End April 2013: new BaBuHe2012 Mutation Rate for standard use: 50 % Probability Average of Ballantyne et al. 2010, Burgarella et al. 2011 and Heinila 2012-04. New Group Colors:
- L1064*H PF5169 PF5174: positive: light blue, by haplotype: cyan
- YSC0000246*D: positive: lime, by haplotype: greenyellow
- PF5197: assumed by haplotype: yellow
- L24 L25 L70 etc.: positive: magenta, by haplotype: violet
- PF5116 PF5119*I (M47) M67 M92 L210 Z489 etc.: positive: coral, by haplotype: pink
- L26*A1 (xZ2221/PF5160 xPF5116): by haplotype: khaki
- L26*C (xZ2221/PF5160): by haplotype: silver
- L26: unsure by haplotype: orange, unknown by haplotype: gold
Mid. April 2013: Two interesting Geno 2.0 results confirm the major new subclade under J2a-L26 (probably after L24 and M67 the biggest): N88317 Yedidia (J2a▷L26▷Z2221/PF5160▷PF5197▷PF5169▷CTS3183.2, most probably related/nearest to *H-L1064), . By comparison with public Y-sequences a split is noted: N76290 Higgins is now J2a▷L26▷Z2221/PF5160▷PF5197▷PF5169▷PF5174▷PF5177. See also current J2a-M410 tree. Some changement in the project grouping and recoloring: *H-L1064 blue/cyan, PF5169-PF5174 cyan/green, PF5197-YSC0000246 dark-green, L24-L25 magenta, PF5116-PF5119 red, xPF5160 xPF5116 grey, unknown/unsure yellow/khaki.
Begin April 2013: 25365 Gattie does need a replacement kit, adress was corrected and the kit send out.
End Mar. 2013: Apart the grouping distance (75 %) from now on mainly 50 % Probability Ballantyne et al. 2010 & Burgarella et al. 2011 Simple Mean mutation rate will be used for comparisons. N65610 Santen Y-Refine12to67 493 ordered 01.12.2012 did come in on 27.03.2013: clearly seem to belong to the L1064 clusters in J-L250 project. Santen seems away ~33 generations from the Iberic/Med cluster (medium confidence) and ~42 generations from the North Sea/English cluster (good confidence). His 12 Marker matches from Southern Italy dont't show up on the 25/37/67 matches, but one (Rega Naples with 67 Markers) would be interesting to compare the haplotype. Ysearch.org again available. Pending results update: 25365 Gattie Y-Refine12to25 491 ordered 20.11.2012 (was expected 09.01.2013, then 18.02.2013, then 11.03.2013, now 01.04.2013), Y-Refine25to37 496 ordered 26.12.2012 (was expected 15.02.2013, then 04.03.2013, then 25.03.2013, now 22.04.2013)
Mid. Mar. 2013: 25 Markers for N65610 Santen; still no results for 25365 Gattie; Kohl/Yaeger has not joined yet. Re-Grouping of L1064 kits and adding of 12-Marker Haplotype designations: .A .B .C
Begin Mar. 2013: 181801 Pelan (Northern Ireland) from J-Project with 37 markers is a good match to *H-L1064 optimized modal (15 shared markers). DYS391 is not 9 (10). Marker upgrade, Geno 2.0 and/or L1064 test would be interesting. Ysearch.org was shut down because of abusive data mining: a great loss for haplotype research.
End. Feb. 2013: N76290 Higgins transferred his Geno2 results: he is L26▷Z2221/PF5160▷Z2397/PF5197▷PF5169▷PF5177. A very interesting result; also by comparison using 1000 Genomes NA21090 (GIH-Gujaratis) who does not share PF5177 etc. Geno2 shows J-PF5169, the same result as for a 12-marker match (Kohl/Yaeger) to the HC cluster (Gatter/Gattie, Kaser, Zanatta). This kit has not yet joined (only in contact). Higgins by haplotype is not far away from L1064+ and L198+. It seems very probable, that PF5169 will become a clade of major interest for this project. 229942 Garcia transferred his Geno2 results: he is in cluster *A1 and the results don't have a more terminal SNP then L26 for him. Cluster *A1 has probably his own (undiscovered) branch sub of L26 (more results needed to confirm). This is an important result because for low-res kits cluster *A1 and *H-L1064 are often near. Conrad (Kirk) donated $20. Pending results update:
- N65610 Santen Y-Refine12to67 493 ordered 01.12.2012 (was expected 23.01.2013, then 11.02.2013, now 04.03.2013)
- 25365 Gattie Y-Refine12to25 491 ordered 20.11.2012 (was expected 09.01.2013, then 18.02.2013, now 11.03.2013), Y-Refine25to37 496 ordered 26.12.2012 (was expected 15.02.2013, now 04.03.2013)
Mid. Feb. 2013: STR-Upgrades for 853 Gatter (boston), 5352 Gatter (phila), 159297 Fadel and most of the results from 027+HR Riyadh Subcluster are available. The Gatter relation is confirmed. Fadel looks nearer to Cluster *H on 37 then on 25 Markers. Still not available the following results: N65610 Santen Y-Refine12to67 and 25365 Gattie Y-Refine12to37. After they are received a major new STR-Marker comparison will be done.
Begin Feb. 2013: result for E4955 is Z2220+ (see J-M410 subclades and clusters overview). Every member who is in a group from 000 to 027 is encouraged to confirm this and do an Advanced SNP order for Z2220 and/or Z2221 and/or Z2222 or you can order Geno 2.0 test if you are interested also in the additional mtDNA and auDNA/X-DNA data and like to have high Y-SNP coverage. Conrad (Kirk) donated $20. Still many STR-Marker upgrade results are pending (FTDNA lab is maybe behind by huge amount of holiday sale orders):
- N65610 Santen Y-Refine12to67 493 23.01.2013 (now 11.02.2013)
- 25365 Gattie Y-Refine12to25 491 09.01.2013 (now 18.02.2013), Y-Refine25to37 496 15.02.2013 (now 15.02.2013)
- 853 Gatter (boston) Y-Refine25to37 ordered 31.12.2012 (now 497 20.02.2013)
- 5352 Gatter (phila) Y-Refine25to37 ordered 31.12.2012 (now 497 20.02.2013)
- 159297 Fadel Y-Refine25to37 ordered 31.12.2012 (now 497 20.02.2013)
- 15 members of 027+HR Riyadh Subcluster Y-Refine67to111 495 06.02.2013 (now 25.02.2013)
Begin Jan. 2013: 91 Members, 6 confirmed L1064+, 23 very good candidates (1 result pending), a bunch of speculative candidates and a dozen unresolved interesting members. Good distribution of DYS391=9 members from different J2a-L26 subclades. Total interesting SNP results at FTDNA:
- L250.2: 7/483, L251.2: 6/484
- L1064: 9/568
Investigation for additional near to *H haplotype and DYS391=9 kits in J-Project with the following interesting candidates:
- 76 168027 Ékes, Szentpéterszeg, 18th c. Hungary (37 Markers, M47 predicted by Bonnie)
- 49 181801 Northern Ireland (37 Markers, DYS391=10)
- 66 84809 Turkey (37 Markers)
- 66 85481 Turkey (37 Markers)
- 78 90848 Turkey (12 Markers)
- 49 E12932 Morlino Italy (37 Markers, DYS391=10)
- 66 105630 Abraham Brown , b 1701 Scotland (37 Markers, DYS391=10)
- 102 86848 Raffaele Aievoli, b.1877 and d.1950 Italy (37 Markers, M67 predicted)
Results: 166314 Maksoudian L1064+ (founder of a new subcluster), E4955 Kaser Z2221+ Z2227- (new ramification of Cluster *H downstream of L26 and upstream of known subclade L24, see J2a-M410 subclades and clusters overview). E4955 donate/orders Z2220.
End Dec. 2012: SNP result for 134080 Costa: he is confirmed L1064+ and by this a legitimate Cluster *H member. 25 Marker result of 159300 Namour: Seems more distant to Cluster *H with generation distance 81 to optimized haplotype. Conrad (Kirk) donated $25. Donation of $35 from Andre Nasr for 159297 Fadel. 33308 Weeks is confirmed L1064+ and by this also a legitimate Cluster *H member. 853 Gatter (boston) and 5352 Gatter (phila) 25 Marker results are back: membership of Cluster *H is strenghtened. N76763 Brochetti joins: at 12 markers he seems more a match to the distant h2a L70 cluster. To take advantage of the the last day of FTDNA sales a Y-Refine25to37 for 853 Gatter (boston) and 159297 Fadel was ordered from the project fund as no other interesting 12 Marker kits have joined in time. P. Gatter funded the Y-Refine25to37 for 5352 Gatter (phila).
Interesting pending results:
- 25365 Gattie Y-Refine12to25 PP3 491 09.01.2013, Y-Refine25to37 PP5 496 15.02.2013
- 33308 Weeks L1064 491 09.01.2013, Y-Refine37to67 MP6-MP8 496 15.02.2013
- 166314 Maksoudian L1064 492 16.01.2013
- 853 Gatter (boston) Y-Refine12to25 PP3 493 23.01.2013, Y-Refine25to37 ordered 31.12.2012
- 5352 Gatter (phila) Y-Refine12to25 PP3 493 23.01.2013, Y-Refine25to37 ordered 31.12.2012
- N65610 Santen Y-Refine12to67 MP6 493 23.01.2013
- 15 members of 027+HR Riyadh Subcluster Y-Refine67to111 495 06.02.2013
- E4955 Kaser Z2221, Z2227 496 15.02.2013
- 159297 Fadel Y-Refine12to25 PP3 496 15.02.2013, Y-Refine25to37 ordered 31.12.2012
Mid. Dec. 2012: First Geno 2.0 Y-DNA results are coming out. David Reynolds compared WTY and Geno 2.0 results for kits 20437, 173880, and 193834 all R1b-L21. 36 SNP where WTY & Geno 2.0 returned different results including L250. WTY allele is A and Geno2 allele is G. Project members with transferred results: N96517 Schliesser, N10172 Anonychuk, 139708 Frank.
37 marker result for 134080 Costa: no myFTDNA matches probably also because of a current Y-DNA "upgrade change" since 12th of Dec. causing loss of matches. Confirmed member of the Cluster *H with generation distance 32 to optimized haplotype and ~36 to YHRD.org 2/303 Central Portugal (genetic distance in mutation steps GD 1/16) and 33308 Weeks (GD 3/28).
Begin Dec. 2012: N65610 Santen ordered an upgrade to 67 Markers. Most of the Rabi'ah cluster have ordered (not paid) an upgrade to 111 Markers. 853 Gatter (boston) and 5352 Gatter (phila) join the project. They are matches on 12 Markers to 25365 Gattie and E4955 Kaser. Chris R. donated $70.
Funding of upgrade to 25 Markers for 853 Gatter and 5352 Gatter.
End Nov. 2012: Funding of L1064 SNP test to 166314 Maksoudian. N65610 Santen joins the project. He is a good match on 12 Markers to both the English, Portuguese and Central European cluster and he has two interesting full 12 marker matches: Rega (Italy, 67 Markers) and Tolva (Italy?, 12 Markers). N87875 Sicignano (Italy) seems another interesting DYS391=9 12 Marker kit.
Conrad (N37321 Taylor) donated $33.
Scanning in YHRD.org and scientific publications was moderately successfull for low confidence matches (17 Markers):
- YHRD.org 1/285 Kuwait City: clearly matching to the Rabi'ah/Bakr ibn Wa'il Micro-Cluster
- YHRD.org 1/202 Turkey: near to Rabi'ah/Bakr ibn Wa'il and Portuguese
YHRD.org 1/200 Minas Gerais Brazil;
YHRD.org 2/303 Central Portugal;
YHRD.org 1/50 Mato Grosso do Sul Brazil;
ETY_117 and ETY_130 in East Tyrol J-M304 (East & North) from Niederstätter et al. 2012 (270 samples, 17 Y-STRs, 27 Y-SNPs): match to E4955 Kaser etc.;
unsuccesfull in Reutte from Erhart et al. 2012 (261 samples, 17 Y-STRs, 19 Y-SNPs);
- Central European:
unsuccessful in Augsburg/Swabia), Rębała et al. 2012 (218 sampes, 39 Y-SNPs, 19 STR)
- YHRD.org 1/163 Palestine-Arab Israel: near to Figawi
The best SMGF.org candidates for J2a-L26*H haplotype cluster (37+ Markers, with distance to optimized haplotype and paternal ancestor indication):
- 14: Eight kits ca. 1870 El-Figawi from Beersheba, Palestine - near to Zanatta and Rot.
- 14: Simao Thomaz (Thuma), b. 1871, Kraibeth Al-Nasrah Syria - near to Joss
- 27: Two kits Luiz Zanatta b. 1896 Sao Paulo, Brazil (Origin Veneto?) Italy - very near to E4955 Kaser
- 27: Eusebio Perez Mexico - near to Portuguese cluster
- 27: Kabir Ullah b. 1895 m. Zubaida Jalal, Multan, Punjab, Pakistan
- 27: Effessoa (Joss), b. 1871 Tiko Cameroon - near to Thomaz
- 54: Unknown surname Azerbaijan
- 54: Unknown surname b. end 19th century? Malayer, Hamadan, C.W. Iran
- 54: Henry Tisdale Lothrop b. 6 Jun 1823 Randolph, Massachusetts (later Wisconsin) USA
- 54: Unknown surname Italy
Mid. Nov. 2012: 159300 Namour, 159297 Fadel and 166314 Maksoudian join the project. Funding of upgrade to 25 markers for 159300 Namour, 25365 Gattie and L1064 test for 134080 Costa, 33308 Weeks. Other invitations and upgrade offers are sended out.
Grouping by calculating the distance in generations to an optimized haplotype (nfm07-J-L1064): Distance nomenclature system is three digits; this nomenclature can change. Different Groups can have the same distance, but are divided by Macro-Cluster namenclature: This is either the part of the Haplogroup Name sub of J2a-L26 (FTDNA J2a4, ISOGG J2a1) and/or a haplotype Cluster Name (Paragroups from J-Project in J2a-L26*: A1, B, C, H, I, etc.). Between distance and group there is an indication of L250 status or presumption: + (positive), ? (unknown), ~ (probably negative), - (negative). Micro-Clusters are kits in the same Group (distance max. 19-39 generations): For already known J2a-L26 subclades the nomenclature in J-Project and L24-Project is used, research and additional naming is done primarily in the big Paragroups of J2a-L26* (A, C) and in J2a-L26*H-L1064. For every Micro-Cluster the lowest distance of a public kit with the highest STR-Marker coverage is choosen for all other kits/members.
Interesting contact to Gatter Surname DNA Project Admin. One private 12 marker kit possibly from Philadelphia is a perfect match to E4955 Kaser. A marker upgrade to 25 is proposed to the possible match. A *H SNP and better time estimate for this branch is more then ever needed to verify some more family history hypotheses: The "Alpine" H* branch could be an Middle East immigrant in Roman Times who spread to the German borders (Gatter/Gattie) and later went back south to Tyrol (Rot.) and also (or stayed) to Veneto (Zanatta). But also a later expansion is possible: the branch went to Veneto (Zanatta) and later to Tyrol (Rot.), while Gatter/Gattie could be religious refugees to Southern German territories from the persecution of the Reformed in Tyrol. Exciting!
FTDNA Holiday Sale 2012! (products link). Also for new 37/67 marker kits. Especially low marker kits should use this period until 31 of December to upgrade.
Go to myFTDNA > Order an Upgrade > Order Special Offers > Select A Product:
12 Marker kits: Y-Refine12to25 $35 ($49), Y-Refine12to37 $69 ($99), Y-Refine12to67 $148 ($189);
25 Marker kits: Y-Refine25to37 $35 ($49), Y-Refine25to67 $114 ($148);
37 Marker kits: Y-Refine37to67 $79 ($99), Y-Refine37to111 $188 ($200);
67 Marker kits: Y-Refine67to111 $109 ($129);
Conrad (N37321 Taylor) is really generous with the project: until 13 Nov. 2012 he has donated $172! Exciting Upgrades can now be proposed to different (potential) members to advance the progress of the project. Interesting kits with only 12 markers (upgrade to 25) or without L1064 SNP test will be contacted regarding interest. Those who respond first and give their consent to the proposed test, receive funding until the fund is exhausted (possibly in the FTDNA sale period).
Begin Nov. 2012: STR-cluster J2a-L26*H-L1064 (ysearch optimized modal GKAAZ, matches) list of the most interesting 12 STR-marker kits. Upgrade of STR-Markers (to 37 or 67) would be very interesting to possibly test/confirm L1064, L250.2 later:
- 25365 Gattie France/Germany (ysearch 2ZVTB, matches): match to PC48P Zanatta from North Italy and therefore probably near to E4955 Kaser.
- Rodriguez Canary Islands Spain (ysearch KBEJN, matches): has not joined yet, possibly near to 134080 Costa and distant to P6845 Santen and 25365 Gattie.
- 159297 Fadel and 159300 Namour from Lebanon (members of J-Project): have not joined yet, probably distant to 122074 Galarneau. Other 12 Marker matches to them: Abidavid, Nassr
- Potenza Calabria Italy (ysearch WFA8A, matches): has not joined yet, probably distant to E4955 Kaser and M6425 UAE.
- Santen (ysearch P6845, matches): has not joined yet, probably distant to 134080 Costa.
- Albertazzi Lombardy Italy (ysearch PZ3H9, matches): has not joined yet, possibility distant to PC48P Zanatta and E4955 Kaser; or J2a L25+ L70+ near to 157734 Zeni Lombardy, 215025 Sivera Piemonte etc.; or J2a M67+ 86848 Aievoli Italy (South?), N54176 Romanelli Italy
- Brochetti North Italy (ysearch PAD4X, matches): has not joined yet, possibility distant to E4955 Kaser.
Other interesting kits and upgrades in STR-cluster J2a-L26*H-L1064:
- 166314 Maksoudian Lebanon/Armenia? (member of J-Project): 37 STR-marker kit, has not joined yet, distant to 122074 Galarneau. Test/Confirmation of L1064, L250.2 and later upgrade to 67 STR-markers would be very interesting.
- M6425 UAE United Arab Emirates (member of J-Project, J2-M172 and J2-Arab): Singleton (own Micro-Cluster), 67 STR-markers, has not joined yet. Test/Confirmation of L1064, L250.2 and upgrade to 111 STR-markers would be very interesting to have good coverage of this Micro-Cluster.
- 122074 Galarneau France (ysearch 78ZU3, matches): Singleton (own Micro-Cluster). Upgrade to 111 STR-markers would be very interesting to have good coverage of this Micro-Cluster.
- 134080 Costa (ysearch T6V9D, matches): refinement from 25 to 37 markers is pending. Check of L1064 would be interesting. If clear Micro-Cluster further marker upgrade interesting.
- 33308 Weeks (ysearch HHQWN, matches): Check of L1064 would be interesting.
- N37321 Taylor (ysearch N9S4R, matches): Geno 2.0 planned for possibly new Y-SNPs. L1064 probably not included to check additionally.
- M5038 Riyadh, 218737 Riyadh and 218734 Riyadh and 183096 Eneza (has not joined yet, member of J2-Arab) most interesting (diverse) Arab cluster kits for upgrade to 111 STR-Markers and/or check of L1064. Cluster kits in ysearch: M5007 Ali NR5FR, 3S23K Shihab (has not joined yet).
End Oct. 2012: Some more possible resources (not invested nearer) of X-to-Y-gene-conversion.
- Thomas Krahn, Recombinational Loss of Heterozygosity (recLOH), 2009?, DNA-Fingerprint, Link
- Rosser, Balaresque and Jobling, July 2009: The rate of X-to-Y conversion (per base per generation) is four to five orders of magnitude more rapid than the rate of Y-chromosomal base-substitution mutation [...], Link
- Cruciani et al. 2012: [...] In October, our group presented evidence for X-to-Y gene conversion within the VCY (MIM 400012) genes,3 a region that lies within the male-specific portion of the Y chromosome (MSY) and is different from the PRKY region. Thus, both studies indicate that a new form of genetic exchange occurs between the sex-specific portions of X and Y and that this process has been active in recent human evolution. [...] Link
- Trombetta, Cruciani, Underhill, et al. 2010: [...] On the other hand, clear evidence for the VCY genes in the P8 palindrome having acted as an acceptor of X-to-Y gene conversion was obtained. A rate of 1.8 × 10−7 X-to-Y conversions/bp/year was estimated for these genes. [...] Link
- Niederstätter , Berger , et al. (2012 preprint): Multiple recurrent mutations at four Y-chromosomal single nucleotide polymorphism sites in a 37 bp sequence tract on the ARSDP1 pseudogene
Mid. Oct. 2012: Communication with admin (see Wayeel J2a4* project) and members mainly from Riyadh (generally Najd region) and a Kuwaiti branch. They mainly claim to be members of the great Bani Wael (Banu Bakr ibn Wa'il) clan with another branch claiming membership in the Eneza (Al Enezi, 'Anizzah?) clan. Interest to upgrade and for further research progress is there. All 18 High-Res kits (16 with 67 and two with 111 STR-markers) join the J-L250 project. First discoveries about the history of Wa'il and Eneza clan especially before the Spread of Islam out of Arabia 632–661 CE. Banu Bakr ibn Wa'il had a 40-year War of Basous (Albasus) from 494-534 CE with cousins from Banu Taghlib ibn Wa'il. Both tribes are reported as Christian Arabs. The connections to the possible center of J2a spread in northern Fertile crescent (see Al-Jazirah - map and Assyria) can be found in classical Arab genealogies: Banu Bakr ibn Wa'il together with 'Anizzah, Taghlib, and Bani Hanifa is member of the large Rabi'ah branch of Adnanite Arab tribes. Bakr's original lands were in Najd, in central Arabia, but most of the tribe's bedouin sections migrated northwards immediately before Islam, and settled in the area of Al-Jazirah, specifically Diyar Rabi'a (Upper Mesopotamia). Also 'Anizzah recorded by early Muslim scholars, had one nomadic branch, living in the northern Arabian steppes bordering Syria and Mesopotamia. Adnan itself is reported living ca. 122 BCE. It will be interesting to discover more and especially how much J1 and J2a and what deep clades are common in these tribes and clans. The first assumption is that the J2a from Assyria (Al-Jazirah) or nearby regions, merged into J1 groups when these clans migrated to that area. Looking at the Arab Tribes project the dominant HG for Adnan-Rabe'a is J1-L858-L222.2 with some J2a, R1b, E1b, G, etc. Later these tribes spread back in to Arabia and other Middle East places.
4/5 Oct. 2012: Communication with Harald Niederstätter (MSc., Innsbruck Medical University) about a possible "gene conversion to Y" of L250, L251 and L252 from other chromosomes. Doing a "quick & dirty" sequence alignment Mr. Niederstätter thinks chr3 is the best candidate to be the source of this multiple SNP changement, if a gene conversion did really occur. To get evidence extended and expensive lab research (sequencing) would be needed. A random parallel mutation of L250 etc. (= recurrent) seems more and more improbable. Maybe Geno 2.0 or public high coverage sequencing helps to find other clades where the same or similar SNPs occured and to find better alternative SNPs. An extended comparison of J-L250 kits and the closest haplotypes was done to have a better overview.
2 Oct. 2012: Resetting based on third haplotype comparison (294 kits including SMGF haplotypes); 9 fastest mutating markers (over 0.005) excluded; used for rebuilding micro-clusters and macro-groups based on haplotype profiles. Y-Utility setup file and NJ-tree PDF here. Bonnie Schrack asked FTDNA lab director Thomas Krahn about the unexpected L250.2- result of kit 110692. He answered: "Yes L250 is probably the culprit. The wholeL15L23L76L79L130L142L147L192... segment seems to be dangerous which involves quite a lot of well established SNPs. We may need to re-thinkphylogeny with those markers removed and see what it'll impact. I checked the sequencing traces but I couldn't find a technical error." I sended another mail with further questions: is L1064 involved and Y-SNP status about two unknown L1064+ kits?
M7424 Al-Saleh L1064+, L250.2+, L251.2+
M7436 Al-Ajeel Al-Askar L1064+, L250.2+, L251.2+
E4955 Kaser L1064+, L250.2+, L251.2+
122074 Boyle (Gardner) L1064+, L250.2+
N37321 Taylor (L1064+, L250.2+, L251.2+)
110692 Amprayil-Cherian L250.2-, M68+
M6882 Jasim Al-Hashimi (L1064-, L250.2+, L251.2+), M68+
1 Oct. 2012: Kit 110692 Amprayil-Cherian India (M68+, 67 markers) result comes back: L250.2-! By this new questions arise about the stability of L250.2/L251.2 and/or M68. Kit M6882 Al-Hashimi Iraq (M68+, 111 markers) is presumed to be positive for L250.2 and L251.2 and negative for L1064 (inofficial internal FTDNA lab result by primers readout of nearby SNP L229, M68+ was tested a bit later by final Deep Clade test results). There is one other Kit with M68+ tested by FTDNA: N12509 Rodrigues India (25 markers), a low marker kit with no SNP tests presumed to be related primarily to 110692: kit 94035 Abraham Karuvelil India (12 markers) and one interesting kit near by haplotype to 110692 and M6882 but tested M68- (L250.2/L251.2 and L1064 are untested): 123673 Demby Unknown Origin (67 markers). For comparison currently on YHRD.org three M68+ haplotypes (17 markers) all from Malaysia are published, the reference is Chang et al 2007. Bonnie in June 2012 published some very helpful information shared by Roy King from Peter Underhill on M68+ samples he knows: Tadjik sample collected by Spencer Wells in Central Asia (M68 was discovered in this one by Underhill); Hindu/Indian sample collected by Ornella Semino, Iraqi sample collected by Ornella Semino. The latter two are found in Semino et al. 2004 paper about E & J (see Table 2 Freq. J).
By my latest STR-comparisons I could observe a good differentiation of J2a-L1064, but not of nearby J2a-M68 and J2a-L26*A. They both mixed up constantly. At least one J2a-M68 haplotype from Chang et al also seems to be very diverse, but more markers would be needed to get more clarity.
By writing to Thomas Krahn, Bonnie Schrack, Tim Janzen and JaG I hope to get all better informed about the situation and maybe Thomas Krahn can help to clarify this puzzle.
Current Y-SNP status - FTDNA kits positive/tested (ytree.ftdna J2a-L26, J2a-L250)
- L26: 412/969, L27: 228/722, L927: 30/96
- L250.2: 7/479, L251.2: 6/482
- L1064: 7/541
- M68: 3/681
Background page information:
Your benefit when you join - description of the group names (00H+, 10d-, 22*A1?~, etc.):
Main quests of this project - you help to clear them by joining
- Bringing high and low resolution kits together: High-res kits (67+ STR-Markers, deepest terminal SNPs) will be used as "anchors" for Low-res kits (37 or less STR-Markers, no SNPs under J2a-L26). The Grouping will be done by building Macro-Clusters: nomenclature system is two digits, the Genetic Distance (GD) is high (30-100 generations by STR) but near enough to differ from most other STR-Clusters; this nomenclature can change when new evidence or better comparisons are available. Different Lineages (Haplogroups) can be in the same Macro-Cluster. Micro-Clusters are kits in the same group: nomenclature are capital letters for haplotype clusters (under research) and small letters for confirmed SNP clades sub of J2a-L26; the GD is low (max. 19-39 generations); nomenclature should remain stable. Additional sign description: + positive for L250.2; - negative for for L250.2;, ~ presumed negative for L250.2; ? SNP not tested or geographical region in the Micro-Cluster not comfirmed by three diverse kits. Group background colors also try to indicate the situation regarding L250.2 and testing situation.
- Understand what Low-Res matches are "false": The FTDNA-Match-calculation is not able to detect the most interesting Low-res matches and J-L250 project tries to help here. If you see your Low-res matches grouped here in different Macro-Clusters, they are probably "false matches" and you don't need to invest in contacting them. Every group will have confirmed (+) or interesting (?) SNPs listed. Micro-Clusters are marked with the probable area of expansion.
- Get help for your best next upgrade: Trough work and cooperation in J-Project, ISOGG-SNP research and with the FTDNA-Lab a suggestion for the next step will be given. It should be easier for you to decide if a single SNP test, a Y-STR-Marker upgrade (Y-Refine) or a huge step like the "new deep clade" test Geno 2.0 is the best. See Help (Glossary).
28 Sep. 2012
- What J-samples/kits are tested L26+ or L27+ or L927+ and also positive for one or more of these SNPs: L250.2, L251.2, L1064, M68?
- What J-samples/kits cluster by STR-haplotype to the previous ones (have a similar/matching STR-marker values pattern)?
- How widespread are all these samples/kits (paternal ancestor locations)?
- Why are J2a-L1064 and J2a-M68 modal haplotypes so diverse and near to many other clades/clusters downstream of J2a-L26?
- Are L250.2/L251.2 reliable and stable SNPs?
: Work on the third haplotype comparison
(241 kits including SMGF haplotypes); 19 fast mutating markers (over 0.0036) excluded
; new quality of cluster separation; Y-Utility setup file here
; kits below 37 markers where excluded (to few markers for comparison). Possible relevant DYS loci values
for haplogroups/clusters under investigation:
27 Sep. 2012
- J2a-L1064 (17 haplotypes): DYS391=9 (all 17), DYS390=22 (12, 5 have 23), DYS461=12 (12, one has modal 13, one 11, one 14), DSY441=13 (11, 2 have L26 modal 14, 2 have 12 and 1 is 16), DYS446=11 (10, 3 have L26 modal 13, two 12, two 10)
- J2a-L26*A (9 haplotypes): DYS531=10 (7)
- J2a-L26*C: DYS388=17, DYF395S1=14-14, DYS643=9
: Resetting based on second haplotype comparison
(212 kits including SMGF haplotypes); 9 fastest mutating markers (over 0.005) excluded
; used for rebuilding micro-clusters and macro-groups based on haplotype profiles. Y-Utility setup file and NJ-tree PDF here
26 Sep. 2012
: a new Y-STR mutation model
will be used in the future. It is the mean DYS loci value between Ballantyne et al. 2010 and Burgarella et al. 2011
. You can find the Y-Utility setup file here
. First base haplotype comparison done (184 kits including SMGF haplotypes); all markers used; used for building micro-clusters and macro-groups based only on haplotype profiles. Project groups created. Current members grouped.
Aug./Sep. 2012: multiple Y-STR comparisons
mainly with McGee Y-Utility
(Burgarella et al. 2011 mutation rates) of many haplotypes partly matching to J2a-L1064 and J2a-M68 kits. J2a-L250 modal haplotype was not used because it is currently very unsure. Haplotypes of SMGF.org where added and similar haplotypes in public FTDNA projects searched. Overlapping haplotypes from other haplogroups and similar haplotype clusters with terminal SNP L26 (nomenclature from J Project Sep. 2012): J2a-M67 (b), J2a-M47 (a), J2a-L24 (h), J2a-L198 (i), J2a-L26*Cl.A, J2a-L26*Cl.B, J2a-L26*Cl.I and Singletons. A very confusing situation, which does not allow for clear assignation of certain interesting kits. Main Project sources: Y-DNA J
, J2 Arab
, J2a4 Levant
, Arab Tribes
, Arab World
, Middle East
, etc. (see Y-DNA J Links
- Finalize the first STR comparisons and GD (genetic distance) calculations by various methods (FTDNA, Burgarella, McDonald, etc.) resulting in various phylogenetic outputs (trees, NJ, etc.).
- Build "micro-clusters" (max. GD 20-40 generations, full STR-Markers use) with nomenclature system A. This nomenclature should remain stable for a longer time.
- Predict a first macro-grouping (GD 30-100 generations, excluding fast mutating Markers) with nomenclature system B. This nomenclature probably changes relatively often when new evidence (test results/upgrades) is available.
- Build Project groups ordered by nomenclature system B.
- Invite to join the Project: J2a-L1064 and J2a-M68 kits - in family/clan/tribe clusters focusing on high STR-Marker coverage and wide SNP testing. Additionally invite the broadest range of nearby haplotypes also of kits proven to be of sibling haplogroups for future research and comparison, giving all members the possibility to better distinguish between matching kits with no SNP evidence.
- Invite to test for missing SNP or STR evidence: focusing on interesting kits/clusters and evaluating single SNP testing vs. upcoming Geno 2.0 test vs. STR-Marker upgrade.
- Additional diversity information from up- and downstreaming SNPs. Currently in 1000 Genomes samples new SNPs positive in J2a-M67 (b) and J2a-M47 (a) where discovered. Some (Z2224-Z2235 in registration) by Bonnie Schrack, Thomas Krahn, et al. (FTDNA Y-SNP research community) and supposedly others (unpublished) by Chris Taylor-Smith et al. mainly for the Genographic Project (Geno 2.0 chip).
- Recurrent SNPs behaviour information: see for example proposed X-to-Y gene conversion for P37, P41, L202, L203 by Niederstätter et al. (not published, DNA in Forensics 2012 speak).
- Searching for help, support and funding of the project goals.
18 Sep. 2012: Current Y-SNP status - FTDNA kits positive/tested
28 Aug. 2012:
- L26: 409/960, L27: 228/716, L927: 30/91
- L250.2: 7/478, L251.2: 6/482
- L1064: 7/535
- M68: 3/680
new evidence provided by Vince Tilroe
in the 1K Genome sample HG01781 (J2a-M319): L1064- L250-
. Like J2a-M67 and J2a-L24 the third major subclade of J2a-L26 has revealed negative for important J-L250 project SNPs by public Y-sequencing samples. Also a statement by Bonnie Schrack "the 1K Genome data sheets we use show only those SNPs that have varied among the samples included in it. If none of those samples had a mutation at that position, or if all of them are null, it won't be listed on the sheet. Such seems to be the case with L250 and L1064.
" So currently probably there are no 1K Genome J-samples with L250+ or L1064+.
23 Aug. 2012
: Project was founded by ChrisR
. As everyone can follow in Y-DNA J Project
and J-L26 J2a1/J2a3/J2a4 subclades SNP discoveries news info
the new subclade of the recurrent SNPs L250.2, L251.2 (first found in E-V13) is almost defined in Aug. 2012 by SNP testing in other clades and clusters. This was the reason to found a project about this new haplogroup containing a former J2a-L26* cluster (FTDNA2009 J2a4* and now J2a-L1064) and the existing J-M68 clade (FTDNA2009 J2a4c).
The new J2a-L250 clade is downstream of J2a-L26 (FTDNA2009 J2a4 defined by L26=Page55/S57, L27=S396 and probably L927). Probably in fall 2012 new SNPs between J2a-L26/L27 and J2a-L250/L251 will be available by Advanced SNP Order at FTDNA and by Geno 2.0 testing.
J2a-L250 in Aug. 2012 has no nomenclature name at FTDNA, ISOGG or YCC. FTDNA, scientists and others have anounced to use primarily shorthands like J-L250 or J2a-L250. This project prefers to use haplogroup names like J2a-L250 or J2a-L1064 (indication of major haplogroup and terminal SNP), while the project name is J-L250.
Pre J-L250 project news
see also J2a3/4* (J-L26*): new SNPs to test: L250.2, L251.2, L1064
22 Aug. 2012
: Current Y-SNP status - FTDNA kits positive/tested:
- L250.2: 6/475, L251.2: 5/481
- L1064: 6/522
- M68: 3/680
: Many J2a-L26* (called also J2a3* by ISOGG in June 2012) cluster kits in J-Project where contacted for testing L250.2 and L1064
. The nearest to J2a3* Custer H and J2a-M68 (J2a3c) and most suspected for a possible positive result are: J2a3* Cluster B, J2a3* Cluster I, J2a3* Cluster A1. The call overlapped with the research on L927
, a SNP tought to be L927- in a WTY kit (23417) from the J2a3* Custer C and by this predicted to be able to split J2a-L26 in two subclades, because it was positive in J2a-L24 and J2a-M67 kits. As later was confirmed, the WTY call for the SNP in 23417 was null (non existant) and all J2a-L26 turned out to be L927+
: Thomas Krahn reported kit M6882 to be L250.2+, L251.2+ and L1064-
(negative)! Thomas Krahn added "Approx. hg: J-L26 L250.2, L251.2, L1064" to his ytree draft
. Later (~19 June) by deep clade test the kit reveals to be M68+
and had 111 markers available. Roy King shares information from Peter Underhill on M68+ samples: Tadjik (collected by Spencer Wells, M68 discovered 2000 by Underhill)
, Indian and Iraqi sample (collected by Ornella Semino and published in the 2004 paper). 5th june 2012 info from ytree (to log the count of derived/tested):
- L250.2: 4/349, L251.2: 3/360
- L1064: 3/359
: Bonnie Schrack (J-Project Admin) and Chris Rоttеnѕtеіnеr (new J-Project Co-Admin) are informed by Thomas Krahn in detail about the discovery of L250, L251 and L1064 in some kits of "cluster H
" in J2a-L26*. This was possible because ytree or ymap system showed more positive results for L250 and L251 than the FTDNA lab thought there should be. L250 and L251 were originally found in E-V13, together with L252, in the same Y-sequence. They searched and found that 3 kits were positive for those two known SNPs, and also for a new one, L1064
. All of these kits have tested (negative) for nearby SNPs. For every SNP test a chromat
is produced. Chromat is a short form of "chromatogram," a term for a lab read-out of a Y-Sequence limited by the primers of the tested SNP. This read-out is often long enogh to include other SNPs. By this evidence the kits should be E4955 (L207.1-), N37321 (L229-) and M7436 (L229-). Their advanced SNP testing has helped in the discovery of the new SNPs! Because these test results were just uncovered by that indirect route, they don't show up on the personal pages or project SNP results of those participants, and they'll have to order these SNPs to have the results "officially" reported. Sorry about that, it's FTDNA policy. By ISOGG SNP List
(L1064 not in list):
There is no rs# (RefSNP ID) so it is not possible to Match rs# to a SNP
. 23andMe Y-tree stops at E1b1b1a2
(ISOGG E1b1b1a1b, i4000247
/ V13, i4000252
/ V36) so probably there is no possibility to get any information out of 23andMe v3 raw data. L1064 position by ytree
Before May 2012
: Bonnie Schrack (J-Project Admin) was able to build the "cluster H
" in J2a-L26* in J-Project. A very important first step, as later was confirmed.