that way. My female line traces to England. My admix shows about 25/30% southwestern European. But I just figured that came from my Sicilian Grandfather. My guess is whoever this female was she left Africa of her own free will and made her way north mixing in with the male Europeans and over time my African admix was lost. How brave of her and I am proud to carry her with me.

Thank you for this info and I will look at it as I want to know all I can. The fast answer of a "slave" child just does not fit into anything I have. And I do not think a slave child would have been raised by the man that fathered it with out there being backlash in the 1600's. All the paperwork I have shows "white" as color of people. No records of even owning slaves. No one in the southern states where I am learning many slaves where.

[xyyman]

no different

To be clear. There may be a misconception or misunderstandings. I don’t think she “left Africa” per se. If is a pre-historical European lineage then it s possbly a MIGRATORY PROCESS how the gene got into Europe. It is not like she decided to take an European Vacation”. (wink) The woman who left was NOT the same person who arrived. We have to stop projecting our prejudices and beliefs into the past. The farmers who left were not the farmers who arrived in Scandanavia. It takes THOUSANDS OF YEARS for the lineage to reach a region and become dominant. Undoubtedly it is a demographic movement but it does NOT occur ovenight. Your L3e2a ancestor was probably wasn’t aware she was “African”. Just as you were unaware you carried L3e2a. She “fitted in “ with others like her on that first leg of the trek to Europe and you are the latest generation. She was probably part of larger group of females carrying H1 and H3 that left Africa (per Kefi et al). She looked no different to others around her.

Quote[whoever this female was she left Africa of her own free will and made her way north mixing in with the male Europeans and over time my African admix was lost }

[xyyman]

surprises

BTW – on Sicilian grandfather thing – Men don’t transmit female lineage to their daughters. You got the L3e2a from your mother and her line. All her sisters/your aunts/grandmothers (blood) will also carry L3e2a. That is why geneaology can be dangerous. Things can be revealed that you refer to keep buried. Eg we know now the Tudors are NOT related to Richard IIII.

[hazel_ion]

BTW – on Sicilian grandfather thing – Men don’t transmit female lineage to their daughters. You got the L3e2a from your mother and her line. All her sisters/your aunts/grandmothers (blood) will also carry L3e2a. That is why geneaology can be dangerous. Things can be revealed that you refer to keep buried. Eg we know now the Tudors are NOT related to Richard IIII.

I know my mtDNA comes only from the female line

I was commenting only on my admix.

And I also understand this took a hell of a long time to happen I am happy to see someone that does not just say " oh it has to be a slave"

[hazel_ion]

To be clear. There may be a misconception or misunderstandings. I don’t think she “left Africa” per se. If is a pre-historical European lineage then it s possbly a MIGRATORY PROCESS how the gene got into Europe. It is not like she decided to take an European Vacation”. (wink) The woman who left was NOT the same person who arrived. We have to stop projecting our prejudices and beliefs into the past. The farmers who left were not the farmers who arrived in Scandanavia. It takes THOUSANDS OF YEARS for the lineage to reach a region and become dominant. Undoubtedly it is a demographic movement but it does NOT occur ovenight. Your L3e2a ancestor was probably wasn’t aware she was “African”. Just as you were unaware you carried L3e2a. She “fitted in “ with others like her on that first leg of the trek to Europe and you are the latest generation. She was probably part of larger group of females carrying H1 and H3 that left Africa (per Kefi et al). She looked no different to others around her.

Quote[whoever this female was she left Africa of her own free will and made her way north mixing in with the male Europeans and over time my African admix was lost }

I agree 100%

[AFH]

BTW – on Sicilian grandfather thing – Men don’t transmit female lineage to their daughters. You got the L3e2a from your mother and her line. All her sisters/your aunts/grandmothers (blood) will also carry L3e2a. That is why geneaology can be dangerous. Things can be revealed that you refer to keep buried. Eg we know now the Tudors are NOT related to Richard IIII.

Do you have a link with the data supporting that conclusion that you can post?

[xyyman]

Richard III

[/B]

Do you have a link with the data supporting that conclusion that you can post?

http://www.nature.com/ncomms/2014/14...ry-information

aDNA is going to make liars of “historians”.

One the things that stands out from this paper is the “hesitation” of the researchers to disclose the MTDNA lineage of Richard III. You need to dig beep in the Supplemental and it is buried away in a parenthesis in a simple sentence. Surprisingly Richards III mother is NOT hg-H the typical modern European lineage but J1 found primarily….where? In fact his male and female is BOTH found where?

So what really happened in Europe during the Middle Ages.

eg

Several pieces of information were disclosed and others strangely NOT included. Are they being deceptive?

1. SLC24A5 and the related SNP was NOT disclosed. They listed SLC24A4. Why?
2. SLC45A2 was disclosed but the related SNP seems different to what is typically used as an indicator.
3. Ditto for TYR/2
4. He was documented as having round face and large teeth and very thin
5. Looks like he did have light eyes, may be blue La Brana
6. No LCT was disclosed

What am I blabbering about?.....Richards was NOT your typical modern European. He seems reminiscent of the Otzi Alps Iceman


======================
QUOTES from the paper—

Identification of the remains of King Richard III -Turi E. King1,2 (Dec2014)


It is also worth noting that we chose to be further conservative and did not include the observation of no matches found in 26,127 European mitochondrial control region haplotypes (LR=6847) (http://empop.org)80. Female mobility among the European nobility is likely to have been much higher than for the general population, because of marriage practices relating to political alliance formation. Such practices would provide some justification for using the European mtDNA database, and so for considering the haplotype found in Skeleton 1 and Michael Ibsen to be extremely rare.



We find a perfect mitochondrial DNA match between the sequence obtained from the remains and one living relative, and a single-base substitution when compared with a second relative. Y-chromosome haplotypes from male-line relatives and the remains do not match, which could be attributed to a false paternity event occurring in any of the intervening generations.


Quote:
In CONTRAST to the Y-haplotypes of the PUTATIVE MODERN RELATIVES, Skeleton 1 belongs to haplogroup G-P287, with a corresponding Y-STR haplotype. Thus, the putative MODERN patrilinear relatives of Richard III are NOT genetically related to Skeleton 1 through the male line over the time period considered. However, this is not surprising, given an estimated average false


QUOTE:
false-paternity between Edward III (1312–1377) and John would mean that John’s son, Henry IV (1367–1413), and Henry’s direct descendants (Henry V and Henry VI) would have had no legitimate claim to the crown.This would also hold true, indirectly, for the entire Tudor dynasty (Henry VII, Henry VIII, Edward VI, Mary I and Elizabeth I) since their claim to the crown also rested, in part, on their descent from John of Gaunt. The claim of the Tudor dynasty would also be brought into question if the false paternity occurred between John of Gaunt and his son, John Beaufort, Earl of Somerset. If the false paternity occurred in either of the three generations between Edward III and Richard, Duke of York, the father of Edward IV and Richard III, then neither of their claims to the crown would have been legitimate.

[xyyman]

Of course no one is making a big deal of it. I saw only one snipet on the news. Plus a lot of " how dare you" hate mail.

People like the way things are. The truth doesn't matter.

I can backup EVERYTHING I post on.