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NealtheRed
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« Reply #25 on: July 31, 2010, 10:29:02 PM »

If you have the FGS's results, show them!

Ciao Signore,

Here they are (Coding Region):

750G
1438G
2706G
4769G
5978G
7028T
7094C
8860G
11389T
11944C
13680T
14518G
15326G
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Y-DNA: R-Z255 (L159.2+) - Downing (Irish Sea)


MTDNA: HV4a1 - Centrella (Avellino, Italy)


Ysearch: 4PSCK



NealtheRed
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« Reply #26 on: July 31, 2010, 10:39:56 PM »

Oetzi was 100% Italian, demonstrated by his tools, linked to the Remedello culture, and, like his mtDNA (K1 from Alpine Region), I think that his Y will astonish everybody.

The latest paper of Malyarchuk has demonstrated that many mtDNA present now in Russia came from Western Europe after the LGM: read it.

Only your prejudices can explain your positions: but truth is truth and at last it will overcome.

Do you have a link to Malyarchuk's paper? The one I read said that HV4 most likely came over the Caucasus from the Near East, after the LGM. If he has something new, I will check it out though.

And as to Otzi's Y-haplogroup? I have not a clue, sir.
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Y-DNA: R-Z255 (L159.2+) - Downing (Irish Sea)


MTDNA: HV4a1 - Centrella (Avellino, Italy)


Ysearch: 4PSCK



Maliclavelli
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« Reply #27 on: August 01, 2010, 01:11:38 AM »

The paper of Malyarchuk is: "The Peopling of Europe from the Mitochondrial Haplogroup U5 Perspective", PlosOne 2010. This is the abstract: "It is generally accepted that the most ancient European mitochondrial haplogroup, U5, has evolved essentially in Europe. To resolve the phylogeny of this haplogroup, we completely sequenced 113 mitochondrial genomes (79 U5a and 34 U5b) of central and eastern Europeans (Czechs, Slovaks, Poles, Russians and Belorussians), and reconstructed a detailed phylogenetic tree, that incorporates previously published data. Molecular dating suggests that the coalescence time estimate for the U5 is ~25–30 thousand years (ky), and ~16–20 and ~20–24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe. In addition, during the Last Glacial Maximum central Europe (probably, the Carpathian Basin) apparently represented the area of intermingling between human flows from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees. Age estimations amounting for many U5 subclusters in eastern Europeans to ~15 ky ago and less are consistent with the view that during the Ice Age eastern Europe was an inhospitable place for modern humans".


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Maliclavelli


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« Reply #28 on: August 01, 2010, 01:44:41 AM »



Ciao Signore,

Here they are (Coding Region):

750G
1438G
2706G
4769G
5978G
7028T
7094C
8860G
11389T
11944C
13680T
14518G
15326G
[/quote]

263G 750G 1438G 2706G 4769G 7028T 7094C 8860G 15326G are the mutations common to all HV4.
You have these your own mutations: 5978G 11389T 11944C 13680T 14518G, and only 13680T you have in common  with the Italian HV4a. You have no mutations in common with the Egyptian, but 13680T defines a cluster we have found so far only in Italy.
Of course we need more data and unfortunately the Ian Logan's site is out so far.
But that yours is an ancient Italian cluster I think very likely.
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Maliclavelli


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Maliclavelli
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« Reply #29 on: August 01, 2010, 01:54:31 AM »

I wondered about the general Alps area.
Before the Roman empire would the Alps have been considered part of Italy?

Of course every modern people is the sum of many ancient tribes. The same for Italians.
But if you know my thousands of posts, you should know that my theory is that the ancient Rhaetians of the Alpine Region were linked to Etruscans and I have always spoken of a "Rhaetian-Etruscan Fatherland".
Italy has overall the same ancient haplogroups, among them all the path of hg. R: R1b1*, R1b1b2*, R1b1b2a (mine), R-L51 (the highest percentage and variance in Italy).
My theory is that this was the time when Italians expanded and peopled Europe.

About Oetzi of course I have no news, but if he was R-L51 (its presence is very high in the Alpine region) for me would be good.
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Maliclavelli


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« Reply #30 on: August 01, 2010, 03:39:27 AM »

Re. the Assyrian who wrote to this forum (Humanist), you can read this posting to Rootsweb and the answer of an expert like Ann Turner to understand how is far from you his HV4, ascertained later by an FGS:

"I would appreciate feedback regarding the following mtDNA results:

HVR2 - 263G, 309.1C, 315.1C
HVR1- 16129A, 16209C, 16287T, 16311C
(tested with GeneTree and classified as L3f)

Comments:

1. The combination of 16129A, 16209C, 16311C would suggest L3f. What is inexplicable, however, is the absence of not only 73G, but 16223T and 16519C as well. It is acknowledged that absence or presence of the latter mutation is ordinarily not useful for phylogenetic purposes. But in this case, however, I believe that combined with the absences of both 73G and 16223T, it might be relevant, considering that 100% of L3f samples have all three.
2. Other perhaps relevant absences between the sample in question and the great majority of L3f samples: 16292T, 189G, and 200G.
3. Other perhaps relevant absences between the sample in question and 20-40% of L3f samples: 150T, 152C.
4. Existence of mutation at 16287T. Not found in any L3f samples.
Questions:
1.These results have proven very difficult to make sense of. Can the absence of all of those mutations, including not only the ones that appear in 100% of L3f samples, but also those that appear in practically all L3f, as well as those that appear less frequently but still in significant numbers, be explained by back mutations?
2.Can some or all of the mutations 16129A, 16209C, and 16311C be explained by homoplasy?
3.Assuming it is not a "private mutation," what is the possible significance of 16287T as far as the phylogenetic tree is concerned?
Thank you very much for taking the time to read this message, and I sincerely hope to hear back from some with their opinions.
Note- L3f samples were referred to on both Mitosearch and the FTDNA L3 Project".





 
« Last Edit: August 02, 2010, 06:40:23 AM by Maliclavelli » Logged

Maliclavelli


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« Reply #31 on: August 01, 2010, 03:59:44 AM »

To answer your question it would be useful this paper. Unfortunately it isn't for free.

O García, R Fregel, J M Larruga, V Álvarez, I Yurrebaso, V M Cabrera and A M González

Using mitochondrial DNA to test the hypothesis of a European post-glacial human recolonization from the Franco-Cantabrian refuge
"It has been proposed that the distribution patterns and coalescence ages found in Europeans for mitochondrial DNA (mtDNA) haplogroups V, H1 and H3 are the result of a post-glacial expansion from a Franco-Cantabrian refuge that recolonized central and northern areas. In contrast, in this refined mtDNA study of the Cantabrian Cornice that contributes 413 partial and 9 complete new mtDNA sequences, including a large Basque sample and a sample of Asturians, no experimental evidence was found to support the human refuge-expansion theory. In fact, all measures of gene diversity point to the Cantabrian Cornice in general and the Basques in particular, as less polymorphic for V, H1 and H3 than other southern regions in Iberia or in Central Europe. Genetic distances show the Cantabrian Cornice is a very heterogeneous region with significant local differences. The analysis of several minor subhaplogroups, based on complete sequences, also suggests different focal expansions over a local and peninsular range that did not affect continental Europe. Furthermore, all detected clinal trends show stronger longitudinal than latitudinal profiles. In Northern Iberia, it seems that the highest diversity values for some haplogroups with Mesolithic coalescence ages are centred on the Mediterranean side, including Catalonia and South-eastern France".

« Last Edit: August 01, 2010, 04:11:30 AM by Maliclavelli » Logged

Maliclavelli


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Maliclavelli
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« Reply #32 on: August 01, 2010, 05:05:25 AM »


21 Apr 2010 ... In a recent global mtDNA phylogenetic tree, based on published complete sequences (van Oven and Kayser, 2009), a branch named HV4a was ...

???????
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Maliclavelli


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Humanist
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« Reply #33 on: August 02, 2010, 04:54:28 AM »

Re. the Assyrian who wrote to this forum --------------you can read this posting to Rootsweb and the answer of an expert like Ann Turner to understand how is far from you his HV4, ascertained later by an FGS:

"I would appreciate feedback regarding the following mtDNA results:

HVR2 - 263G, 309.1C, 315.1C
HVR1- 16129A, 16209C, 16287T, 16311C
(tested with GeneTree and classified as L3f)

Comments:

1. The combination of 16129A, 16209C, 16311C would suggest L3f. What is inexplicable, however, is the absence of not only 73G, but 16223T and 16519C as well. It is acknowledged that absence or presence of the latter mutation is ordinarily not useful for phylogenetic purposes. But in this case, however, I believe that combined with the absences of both 73G and 16223T, it might be relevant, considering that 100% of L3f samples have all three.
2. Other perhaps relevant absences between the sample in question and the great majority of L3f samples: 16292T, 189G, and 200G.
3. Other perhaps relevant absences between the sample in question and 20-40% of L3f samples: 150T, 152C.
4. Existence of mutation at 16287T. Not found in any L3f samples.
Questions:
1.These results have proven very difficult to make sense of. Can the absence of all of those mutations, including not only the ones that appear in 100% of L3f samples, but also those that appear in practically all L3f, as well as those that appear less frequently but still in significant numbers, be explained by back mutations?
2.Can some or all of the mutations 16129A, 16209C, and 16311C be explained by homoplasy?
3.Assuming it is not a "private mutation," what is the possible significance of 16287T as far as the phylogenetic tree is concerned?
Thank you very much for taking the time to read this message, and I sincerely hope to hear back from some with their opinions.
Note- L3f samples were referred to on both Mitosearch and the FTDNA L3 Project".

Yes, my question was in regard to an obviously flawed haplogroup classification by GeneTree.  They have yet to adjust my classification!  It has been since November of '09. 

By the way, since we are discussing full sequencing, and as consequence, coding mutations, I would appreciate if you would edit your post and remove my real name.  I do not care that you know my name, or that anyone here knows my name, but I would prefer that my real name and potentially sensitive data not be so easily associated via a simple web search. 

Thanks and look forward to continuing our discussion of HV4 and Oetzi.



« Last Edit: August 02, 2010, 05:03:18 AM by Humanist » Logged

Maliclavelli
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« Reply #34 on: August 02, 2010, 06:52:18 AM »

Done, Humanist. I apologize, but who knows me knows that I don't like who hides himself, even as in the internet age nobody can hid nobody.
I have said many times that science is undestanding particular cases in their particular circumstancies, and the name, the origin (your G1*) is fundamental for science itself. I understand that someone can have some problem to reveal his name and his genetical data (I published my mutation 11204C that could have medical consequences, because I think that truth and its quest it's worth above all).

This said, I appreciated your diagram and will be always glad to converse with you.
« Last Edit: August 02, 2010, 08:16:11 AM by Maliclavelli » Logged

Maliclavelli


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« Reply #35 on: August 02, 2010, 07:22:44 AM »

Thanks, my friend.  Please take a look at this Google Doc spreadsheet, if you will, of all HV4 and HV4a samples listed on Ian's site, plus 'theReds' CR mutations: https://spreadsheets.google.com/ccc?key=0AksEb_ijCNKYdFM3bDRKelFKTzJlZ05FZUFnSTRCRHc&hl=en&authkey=CImnt-oO

Interesting to note that the three Near Eastern specimens are the only samples to share differences at loci 7805 and 16129.  

I am curious why the Jordanian is assigned to HV4a, considering that the difference at the defining locus, 16221, appears not to exist.  Save for my difference at 16209,  the Jordanian sample and I would be a perfect match.  

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« Reply #36 on: August 02, 2010, 07:28:15 AM »

I have said many times that science is undestanding particular cases in their particular circumstancies, and the name, the origin (your G1*) is fundamental for science itself.

Tell me about it.  I am still awaiting my first 12-marker match, for Pete's sake! 
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Maliclavelli
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« Reply #37 on: August 02, 2010, 09:19:28 AM »

Dear Humanist, re. your Y (after I will exam also your mtDNA) I think you first should correct
your data: DYS461=13, A10=11 and DYS441=15 and complete, from SMGF, 3NV5M, who has the same your
43 values except DYS447=23 AND DYS464d=15, then he is very close related to you.
Certainly it is very strange that the closest to you over the world are all Western Europeans
and the closest an Italian. Perhaps I will demonstrate the also hg. G doesn't come from Caucasus
but from the Italian Refugium. Aaaaahhhhh

1 14 13 32 23 10 12 13 14,15 10 13 16 -1 -1 -1 -1 -1
1 of 29 Ragusa, Italy [Italian]

1 14 13 32 23 10 11 13 14,15 -1 -1 -1 -1 -1 -1 -1 -1
1 of 411 Bydgoszcz, Poland [Polish]

1 14 13 31 23 10 11 13 14,15 -1 -1 -1 -1 -1 -1 -1 -1 >>
1 14 13 31 23 10 11 13 14,15 10 11 15 20 17 17 25 11 >>
1 of 43 Pennsylvania, United States [African American]
1 of 738 Cologne, Germany [German] Eurasian - European

(from YHRD)




 
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Maliclavelli


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« Reply #38 on: August 02, 2010, 09:55:15 AM »

Thanks.  Did not notice that they had reported my additional markers.  I had attempted to use their conversion chart for some of the SMGF markers.  But other than DYS461, I do not see a difference between YSearch and Ray Banks's site.  Did you compare the marker values to YSearch from Ray's site or the Haplogroup G Project site's page? 

I knew about the Ragusa man, but not about the others.  Many thanks! 

The close match on YSearch was known to me. It is from the SMGF database.  In fact, I created the Ysearch account, 3NV5M.  A paternal relative tested a few years ago, and we believe it to be his Y-DNA specimen.  We are not certain, however, because he tested as part of some supposed academic study. 
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« Reply #39 on: August 02, 2010, 10:47:06 AM »

I extracted your values (and those of your related Iranian) from SMGF as FTDNA. I think that these are the values to put on Ysearch.
I don't know "Ray Bank's site".

Re. your mtDNA,  first of all I thank you very much for the Ian Logan's spreadsheet, being his site out now (probably he is working over it).

N° 40 from Italy is a perfect match of the CR with NealtheRed (his mother is from Italy), and if
is he, why there isn't the control region he has? If he is another person, I'd win completely my
bet with him.

Also the three Spaniards have C13680T, then this is a Western European clade, for now found only
in Italy and Spain.

Of course all these indipendent mutations demonstrate the ancient dispersal of this haplogroup.

Probably you, the Egyptian and the Jordanian belong to a Middle Eastern clade, even though separated
long time ago and you and the Jordanian are closely related.
« Last Edit: August 02, 2010, 12:14:27 PM by Maliclavelli » Logged

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« Reply #40 on: August 02, 2010, 12:43:59 PM »

(For Humanist)

2 14 13 32 24 10 11 13 14,15
1 of 266 Kiev, Ukraine [Ukrainian] Eurasian - European 
1 of 743 Chemnitz, Germany [German] Eurasian - European   

2 15 13 32 24 10 11 13 14,15 10 12 15 -1 -1 -1 -1 -1 
1 15 13 32 24 10 11 13 14,15 -1 -1 -1 -1 -1 -1 -1 -1 
1 15 13 32 24 10 11 13 14,15 10 13 -1 -1 -1 -1 -1 -1 
1 15 13 32 24 10 11 13 14,15 10 13 15 19 15 18 23 11 
1 15 13 32 24 10 11 13 14,15 10 13 15 20 15 17 22 11 
1 15 13 32 24 10 11 13 14,15 10 13 15 20 15 17 23 11 
1 15 13 32 24 10 11 13 14,15 10 14 15 -1 -1 -1 -1 -1
2 of 32 Palota, Bihor, Romania [German] Eurasian - European 
1 of 200 Novi Sad, Serbia [Slovakian] Eurasian - European 
1 of 129 Bialystok, Poland [Old Believers] Eurasian - European 
1 of 191 Northern Greece, Greece [Greek] Eurasian - European 
1 of 942 Gdansk, Poland [Polish] Eurasian - European 
1 of 73 Orel, Russian Federation [Russian] Eurasian - European 
1 of 645 Prague, Czech Republic [Czech] Eurasian - European 

You can see that, going to values nearer to the modal, we are carried
to East. You can amuse yourself going on with the research:

15 13 32 24 10 11 13 14,15         8 
14 13 31 24 10 11 13 14,15         4 
14 12 31 24 10 11 13 14,15         3 
14 13 32 23 10 11 13 14,15         1 
       

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Maliclavelli


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« Reply #41 on: August 02, 2010, 09:34:07 PM »

Of course your clade is characterized by DYS392=12, then only the guy from Ragusa should be taken in consideration. We have two other guys with DYS392=12 from Ascoli (Marche). Unfortunately the researches on Sardinians haven't tested this marker.
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Maliclavelli


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« Reply #42 on: August 02, 2010, 09:39:56 PM »

I think we should learn from mtDNA HV4 to explain YDNA R: there are two clades who developed independently in Middle East and in the Mediterranean Western Europe (above all Italy and Spain) for 20/25,000 years. Hg. R is younger, but probably not so young as many are thinking.
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Maliclavelli


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« Reply #43 on: August 03, 2010, 02:17:35 AM »

If we consider the mutations in the Coding Region (the three Italians=16, the three Middle Easterners=4, the three Spaniards=4), it isn't difficult to understand that Italy had at least a HV4-populations fourfold the other two. To imagine that it was the land of origin of this haplogroup and from the Paglicci time (24,000 YBP) it isn't difficult too.
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Maliclavelli


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« Reply #44 on: August 04, 2010, 06:31:33 AM »

Last news on Oetzi.

Sir William R. Hurst put the Oetzi's data on Mitosearch (ID: 4q6ja), writing that he was found in the "Austrian Alps" and that his country of origin is "Austria".
You can now find the emendate version under ID: 27NEU.
Sir Hurst is free to maintain his opinion or to accept the truth of the facts (I don't repeat what I have said many times, id est  the origin of Oetzi from South of the Alps, in the Remedello culture, etc.).
 
Probably also Hurst's ancestors have replied to me from afterlife, saying that the correct Oetzi's ID is 27NEU, id est 27NEW. Of course Hurst's ancestors speak in their language: Germanic.

The fact that we find now the most part of K1* in the British Isles and less in Central and North Europe (only one sample in Italy and another in Turkey, but of Greek extraction) demonstrates only the path of the migration from Italy, like I have said many times, also for many Y. When someone will be able to find some K1* more ancient of Otzi out of Italy, we'll discuss the new finding.
« Last Edit: August 04, 2010, 08:20:02 AM by Maliclavelli » Logged

Maliclavelli


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« Reply #45 on: August 04, 2010, 10:20:04 AM »

Very interesting for NealtheRed. This FGS has been published recently:

HM765460 Zaragoza Haplogroup HV4a 01-AUG-2010
T146C A263G 315.1C A750G A1438G A2706G T3645C A4769G A5978G C7028T
T7094C A8860G C11389T T11944C C13680T A14518G A15326G C16221T

It's a match -1/+1: -309.1C, +3645C. When it is published on GenBank we'll know also his nationality.
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« Reply #46 on: August 05, 2010, 08:31:59 AM »

Perhaps Oetzi is a G2a man.  :)  The Tirol is fertile territory for G2a men.  At least relatively speaking with regard to its general frequency among the European nations.
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« Reply #47 on: August 05, 2010, 11:17:06 AM »

It is possible. Italy have an high frequence overall of G2a (but as I have said these last days, also of your G1a: certainly 3 cases) and Sardinia is a centre of dispersion for the whole Western Europe, then this haplogroup arrived there very early.
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« Reply #48 on: August 08, 2010, 08:17:13 AM »

A little more on Ötzi

Gene Map to Give Insight into 5,200-year-old Iceman.
http://www.livescience.com/history/ice-man-genome-sequenced-100804.html
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R1b1a2a1a1b4


R-DF13**(L21>DF13)
M42+, M45+, M526+, M74+, M89+, M9+, M94+, P108+, P128+, P131+, P132+, P133+, P134+, P135+, P136+, P138+, P139+, P14+, P140+, P141+, P143+, P145+, P146+, P148+, P149+, P151+, P157+, P158+, P159+, P160+, P161+, P163+, P166+, P187+, P207+, P224+, P226+, P228+, P229+, P230+, P231+, P232+, P233+, P234+, P235+, P236+, P237+, P238+, P239+, P242+, P243+, P244+, P245+, P280+, P281+, P282+, P283+, P284+, P285+, P286+, P294+, P295+, P297+, P305+, P310+, P311+, P312+, P316+, M173+, M269+, M343+, P312+, L21+, DF13+, M207+, P25+, L11+, L138+, L141+, L15+, L150+, L16+, L23+, L51+, L52+, M168+, M173+, M207+, M213+, M269+, M294+, M299+, M306+, M343+, P69+, P9.1+, P97+, PK1+, SRY10831.1+, L21+, L226-, M37-, M222-, L96-, L193-, L144-, P66-, SRY2627-, M222-, DF49-, L371-, DF41-, L513-, L555-, L1335-, L1406-, Z251-, L526-, L130-, L144-, L159.2-, L192.1-, L193-, L195-, L96-, DF21-, Z255-, DF23-, DF1-, Z253-, M37-, M65-, M73-, M18-, M126-, M153-, M160-, P66-

12 24 14 10 11 14 12 12 12 13 13 29 18


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« Reply #49 on: August 09, 2010, 03:57:17 PM »

Haplogroup HV is a west Eurasian haplogroup found throughout the Middle East, including Iran, Anatolia (present-day Turkey) and the Caucasus Mountains of southern Russia and the republic of Georgia. It is also found in parts of East Africa, mainly in the Sudanese Arabs  who also have a very high frequency of y-chromosome haplogroup J.

Much earlier, around 30,000 years ago, some members of HV moved north across the Caucasus Mountains and west across Anatolia, their lineages being carried into Europe for the first time by the Cro-Magnon. Their arrival was the second group(s) of anatomically modern humans in Europe (the first being mtDNA haplogroup U5). These continued migrations sounded the end of the era of the Neandertals, a hominid species that inhabited Europe and parts of western Asia from about 230,000 to 29,000 years ago. Better communication skills, weapons, and resourcefulness probably enabled them to outcompete Neandertals for scarce resources. Importantly, some descendants of HV had already broken off and formed their own group, haplogroup H, and continued the push into Western Europe.

A 2003 study was published reporting on the mtDNA sequencing of the bones of two 24,000-year-old anatomically modern humans of the Cro-Magnon type from Southern Italy. The study showed one was of either haplogroup HV or R0.
(from Wikipedia)
Has aiy one made aiy sense of the Neanderthal commonality with Eurasian (western i think) by the Max Plankl abs
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