The Southern European DNA enigma. Option 2. The DNA is Ancient.

The above photograph taken by me, of Neolithic skulls from the Tomb of the Sea Eagles, Orkney.

I'm not the only English person reporting "Southern European" on their Autosomal DNA for Ancestry test results.  I've noticed that on 23andMe, for example, that English often report these strange low percentages of "Southern European" in their ancestry composition results.

There may be something odd about the ancient ancestry of the English, that we do not yet know.  Others have also pointed out that in ancient admixture calculators, that the English receive lower percentages of ANE (Ancient North Eurasian) than do the Irish, Scottish, or other nearby neighbours.  POBI (People of the British Isles 2015) suggested a unknown immigration into Southern Britain during Late Prehistory perhaps from the area that is now France.

Some point to perhaps, more Neolithic survival in lowland Britain, relating perhaps to Sardinian patterns.  Others suggest immigration from Southern Europe and elsewhere during 360 years of Roman occupation.

Option 2 is a possibility - perhaps these is something about English ancestry that we do not yet know about, that confuses the algorithms of commercial DNA companies, when trying to identify our more recent ancestry.

The Southern European DNA enigma. Option 1. The DNA Analysis is true

My great grandfather Fred Smith, and my great Uncle Lenny.

Option 1.  The DNA Analysis for Ancestry is true

This option supports the commercial DNA for ancestry companies claim, that I have Southern European ancestry.  For this to be the case, my Southern European ancestors must have either a) been hidden in the gaps, the missing ancestors.  b) be NPE (non parental events - biological ancestors that are contrary to recorded ancestors.  Usually male). c) predate my genealogical record over the past 360 years or d) my recorded genealogy is faulty.  I have badly researched my ancestry and have made mistakes.

What gaps are there?  All of my generations are complete to and including my Generation 5.  I have all of the names of my 16 direct ancestors at that generation (great great grandparents).  All appear totally English, of English religious denominations.  Their surnames and location were: Brooker of London (previously Oxfordshire), Shawers of London, Baxter of Norfolk, Barber of Norfolk, Smith of Norfolk, Peach of Norfolk, Barber (again) of Norfolk, Ellis of Norfolk, Curtis of Norfolk, Rose of Norfolk, Key of Norfolk, Goffen of Norfolk, Tammas-Tovell of Norfolk, Lawn of Norfolk, Thacker of Norfolk, and Daynes of Norfolk.

I have photographs of three of them.

Everything looks utterly English - the majority East Anglian.

The gaps start to appear at Generation 6 (G.G.G Grandparents)  Three missing male ancestors - all missing fathers of illegitimate births.  29 out of 32 direct ancestors recorded though.  All appear English again:  

Brooker of Oxfordshire, Edney of Oxfordshire, Shawers of London, Durran of London (previously Oxfordshire), Baxter of Norfolk, Barber of Norfolk, Smith of Norfolk, Hewitt of Norfolk, Peach of Lincolnshire, Riches of Norfolk, Barber of Norfolk, Ellis of Norfolk, Goodram of Norfolk, Curtis of Norfolk, Larke of Norfolk, Rose of Norfolk, Barker of Norfolk, Key of Norfolk, Waters of Norfolk, Goffen of Norfolk, Nichols of Norfolk, Tovell of Norfolk, Tammas of Norfolk, Lawn of Norfolk, Springall of Norfolk, Thacker of Norfolk, Daynes of Norfolk, Quantrell of Norfolk.  Oh, and a "Mary Ann" of Norfolk.

Again, all English, English religious denominations.  Mainly rural working class East Anglian.  No sign of any foreigners.

The record does start to really fall away at Generation 8.  From then on, it's a minority of lines recorded, stretching back to the 1680's.  However, at no where on my record of 207 direct ancestors, do I see anything that looks remotely non-English, never mind Southern European.  No sign of any Catholicism anywhere.

Let's just consider percentages of DNA though.

Each grandparent gives me 25% on average.

Generation 3 (grandparent) 12.5%

Generation 4 (great grandparent) 6%

Generation 5 (great great grandparent) 3%

Generation 6 (G.G.G grandparent) 1.5%

Beyond then genetic recombination starts to really kick in, and you may have zero DNA from any particular ancestral lineage.  It get's washed out.  Only if it comes down from a number of lines is admixture highly likely to survive further back.

23andMe (V4 AC in spec after phasing with one parent) claims that both of my parents had 2% Southern European DNA.  That takes it back to around MY Generation 6 or 7.  Sure, I'm missing 9% of Generation 6, and 20% of Generation 7.  My Southern European ancestors could have admixed then.  But what are the chances of it happening on both sides?  Possible, yes.  I think unlikely though.  No Southern European names or religions passed down.  When was this? Around 1780 to 1820.  Okay, if I want to piece national history into it, how about The Peninsular Wars (1807-1814)?  The Royal Norfolk Regiment took an active part in that campaign.  Could I have (presumably male) ancestors through both of my parents, that brought back Portuguese wives?  It is a possibility.  I'll acknowledge that.  But am I weaving history in order to make it fit the DNA analysis?

FT-DNA (FF My Origins) claims that I have 32% "Southern European" ancestry.  No sign of it in family history or photography.  Too much likeness of recorded fathers.  Okay, maybe it goes further back, but on multiple lines?  I think that we are pushing this one.  What is the chance of so many Southern Europeans given my above recorded or known English ancestry.  It couldn't have happened.

DNA.land gives me 19% Southern European, including 13% Balkan.  The same problem as the FT-DNA analysis.  It just doesn't wash.  It cannot fit.

Therefore I conclude:

  1. FT-DNA and DNA.land claims of my Southern European percentages cannot realistically be explained by gaps or missing ancestors.
  2. 23andMe claims of 2% Southern European could be explained by the missing gaps - just!  But would need quite a coincidence to be on both sides, just in those gaps.

That pretty much covers it for gaps, NPE's, etc.  If any Southern European on the other hand, predates my genealogical record, then it would need to be on multiple lines, and to have lost all sign of Southern European surnames, religions, and traditions.  I haven't seen any history of a mass Southern European migration to England 600 - 400 years ago.

So which is it?

Following on from my last two posts.  Simple.

  1. The DNA companies are correct in their assessment of my ancestry.  I have Southern European Ancestry within the past 500 years.  Perhaps Iberian, perhaps Balkan?  Maybe via both my father and mother?
  2. The Southern European picked up by atDNA tests for ancestry, relate to ancient patterns, shared by the English.  They could be Neolithic, or other Late Prehistoric.  They could be Roman.
  3. Commercial autosome DNA Tests for Ancestry fail.  There is no Southern European, neither within the past 500 years, nor ancient.  It's all bogus.  Current chips and references fail to differentiate successfully between European populations of the past.

So which one is it? I'll be looking at answering this in my next few posts.


Revisiting Southern European for Ancestry

This photo of A Capela dos Ossos (the bone chapel) in Évora, Portugal.  Taken by myself.

First, a recap

I'm English by ethnicity, birth, upbringing, known family history, and by record.  That record, I've researched on and off for more than 25 years, primarily in record offices, but in more recent years also online.  On my personal database I presently have 207 direct ancestors recorded.  All lived in Southern England, with the majority in East Anglia.  All appear to have English surnames.  All recorded religious denominations, English.  The majority were rural working class.  I have a typical English ethnicity and phenotype.  My recorded genealogy stretches back at the furthest to the 1680's.

I'd expect some admixture in there.  I know from my Y-DNA that I have Asian admixture from between 500 and 1,800 years ago on my paternal lineage.  Surely some Hugeonauts, Strangers, Romany, or others at some point.  However, a rare and single event on one line of ancestry doesn't hang around very long in autosomal DNA.  It can be washed out very quickly by genetic recombination - as my Asian, as detected by my Y-DNA, has been.  You should only really see significant traces of admixture, when it is either recent (within the past few hundred years at most), or entered on multiple lines of ancestry.

Therefore, I'd have expected a commercial Autosomal DNA test for ancestry to come fairly close to 100% for British, or even English.  But instead, so far, I've received:

From 23andMe Ancestry Composition in Speculative mode, before any phasing with mother alone:

32% British & Irish
27% French & German
7% Scandinavian
29% Broadly NW European
2% Broadly Southern European (including 0.5% Iberian)

and after phasing with one parent:

37% British & Irish  (23% from father, 14% from mother)
22% French & German  (12% from father, 10% from mother)
1% Scandinavian  (from mother alone)
36% Broadly NW European  (23% from father, 13% from mother)
2% Broadly Southern European (1% from father, 1% from mother)

From FTDNA Family Finder My Origins, I recently received:

36% British Isles
32% Southern European
26% Scandinavia
6% Eastern Europe

Wegene using my 23andMe raw data gives me:

81% French
19% British

DNA.land using my 23andMe raw data gives me:

77% Northwest European
19% South European broken into 13% Balkan and 6% Central/South European
2% Finnish
1% ambiguous West Eurasian.

GEDmatch Eurogenes K13 on Oracle using my FT-DNA raw data gives me as my nearest Genetic Distance:

Southeast English 3.75 GD

On Oracle 4 I get as my nearest single population Genetic Distance:

Southeast English 4.28 GD

Best three way on K13 Oracle 4 mix is:

50% Southeast_English +25% Spanish_Valencia +25% Swedish @ 1.86 GD

Eurogenes K13 does often suggest Iberian references for admixtures on my results further down the proposal list.  Still, thumbs up for Eurogenes K13!  It gets me as Southeast English correctly!

So... 23andMe claims that I have 2% Southern European and that it comes from both parents, although before phasing, it hinted at Iberian.  FT-DNA claims that I have a whopping 32% Southern European!  DNA.land claims that I'm 19% South European, but Balkan with some Italian, rather than Iberian!  Eurogenes K13 Oracle 4 suggests that if I do have admixture, that it most likely includes Iberian.  My family tree has no evidence of any Southern European people, names, or any Catholicism, etc.  Confusing or what?


FTDNA (Family Tree DNA) My Origins Autosome Test for Ancestry

I know I should have smiled!  Me, myself sitting outside of the archaeology museum earlier this year, at Sofia, Bulgaria.South-West Europe.

FT-DNA Family Finder My Origins

I haven't posted much coherent lately, because, well, my Life changed, and consequently I've been pretty busy, in a very good way.  However, my exploration into genetic genealogy hasn't ceased at all.  Indeed, I took advantage of the Family Tree DNA (FTDNA) Summer sale, and bought the USD $79 Family Finder test.

No need to send a fresh sample, this was the third test from the sample that I sent to FT-DNA's US lab earlier this year.  FTDNA Family Finder is an autosomal DNA test only, without haplogroup results - but I've tested my Y-DNA to death already, and I know my mtDNA haplotype.  The services supplied include relationship matching, raw file download, and an Ancestry analysis named My Origins.  Hey, for that price, in GBP £, that is el cheapo good value.  And it's a good test, with about 690,000 SNPs tested, against 23andMe's current 577,382.  Smoking.

My prime interests was in 1) comparing the raw data with 23andMe on GEDmatch, and 2) seeing what FTDNA My Origins has to say about my autosomal DNA for ancestry.

So what did I find.

The former, comparing raw data files, I've done.  But briefly, the calculators DO vary for the two files, but not by very much - except maybe, that on Eurogenes K13, the nearest GD on my FT-DNA file is closer to correct - putting SE English closer this time than South Dutch.

The latter?

Family Tree DNA reported My Origins as:

100% European.

Broken into:

36% British Isles
32% Southern Europe
26% Scandinavia
6% Eastern Europe

This is a pretty bizarre result.  36% almost hits dead on my 23andMe Ancestry Composition (spec) result for British Isles (32% before phasing, 37% after phasing with one parent).  Perhaps they are using a similarly biased reference?  I'll blog on that soon as well.

26% Scandinavian is massive.  23andMe AC spec reported 7% before phasing, and 2% after phasing with one parent.

That's pretty much my first report for Eastern European, except for DNA.land's claim of some Balkans (hence my excuse for the above photograph).

but .... 32% Southern Europe, really?  Let's go there next, off to Southern Europe now:



Family Tree DNA Family Finder data V 23andMe raw data on GEDMATCH

Background

I'm South-east English in known paper ancestry, ethnicity, and heritage - mainly Norfolk East Anglian, where I still live, close to many known ancestors. I have 207 recorded ancestors on my tree, over the past 380 years. The majority lived in Norfolk, but some were Oxfordshire, Lincolnshire, Suffolk, and Berkshire. All appear to be English, with English surnames, English religions and denominations, overwhelmingly East Anglian:

Generation 1 has 1 individual. (100.00%)

Generation 2 has 2 individuals. (100.00%)

Generation 3 has 4 individuals. (100.00%)

Generation 4 has 8 individuals. (100.00%)

Generation 5 has 16 individuals. (100.00%)

Generation 6 has 29 individuals. (90.62%)

Generation 7 has 51 individuals. (79.69%)

Generation 8 has 47 individuals. (36.72%)

Generation 9 has 36 individuals. (14.84%)

Generation 10 has 10 individuals. (2.34%)

Generation 11 has 4 individuals. (0.39%)

Total ancestors in generations 2 to 11 is 207

I have previously tested 23andMe, FTDNA Y111, and FTDNA Big Y. My Y line is unusual, because it does originate in Western Asia, within the past few thousand years (L1b2c). However, there is no evidence of anything but European in any autosomal tests so far, so other than the Y, it appears to be washed out.

My 23andMe AC in spec mode (after phasing with one parent) is:

100% European

96% NW European

2% South European

2% broadly European


37% British & Irish

22% French & German

1% Scandinavian

36% broadly NW European

2% broadly South European


FTDNA Family Finder - My Origins


36% British Isles

32% Southern European

26% Scandinavian

6% Eastern European

I thought that it would be interesting to compare how a few important GEDMATCH calculators, see my raw data from Family Tree DNA, in comparison to the raw data from 23andMe:

GEDMATCH

23andMe raw data V ftDNA raw data

Eugenes K13 Oracle

23andMe data

Admix Results (sorted):

# Population Percent

1 North_Atlantic 47.58

2 Baltic 22.36

3 West_Med 15.65

4 East_Med 8.03

5 West_Asian 3.05

6 Red_Sea 1.42

7 Amerindian 0.74

8 South_Asian 0.71

9 Oceanian 0.46


Single population Sharing:


# Population (source) Distance

1 South_Dutch 3.89

2 Southeast_English 4.35

3 West_German 5.22

4 Southwest_English 6.24

5 Orcadian 6.97

6 French 7.63

7 North_Dutch 7.76

8 Danish 7.95

9 North_German 8.17

10 Irish 8.22


Family Tree DNA data

Admix Results (sorted):

# Population Percent

1 North_Atlantic 47.89

2 Baltic 22.68

3 West_Med 15.45

4 East_Med 7.41

5 West_Asian 3.11

6 Red_Sea 1.38

7 South_Asian 0.84

8 Amerindian 0.72

9 Oceanian 0.52


Single Population Sharing:


# Population (source) Distance

1 Southeast_English 3.75

2 South_Dutch 4.03

3 West_German 5.42

4 Southwest_English 5.68

5 Orcadian 6.33

6 North_Dutch 7.15

7 Danish 7.36

8 Irish 7.59

9 West_Scottish 7.62

10 North_German 7.7


Euogenes EUtest V2 K15

23andMe data

Admix Results (sorted):


# Population Percent

1 North_Sea 33.42

2 Atlantic 27.98

3 West_Med 12.24

4 Baltic 10.42

5 Eastern_Euro 7.04

6 West_Asian 3.52

7 East_Med 3.14

8 Red_Sea 1.48

9 Amerindian 0.39

10 Oceanian 0.19

11 South_Asian 0.18


Single Population Sharing:


# Population (source) Distance

1 Southwest_English 2.7

2 South_Dutch 3.98

3 Southeast_English 4.33

4 Irish 6.23

5 West_German 6.25

6 North_Dutch 6.79

7 West_Scottish 6.84

8 French 6.85

9 North_German 6.89

10 Danish 7.26


Family Tree DNA data

Admix Results (sorted):


# Population Percent

1 North_Sea 33.81

2 Atlantic 28.23

3 West_Med 12.04

4 Baltic 10.59

5 Eastern_Euro 6.84

6 West_Asian 3.66

7 East_Med 2.47

8 Red_Sea 1.46

9 Amerindian 0.35

10 South_Asian 0.31

11 Oceanian 0.25


Single Population Sharing:


# Population (source) Distance

1 Southwest_English 2.29

2 Southeast_English 4.02

3 South_Dutch 4.48

4 Irish 5.78

5 West_Scottish 6.41

6 North_Dutch 6.43

7 West_German 6.63

8 North_German 6.73

9 Danish 7.01

10 Orcadian 7.19


Gedrosia Eurasia K6 Oracle

23andMe data

Admix Results (sorted):


# Population Percent

1 West_European_Hunter_Gartherer 39.18

2 Natufian 38.8

3 Ancestral_North_Eurasian 20.85

4 Ancestral_South_Eurasian 0.82

5 East_Asian 0.35


Family Tree DNA data

Admix Results (sorted):


# Population Percent

1 West_European_Hunter_Gartherer 39.57

2 Natufian 38.66

3 Ancestral_North_Eurasian 20.75

4 East_Asian 0.86

5 Ancestral_South_Eurasian 0.16

Novel SNPs for Paul Brooker Y Haplogroup L-M317 (+SK1414) Family Tree DNA kit 491864

I've just stored this data here, as a "in case it was lost".  All of the Novel SNPs as listed by FTDNA Y Haplogroup L project administrator, Gareth Henson, based on my FTDNA Big Y test, including both YFull and FullGenomes analysis of the Big Y data.

117 Novel SNP's not yet recorded on any other sample.

Position Reference Derived Reads YFULL FTDNA FGC YFull Temp Name YFQ YFull Qual Desc FGC Name FGC Qual

Comments
2872307 C A 80 Y Y Y YFS1985627 100 Best qual FGC51036 100


3440120 T C 22 Y N Y YFS1985628 100 Best qual
40


3650777 G A 2 Y N N YFS1985629 100 Ambiguous qual



Probably just "noise"
3851037 C A 2 Y N Y YFS1985630 100 Ambiguous qual
10

Probably just "noise"
4676699 T A 2 Y N N YFS1985635 100 Ambiguous qual



Probably just "noise"
4953978 A T 2 Y N N YFS1985636 100 Ambiguous qual



Probably just "noise"
5627893 T A 3 Y N N YFS1985637 100 Acceptable qual



Reads below FTDNA threshold
6134978 G T 77 Y Y Y YFS1985638 91 Acceptable qual
10


6391676 G A 73 Y Y Y YFS1985641 100 Best qual
10


6419919 G T 2 Y N Y YFS1985642 100 Ambiguous qual
10

Probably just "noise"
6643664 C T 33 Y Y Y YFS1985643 100 Best qual FGC51038 100


6701612 A G 51 Y Y Y YFS1985644 100 Best qual FGC51039 100


6715132 A G 5 Y N Y YFS1985645 100 Best qual FGC51040 95

Reads below FTDNA threshold
6893378 T C 30 Y Y Y YFS1985646 95 Acceptable qual FGC51041 100


7032017 C A 80 Y Y Y YFS1985649 100 Best qual FGC51042 100


7327691 G A 78 Y Y Y YFS1985652 97 Acceptable qual FGC51043 100


7377200 G A 47 Y Y Y YFS1985653 100 Best qual FGC51044 100


7517429 G A 54 Y Y Y YFS1985656 100 Best qual FGC51045 100


7581204 G T 41 Y Y Y YFS1985658 96 Acceptable qual FGC51046 100


7750714 A T 8 Y N Y YFS1985660 100 Best qual
40

Reads below FTDNA threshold
7764687 G T 30 Y Y Y YFS1985661 100 Best qual FGC51047 100


7799504 G A 82 Y Y Y YFS1985662 98 Acceptable qual FGC51048 100


7957071 A C 11 Y Y Y YFS1985663 100 Best qual FGC51049 100


8208710 T C 39 Y Y Y YFS1985664 96 Acceptable qual FGC51050 100


8461000 C A 70 Y Y Y YFS1985666 98 Acceptable qual FGC51051 100


8468697 T C 17 Y Y Y YFS1985667 100 Best qual FGC51052 100


8485396 T G 102 Y Y Y YFS1985668 100 Best qual FGC51053 100


8573893 C T 86 Y Y Y YFS1985669 100 Best qual FGC51054 100


8637541 G A 6 Y N Y YFS1985670 100 Best qual FGC51055 95

Reads below FTDNA threshold
8801867 A G 48 Y Y Y YFS1985672 100 Best qual FGC51056 100


8872964 G A 25 Y Y Y YFS1985673 100 Best qual FGC51057 95


9124517 C T 89 Y Y Y YFS1985674 100 Best qual FGC51058 100


9139036 G T 41 Y Y Y YFS1985675 100 Best qual FGC51059 100


9169290 A T 30 Y Y Y YFS1985677 100 Best qual FGC51060 100


9754516 T C 26 Y Y Y YFS1985683 100 Best qual
40


9838293 G C 64 Y Y Y YFS1985684 100 Best qual FGC51061 100


13135709 C T
N Y Y


FGC41711 100

Recurrent mutation?
13679122 C T
N Y Y


FGC51064 100


13855794 C A 2 Y N Y YFS1985793 100 Ambiguous qual
10

Probably just "noise"
14031785 C A 8 Y N Y YFS1985860 100 Best qual
40

Reads below FTDNA threshold
14426597 G A 56 Y Y Y YFS1985862 98 Acceptable qual FGC51065 100


14612339 A T
N Y Y


FGC51066 100


14638509 T C 55 Y Y Y YFS1985864 92 Acceptable qual SK1414 100


14751018 C T 56 Y Y Y YFS1985865 100 Best qual FGC51067 100


15039403 T C 63 Y Y Y YFS1985868 100 Best qual FGC51068 100


15160593 C T 16 Y Y Y YFS1985870 100 Best qual FGC51069 100


15311752 C G 64 Y Y Y YFS1985872 100 Best qual FGC51070 100


15349365 G A 68 Y Y Y YFS1985873 100 Best qual FGC51071 100


15491978 T C
N Y Y


FGC22105; YFC006597 10

Recurrent mutation (boundary between TA and CA repeats)
15584574 G A 5 Y N Y YFS1985874 100 Best qual FGC51072 95

Reads below FTDNA threshold
15633507 G A 49 Y Y Y YFS1985875 100 Best qual FGC24349 100

Recurrent mutation?
15777291 G T 18 Y Y Y YFS1985876 100 Best qual FGC51073 100


16042702 C G 7 Y N Y YFS1985877 100 Best qual FGC51074 95

Reads below FTDNA threshold
16134641 G C 8 Y N Y YFS1985878 100 Best qual FGC51075 95

Reads below FTDNA threshold
16309939 T A 49 Y Y Y YFS1985879 100 Best qual FGC51076 100


16406336 C T 88 Y Y Y YFS1985880 94 Acceptable qual FGC51077 100


16547983 C T 66 Y Y Y YFS1985881 100 Best qual FGC51078 100


16611208 C T 46 Y Y Y YFS1985882 100 Best qual FGC51079 100


16764043 T C 40 Y Y Y YFS1985883 93 Acceptable qual FGC51080 100


17099361 T C 48 Y Y Y YFS1985884 94 Acceptable qual FGC51081 100


17394936 T C 54 Y Y Y YFS1985886 97 Acceptable qual FGC51082 100


17448259 A G 8 Y N Y YFS1985887 100 Best qual FGC51083 95

Reads below FTDNA threshold
17463141 G A 11 Y Y Y YFS1985888 100 Best qual FGC51084 100


17504007 C A 2 Y N Y YFS1985889 100 Ambiguous qual
40

Probably just "noise"
17575329 G T 31 Y Y Y YFS1985890 100 Best qual FGC51085 100


17774733 T A 19 Y N Y YFS1985891 100 Best qual
10

3 SNPs close together - probably a single mutation event
17774735 G A 19 Y N Y YFS1985892 100 Best qual
10

17774737 T C 19 Y N Y YFS1985893 100 Best qual
10

17938564 C T 95 Y Y Y YFS1985894 100 Best qual FGC51086 100


18045221 A T 55 Y Y Y YFS1985895 100 Best qual FGC51087 100


18557184 G A 64 Y Y Y YFS1985898 98 Acceptable qual FGC51088 100


18675826 A T 18 Y Y Y YFS1985899 100 Best qual FGC51089 100


18919156 G A 76 Y Y Y YFS1985901 100 Best qual FGC51090 100


19057204 G A 19 Y Y Y YFS1985902 100 Best qual FGC17900 100

Recurrent mutation?
19119491 A C 23 Y Y Y YFS1985903 100 Best qual FGC51091 100


19508605 A G 62 Y Y Y YFS1985905 98 Acceptable qual FGC51092 100


19544681 G T 8 Y N Y YFS1985906 100 Best qual FGC51093 95

Reads below FTDNA threshold
20692245 T C
N Y Y



40


21037375 C T 4 Y N Y YFS1985916 100 Acceptable qual FGC51094 95

Reads below FTDNA threshold
21141871 G C 51 Y Y Y YFS1985917 97 Acceptable qual FGC51095 100


21152868 T G
N Y Y


DC323 (also known as S4815) 10

Recurrent mutation
21374612 G C 68 Y Y Y YFS1985919 100 Best qual FGC51096 100


21392171 G A 22 Y Y Y YFS1985920 100 Best qual FGC51097 100


21412260 C A 7 Y N Y YFS1985921 100 Best qual
40

Reads below FTDNA threshold
21504880 G A 18 Y Y Y YFS1985922 100 Best qual FGC51098 100


21550243 A C 20 Y Y Y YFS1985924 100 Best qual FGC51099 100


21554777 G T 2 Y N Y YFS1985925 100 Ambiguous qual
40

Probably just "noise"
21628664 C T 81 Y Y Y YFS1985926 100 Best qual FGC51100 100


22230862 A G 55 Y Y Y YFS1985927 92 Acceptable qual FGC51101 95


22240008 T C
N Y Y


ZS5617 40

In volatile DYZ19 region
22259810 G C
N Y Y



40

In volatile DYZ19 region
22261622 T C
N Y Y



40

In volatile DYZ19 region
22262437 T A
N Y N






In volatile DYZ19 region
22262459 G C
N Y Y


site of BY1891 40

In volatile DYZ19 region
22262502 A G
N Y Y



10

In volatile DYZ19 region
22268591 A T
N Y Y



40

In volatile DYZ19 region
22423571 C A
N Y Y



10

In volatile DYZ19 region
22521253 T C 18 Y Y Y YFS1986012 100 Best qual FGC51102 100


22523410 G A 44 Y Y Y YFS1986013 100 Best qual FGC51103 100


22573608 A G 57 Y Y Y YFS1986014 95 Acceptable qual FGC51104 100


22675321 T C 45 Y Y Y YFS1986015 97 Acceptable qual FGC51105 100


22749142 A C 65 Y Y Y YFS1986016 100 Best qual FGC51106 100


22760336 A G 35 Y Y Y YFS1986017 100 Best qual FGC51107 100


23081618 G A 34 Y Y Y YFS1986018 96 Acceptable qual
10


23249958 T C 66 Y Y Y YFS1986019 100 Best qual FGC51108 100


23283344 T C 72 Y Y Y YFS1986020 88 Ambiguous qual
40


23324862 T A 63 Y Y Y YFS1986023 98 Acceptable qual FGC51109 100


23401635 A G 15 Y Y Y YFS1986024 100 Best qual FGC51110 100


23479996 A T 59 Y Y Y YFS1986025 100 Best qual FGC51111 100


23563109 G A
N Y Y


YP5075


Recurrent mutation?
23633302 T C 22 Y Y Y YFS1986027 95 Acceptable qual FGC51112 100


23638466 A C 81 Y Y Y YFS1986028 98 Acceptable qual FGC51113 100


23832496 G C 33 Y Y Y YFS1986030 100 Best qual FGC51114 95


23899850 T C
N Y Y



40


24001198 C T 13 Y N Y YFS1986033 100 Best qual FGC51115 100

Reads below FTDNA threshold
24026825 G T 2 Y N N YFS1986035 100 Ambiguous qual



Probably just "noise"
24428691 T C 26 Y Y Y YFS1986036 100 Best qual FGC51116 100


Y Haplogroup L Resource page

Distribution Haplogroup L Y-DNA

By Crates (Own work) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY-SA 4.0-3.0-2.5-2.0-1.0 (http://creativecommons.org/licenses/by-sa/4.0-3.0-2.5-2.0-1.0)], via Wikimedia Commons.  Unmodified.

Introduction - Y-DNA, Haplogroups, SNPs, Haplotypes

The Y chromosome, and it's Y-DNA, are copied from father to son, down a strictly paternal lineage.  If I were to trace my entire direct ancestry back, I have two parents, four grandparents, eight great grandparents, sixteen great great grandparents.  Yet out of those sixteen great great grandparents (generation 5), who were born only circa 160 years ago, only one carried the Y-DNA that was passed down to me.  My eight great great grandmothers did not not inherit a Y chromosome from their fathers.  Most likely, my other seven great great grandfathers, carried distinctive differently marked Y-DNA.  Yet all sixteen biological great great grandparents have contributed to my overall atDNA (autosomal DNA).  Only one gave me my Y-DNA.  So you can see that Y-DNA represents only one narrow lineage.

Y-DNA, may on the face of it, appear to offer a limited understanding of total biological ancestry.  All sixteen of my great great grandparents were direct ancestors, not just the Y great great grandfather.  However, this lineage offers us evidence that can be genetically tracked, then mapped into relationship.  It could be done to ascertain parental, or non parental events.  It can be used to check the biological validity of relationship to cousins.  As more people investigate and record their haplogroups, haplotypes, STR markers, and SNPs, so we can for example, start to use them to map biological relationship further back.  Y-DNA is particularly useful, not only because of it's markers, but also because it can be plotted to surname studies.  In Western societies, the surname often follows the Y lineage for several generations.

However, Y-DNA (nor the maternal mtDNA) evidence doesn't just stop there.  As more people investigate, submit, and record their data from around the World - and as anthropologists and archaeologists add ancient DNA data from ancient and provenanced human remains to that record, so we can build and plot a world map of the human family, how it relates, how it was distributed globally throughout prehistory.

Both Y and mt DNA carries mutation markers, that define a HaplogroupA haplogroup is a family of shared descent.  These haplogroups are ancient.  The paternal Y-DNA haplogroup that this resource page is dedicated to has been designated as L.

However, mutations do not stop with the formation of a new haplogroup.  They continue through the generations.  As lineages divide between different sons, across many generations, so these mutations in the Y-DNA for example, continue to accumulate down the diverging lineages that once shared common descent.  We are all unique.  The sub clade of L that this page focuses on is L1b.  All male carriers of L1b will carry a SNP (Single Nucleotide Polymorphism) on their Y-DNA that has been designated as M317. This SNP will be downstream of another SNP that has been designated as M22.  Finally, a Y-DNA can be said to have a terminal SNP.  A terminal, refers not to the Haplogroup (in this case L), but can be used to define right down to the last SNP on the Y-DNA, that is shared with others on a record.  If someone for example, carries Y-DNA that is proven (or predicted by comparison) to be Y Haplogroup L, and to carry M317, then their Y terminal could be designated as L-M317, or alternatively, as L1b.  This is also sometimes referred to as a haplotype.  However, a haplotype can also refer to a particular STR.

Y Haplogroup L M20

The above image illustrates a modern day distribution of Y Haplogroup L (M20) as proposed and created by Anthropogenica user Passa.

Y Haplogroup K formed from Y Haplogroup IJK in the Y-DNA of hunter-gatherer fathers and sons, that share a MRCA (most recent common ancestor) during the Upper Palaeolithic, circa 45,400 years ago.  Where did these Y ancestors live at that time?  We think that they lived in Western or Southern Asia.  Iran is a favourite proposal. Earlier Y ancestors had most likely exited Africa 20,000 years earlier, and were well established in Asia.  They had most likely met and confronted another archaic human species, The Neanderthal. This was however, a time of great expansion by humans.  The first anatomically modern humans had recently entered Europe, while other modern humans were arriving in Australia.  The Ice Age was in a flux, but glaciation was advancing.

The most recent common Y ancestor to carry Y Haplogroup LT lived circa 42,600 years ago.  Then a mutation in the Y-DNA lead to the formation of Y Haplogroup L, with a most recent common ancestor 23,200 years ago, close to the time of the Last Glacial Maximum, when ice sheets were reaching their maximum positions.  K, LT, and early L, most likely all originated in Upper Palaeolithic hunter-gatherer populations living during the last Ice Age, in the area of modern day Syria, Iraq, Iran or Pakistan.  It was a time of increased stress on human populations, that were having to adapt to some severe environmental challenges, and may have at times faced isolation into a number of Ice Age Refuges.  Some of these Upper Palaeolithic, Ice Age hunter-gatherer refuges may have been close to the Black Sea, others close to the Caspian Sea, but they were most likely located somewhere between Eastern Anatolia, and Eastern Iran, south of the Caucasus.

L1 / L2 Divergence - the Odd L2's

The oldest divergence within Y Haplogroup L.  L1, as characterised by the SNP M22, diverged from L2, as characterised by the SNP L595.  L2 was only recently discovered, and forced an ISOGG revision of Y Haplogroup L and it's nomenclature that is still causing problems.  In this article, unless stated otherwise, I am using 2017 Nomenclature.  L2 or L-L595 is very rare, but has so far cropped up sporadically across Western Eurasia, including in Azeribaijan, Turkey, Sardinia, England, and Tartaristan.

That is L2 dealt with.  However, most Y Haplogroup L falls into L1. Let us start to look at the main branches of L1.  Remember, L1 is defined by the SNP M22:

Unofficial proposed tree for L1 (L-M22) 2016.  By Gökhan Zuzigo, modified by Paul Brooker.

Proposed Migration Map of L-M22 (L1) by Phylogeographer at https://phylographer.com/mygrations/?

The Big L1 Split - L1a and L1b

As can be seen above, this split occurred around 18,400 years ago, possibly somewhere between what is now Iran and Pakistan.  The L1a branches inherit the SNP M2481, and the L1b branches inherited M317.

First of all, let's look at L1a, because although it is not my sub clade, in terms of modern day population size, it appears to greatly outnumber any other L sub clade.

Pakistan and India - Present Day Home of L1a1 and L1a2

L1a splits again into two sub clades.  The split occurred around 17,400 years ago.  L1a1 (L-M27) and L1a2 (L-M357)

L1a1 (L-M27)

Defined by SNP M27 (on older nomenclature as still used by 23andMe, this was formerly L1*) is mainly found in India, particularly South West India, and in Sri Lanka. This is perhaps the most populous modern day L sub clade, found in 15% of Indian males.  However, it is not restricted to India, and has also been found in 20% of Balochi in Pakistan, and has also been reported in Kirghiz, Pashtun, Tajik, Uzbek, and Turkmen males across Central Asia.

L1a and L1a1 (L-M27) at Birds Eye Cave, Armenia 6161 years before present.

Ancient Y DNA from the Copper Age has emerged from this location in Armenia, and included L1a, and L1a1.  This might suggest, that although very successful today in India and Pakistan, that it has a Western Asian origin.

L1a2 (L-M357)

Has defined by SNP M357 (on older nomenclature as still used by 23andMe, this was formerly L3*).  This sub clade is mainly found in Pakistan, but also Saudi Arabia, Kuwait, The Chechen Republic, Tajikistan, India, and Afghanistan.  It has been found at 15% in Burusho populations, and at 25% in Kalash populations.  It is much more common in Pakistan than in India.

So, the L1a sub clades - spreading down into Southern Asia, and accounting for potentially millions of Y Men there.  Far more than any other branches of Y Haplogroup L.  However, Southern Asia is unlikely to be the origin of L.  That origin is more likely, as stated earlier, to be the place with the most diversity in branches.  That points more towards again towards Western Asia.  It's just that ancient carriers of L, appear to have been particularly successful in Southern Asia, and to have fathered more sons there.

L-M317 or L1b of Western Asia

We now move onto the branches of particular interest to myself, because I carry a Y Haplotype that belongs here.  L1b is defined by the SNP M317, that formed circa 18,400 years ago, most likely in the area of modern day Iran, or elsewhere in Western Asia.

Phylogenetic tree of L1b by Anthrogenica user Caspian (with permission):

Click on above hyperlink for full sized image

L1b is mainly distributed across Western Asia, from modern day Turkey, across to Pakistan.  However, as we will see, it also spreads in low densities across parts of Europe.  it is very much, the "Western L".

The Next split - L1b1 or L-M349.  The Levant, and Europe!

Around 14,000 years ago, another split occurred in the L1b (M317) branch. A new SNP, M349, defined L1b1.  Today, L1b1, or L-M349, is found in Western Asia, in Lebanon, Syria, Turkey, Armenia, etc.  However, it is also found scattered in low densities through parts of Europe.  It crops up in South Europe, often close the the Mediterranean Sea, including particularly in parts of Italy.  It also forms a light cluster in Central Europe.

A working map of Y haplogroup L sub clades by Edward Chernoff.  This map is incomplete, but is published here with permission of Edward Chernoff.  Copyrights applied.

Branching away from a common Y ancestor with L1b1 (M349), is another 14,000 year old line defined by SNP SK1412, L1b2.

L1b2 (L-SK1412) splits - Pontic Greeks, and the others...

13,000 years ago,, during a cold stage towards the end of the last Ice Age, the L1b2 (SK1412) Y branch divides again.  Very recent research suggests that it split into three lines: L-SK1415 (L1b2a), L-PH8 (L1b2b), and L-SK1414 (L1b2c).

L1b2a (L-SK1415), has as far as I know, only been detected in a Makrani Balochi survey in SW Pakistan.

L1b2b (PH8), is found in Turkey, Greece, Armenia, Chechen Republic, Iraq, etc.  It is associated particularly with the Pontic Greek ethnicity from Eastern Anatolia, and around the Black Sea.  A further division within PH8 has been detected at around 3,000 years ago.

Finally ... mine:

L1b2c (L-SK1414, FGC51074), has so far been SNP detected only in Makrani Balochi, in SW Pakistan, Gujarat, India, Turkey, Cyprus, Saudi Arabia, Lebanon (Druze), and in England. STR predictions for L-SK1414 have also been found in Goa, Syria, Iraq, Kuwait, UAE, Tartaristan, France, Italy, Iran, and Azores.  In addition to SK1414, I have with the assistance of Gareth Henson, a FT-DNA Big Y test, accompanied by further analysis of their raw data, by Yfull, and FullGenomes, ascertained 117 novel SNPs looking for first time matches.  As can be imagined, I'm very keen that further L Y-Men should test.

Distribution may be connected to the dispersal of the recently identified group known as the Iranian Neolithic Farmers after 10,000 BCE:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5113750/#:~:text=We%20sequenced%20Early%20Neolithic%20genomes,significantly%20to%20the%20ancestry%20of

In addition there would appear to be a potential link between this group, and the inhabitants of the Harappan or Indus Valley civilization. Below is my proposed distribution of L SK1414 / FGC51074:

Those tentative European Y haplogroup L links

We have seen above, that again, and again, Y haplogroup L (M20), and several of it's sub clades appear to have Western Asian origins, despite success of some of those sub clades today in India and Pakistan.  Y haplogroup L has not been linked to the Yamna hypothesis, that has taken credit for the origin of many haplogroups that are successful today in Europe.  Y-DNA L was located to the southern side of the Caucasus, between present day Turkey and Pakistan.  However, two particular Y-DNA L sub clades do make mysterious appearances across Europe.

1) L-L595 (L2) has only recently been discovered, so far, exclusively across Europe, in very low numbers.

2) L-M349 (L1b1), downstream of M317, also spreads across South Europe, and clusters at the Rhine-Danube.  I have on 23andMe forums, seen a number of testers that unfortunately have not tested their Y elsewhere, claim Ashkenazi paternal ancestry, but this is far from common to all European L-M349 samples. Although rarely forming much more than 1% of all Y along the Mediterranean coast of Southern Europe, this percentage does occasionally rise higher, for example, in parts of Italy.

When did L2 or even L1b1 enter Europe?  L2 has only so far been found in Europe.  There are some suggestions that some European L could be survivors from the Eurasian Neolithic.  However, ancient DNA has not yet been found to support this hypothesis. 

Prime resources

L Yfull Tree

https://www.yfull.com/tree/L/

Wikimedia entry for Y Haplogroup L-M20

https://en.wikipedia.org/wiki/Haplogroup_L-M20

FTDNA L The Y Haplogroup L Project

https://www.familytreedna.com/public/Y-Haplogroup-L/

Marco Cagetti's Y Haplogroup L

http://www.cagetti.com/Genetics/L-haplogroup.html

Anthropogenica Y Haplogroup L Forum Board

http://www.anthrogenica.com/forumdisplay.php?37-L

ISOGG 2009 Y Haplogroup L (Useful for understanding 23andMe Y haplogroup result of L2*)

http://isogg.org/tree/2009/ISOGG_HapgrpL09.html

ISOGG 2017 Y Haplogroup L

http://isogg.org/tree/ISOGG_HapgrpL.html

Other resources

Europedia Y-DNA Haplogroup L

http://www.eupedia.com/europe/origins_haplogroups_europe.shtml#L

23andMe users should note that the company in 2016, still used a very outdated ISOGG nomenclature system.  My 23andMe reported haplotype was L2*.  However, using ISOGG 2016, this is now L1b (L-M317).  NOT to be confused with modern day L2 (L-L595).

Facebook Y Haplogroup L Group

https://www.facebook.com/groups/773887796013634/

L-M317 STR Alpine cluster article

https://figshare.com/articles/L_M317_STR_marker_likelihood_tree_focuing_Alpine_cluster/105684

Familypedia Wiki for Haplogroup L

http://familypedia.wikia.com/wiki/Haplogroup_L_(Y-DNA)

For personal note  as of 2018-08-28.

My Y Haplogroup L Designation:

L +M20 +M22 +M317 +SK1412 +SK1414 (or FGC51074) +FGC51041 (or Y31947) +FGC51036

L-SK1414 = L1b2c

SK1414/FGC51074 age estimate current 9,300 years bp.

L-FGC51041 is a verified terminal

FGC51041/Y31947 age estimate current 6,000 years ago but only 2 samples on Ytree.

L-FGC51036 on terminal on FT-DNA

L-Y31947 is terminal on yFull

115 novel SNPs