Author Topic: Independent-made R2a phylogenetic tree  (Read 3731 times)

DMXX

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Independent-made R2a phylogenetic tree
« on: June 19, 2011, 08:16:12 PM »
I took the initiative of reconstructing the Y-DNA R2a phylogenetic tree that was showcased here a couple of years ago. It largely agrees with UG's current cluster arrangement, which shows I worked in the right direction. With over 60 members testing upto 67 markers, the results are illuminating;

[attachment=5394:r2a reworked.jpg]

Phylogenetic tree made using McGee's Y-Utility, Phylip and FigTree. Again, I have to thank Vineviz on DNA-Forums for kindly laying down the roots for tree-building (pardon the pun) on this forum.

Several comments;

The Indian R2a's, who were largely absent in the previous run, now seem to be distributed across the entire tree on different branches. The preconception of Indian R2a being distinct from West Eurasian R2a was heavily supported based on the data by some (such as myself) and presumed by others.
That clearly isn't the case based on this chart. I'll have a proper look into the haplotypes later today, but this either suggests Indian R2a diversity is so great that they're quite literally omnipresent, or a hefty portion of Indian R2a arrived through multiple sources.

Relating the discussion to India, several of the clusters seem to have a combination of Subcontinental and European/Near-Eastern constituents. For instance;

o India, Tunisia, Iran-Caucasus (Aqua)

o Slovakia, India (Pink)

o India, Syria (Beige)

o India, Saudi Arabia, Scotland (Purple)

Strangely, the greatest "explosion" in R2a differentiation and growth seems to have occurred ~2750ybp. By coincidence, all of these Indian+NE/Euro clusters seem to fall after that point in time. Whether we're witnessing a real physical change in R2a's structure or an artificial construct caused by other reasons (sampling bias, program use) is yet to be seen.

To conflate the mystery of R2a further, the oldest lineages found to date seem to be from the British Isles of all places! Again, I'll have to review the data to confirm whether they actually are that divergent.

As ever, I welcome comments and appreciate the input of other users.
« Last Edit: June 20, 2011, 05:14:38 AM by DMXX »

Rj

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Re: Independent-made R2a phylogenetic tree
« Reply #1 on: June 20, 2011, 12:43:47 AM »
Hi DMXX,

The attachment isn't linked.

Quote
Strangely, the greatest "explosion" in R2a differentiation and growth seems to have occurred ~2750ybp.

Does it coincide with a similar differentiation with R1a within the same time period? Would be interesting if there's a connection between migrations and this differentiation.


Quote
To conflate the mystery of R2a further, the oldest lineages found to date seem to be from the British Isles of all places!

I'm assuming you're talking about the Simpsons? Isn't there a South Asian connection there? Even if that's not the case one can safely say that R2a doesn't have a presence in the British Isles and this is just an anomaly right?
« Last Edit: June 20, 2011, 12:47:47 AM by Rj »
Y-DNA Haplogroup: R2
YSearch: ZYERN
Indian(West Bengal - Brahmin)

DMXX

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Re: Independent-made R2a phylogenetic tree
« Reply #2 on: June 20, 2011, 05:23:03 AM »
Hi DMXX,

The attachment isn't linked.

Does it coincide with a similar differentiation with R1a within the same time period? Would be interesting if there's a connection between migrations and this differentiation.

I'm assuming you're talking about the Simpsons? Isn't there a South Asian connection there? Even if that's not the case one can safely say that R2a doesn't have a presence in the British Isles and this is just an anomaly right?

Thanks for pointing that out Rj, it is now there.

I don't know about the correlation with R1a1a, but Jean M on DNA-Forums has suggested the "explosion" coincides with the Copper Age back-migration of Scythians from Asia into Europe/European steppelands.

Also, I "blinded" the participant names to ensure there wasn't any sort of bias. That's why only ID's are shown on the original chart. I manually looked up the ID locations after the tree was formed.

I don't know the story regarding the Simpsons, but the tree suggests they're a very old branch from the main one. If you examine the chart you'll also see that Indian R2a's form "the other side", though this might simply be the tree splitting ends of what may constitute a similar branch. Again, I'll have to check out the haplotypes later today.

I think this tree is largely correct as it largely agrees with the project's own clusters. The only major difference comes with the South Asian R2a's, who are distributed across the whole thing. I can only presume UG either hasn't had the time to find an appropriate place for them (real-life commitments perhaps) or, returning to a criticism I had of the project's structure, clusters are artificial as they are created based on known ancestries.

By blinding the ancestries, we've come up with a very different R2a tree.

[Edit]: Just looked up the Simpson ID's. As you can see, they're quite divergent from the others, but seem to be intertwined with some similarly divergent Indian R2a's. That certainly does indicate a South Asian link, one that apparently exceeds 3000 years.
« Last Edit: June 20, 2011, 05:51:06 AM by DMXX »

Rj

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Re: Independent-made R2a phylogenetic tree
« Reply #3 on: June 20, 2011, 08:23:57 AM »
Thanks for the reply. I think you're approaching this in the right manner by looking at the raw data instead of going by known ancestry. I haven't looked at your tree in detail but it'll be interesting to go deeper and check out individual kit numbers and see whom they belong to and where they're from.

I have a question regarding DYS19. For me  it's 13 and only 2 others have this value on FTDNA. All three of us happen to ancestrally be from the same area (West Bengal). For everyone else it is 14, 15 or 16.Any thoughts on this?
Y-DNA Haplogroup: R2
YSearch: ZYERN
Indian(West Bengal - Brahmin)

DMXX

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Re: Independent-made R2a phylogenetic tree
« Reply #4 on: June 20, 2011, 09:12:28 AM »
Thanks for the reply. I think you're approaching this in the right manner by looking at the raw data instead of going by known ancestry. I haven't looked at your tree in detail but it'll be interesting to go deeper and check out individual kit numbers and see whom they belong to and where they're from.

I have a question regarding DYS19. For me  it's 13 and only 2 others have this value on FTDNA. All three of us happen to ancestrally be from the same area (West Bengal). For everyone else it is 14, 15 or 16.Any thoughts on this?

The tree may be revised in the next day or so after I consult with genetic genealogists who have used this software before, but I'm fairly confident we're looking at the actual structure of our lineage.

DYS19/394 is a fairly fast-mutating marker making it fairly applicable to genealogical tracing. That you and the other West Bengali R2a's share this mutation is very indicative of a common ancestor. I'll open up a new thread investigating this for you.

Rj

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Re: Independent-made R2a phylogenetic tree
« Reply #5 on: June 20, 2011, 12:07:46 PM »
The tree may be revised in the next day or so after I consult with genetic genealogists who have used this software before, but I'm fairly confident we're looking at the actual structure of our lineage.

DYS19/394 is a fairly fast-mutating marker making it fairly applicable to genealogical tracing. That you and the other West Bengali R2a's share this mutation is very indicative of a common ancestor. I'll open up a new thread investigating this for you.

Thanks for your effort, much appreciated  :) One of those guys is a 12 marker match so I was pretty certain that DYS19 had something to do with a recent(relatively) ancestor. It's just that everyone else shares 14,15 or 16 but are spread out all over the place without showing any particular 'clustering'. I found that intriguing.

Your phylogenetic tree seems to mirror results from ysearch visually. Good stuff..
Y-DNA Haplogroup: R2
YSearch: ZYERN
Indian(West Bengal - Brahmin)

Rj

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Re: Independent-made R2a phylogenetic tree
« Reply #6 on: June 20, 2011, 12:56:48 PM »
BTW, one of the samples on the oldest branch of the tree happens to be from from MP, India. If you read about the history of R2's from the British Isles you'll notice that they were in India during the British raj. Just an observation I made a long time back but I don't want to speculate too much about it. If you plot geographical locations over where clusters branch off you notice a pattern here. MP>South India>Bengal>Iran/Punjab>Armenia/Greece>East Europe>etc... not exactly in that order but more or less so. Of course there aren't that many samples here and that gap between MP and the 'explosion' is a bit odd. Just trying to find some pattern here. Maybe it's all in my head!  :P
« Last Edit: June 20, 2011, 01:09:40 PM by Rj »
Y-DNA Haplogroup: R2
YSearch: ZYERN
Indian(West Bengal - Brahmin)

PCSensei

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Re: Independent-made R2a phylogenetic tree
« Reply #7 on: June 29, 2011, 01:37:01 PM »
I'm assuming you're talking about the Simpsons? Isn't there a South Asian connection there? Even if that's not the case one can safely say that R2a doesn't have a presence in the British Isles and this is just an anomaly right?
I don't know the story regarding the Simpsons, but the tree suggests they're a very old branch from the main one. If you examine the chart you'll also see that Indian R2a's form "the other side", though this might simply be the tree splitting ends of what may constitute a similar branch. Again, I'll have to check out the haplotypes later today.
I think this tree is largely correct as it largely agrees with the project's own clusters. The only major difference comes with the South Asian R2a's, who are distributed across the whole thing. I can only presume UG either hasn't had the time to find an appropriate place for them (real-life commitments perhaps) or, returning to a criticism I had of the project's structure, clusters are artificial as they are created based on known ancestries.
By blinding the ancestries, we've come up with a very different R2a tree.
[Edit]: Just looked up the Simpson ID's. As you can see, they're quite divergent from the others, but seem to be intertwined with some similarly divergent Indian R2a's. That certainly does indicate a South Asian link, one that apparently exceeds 3000 years.

Don't get too hung up on the Simpson Indian connection.  13 of the group are in the USA and 1 in the UK.  12 have UK roots back to c1600.  The two who show Mhow India as oldest ancestor are a father and son, living in the US, and the father was adopted.  Our current thinking is that he descends from a liaison between an Indian woman and a (Simpson) British soldier in the late 1800's-early 1900's - Mhow was the main base for the (British) Indian Army.  If we are able to trace the actual ancestor it means that these two would also show UK roots.
Y-DNA: R2, Cluster A, ancestry UK both sides pre 1800 (possibly to 1600)
mt-DNA: H* (meaning no-one has yet identified the sub-clade!)
"Genealogy - the only area where a step backwards is progress!"

Rj

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Re: Independent-made R2a phylogenetic tree
« Reply #8 on: June 29, 2011, 04:46:09 PM »
Our current thinking is that he descends from a liaison between an Indian woman and a (Simpson) British soldier in the late 1800's-early 1900's - Mhow was the main base for the (British) Indian Army.

And perhaps the other way around. Indian man and a (Simpson) British woman? That makes more sense. R2 is not from the British Isles for sure. Simpson R2 clusters with Indian R2, am I correct? Or is there a gypsy ancestor in the Simpson family? East European R2(mostly Jewish and Gypsy) is distinct so I see a South Asian connection here. Y-chromosome. But yes, I would not get too hung up about it. We don't know enough and it is clearly an anomaly.
« Last Edit: June 29, 2011, 05:07:47 PM by Rj »
Y-DNA Haplogroup: R2
YSearch: ZYERN
Indian(West Bengal - Brahmin)

Birko19

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Re: Independent-made R2a phylogenetic tree
« Reply #9 on: June 29, 2011, 05:39:34 PM »
Our current thinking is that he descends from a liaison between an Indian woman and a (Simpson) British soldier in the late 1800's-early 1900's - Mhow was the main base for the (British) Indian Army.

And perhaps the other way around. Indian man and a (Simpson) British woman? That makes more sense. R2 is not from the British Isles for sure. Simpson R2 clusters with Indian R2, am I correct? Or is there a gypsy ancestor in the Simpson family? East European R2(mostly Jewish and Gypsy) is distinct so I see a South Asian connection here. Y-chromosome. But yes, I would not get too hung up about it. We don't know enough and it is clearly an anomaly.

I too suspected that the Simpsons could have a Roma connection, but after looking at the Simpson FTDNA project I don't think that was the case, they clearly lack haplogroup H1a among them, if there was any Gypsy ancestry you would at least see some H1a, that along with the lack of oral tradition makes the Gypsy connection unlikely:

http://www.familytreedna.com/public/simpson/default.aspx?section=yresults

As far as the Simpson sample from India, based on the evidence it seems very clear that the theory PCSensei mentioned makes more sense, the reason for that is because if we look at the mtDNA of the Simpson project, they lack South Asian mtDNA with the exception of the two samples PCSensei was talking about, one of them seems to have an Indian mother that carried haplogroup U7 while the other one has unknown parents, but mtDNA M seems to be a clear indication of Indian maternal ancestry, now I'm not trying to dismiss a South Asian origin here, but R2 within the Simpsons seems to be older than what these two samples indicate, meaning if the Stephens are indeed Simpsons, based on the data available it makes more sense to believe that this is a union of a British Simpson male with an Indian female rather than the other way around.

Also one more question, you said East European R2 (Jewish and Gypsy) is distinct, I've seen the Jewish samples, do you have data on Gypsy R2 to call it Gypsy R2?
« Last Edit: June 29, 2011, 05:41:49 PM by Birko19 »

Rj

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Re: Independent-made R2a phylogenetic tree
« Reply #10 on: June 30, 2011, 02:09:09 AM »
Also one more question, you said East European R2 (Jewish and Gypsy) is distinct, I've seen the Jewish samples, do you have data on Gypsy R2 to call it Gypsy R2?

What I meant by 'Gypsy R2' are the Sinte samples in Spencer Wells' paper.

R. Spencer Wells et al., “The Eurasian Heartland: A continental perspective on Y-chromosome diversity,” Proceedings of the National Academy of Sciences of the United States of America 98, no. 18 (2001): 10244-10249.

Quote
The Sinte Romani, or Gypsies, group with the Hunza and Bartangi (from the Pamir region of Central Asia) populations in our tree. This finding is primarily due to the M124 haplotype, which is present at high frequency in all three populations. M124 is not found in Eastern Europe (17), where the Sinte Romani lived before being resettled in Central Asia in the 1940s. It is, however, common in Central and Southern Asia. Thus, the Y-chromosome results provide clear genetic evidence of a link between the Gypsies and their Asian kin.

But yes, I have not seen their haplotype data.
Y-DNA Haplogroup: R2
YSearch: ZYERN
Indian(West Bengal - Brahmin)

Birko19

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Re: Independent-made R2a phylogenetic tree
« Reply #11 on: June 30, 2011, 12:18:03 PM »
Also one more question, you said East European R2 (Jewish and Gypsy) is distinct, I've seen the Jewish samples, do you have data on Gypsy R2 to call it Gypsy R2?

What I meant by 'Gypsy R2' are the Sinte samples in Spencer Wells' paper.

R. Spencer Wells et al., “The Eurasian Heartland: A continental perspective on Y-chromosome diversity,” Proceedings of the National Academy of Sciences of the United States of America 98, no. 18 (2001): 10244-10249.

Quote
The Sinte Romani, or Gypsies, group with the Hunza and Bartangi (from the Pamir region of Central Asia) populations in our tree. This finding is primarily due to the M124 haplotype, which is present at high frequency in all three populations. M124 is not found in Eastern Europe (17), where the Sinte Romani lived before being resettled in Central Asia in the 1940s. It is, however, common in Central and Southern Asia. Thus, the Y-chromosome results provide clear genetic evidence of a link between the Gypsies and their Asian kin.

But yes, I have not seen their haplotype data.

Very well, but if you have not seen the Sinte STR values, how can you say they're distinct? In any case, the Sinte R2a is probably not that significant given the sample nature (Genetic drift), so far this has been proven by the extensive studies done on the Roma groups in Europe which seriously lack the R2a lineage, I have only seen one sample tested positive for the M124 among the European Gypsies, my gut feeling is the Sinte group probably come from a very tiny R2a family.

Rj

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Re: Independent-made R2a phylogenetic tree
« Reply #12 on: June 30, 2011, 03:46:56 PM »
Very well, but if you have not seen the Sinte STR values, how can you say they're distinct? In any case, the Sinte R2a is probably not that significant given the sample nature (Genetic drift), so far this has been proven by the extensive studies done on the Roma groups in Europe which seriously lack the R2a lineage, I have only seen one sample tested positive for the M124 among the European Gypsies, my gut feeling is the Sinte group probably come from a very tiny R2a family.

It is very likely that the Sinte sample was from a very small family.. :) Even the WB Karmali sample at 100% R2 is most likely to be 'related' people. However, going by the known history of Gypsies(originating in South Asia) and what is written in this paper and others as well one can take it for granted that Gypsies did not migrate from the British Isles. Perhaps Gypsies do not cluster with South Asians, and maybe they do with Central South Asians (whatever and wherever that may be is debatable, it's a matter of semantics and opinion). But going back to the Simpsons, I'd still say it is more likely that there was a male Indian ancestor. I think it would be wise to leave the Simpsons aside for now. We are barely scratching the surface of the intricacies of our haplogroup in general and the Simpsons just confuse and confound.
Y-DNA Haplogroup: R2
YSearch: ZYERN
Indian(West Bengal - Brahmin)

Birko19

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Re: Independent-made R2a phylogenetic tree
« Reply #13 on: June 30, 2011, 04:19:25 PM »
Very well, but if you have not seen the Sinte STR values, how can you say they're distinct? In any case, the Sinte R2a is probably not that significant given the sample nature (Genetic drift), so far this has been proven by the extensive studies done on the Roma groups in Europe which seriously lack the R2a lineage, I have only seen one sample tested positive for the M124 among the European Gypsies, my gut feeling is the Sinte group probably come from a very tiny R2a family.

It is very likely that the Sinte sample was from a very small family.. :) Even the WB Karmali sample at 100% R2 is most likely to be 'related' people. However, going by the known history of Gypsies(originating in South Asia) and what is written in this paper and others as well one can take it for granted that Gypsies did not migrate from the British Isles. Perhaps Gypsies do not cluster with South Asians, and maybe they do with Central South Asians (whatever and wherever that may be is debatable, it's a matter of semantics and opinion). But going back to the Simpsons, I'd still say it is more likely that there was a male Indian ancestor. I think it would be wise to leave the Simpsons aside for now. We are barely scratching the surface of the intricacies of our haplogroup in general and the Simpsons just confuse and confound.

The Gypsies are South Asian in origin and did indeed migrate to the British Isles, it would be false to say they did not since there are a number of Gypsies that live there today and many of them carry haplogroup H1a as evidence for it, the main obstacle here is claiming that European R2's are of Gypsy origin when in fact the Gypsies themselves carry it in rare numbers, I would be convinced that R2 is a Gypsy connection when I see a study where it's found in common numbers, to this date there has not been such study with the exception of Wells which obviously shows the insignificance of the sample due to genetic drift (Similarly the Yezidie group in Georgia tested 44% R2), the best way to analyze a proper Gypsy R2 lineage is to see the overall count of R2 among all Gypsy groups, since they all carry H1a as a clear relative marker, R2 should show up in a similar fashion, but since it does not one can easily dismiss that connection.

As for the Simpsons, I understand that the connection may be South Asian, but it clearly cannot be a recent one (Recent being the past 300 years or so), the Stephen case is clearly a result of a Simpson British man and an Indian woman, whether over 300 years ago the Simpson family had an Indian ancestor or not is up to debate.

As for the topic itself, a tree based on STR values is not very useful to be honest, in fact the Simpsons carry the L295 marker, meaning they should be grouped with the few other members that tested positive for this SNP, instead we see them all the way distant from these other L295+ members, it's true that STR can have some significance, but one needs to remember that the mutation is random and the only way to build a proper tree is by SNP comparison, which on that note, since you have a Brahmin background from the Bengal area, you may also carry the L295 SNP because the Indian member that tested positive for it is also a Brahmin from the same area, I'm eagerly waiting for the next Indian sample that tested for the L295 (From Rajasthan), it should be interesting.

PCSensei

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Re: Independent-made R2a phylogenetic tree
« Reply #14 on: July 06, 2011, 02:13:33 PM »

[attachment=5394:r2a reworked.jpg]

Phylogenetic tree made using McGee's Y-Utility, Phylip and FigTree.

To conflate the mystery of R2a further, the oldest lineages found to date seem to be from the British Isles of all places! Again, I'll have to review the data to confirm whether they actually are that divergent.


Hi DMXX

Having looked at the latest version of the tree there's just a couple of comments which I hope will be helpful.  I don't know how this kind of software works, but if you can 'tweak' the results it would be helpful to have 114870 and 66590 at the bottom of the chart, which would place them with the other Simpsons.  These two are both exact matches for the Simpson modal value at 67 markers, and it would be helpful to show them near 10674 who is also a Simpson and only one off the Simpson modal at 67.

Although people may have reported their origins in various different ways we have some good paper trails which make it most likely that the common ancestor for all these Simpsons (and myself 112058) was in England, quite probably Staffordshire, around 1600.  But where they were before that, en route from Central Asia (or wherever the latest view locates the origin of R2a1*) is anybody's guess!
Y-DNA: R2, Cluster A, ancestry UK both sides pre 1800 (possibly to 1600)
mt-DNA: H* (meaning no-one has yet identified the sub-clade!)
"Genealogy - the only area where a step backwards is progress!"