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MfA
01-07-2014, 04:14 PM
Marker path from rCRS to haplogroup J1b3:
H2a2a1(rCRS) ⇨ 263G ⇨ H2a2a ⇨ 8860G 15326G ⇨ H2a2 ⇨ 750G ⇨ H2a ⇨ 4769G ⇨ H2 ⇨ 1438G ⇨ H ⇨ 2706G 7028T ⇨ HV ⇨ 14766T ⇨ R0 ⇨ 73G 11719A ⇨ R ⇨ 4216C ⇨ R2'JT ⇨ 11251G 15452A 16126C ⇨ JT ⇨ 295T 489C 10398G 12612G 13708A 16069T ⇨ J ⇨ 462T 3010A ⇨ J1 ⇨ 8269A 16145A (16222T) 16261T ⇨ J1b ⇨ 8460G 16235G ⇨ J1b3

J1b3 Armenian, Assyrian, Irish, Italian, Kurdish(all 23andMe), Armenian (Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5)) (A8460G, A16235G)
-J1b3a HM594676 (http://www.ncbi.nlm.nih.gov/nuccore/HM594676) Armenian (FTDNA), EF583175 (http://www.ncbi.nlm.nih.gov/nuccore/EF583175) Slovakia, EF583177 (http://www.ncbi.nlm.nih.gov/nuccore/EF583177) Slovakia(Malyarchuk 2008) (T16271C)
-J1b3b JQ797775 (http://www.ncbi.nlm.nih.gov/nuccore/JQ797775) Greece, HM852838 (http://www.ncbi.nlm.nih.gov/nuccore/HM852838) Iranian, Kurdish(23andMe) (T15530C)
--J1b3b1(15172T, 15490)
---J1b3b1a Persian(Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5)) (152<, 10685<)
---J1b3b1b Persian(Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5)) (2833, 3010)

http://abload.de/img/desktop_2014_01_07_18zacdi.png
http://download.cell.com/AJHG/mmcs/journals/0002-9297/PIIS0002929712002042.mmc1.pdf

According to this (http://download.cell.com/AJHG/mmcs/journals/0002-9297/PIIS0002929712001462.mmc1.pdf) paper J1b3 is ~3 kyo.

newtoboard
01-07-2014, 04:23 PM
Nice work. Seems like a good candidate for a Neolithic dispersal to Central Asia and maybe South Asia.

MfA
01-07-2014, 04:34 PM
Nice work. Seems like a good candidate for a Neolithic dispersal to Central Asia and maybe South Asia.
You are talking about J1b though.
J1b3 is quite young and haven't spread much out of Anatolia-Iranian plateau.

newtoboard
01-07-2014, 05:08 PM
Yea my mistake. Statement applies to J1b and likely J1b1. J1b3 seems to have a similar distribution to J1b4 in that it is most concentrated in the South Caucasus, Iranian plateau and Eastern Anatolia.

Humanist
01-08-2014, 04:40 AM
J1b3 Armenian, Assyrian, Italian, Kurdish(all 23andMe), Armenian (Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5))
-J1b3a HM594676 (http://www.ncbi.nlm.nih.gov/nuccore/HM594676) Armenian (FTDNA), EF583175 (http://www.ncbi.nlm.nih.gov/nuccore/EF583175) Slovakia, EF583177 (http://www.ncbi.nlm.nih.gov/nuccore/EF583177) Slovakia(Malyarchuk 2008)
-J1b3b Greece(JQ797775 (http://www.ncbi.nlm.nih.gov/nuccore/JQ797775)), Iranian(HM852838 (http://www.ncbi.nlm.nih.gov/nuccore/HM852838)), Kurdish(23andMe)
--J1b3b1
---J1b3b1a Persian(Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5))
---J1b3b1b Persian(Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5))

http://abload.de/img/desktop_2014_01_07_18zacdi.png
http://download.cell.com/AJHG/mmcs/journals/0002-9297/PIIS0002929712002042.mmc1.pdf

According to this (http://download.cell.com/AJHG/mmcs/journals/0002-9297/PIIS0002929712001462.mmc1.pdf) paper J1b3 is ~3 kyo.

Pala et al. (http://www.sciencedirect.com/science/article/pii/S0002929712002042) and Behar et al. ages are significantly different.

Pala et al.

http://i1096.photobucket.com/albums/g326/dok101/Faces/J1b3.jpg


Also, it is interesting to note that Italians are among the populations. Again.

Humanist
01-08-2014, 08:13 AM
M5a1, M18, M25, M35b, U3, H7, J1b, J1b3, J1c1, X2e and X2d represent the minimum component of ancestral lineages already present in the most ancient Roma groups settled in Europe. Probably most of these lineages were incorporated in the Roma before the arrival to the European continent.

Reconstructing the Indian Origin and Dispersal of the European Roma: A Maternal Genetic Perspective (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015988)

Mendizabal et al.

MfA
01-08-2014, 12:57 PM
Reconstructing the Indian Origin and Dispersal of the European Roma: A Maternal Genetic Perspective (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015988)

Mendizabal et al.

Very interesting, thanks for the paper..

Even so, the conservative identification of the founder lineages M5a1, M18, M25, M35b, U3, H7, J1b, J1b3, J1c1, X2e and X2d allowed us to obtain maximum admixture proportions with host populations. Overall, the incorporation of female lineages from non-Roma appears to have been low since most of the sequences present in current Roma are rare in the European host populations, suggesting that the majority of lineages were already present in Roma before their arrival in Europe. The phylogeography of the Roma founder lineages demonstrates a broad West Eurasian origin (except those belonging to macrohaplogroup M) not confined to Western Europe. In fact, haplogroups such HV, pre-HV, J-T, U-K, I, W and X are present in highest frequencies in the Anatolian/Caucasus and Iranian regions [38] being moreover still present at relatively high frequencies in the Indus Valley and Central Asia [38], [43]. Given this distribution, higher phylogeographic resolution is needed to distinguish among lineages from such a broad geographical area.

Some of them may be found there but not J1b3 as it is strictly E Anatolian/NW Iranian. So they received J1b3 on their journey somewhere in these route before arrival to Europe.

I identified all samples are belong to J1b3a with 16271 mutation, Hap25 is similar to Slovakian samples, while Hap26,27,28 similar to Armenian with extra 16519 mutation..



Sample ID Polymorphic sites (16024-576) Haplogroup N RoPor N RoBarc SNP*
Hap25 16069 16126 16145 16222 16235 16261 16271 73 263 295 309.1C 315.1C 462 489 J1b3 0 1 n.d.
Hap26 16069 16126 16145 16222 16235 16261 16271 16519 73 146 263 295 315.1C 462 489 J1b3 1 0 n.d.
Hap27 16069 16126 16145 16222 16235 16261 16271 16519 73 263 295 309.1C 315.1C 462 489 J1b3 7 0 n.d.
Hap28 16069 16126 16145 16222 16235 16261 16271 16519 73 263 295 315.1C 462 489 J1b3 6 0 n.d.


J1b3a was found in all Roma except the Lithuanian(maybe something to do with low sample size of the latter).. It was distributed mainly on Iberian and Polish Roma..

http://abload.de/img/journal.pone.0015988.ldegh.png

MfA
01-08-2014, 01:05 PM
BTW I found a Irish J1b3 from Little bit's spreadsheet (https://docs.google.com/spreadsheet/ccc?key=0AqARKoDx3EVHdGJkd3ptRVhDSll2WHFocmg0SU0ta UE&hl=en_US#gid=0). Not sure if that will be a J1b3a like Romas at mthap tool or related with Irish travellers although they seem to be not connected with Romas other than living style.


Pala et al. (http://www.sciencedirect.com/science/article/pii/S0002929712002042) and Behar et al. ages are significantly different.

Pala et al.

http://i1096.photobucket.com/albums/g326/dok101/Faces/J1b3.jpg

Also, it is interesting to note that Italians are among the populations. Again.

Which one should we take consider? I see Pala et al is a month newer than Behar et al..

MfA
01-13-2014, 11:09 PM
I can't edit the first message anymore so I'll repost the updated scheme. Italian sample in the OP turns out J1b3b from Central-South Italy, so Greece, Italian J1b3b might be linked.

There is a new paper (http://biorxiv.org/content/early/2014/01/13/001792) which brought 3 new J1b3 to table, no further clades reported, 2 Balochis and a Brahui.
Don't want to sound biased here but Balochi people speaks Northwest Iranic language and Balochi and Brahuis are very similar folks in terms of genetics.. So this might be a signature of the Balochis brought J1b3 from E Anatolia/NW Iran to their current location.

http://abload.de/img/desktop_2014_01_14_00lii64.png

J1b3 Armenian, Assyrian, Irish, Kurdish(all 23andMe), Armenian (Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5)), HGDP00052 Balochi, HGDP00078 Balochi, HGDP00023 Brahui(Lippold 2014 (http://biorxiv.org/content/early/2014/01/13/001792.figures-only))(A8460G, A16235G)
-J1b3a HM594676 (http://www.ncbi.nlm.nih.gov/nuccore/HM594676) Armenian (FTDNA), EF583175 (http://www.ncbi.nlm.nih.gov/nuccore/EF583175) Slovakia, EF583177 (http://www.ncbi.nlm.nih.gov/nuccore/EF583177) Slovakia(Malyarchuk 2008) (T16271C)
-J1b3b JQ797775 (http://www.ncbi.nlm.nih.gov/nuccore/JQ797775) Greece, HM852838 (http://www.ncbi.nlm.nih.gov/nuccore/HM852838) Iranian, Italian, Kurdish(23andMe) (T15530C)
--J1b3b1(15172T, 15490)
---J1b3b1a Persian(Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5)) (152<, 10685<)
---J1b3b1b Persian(Derenko 2013 (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0080673#s5)) (2833, 3010)

MfA
07-16-2014, 06:48 PM
Ian Logan is very kind to add me GenBank.
http://www.ianlogan.co.uk/sequences_by_group/j1b_genbank_sequences.htm

For those who interests, all you need to do is uploading your 23andMe raw data to OpenSNP.org (https://opensnp.org)

Dr_McNinja
07-17-2014, 03:05 AM
Ian Logan is very kind to add me GenBank.
http://www.ianlogan.co.uk/sequences_by_group/j1b_genbank_sequences.htm

For those who interests, all you need to do is uploading your 23andMe raw data to OpenSNP.org (https://opensnp.org)
Do you have to upload the whole thing or only the mtDNA?

Humanist
07-17-2014, 04:52 AM
Do you have to upload the whole thing or only the mtDNA?

I do not know about MfA, but I have my entire raw data file uploaded at OpenSNP.

MfA
07-17-2014, 07:15 AM
Do you have to upload the whole thing or only the mtDNA?

No you don't, only mtDNA raw data is enough.

MfA
03-22-2017, 11:52 AM
Looks like J1b3 originated in or around Iranian plateau, having both basal and the daugther clades based on modern samples. J1b3a seems to be found in Armenia.

Joana B. Pereira et al. 2017, Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe
(http://rspb.royalsocietypublishing.org/content/284/1851/20161976)

https://abload.de/img/j1b3f7uyz.png

Age estimates:, J1b3a has a very recent mrca data, from Armenia to Iberia, Slovakian samples are Romani people.

https://abload.de/img/age_j1b39judv.png

genbank submissions:
https://abload.de/img/j1b3_genbankxmusk.png

http://www.ianlogan.co.uk/sequences_by_group/j1b_genbank_sequences.htm