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alan trowel hands.
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« on: August 12, 2012, 05:45:19 AM »

I think I have probably asked this before but I wonder if its any clearer these days.  I presume that all L23XL51 that has an intervening SNP that does not occur in L51/L11 can be ignored as being ancestral to L51/L11.  In terms of STRs too is there any L23* group who resemble more the L51/L11 STRs.  Finally what is the geography of this group?
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alan trowel hands.
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« Reply #1 on: August 12, 2012, 06:41:29 AM »

I also wonder if this entry in Wikipedia has been factored in fully in discussions:

R1b1a2 (2011 name) is defined by the presence of SNP marker M269. R1b1a2* or M269(xL23) is found at highest frequency in the central Balkans notably Kosovo with 7.9%, Macedonia 5.1% and Serbia 4.4%.[7] Kosovo is notable in also having a high percentage of descendant L23* or L23(xM412) at 11.4% unlike most other areas with significant percentages of M269* and L23* except for Poland with 2.4% and 9.5% and the Bashkirs of southeast Bashkortostan with 2.4% and 32.2% respectively.[7] Notably this Bashkir population also has a high percentage of M269 sister branch M73 at 23.4%.[7] Five individuals out of 110 tested in the Ararat Valley, Armenia belonged to R1b1a2* and 36 to L23*, with none belonging to subclades of L23.[
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vineviz
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« Reply #2 on: August 12, 2012, 08:31:54 AM »

I think I have probably asked this before but I wonder if its any clearer these days.  I presume that all L23XL51 that has an intervening SNP that does not occur in L51/L11 can be ignored as being ancestral to L51/L11.  In terms of STRs too is there any L23* group who resemble more the L51/L11 STRs.  Finally what is the geography of this group?

We have two new markers (Z2103 and Z2105) that we are investigating.  But in 1000 Genomes, all the men who are L23+ L51- are also Z2103+ Z2105+.  If that hold true, then the answer to the question in your Subject line will be "not any".
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vineviz
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« Reply #3 on: August 12, 2012, 08:34:26 AM »

I also wonder if this entry in Wikipedia has been factored in fully in discussions:

R1b1a2 (2011 name) is defined by the presence of SNP marker M269. R1b1a2* or M269(xL23) is found at highest frequency in the central Balkans notably Kosovo with 7.9%, Macedonia 5.1% and Serbia 4.4%.[7] Kosovo is notable in also having a high percentage of descendant L23* or L23(xM412) at 11.4% unlike most other areas with significant percentages of M269* and L23* except for Poland with 2.4% and 9.5% and the Bashkirs of southeast Bashkortostan with 2.4% and 32.2% respectively.[7] Notably this Bashkir population also has a high percentage of M269 sister branch M73 at 23.4%.[7] Five individuals out of 110 tested in the Ararat Valley, Armenia belonged to R1b1a2* and 36 to L23*, with none belonging to subclades of L23.[

Probably, although that Wiki quote is kind of a jumble of random facts.

No doubt, the Balkans are an important area in the history of R-M269's expansion into Europe from SW Asia but the testing there is still too spotty to draw reasonable conclusion about the region's precise role.
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alan trowel hands.
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« Reply #4 on: August 12, 2012, 09:29:21 AM »

I also wonder if this entry in Wikipedia has been factored in fully in discussions:

R1b1a2 (2011 name) is defined by the presence of SNP marker M269. R1b1a2* or M269(xL23) is found at highest frequency in the central Balkans notably Kosovo with 7.9%, Macedonia 5.1% and Serbia 4.4%.[7] Kosovo is notable in also having a high percentage of descendant L23* or L23(xM412) at 11.4% unlike most other areas with significant percentages of M269* and L23* except for Poland with 2.4% and 9.5% and the Bashkirs of southeast Bashkortostan with 2.4% and 32.2% respectively.[7] Notably this Bashkir population also has a high percentage of M269 sister branch M73 at 23.4%.[7] Five individuals out of 110 tested in the Ararat Valley, Armenia belonged to R1b1a2* and 36 to L23*, with none belonging to subclades of L23.[

Probably, although that Wiki quote is kind of a jumble of random facts.

No doubt, the Balkans are an important area in the history of R-M269's expansion into Europe from SW Asia but the testing there is still too spotty to draw reasonable conclusion about the region's precise role.

I actually didnt realise M412 was L51.  Anyway it is interesting that L23XL51 and M269* are both located together in the Balkans and Poland too.  Between that and the M73 I am less inclined now to see Anatolia as a likely origin point.  I also believe Anatolia is far to early involved in farming to explain the lack of early branching and general lack of impressive take off of R1b in the early Neolithic era.  I am more inclinded to see Anatolia as an arrival point from the source area of M269 albeit that the source of Anatolian M269 was relatively close to the origin point. 
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vineviz
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« Reply #5 on: August 12, 2012, 09:55:29 AM »

Well, R-M73 is a complete red herring at least as far as the data above are concerned.

And while Anatolia is not the most likely point of origin for R-M269, the data above are not sufficient to rule it out as being among the possibilities.
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acekon
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« Reply #6 on: August 12, 2012, 10:27:16 AM »

The problem as I see it is that there is a lack of conviction. For example you have given a rough approximate area of the location of L23*[alan trowel hands] with a rough timeline. However, no offense to V.V. Maps are made with only snp's not str's and even then, there are no dates given,  even with +/- . There are no corresponding signature STR's-SNP tables. ISOGG tree there are no corresponding dates to SNP's except in very broad terms, for the R line, [maybe I'm not on the right ISOGG page] however all I see is,

M207-27,000
R1-M173-18,500
R1b1a2-M269-4000-8000

Familytree uses only snp's in there tree.  If all the science is sound then the calculations should also be. If the calculations are sound then the next step would be to translate inter-changeable  snp and str tree, with dates, IMO.

Another problem is the migration of ancient peoples. For example[one example] the Phillistines who were inhabitants of Levant [1200BC?]. Were they associated with Phrygians, or from around that area, or the Aegean Sea. Were the Phrygians associated with the Armenians? Was there an expansion from the Balkan's?Was Phrygian language into Pakistan? If so, I would tend to think that there would be genetic evidence left behind, besides traditional ancient writings connecting groups. Phrygian is just one example. How do we know when taking a str/snp sample from the Levant/Balkans/Caucasus, it is not an ancestor of one of these ancient migrants?

http://www.worldfamilies.net/forum/index.php?topic=10730.0
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alan trowel hands.
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« Reply #7 on: August 12, 2012, 10:33:21 AM »

Well, R-M73 is a complete red herring at least as far as the data above are concerned.

And while Anatolia is not the most likely point of origin for R-M269, the data above are not sufficient to rule it out as being among the possibilities.

My main point though is Anatolia is one of the earliest farming areas.  M269 or its immediate ancestor does not have the hallmarks of being swept up in the early farming demographic boom.  Ancient DNA also suggests it wasnt swept into Europe with the first farmers.  it just seems very unlikely that it was in Anatolia as early as that to me.  It seems more likely it was not in the early farming zone.   Anatolia just doesnt seem compatible to me.  I favour the idea it was in some area where farming came late or a very marginal area prior to 5000/4000BC. 
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alan trowel hands.
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« Reply #8 on: August 12, 2012, 10:37:22 AM »

The problem as I see it is that there is a lack of conviction. For example you have given a rough approximate area of the location of L23*[alan trowel hands] with a rough timeline. However, no offense to V.V. Maps are made with only snp's not str's and even then, there are no dates given,  even with +/- . There are no corresponding signature STR's-SNP tables. ISOGG tree there are no corresponding dates to SNP's except in very broad terms, for the R line, [maybe I'm not on the right ISOGG page] however all I see is,

M207-27,000
R1-M173-18,500
R1b1a2-M269-4000-8000

Familytree uses only snp's in there tree.  If all the science is sound then the calculations should also be. If the calculations are sound then the next step would be to translate inter-changeable  snp and str tree, with dates, IMO.

Another problem is the migration of ancient peoples. For example[one example] the Phillistines who were inhabitants of Levant [1200BC?]. Were they associated with Phrygians, or from around that area, or the Aegean Sea. Were the Phrygians associated with the Armenians? Was there an expansion from the Balkan's?Was Phrygian language into Pakistan? If so, I would tend to think that there would be genetic evidence left behind, besides traditional ancient writings connecting groups. Phrygian is just one example. How do we know when taking a str/snp sample from the Levant/Balkans/Caucasus, it is not an ancestor of one of these ancient migrants?

http://www.worldfamilies.net/forum/index.php?topic=10730.0

To be honest I think a lack of conviction is only sensible.  There are just too many unknowns.  Conviction in the current state of knowledge would seem a bad idea to me.  It would be different if we had some certaint fixed points but there are just so many uncertainties and areas of disagreement.  Despite all that I think its a lot better than it was a couple of years ago.
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acekon
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« Reply #9 on: August 12, 2012, 10:48:11 AM »

The problem as I see it is that there is a lack of conviction. For example you have given a rough approximate area of the location of L23*[alan trowel hands] with a rough timeline. However, no offense to V.V. Maps are made with only snp's not str's and even then, there are no dates given,  even with +/- . There are no corresponding signature STR's-SNP tables. ISOGG tree there are no corresponding dates to SNP's except in very broad terms, for the R line, [maybe I'm not on the right ISOGG page] however all I see is,

M207-27,000
R1-M173-18,500
R1b1a2-M269-4000-8000

Familytree uses only snp's in there tree.  If all the science is sound then the calculations should also be. If the calculations are sound then the next step would be to translate inter-changeable  snp and str tree, with dates, IMO.

Another problem is the migration of ancient peoples. For example[one example] the Phillistines who were inhabitants of Levant [1200BC?]. Were they associated with Phrygians, or from around that area, or the Aegean Sea. Were the Phrygians associated with the Armenians? Was there an expansion from the Balkan's?Was Phrygian language into Pakistan? If so, I would tend to think that there would be genetic evidence left behind, besides traditional ancient writings connecting groups. Phrygian is just one example. How do we know when taking a str/snp sample from the Levant/Balkans/Caucasus, it is not an ancestor of one of these ancient migrants?

http://www.worldfamilies.net/forum/index.php?topic=10730.0

To be honest I think a lack of conviction is only sensible.  There are just too many unknowns.  Conviction in the current state of knowledge would seem a bad idea to me.  It would be different if we had some certaint fixed points but there are just so many uncertainties and areas of disagreement.  Despite all that I think its a lot better than it was a couple of years ago.

Sorry I can't help myself. Starting to sound a little cheesy, however should we have faith, with all the complex computer simulations on  mutation rates, being translated into STR/SNP data?  There are some pretty big intellectual guns here, nobody wants to put there b*lls on the line, with firm anchor dates snp/str tree.

noun 1. confidence or trust in a person or thing:
« Last Edit: August 12, 2012, 10:50:30 AM by acekon » Logged

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vineviz
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« Reply #10 on: August 12, 2012, 11:07:09 AM »

M269 or its immediate ancestor does not have the hallmarks of being swept up in the early farming demographic boom.  Ancient DNA also suggests it wasnt swept into Europe with the first farmers. 

I think the second statement is more defensible than the first.  About the only thing we know of the early farmers (genetically speaking) is the impact they had on Europe.  Inferring that all early farmers in the Near East resembled genetically the first farmers to migrate to Europe requires some assumptions about homogeneity of the source population that I don't think are warranted.

After all, the first migrants from Europe to America were not fully representative genetically of all Europeans at the time the migration began.
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vineviz
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« Reply #11 on: August 12, 2012, 11:09:37 AM »

Sorry I can't help myself. Starting to sound a little cheesy, however should we have faith, with all the complex computer simulations on  mutation rates, being translated into STR/SNP data?  There are some pretty big intellectual guns here, nobody wants to put there b*lls on the line, with firm anchor dates snp/str tree.

There is such a thing as over-confidence as well, and it is a well-know contributor of bias and error.

http://en.wikipedia.org/wiki/Overconfidence_effect

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"Overconfidence has been called the most “pervasive and potentially catastrophic” of all the cognitive biases to which human beings fall victim."
« Last Edit: August 12, 2012, 11:10:36 AM by vineviz » Logged
acekon
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« Reply #12 on: August 12, 2012, 12:10:03 PM »

Sorry I can't help myself. Starting to sound a little cheesy, however should we have faith, with all the complex computer simulations on  mutation rates, being translated into STR/SNP data?  There are some pretty big intellectual guns here, nobody wants to put there b*lls on the line, with firm anchor dates snp/str tree.

There is such a thing as over-confidence as well, and it is a well-know contributor of bias and error.

http://en.wikipedia.org/wiki/Overconfidence_effect

Quote
"Overconfidence has been called the most “pervasive and potentially catastrophic” of all the cognitive biases to which human beings fall victim."


There is a difference between overconfidence, bias, error and bluffing.

Have you ever played a family night of chess, and given all the pieces away. If the position is strong, it does not matter the game is already won. The game cannot be won on a unattainable position, no matter how many errors/bias opponent  makes in giving away all his good pieces.

 On the other hand p*ker  is totally opposite. The game can be won with a totally unattainable position, in other words by bluffing with a bad hand.

Overconfidence, errors and bias are human nature, some like myself, have more of these poor qualities than the rest.



"In the card game of , a bluff is a bet or raise made with a hand which is not thought to be the best hand."

"Science (from Latin scientia, meaning "knowledge") is a systematic enterprise that builds and organizes knowledge in the form of testable explanations"
« Last Edit: August 12, 2012, 12:13:22 PM by acekon » Logged

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vineviz
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« Reply #13 on: August 12, 2012, 12:23:38 PM »

The questions being discussed here are, or should be, scientific ones.  Bluffing has no place, and overconfidence is a definite liability.
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acekon
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« Reply #14 on: August 12, 2012, 12:38:16 PM »

The questions being discussed here are, or should be, scientific ones.  Bluffing has no place, and overconfidence is a definite liability.


Yes thank you exactly my hand is very weak, you can attribute all of the following sentence to me, you can put me in check-mate.

" There is such a thing as over-confidence as well, and it is a well-know contributor of bias and error."

However at the outset  I quoted "cherry-picking"

"Good science looks at all the evidence (rather than cherry picking only favorable evidence), controls for variables so we can identify what is actually working, uses blinded observations so as to minimize the effects of bias, and uses internally consistent logic."

I'm calling your hand, [dates +/-, placement of str's and snp's].  If you do not know just say so, you do not have to be ashamed. You have a lot more humility coming to our forums and teaching us a thing, or comparing  different competing ideas. We cannot do that unless you give more information.
« Last Edit: August 12, 2012, 12:39:23 PM by acekon » Logged

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« Reply #15 on: August 12, 2012, 01:22:59 PM »

The questions being discussed here are, or should be, scientific ones.  Bluffing has no place, and overconfidence is a definite liability.


Yes thank you exactly my hand is very weak, you can attribute all of the following sentence to me, you can put me in check-mate.

" There is such a thing as over-confidence as well, and it is a well-know contributor of bias and error."

However at the outset  I quoted "cherry-picking"

"Good science looks at all the evidence (rather than cherry picking only favorable evidence), controls for variables so we can identify what is actually working, uses blinded observations so as to minimize the effects of bias, and uses internally consistent logic."

I'm calling your hand, [dates +/-, placement of str's and snp's].  If you do not know just say so, you do not have to be ashamed. You have a lot more humility coming to our forums and teaching us a thing, or comparing  different competing ideas. We cannot do that unless you give more information.

What's the big deal? I wasn't aware we were playing a card game. I would like to learn something. I just came from church. That arena is where the confidence of my convictions comes from. This arena of genetic genealogy and population genetics is still in its infancy. Realism about that is a good thing, not a bad thing.

We are just exchanging ideas and data on this forum. Hopefully we can learn something, and every now and then there will be an outcome* that directly contributes to the genetic genealogy and population genetics communities.

* Example 1: Citizen-scientist paper: "Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach" by Richard A. Rocca, Gregory Magoon, David F. Reynolds, Thomas Krahn, Vincent O. Tilroe, Peter M. Op den Velde Boots, Andrew J. Grierson http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0041634

* Example 2: Citation from a scientific paper: "A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe"
Quote
Acknowledgements: We thank all the men who donated DNA samples used in this study. We thank Vincent Vizachero for alerting us to the potential of M520, M529, S116, L11, L23 SNPs and for insight regarding the DYS390, 19 repeat allele and M73.
http://www.nature.com/ejhg/journal/v19/n1/full/ejhg2010146a.html

* Example 3: International Society of Genetic Genealogy publications, links and haplogroup tree.  http://isogg.org/tree/index.html
« Last Edit: August 12, 2012, 01:26:49 PM by Mikewww » Logged

R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
vineviz
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« Reply #16 on: August 12, 2012, 01:31:41 PM »


I'm calling your hand, [dates +/-, placement of str's and snp's].  If you do not know just say so, you do not have to be ashamed. You have a lot more humility coming to our forums and teaching us a thing, or comparing  different competing ideas. We cannot do that unless you give more information.


I still don't know what your question is.

If you pose some specific questions, I'll give my answers as best I can in the time I have to devote to it.

I will  say that a complete accounting of the background for that map would require many thousands of words that I do not at the moment  have time to write. If that bothers you, feel free to think less of me.
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alan trowel hands.
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« Reply #17 on: August 12, 2012, 02:07:39 PM »

M269 or its immediate ancestor does not have the hallmarks of being swept up in the early farming demographic boom.  Ancient DNA also suggests it wasnt swept into Europe with the first farmers. 

I think the second statement is more defensible than the first.  About the only thing we know of the early farmers (genetically speaking) is the impact they had on Europe.  Inferring that all early farmers in the Near East resembled genetically the first farmers to migrate to Europe requires some assumptions about homogeneity of the source population that I don't think are warranted.

After all, the first migrants from Europe to America were not fully representative genetically of all Europeans at the time the migration began.

That is a fair point and I would add there is some evidence (although I wouldnt say conclusive) that Anatolia was not as important as was originally thought in the initial European Neolithic compared to the Levant.  I agree that my first point is more significant i.e. R1b does not seem to have deep and varied branching dating to the initiation of faming which does make an Anatolian origin less likely. 
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acekon
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« Reply #18 on: August 12, 2012, 03:04:23 PM »


I'm calling your hand, [dates +/-, placement of str's and snp's].  If you do not know just say so, you do not have to be ashamed. You have a lot more humility coming to our forums and teaching us a thing, or comparing  different competing ideas. We cannot do that unless you give more information.


I still don't know what your question is.

If you pose some specific questions, I'll give my answers as best I can in the time I have to devote to it.

I will  say that a complete accounting of the background for that map would require many thousands of words that I do not at the moment  have time to write. If that bothers you, feel free to think less of me.

Don't be so silly, everyone appreciates your expertise and time you put into the  fields of genetics and history, ideas/viewpoints,including me!

I tried to make myself clear, about a proper format, instead of thousands of ambiguous words and snps; to format your map in signature STR's.


This is totally inappropriate, and I appreciate rms2 for allowing open debate again!

I thought your ability to read and perhaps translate snp's into signature str's on your map.

http://www.youtube.com/watch?v=SdkdQtlF-RU
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YDNA: R-Z2105* Śląsk-Polska
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