phylogenetic structure of q-m378 subclade based on full y-chromosome sequencing

8/11/2019 Phylogenetic Structure of Q-M378 Subclade Based On Full Y-Chromosome Sequencing

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The Russian Journal of Genetic Genealogy ( ): 5, 1, 2013 ISSN: 1920-2997 http://ru.rjgg.org RJGG

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Received: December 14 2013; accepted: December 16 2013;published: January 8 2014Correspondence: [email protected] [email protected]@yfull.com

Phylogenetic Structureof Q-M378 Subclade

Based On FullY-Chromosome Sequencing

Vladimir Gurianov1Leon Kull2Roman Sychev3Vladimir Tagankin3Vadim Urasin3

1 The Q-L275 Research Project, Russia,2 Full Genomes Corporation, USA,3 YFull research group, Russia.

Abstract

Q-M378 subclade, which is downstream of Q-L275 haplogroup, is marked by a wide area of its distributionand a minor share of presence in modern populations of Eurasia. Phylogenetic structure of the subclade, knownso far, did not allow for matching SNP Y-chromosomes to specific populations and to reconstruct possible direc-tions of their migrations in retrospect.

The conducted research enabled us to form a consistent phylogenetic structure of Q-M378 subclade, validatedby analysis of SNP and STR-markers, based on the data of full Y-chromosome sequencing using next generationsequencers. As part of the research, new phylogenetic levels of Q-Y2250 (downstream of Q-M378 and includingQ-L301), Q-Y2220 (downstream of Q-L245), Q-Y2200 (downstream of Q-Y2220) were defined.

SNPs, which, in the future, may possibly mark certain European and Asian subclusters of Q-Y2220 (includingthe Armenian subcluster), as well as separate branches of the Jewish cluster Q-Y2200, were defined as well.

The research also confirmed connection of Q-M378 subclade distribution with migration of Indo-Europeanlanguage carriers from Central Asia via Afghanistan and Iran to the West.

Introduction

The Q-M378 subclade1, downstream of Q-L275 haplogroup, is present in a number of pop-ulations in Europe, Southwest (Western)2 andSouthern Asia3, and also in the Central Asia allthe way to North-West China4.

1yDNA Haplogroup Q and its Subclades 2013 -http://www.isogg.org/tree/ISOGG_HapgrpQ.html. Hereinafter subclades are referenced in

line with ISOGG notation (International Society of Genetic Genealogy) specifyingsingle nucleotide polymorphism (SNP) typical for a respective subclade.2Cinnioglu et al, Excavating Y-chromosome haplotype strata in Anatolia, 2003.Haplotypes 337-339 according to predictor by Urasin (http://predictor.ydna.ru/) are

positive to SNP M378. All samples belong to Central-Anatolian and East-Anatolianregions of Turkey.3Sanghamitra Sengupta et al., Polarity and Temporality of High-Resolution Y-

Chromosome Distributions in India Identify Both Indigenous and Exogenous Ex-pansions and Reveal Minor Genetic Influence of Central Asian Pastoralists, Am JHum Genet. 2006 February; 78(2): 202221.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1380230/(among the tested inhabitants of

Pakistan 2 out of 176 or 1.14% were positive to SNP M378; SNP M378 was not

identified among sample groups in India and Eastern Asia).4Zhong et al., Extended Y-chromosome investigation suggests post-Glacial mi-

grations of modern humans into East Asia via the northern route // Molecular Bi-ology and Evolution, First published online: September 13, 2010, doi:10.1093/molbev/msq247 (among four populations of Uigurs from Xinjiang onesuch person was found in each of the two populations: 1 out of 71, 1 out of 18).

One of the peculiar features of Q-M378 sub-clade is a relatively wide area of its distribution(connected with migrations of ancestral popula-tions of the Indo-European language family) andan extremely low percentage in almost all popu-lations (modern ethnic groups), where it hasbeen reported by now. The exception is the Jew-

ish Diaspora (primarily Ashkenazi Jews), whereQ-M378 subclade share reaches 5.2 to 7 percent(Behar 20045, Hammer 20096). Therefore, Q-M378 locality is often associated with the MiddleEast. In the meantime, a more comprehensiveanalysis of research data and publicly availabledata of commercial tests enables us to draw aconclusion on more complex and rather unob-

5 Behar DM, Garrigan D, Kaplan ME, Mobasher Z, Rosengarten D, Karafet TM, Quintana-Murci L, Ost-

rer H, Skorecki K, Hammer MF. (2004)."Contrasting patterns of Y chromosome variation in AshkenaziJewish and host non-Jewish European populations". Hum Genet114(4): 354365.doi:10.1007/s00439-003-1073-7. PMID 14740294

6Hammer MF, Behar DM, Karafet TM,et al.(November 2009). "Extended Y

chromosome haplotypes resolve multiple and unique lineages of the Jewishpriesthood".Human Genetics126(5): 707717. doi:10.1007/s00439-009-0727-

5.PMC2771134. PMID19669163.


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vious correlations between carriers of this Y-chromosome mutation for the last millennium.

The article's aim is to, based on the available

data from open sources and conducted researchdata, specify phylogenetic structure of Q-M378subclade and provide classification of its majorclusters (haplotypes, combined according to thefollowing criteria: pertaining to a sequence of asingle SNP - single nucleotide polymorphisms,phylogenetic similarity, geographical distribu-tion).

Source data and methodology

Data sets for comparison

Data from the Personal Genome Project7

and the 1000 Genomes Project8 were usedwithin the framework of the conducted research.Samples, taken from the specified projects (Ta-ble 1), have PGP and HG prefixes respectively.

7 http://www.personalgenomes.org/ See also: Ball, M.P., et al., A publicresource facilitating clinical use of genomes. Proceedings of the NationalAcademy of Sciences, 2012. 109(30): p. 11920-11927.8http://www.1000genomes.org/ See also: 1000 Genomes Project Consortium.An integrated map of genetic variation from 1,092 human genomes. Nature,2012. 491(7422): p. 56-65.

Table 1. Information based on the data from The Personal Genome Project and 1000 Genomes Project.

Sample code Population Verified origin

HG03914 Bengali (BEB) Bangladesh

HG03652 Punjabi (PJL) Pakistan (Lahore)

HG03864 Telugu (ITU) India

PGP130 N/A Northern Africa (Morocco)

Samples HG03914, HG03652, HG03864 thatdo not belong to Q-M378 subclade were used forcomparison.

Additionally, data from targeted Y-chromosome sequencing of five individuals,tested at Full Genomes Corporation (FGC)9,were analyzed.

9

https://www.fullgenomes.com/

Table 2. Information based on test participants' data at Full Genomes Corporation.

Sample code Population Verified origin

AJ1 Ashkenazi Jews Eastern Europe

AJ2 Ashkenazi Jews Eastern Europe

Ar1 Armenians Eastern Turkey

Ir1 Iranians Iran, Khuzestan province

Kz1 Kazakhs Kazakhstan, kozha lineage


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Genotyping

Data sets in BAM format (BAM/SAM Specifi-cation10) and, in case of PGP130, TSV11 format

were used for the research.

Next-generation sequencing12, performedby Full Genomes Corporationat Beijing Ge-nomics Instituteusing Illumina HiSeq 2000sequencer, is characterized by the following pa-rameters: 50x coverage at read length of 100base pairs, with paired end reads. Mapped cov-erage at about 23 million base pairs out of ap-proximately 59 million base pairs, present in ahuman Y-chromosome, was obtained.

Data processing and analysis

Clusterization of Q-M378 subclade haplo-types (including haplotypes that belong to Q-L275 upstream level and downstream levels)was carried out based on 222 haplotypesprocessing (67 STR-markers13), obtained frompublic sources14. MURKA software15was used toconstruct the phylogenetic tree.

Processing and analysis of full Y-chromosomesequencing data was made using FGC software,

along with the software developed by YFull re-search group16.

Samples pertaining to Q-L275 subclade andhaving no M378 mutation were used as refer-ence, along with the samples of an upstreamand parallel subclades on a case-by-case basis.Each sample was genotyped for both SNPs dis-covered during the research and SNPs includedin the ISOGG list under Q-L275 subclade and itsdownstream subclades.

Presence of mutation in more than two sam-ples served as the criterion of a new SNP dis-covery, as well as data consistency between thenew SNPs inter seand the previously known in-10An up-to-date specification version can be found at.https://github.com/samtools/hts-specs11 TSV (Tab Separated Values) text format for storing and viewing tabular da-ta.12Behjati & Tarpey, What is next generation sequencing?, Arch Dis Child EducPract Ed 2013;98:236-238 doi:10.1136/archdischild-2013-304340http://ep.bmj.com/content/98/6/236.full13STR-markers (short tandem repeats).14 Public projects data from the Family Tree DNA website:http://www.familytreedna.com/projects.aspx. Hereinafter haplotypes from thespecified source are marked as follows - FTDNA kit and haplotype number.15 MURKA by Valery Zaporozhchenko (Research Center of Medical Genetics of the

Russian Academy of Medical Sciences, Moscow, Russia).http://sourceforge.net/projects/phylomurka/16 http://www.yfull.com/

formation on phylogenetic structure of a respec-tive subclade.

Results

Clusterization of Q-M378 subcladebased on SNP and STR-markers analysis

Given that SNPs characterize distribution ofhaplotypes into clusters in a more specific way,primary clusterization was made taking into ac-count the known data on SNPs, defining sub-levels of Q-M378 subclade.

There are three downstream subclades cur-rently known17 Q-L245, Q-L301, Q-L327. SNPswith an L prefix, defining the above subclades,were identified at the Family Tree DNA lab ledby Dr. Thomas Krahn.

Geography of Q-L245 distribution essentiallyrepeats geography of M378 distribution (exceptfor Central and Southern Asia).

Q-L301 subclade is localized exclusively inIran18. Simultaneous presence of two subcladesQ-L301 and Q-L245 in Iran and Iraq among au-tochthonous population is indicative of the long

duration of residence of M378 mutation carriesamong the people living in this region1920.

L327 is a private SNP, represented by a sin-gle haplotype of a Portuguese from Azores21.

Another private SNP22 is P306, localized inone Indian. That being said, it was not foundamong the tested representatives of Q-M378subclades (including Q-L301)23.

Until recently only two SNPs were acknowl-

edged as downstream of L24524: L272.1, de-tected in Europe (Sicily) and L315 (discovered in

17 Y-DNA Haplogroup Q and its Subclades 2013 -http://www.isogg.org/tree/ISOGG_HapgrpQ.html18FTDNA kit 178026, M7540, M7949.19 Nadia Al-Zahery et al, In search of the genetic footprints of Sumerians: a sur-vey of Y-chromosome and mtDNA variation in the Marsh Arabs of Iraq (2011).http://www.biomedcentral.com/1471-2148/11/288 This work has some data onQ haplotypes present in the Marsh Arabs (n=143) and Iraqis (n=154). Q-M378has a frequency of 2.1% in the first case and 1.9% in the second one.20Grugni et al., Ancient Migratory Events in the Middle East: New Clues from theY-Chromosome Variation of Modern Iranians (2012). DOI:10.1371/journal.pone.0041252. Among those positive to SNP M378 the followingethnic groups come under notice Khorasan Persians - 3 out of 59 (5.1%), Es-fahan Persians - 1 out of 11 (9.1%), Lurs - 2 out of 50 (3.9%), Assyrians - 1 outof 39 (2.6%), Azerbaijani - 1 out of 63 (1.6%).21FTDNA kit 13254.22 FTDNA kit N78873.23 FTDNA kit 178026, M7540, 193005, 95307 respectively.24 Both are private SNPs, i.e. found so far in a single carrier of such mutation.L315 FTDNA kit 51 and L272.1 (FTDNA kit 95307). L315 may not be stable asit was positive in HG02291 sample.


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East European Ashkenazi). Below L245 SNPL619.2 is located as well, discovered in two rep-resentatives of Armenian Diaspora25. Further-more, the fact that this SNP emerged relatively

recently is confirmed by existence of ArmenianDiaspora representatives, who showed no signof this polymorphism26.

Consequently, until very recently Q-L245subclade could not be clusterized using SNPs.Thereby phylogenetic definitions and analysis ofSTR-markers were used for clusterization. Asegment of DYF395S1 chromosome of low va-riability27 was used for clusterization (the ap-proach was initially proposed by Q yDNAProject28 administrator Rebekah A. Canada),which allowed formation of stable clusters withrespective geographical and ethnic reference.

For example, the following clusters were hig-hlighted using this approach.

DYF395S1=14-17

It includes four haplotypes: two Dagestanis(identifiers according to the cited publication29-Avar Dag 511 and Kaitag Dag06 894), a Turk30and an Arab of Iraq31. The latter belongs to thelegendary tribe of Quraysh (Adnan-Modar tribal

self-definition).

This cluster is located closer to the tree rootL245 than any other one and, apparently, is thenearest to the ancestral haplotype.

DYF395S1=15-17

It includes a whole group of haplotypes ofpeople of various origin. One can pinpoint thefollowing subclusters in the cluster:

-Central European (localization of most

ancestral lineages Switzerland32, part of themis linked to a Mennonite community);

25FTDNA kit E5340, 191379.26 FTDNA kit 173902, 178717.27Vladislav Ryzhkov, Calculating time to the most recent common ancestor byseparate panels of Y-STR markers, sorted by increasing mutation rate constants,The Russian Journal of Genetic Genealogy (Russian version): Vol. 3, No. 2, 2011,ISSN: 1920-2997 http://ru.rjgg.org28Q yDNA Project http://www.familytreedna.com/public/yDNA_Q/29Balanovsky et al, Parallel Evolution of Genes and Languages in the CaucasusRegion. Molecular Biology and Evolution, 13 May 2011.30FTDNA kit 303617.31FTDNA kit 197506.32 The SCHACKE surname appeared in Germany at least as early as the 1600sand perhaps earlier. The JAGGI surname in Switzerland goes back much further.With this DNA Project we hope to learn more about our early ancestors and

where our ancestors originated. Johann Christoffel SCHACKE, the paternalancestor of most who carry the SHOCKEY surname, was born inKirchheimbolanden, Pfalz, Germany in 1720 to Swiss parents. He arrived inPhiladelphia PA in 1737. The Anglicized version of his name became JohnChristopher Shockey. He and his wife Barbara had nine children between 1739

- North-European (localization of mostancestral lineages Netherlands33);

- Italian (including haplotypes with partial

SNP L272.1);

- Armenian;

- Southwest Asian.

It should be noted that according toDYF395S1=15-17 attribute, a number of haplo-types with no L245 mutation, are part of thecluster, in particular haplotypes of a level, whichwill be further described as Q-Y2250, as well ashaplotypes of level Q-L327, and Q-P306. How-ever, in view of a thesis adopted by us on priori-ty of SNP application during clusterization, wewill not do that. This also implies a conclusionthat clusters DYF395S1=14-17 and/or 15-17were formed already as a part of Q-M378 level.This hypothesis however can be made morespecific only with the growth of a number oftested representatives of the cluster.

DYF395S1=15-18

DYF395S1=15-19

These two clusters are represented exclu-sively by people of Jewish origin.

Individual haplotypes, having RecLOH (theso-called Recombinational Loss of Heterozygosi-ty) in this part of Y-chromosome, were not con-sidered under this clusterization.

It is expected to identify SNPs, correspondingto each of the above-mentioned STR-based clus-ters, as part of further research.

and 1756, six sons and three daughters. After Barbara died John Christophermarried Anna Marie COMPTON. John Christopher and Anna Marie had one sonborn in 1774 or 1775. This project hopes to help identify the descendants of theseven sons of John Christopher SHOCKEY as well as learn more about his Swissancestors and their related families from Germany and/or Switzerland.http://www.familytreedna.com/public/shockey-schacke/default.aspx33 Huff/Hough Surname Project -http://www.familytreedna.com/public/HOUGH/default.aspx A Dutch namedDerrick Pauluszen Hoff (1649-1730), who arrived in New Amsterdam (New York)no later than 1660, is considered to be the common ancestor of the family.


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New phylogenetic structureof Q-M378 subclade,upstream and parallel subclades

As a result of processing and analysis of fullY-chromosome sequencing data some new sin-gle nucleotide polymorphisms were discovered,their placements defined on Y-chromosome (ac-cording to the reference sequence of human ge-

nome hg1934), as well as phylogenetic place-ments on the SNP tree.

The data on the new SNPs was summarized

in Tables 3-5 along with Diagram 1, specifyingSNP tagging according to Y notation35 and FullGenomes Corporation notation36.

34hg19 reference sequence or GRCh37. See also: Human Genome Overview.http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/35 Y SNP prefix according to YFull.36 FGC SNP prefix according to Full Genomes Corporation.


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As can be seen from the above, below L275SNP level the following levels, not described tothis day, were discovered:

1)

Q-Y1150 level, which is downstream ofQ-L275 and parallel to Q-M378. SNPs of thislevel were discovered in only three natives ofHindustan (HG03914, HG03652, HG03864)37.

2) Q-Y2250 level, downstream of Q-M378and parallel to Q-L245. SNPs of this level (Table3) were found in Ir1 and Kz1 samples. Seeingthat Ir1 sample has a positive SNP L301 value,and Kz1 is negative to this SNP, it is evidentthat Q-L301 level is downstream of Q-Y2250.Private SNPs of Kz1 sample are listed in Appen-dix 3. Private SNPs of Ir1 sample are listed inAppendix 7.

3) Q-Y2220 level, downstream of Q-L245.This level combines haplotypes of Jewish andArmenian clusters Q-L245. All tested samples ofthis cluster representatives (AJ1, AJ2, Ar1) hadpositive SNPs of this level (see Table 4),excluding PGP130 sample (Moroccan origin).

37G.R. Magoon, R.H. Banks, C. Rottensteiner, B.E. Schrack, V.O. Tilroe, T. Robb,A.J. Grierson, Generation of high-resolution a priori Y-chromosome phylogeniesusing next-generation sequencing data, 2013, doi:10.1101/00802 (in prepara-tion, preprint on bioRxiv.org).

4) There is also Q-Y2220 level parallel to Q-Y2200 (xQ-Y2200) that contains SNPs, definingArmenian segment of DYF395S1=15-17 cluster.Due to the fact that these SNPs were found in

only one sample (Ar1) they have a status of pri-vate ones. Although one can assume the follow-ing with high probability:

- that part of these SNPs will be characte-rized by a rather wide range of haplotypes ofDYF395S1=15-17 cluster;

- Q-L619.2 level will be downstream of Q-Y2220 (xQ-Y2200), since only a part of Arme-nians, who are positive to SNP L245, belong toit. Ar1 sample, tested by us, showed no sign ofL619.2 mutation.

5) Q-Y2200 level, downstream of Q-Y2220.SNPs of this level define Jewish cluster Q-L245(see Table 5). Private SNPs of samples AJ1 andAJ2 are listed in Appendices 5, 6. In addition,both tested samples had no L315 mutation.


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Table 3. Q-Y2250 level. New SNPs, downstream of positive SNP M378.

Position(hg19)

Ancestralvalue

Derivedvalue

SNP name (Y)SNP name (FGC)

or synonym

7115834 C T Y2244 FGC4626

6894323 C T Y2245 PR683

3544336 C G Y2246 FGC4613

2765038 T G Y2247 FGC4607

4070598 G A Y2248 FGC4618

4242831 A G Y2249 FGC4619

4852955 G A Y2250 FGC4620

6537988 A G Y2251 FGC4624

6724553 C T Y2252

8671530 A G Y2255 FGC4631

10077457 T C Y2256 FGC4635

15766997 A C Y2263 FGC4646

18169503 A C Y2264 FGC4656

18803364 C T Y2265 FGC4657

18990293 A G Y2266 FGC4659

22525954 AT A Y2268

23956540 A T Y2269 FGC4675

24452225 G C Y2270 FGC4676

15684681 A T CTS4507

13643442 T C FGC4638

___________________________

Note:Y2268 deletion.

Table 4.Q-Y2220 level. New SNPs, downstream of positive SNP L245.

Position(hg19)

Ancestralvalue

Derivedvalue

SNP name (Y) SNP name (FGC)

9408770 G T Y2220 FGC1904

18051798 A C Y2209 FGC1917

22017904 G T Y2202 FGC1925

4914530 A G Y2229


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Table 5. Q-Y2200 level. New SNPs, downstream of positive SNP L245.

Position(hg19)

Ancestralvalue

Value positiveto SNP

SNP name (Y) SNP name (FGC)

23646920 C T Y2196 FGC1934

22953894 A G Y2197 FGC1933

22825080 A G Y2198 FGC1932

22588598 C T Y2200 FGC1929

22471554 A T Y2201 FGC1928

21277083 G A Y2203 FGC1923

19425984 G A Y2206

19053060 C T Y2207 FGC1919

18207170 A G Y2208 FGC1918

18046486 T C Y2210 FGC1916

18043999 G A Y2211 FGC1915

16994660 T A Y2212 FGC1914

15834557 G A Y2213 FGC1912

14385853 T G Y2215 FGC1911

14353022 A C Y2216 FGC1910

14184253 C A Y2218 FGC1909

9892635 C T Y2219 FGC1906

9401947 C A Y2221 FGC1903

8662585 C A Y2224 FGC1899

6949449 C T Y2225 FGC1897

4606181 C T Y2231 FGC1890

3995524 G A Y2232 FGC1888

3148720 A G Y2233 FGC1886


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Placement of SNPs, listed by ISOGG as SNPsunder Investigation, was specified within thescope of this work: F108, F803, F815, F1082,F1126, F1169, F1213, F1337, F1349, F1528,

F1537, F1594, F1734, F1780, F1836, F1839,F1858, F1875, F1974, F2023, F2145, F2230,F2313, F2343, F2440, F2628, F2657, F2777,F2851, F2877, F2894, F2934, F3084, F3121,F3193, F3207, F3389, F3621, F3680. On May 8,2013 all of the above SNPs were classified byISOGG as pertaining to level L245 or below. Theanalysis showed necessity to modify the pro-posed scheme. All SNPs, apart from F1213,F1349, F1594, F1734, F1780, F1836, F1839,F2230, F2877, pertain to level Q-L275, as theyare positive for samples HG03914, HG03652,HG03864, AJ1, AJ2, Ar1, Ir1. The remainingSNPs, in their turn, are positive to all samples inthe research that are positive to M378 and L245.Consequently, the said SNPs are at the samelevel with Q-L275 and Q-M378 respectively38.

Besides, a considerable amount of new SNPswas discovered at the same level with L275,M378 and L245.

For example, the following SNPs pertain tolevel Q-L275 - Y1014-Y1022, Y1024-Y1057,Y1059-Y1069, Y1071-Y1137, Y1139, Y1142,

Y1153, Y1160, Y1164, Y1166, Y1167, Y1169,Y1195, Y1220, Y1240, Y1978-Y1983, Y1985-Y1989, Y1991-Y1993, Y1995, Y1996-Y1997,Y2003, Y2005-Y2007, Y2009, Y2239, Y2243;

to level Q-M378 - Y2012, Y2013, Y2016-Y2082, Y2084-Y2095, Y2097, Y2098, Y2113-Y2115, Y2226, Y2361 (Appendix 1, Table 6);

to level Q-L245 - Y2116-2149, Y2195,Y2199, Y2204, Y2217, Y2222, Y2223, Y2235,Y2237 (Appendix 2, Table 7).

The said SNPs do not at the moment haveany phylogenetic meaning, but it can be as-38 It should be noted that FTDNA research team led by Dr. Thomas Krahn, withthe participation of Q yDNA Project administrator Rebekah A. Canada, came to asimilar conclusion earlier. Respective data can be found on the SNP tree draftversion page of the Family Tree DNA website:http://ytree.ftdna.com/index.php?name=Draft&parent=31182976 There was nopublished justification of such conclusions, but, presumably, samples, tested un-der National Geographic Geno 2.0 project, were used for the analysis.

signed to them later after a full sequencing ofsamples, pertaining to these levels and withoutSNP mutation, defining downstream levels.

Summary

The research proved high efficiency of full Y-chromosome sequencing to define phylogeneticstructure, allowed for forming a consistent phy-logenetic structure of Q-M378 subclade, con-firmed by analysis of SNP and STR-markers.

As part of the research, new phylogenetic le-vels of Q-Y2250 (downstream of Q-M378 and in-cluding Q-L301), Q-Y2220 (downstream of Q-L245), Q-Y2200 (downstream of Q-Y2220) weredefined. SNPs, which, in the future, may possi-bly mark certain European and Asian subclustersQ-Y2220 (including the Armenian subcluster), aswell as separate branches of the Jewish clusterQ-Y2200, were also defined.

The research confirmed connection of Q-M378 subclade distribution with migration of In-do-European language carriers from Central Asiavia Afghanistan and Iran to the West. That beingsaid, the amount of materials at the researchers'disposal at the moment is not enough to form

an entire picture of the mentioned migrationprocesses. The specified task can be resolved inthe near future, while statistically significant da-ta is being accumulated.

Acknowledgements

The authors of the article wish to thank thefollowing people, who rendered their assistancein its preparation and conducting the research:

Mikhail Edelstein (Russia)Askar Abdullin (Kazakhstan)Igor Bukharov (Russia)Nazaret Chitilian (Lebanon)Justin Allen Loe (United States)Gregory Magoon (United States)


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Appendix 1.Table 6. SNPs at the same level with M378.

Position(hg19)

Ancestralvalue

Derived valueSNP name (Y)or synonym

SNP name (FGC)

2806676 A G Y2012 FGC1770

3111159 G C Y2013 FGC1758

3815203 G C Y2016 FGC1774

3929337 C A Y2017 FGC1988

4234101 A G Y2018 FGC1775

4332151 G A Y2019 FGC1776

4634427 C A Y2020 FGC1777

4775787 T C Y2021 FGC1779

4778576 A G Y2022 FGC1780

4783438 T C Y20234961249 C A Y2024 FGC1781

5011266 A G Y2025

5266522 A G Y2026 FGC1782

5496739 A C Y2027 FGC1783

5687522 T A Y2028 FGC1784

5751055 T G Y2029 FGC1785

5872168 C T Y2226

5963558 G A Y2030

6085717 C A Y2031 FGC1788

6430659 T G Y2032 FGC1789

6617825 T C Y2033 FGC1790

6618215 T C Y2034 FGC1791

6746675 T C Y2035 FGC1792

6774328 T C Y2036 FGC1793

6986250 T C Y2037 FGC1794

7045044 C T Y2038 FGC1795

7071796 C G Y2039 FGC1796

7094691 A G Y2040 FGC1797

7159039 C G Y2041 FGC1798

7160439 G A Y2042 FGC1799

7339849 G T Y2043 FGC1801

7431253 C T Y2044 FGC1803

7437821 C G Y2045 FGC1804

7550568 G C Y2046 FGC1805

7652630 G A Y2047

7778164 G A Y2048 FGC1807

7856334 A G Y2049 FGC1808

7952263 C T Y2050 FGC1809

8067818 C G Y2051 FGC1810

8681004 T C Y2052 FGC1812


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8682184 C T Y2053 FGC1813

8821295 A G Y2054 FGC1814

9074666 C T Y2055 FGC1815

9170505 G T Y2056 FGC181713127815 A G Y2057 FGC1818

13928638 G C Y2058 FGC1820

14017272 A G Y2059 FGC1825

14193680 G A Y2060 FGC1827

14293849 T A Y2061 FGC1830

14435779 A G Y2062 FGC1833

14540558 C T Y2063 FGC1834

14674385 C T Y2064 FGC1835

14733633 C A Y2065 FGC1836

15498011 C A Y2066

15521110 T C Y2067 FGC1838

15699493 C T Y2068 FGC1841

16217389 A AT Y2069

16654310 C G Y2070 FGC1842

16678163 C T Y2071 FGC1843

17230548 G A Y2072 FGC1844

17447489 C T Y2073 FGC1845

17959860 A G Y2074 FGC1850

18243302 C T Y2075 FGC1852

18714407 C A Y2076 FGC1854

18768735 G T Y2077

18768736 C A Y2078

18769454 A G Y2079 FGC1767

18803642 T G Y2080 FGC1855

18856911 G C Y2081 FGC1856

19373808 A T Y2082 FGC1858

21365952 G A Y2084 FGC1861

21479863 G A Y2085 FGC1862

21647670 G C Y2086 FGC186321832029 C A Y2087 FGC1864

22022365 A G Y2088 FGC1865

22101157 C T Y2089 FGC1866

22440644 G A Y2361

22624047 G A Y2090 FGC1768

22931328 T A Y2091 FGC1869

23053626 A G Y2092 FGC1872

23078557 G T Y2093 FGC1873

23166596 T C Y2094 FGC1874

23279919 G T Y2095 FGC1875

23566714 C T Y2097 FGC1877


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23615574 AT A Y2098

28516009 A T Y2113

28593688 T C Y2114

28687807 A G Y2115

________________________

*Note:Y2098 deletion, Y2069 insertion.

Appendix 2.Table 7. SNPs at the same level with L245.

Position(hg19)

Ancestralvalue

Derived value SNP name (Y) SNP name (FGC)

2794289 C G Y2116 FGC1987

3127708 T C Y2117 FGC1771

3709585 A C Y2118 FGC1773

4502969 T C Y2119 FGC1759

4671322 C A Y2120 FGC1778

7219594 T C Y2121 FGC1800

7408851 C A Y2122 FGC1802

7590793 C T Y2123 FGC1806

8614513 C G Y2124 FGC1811

9144039 A T Y2223 FGC1901

9382621 G T Y2222 FGC1902

9798919 G A Y2125 FGC181613956388 G A Y2126 FGC1821

13982835 C T Y2127 FGC1823

14012662 G A Y2128 FGC1824

14045736 T C Y2129 FGC1826

14202870 A G Y2130 FGC1828

14285880 C G Y2131 FGC1829

14296099 C A Y2217 FGC1831

14402304 G A Y2132 FGC1832

15569048 C T Y2133 FGC1839

15614105 C G Y2134 FGC1840

16519324 A G Y2135

16757414 G GA Y2237

17686482 T C Y2136 FGC1846

17686883 A G Y2137 FGC1847

17763793 T A Y2138 FGC1848

17860015 G T Y2139 FGC1849

18134822 T C Y2140 FGC1851

18575106 G A Y2141 FGC1853

19300050 C T Y2142 FGC1857

21118566 T C Y2143 FGC1859

22015887 C A Y2144 FGC1989


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22934317 ATC A Y2235

23010582 C T Y2145 FGC1870

23042385 C A Y2146 FGC1871

23648959 T G Y2147 FGC187823733052 A G Y2148 FGC1879

28520821 A G Y2149

28646637 C G Y2195 FGC1883

22767464 G A Y2199 FGC1868

21235857 A G Y2204 FGC1860

________________________

*Note:Y2235 deletion, Y2237 insertion.

Appendix 3. Table 8. Private SNPs for Kz1 sample.

Position(hg19)

Ancestralvalue


2980949 T C YFS026208

3027441 C A YFS026210 FGC4858

3751684 G A YFS026242 FGC4859

4164029 A G YFS026250 FGC4860

4515848 G A YFS026257 FGC4862

4714529 G T YFS026264 FGC4864

5394870 T C YFS026279 FGC4865

5398133 A T YFS026280 FGC4866

6088200 T C YFS026301 FGC4867

6675390 A G YFS026321 FGC4868

7058898 G A YFS026329 FGC4869

7208802 C T YFS026339 FGC4870

7278041 G A YFS026340 FGC4871

7704050 C T YFS026351 FGC4856

7929100 A C YFS026356 FGC4872

8268654 G A YFS026361 FGC4873

8684090 G A YFS026366 FGC4874

8714870 C T YFS026367 FGC4875

9154952 G A YFS026372 FGC4876

9990725 C G FGC4878

13230336 G A FGC4879

13313894 G C FGC4880

13637299 G A FGC4881

14599760 G A YFS026426 FGC4882

15353330 C T YFS026439 FGC4883

15540398 G A YFS026445 FGC488415617600 G A YFS026447 FGC4885

15656595 A C YFS026448


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15881099 G A YFS026457 FGC4886

17344441 A G YFS026496 FGC4887

17455705 C G YFS026499 FGC4888

17619239 A C YFS026502 FGC488918132430 T A YFS026506 FGC4890

18205189 C A YFS026508 FGC4891

18235952 C A YFS026509 FGC4892

18427622 C T YFS026514 FGC4893

18699065 G A YFS026522 FGC4894

19119009 G A YFS026534 FGC4895

21794826 T C YFS026585 FGC4896

21824228 C T YFS026586 FGC4897

22216997 C A YFS026594 FGC4898

22263424 G T FGC4899

22464918 G A YFS029304

22470401 G T YFS029305 FGC4901

22476862 T A FGC4902

22779292 G A YFS026598 FGC4904

22845858 T A YFS026600 FGC4905

22980932 G A YFS026603 FGC4906

23097922 G T YFS026606 FGC4907

23188736 C T YFS026608 FGC4908

23574588 G T YFS026618 FGC4909

28577678 T G FGC4857

28556325 T G YFS026709

Appendix 4.Table 9. Private SNPs for Ar1 sample.

Position(hg19)

Ancestralvalue


2837084 G A YFS030295

4687602 C T YFS030307

3264534 G T YFS030298

3692600 G A YFS030300

6849037 A G YFS030309

7389018 T C YFS030314

7809088 C T YFS030318 FGC2000

8227956 C T YFS030321 FGC2001

8310172 G A YFS030322 FGC2002

8891034 A G YFS030324 FGC2003

9455617 G C YFS030326 FGC2004

9507128 G A YFS030327 FGC2005

13207417 C T FGC2006

13862984 G A YFS030335 FGC2007


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99

14037704 A G YFS030339 FGC2008

14266100 G A YFS030343

14271743 G T YFS030344 FGC2009

14645998 A T YFS03035015487465 T C YFS030354 FGC2010

15532493 G C YFS030355 FGC2011

15562737 G A YFS030356 FGC2012

15649426 C G YFS030357

15949197 C T YFS030358 FGC2013

16033272 G A YFS030359 FGC2014

16914913 A T YFS030368

17143642 G A YFS030370 FGC2015

17264341 C T YFS030371 FGC2016

17350212 G T YFS030372 FGC2017

17468836 G A YFS030374 FGC2018

17522056 C A YFS030375 FGC2019

17547056 C T YFS030376 FGC1986

17969724 T C YFS030377 FGC2020

18005360 G A YFS030378 FGC2021

18082500 T C YFS030379 FGC2022

18143358 C T YFS030380

18269281 T C YFS030381 FGC2023

19295864 G A YFS030386 FGC2024

19305808 C G YFS030387 FGC2025

21920836 G T YFS030396 FGC2026

22195671 T G YFS030398 FGC2027

22546195 T C YFS030431 FGC2029

23036871 A C YFS030432 FGC2030

23193319 C G YFS030433 FGC2031

23633830 T C YFS030434 FGC2032

23749442 C G YFS030435 FGC2033

23952561 G A YFS030438 FGC2034

28546577 A G YFS030460 FGC203528697215 C T YFS030463 FGC2036

28728861 A G YFS030465 FGC2037

28773229 G A YFS030466 FGC2038


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Appendix 5.Table 10. Private SNPs for AJ1 sample.

Position(hg19)

Ancestralvalue


3014878 G C YFS028077

3279492 T C YFS028084

4705139 G A YFS028121

4734829 G T YFS028122

5007712 T C YFS028135

6028097 T C YFS028158 FGC4835

6671453 T A YFS028174

6985833 G C YFS028180 FGC4836

7116693 C G YFS028187 FGC4837

13225084 C A FGC483913227006 C T FGC4840

14174284 C T YFS028277 FGC4841

14683323 G A YFS028303

15749472 C G YFS028328 FGC4842

15911171 T A YFS028333 FGC4843

17216758 C G YFS028365 FGC4844

17842405 G A YFS028379 FGC4845

18697269 A G YFS028399 FGC4846

22541678 G A YFS028484

22545510 G T YFS028485 FGC4850

22809218 A T YFS028490 FGC4851

22816094 C T YFS028491 FGC4852

22989959 T C YFS028498 FGC4853

23338485 T C YFS028509 FGC4854

Appendix 6.Table 11. Private SNPs for AJ2 sample.

Position

(hg19)

Ancestral

value


3085515 C A YFS030088 FGC1885

4157714 C T YFS030093 FGC1889

7357489 C T YFS030117 FGC1898

8757232 C A YFS030130 FGC1900

9761433 C T YFS030140 FGC1924

16933881 C T YFS030164 FGC1913

19228285 T C YFS030189 FGC1920

21322098 A G YFS030210 FGC1924

22128896 C T YFS030218 FGC1926

22612418 A T YFS030247 FGC1930

22720359 C T YFS030248 FGC1931


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Appendix 7.Table 12. Private SNPs for Ir1 sample.

Position (hg19) Ancestral value Derived value SNP name (Y)

2808294 G A YFS0304862848925 C T YFS030487

3241019 G A YFS030493

3331565 C T YFS030495

3617298 G A YFS030498

3905106 T C YFS030501

3983695 G A YFS030503

4048861 C G YFS030505

4976524 T C YFS030521

4976526 T C YFS030522

5021496 G C YFS030523

5219277 T A YFS030526

5844571 C T YFS030529

6531744 G A YFS030531

7398730 T C YFS030543

7685828 G T YFS030547

7997281 G C YFS030548

8350958 G A YFS030550

8482074 C G YFS030551

8874735 C A YFS0305539459692 A G YFS030555

9832592 A G YFS030556

14022660 C A YFS030564

14273656 A G YFS030573

14401614 C T YFS030575

14532575 G T YFS030582

14916116 G A YFS030585

14996654 G A YFS030588

15012864 C A YFS030589

15240341 G C YFS030591

15799031 G C YFS030596

15933501 T A YFS030599

16253494 C T YFS030602

16280147 C T YFS030603

16304710 T C YFS030604

16875622 C T YFS030608

17529042 G A YFS030616

18106050 C T YFS030618

18903761 A C YFS030626

19157289 G A YFS030633

19198307 A T YFS030634


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19526472 A C YFS030637

21359025 C G YFS030656

21567329 G A YFS030657

22564450 C T YFS03068422621906 G T YFS030685

22687343 A T YFS030686

22910874 G A YFS030688

23018638 T C YFS030689

23054174 T G YFS030690

23198785 A T YFS030691

23435852 A C YFS030694

24484883 T C YFS030706

28759876 C T YFS030732

17188634 T C YFS030609

19001468 C T YFS030630

20534862 T C YFS030645

21599239 A G YFS030658

21836635 A T YFS030661

phylogenetic structure of q-m378 subclade based on full y-chromosome sequencing

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