S26 (aka Null DYS439, Little or L1 SNP)

 

John McEwan

 

4th Dec 2005 (last updated 30th April 2006)

 

The discovery and elucidation of this R1b subclade SNP is well described (and kept updated) by Leo Little at  http://www.familytreedna.com/public/null439/index.aspx  Briefly, a SNP was discovered by Leo Little and FTDNA in the flanking regions of DYS439 based on the observation that a null allele was appearing in this STR associated with a certain cluster of haplotypes within R1b. FTDNA now officially identify these null individuals. More recently based on a SNP tested individual it appears that L1 is a sub-clade of S21 and it is now shown as such on the new ISOGG haplogroup tree. This work seeks to examine this SNP from the perspective of its properties, relative to other R1b SNPs.

 

Data

The file of putative nulls supplied by Leo Little on the 3rd Dec 2005 was examined and edited to remove close matches within the same surname, most likely due to sampling within the same recorded family. Similarly, only those with 37 FTDNA STR marker results were kept.

 

Before editing there were 32 individuals with 37 FTDNA markers. On this basis, compared to the phase 3 cluster analysis, this subgroup makes up 32/3996 ~ 0.8% of Ysearch with 37 marker results and 32/2553 ~1.3% of R1b. This identifies that the subgroup is a minor fraction of R1b.

 

Results

The edited results were then analyzed in Dean McGee’s site http://www.mymcgee.com/tools/yutility.html . The modal haplotype and haplotypes used are listed in table 1 below. Table 2 compares these haplotypes using the infinite allele model. The major observation is the high level of diversity observed between the different families. The number of mismatches ranges from 2-17.  This is surprising given the small observed fraction of R1b that this group represents, which in turn implicitly suggests a recent and common origin.

 

Using conservative anthropological parameters of 0.0007 mutations/STR/generation and 28 years for the generation interval inferred a TMRCA estimate of 7681 yrs bp. While this estimate has large standard errors, this is very long ago.

 

In order to identify what relationship L1 individuals and modal have with the phase 3 R1b cluster analysis the relevant haplotypes were compared. First the L1 modal haplotype had a best fit with R1bSTR32 with 4 mismatches, followed by R1bSTR42 with 5 mismatches. The next best was 7 mismatches. Individuals ranged from 5-12 mismatches with R1bSTR32 and 6-13 with R1bSTR42.  The latter group R1bSTR42 is mentioned because other S21+ individuals have been identified within that cluster.

 

Geographical distribution

Only a limited number of surnames are available that have the L1 SNP. Most appear to have English origins and those with 37 FTDNA haplotypes have been graphically tabulated below. With some exceptions there appears to be a centre of gravity located in central England with both Wales and Scotland underrepresented.

 

Discussion

Three points emerge from these results: the diversity of the individuals relative to the size of the group, the age of the estimated mutation and the geographical distribution of the individual surnames. 

 

For a comparison the TMRCA estimates for other R1b SNPs calculated on the same basis are listed below. They show that L1 most likely occurred after S21 and M167. This is also consistent with it potentially being a subclade of S21.

 

R1b SNP       yrs bp

S21                 9231   (derived from 10 S21 positive individuals)

M167              9048   (derived from average of 3 estimates 9072 yr bp, 8198 yrs bp and 9874 yrs bp)

L1                   7681   (derived from 21 semi unrelated individuals) 

 

The current hypothesis is that S21+ is an early mutation within R1b that was geographically European in localization. In more recent times in Britain it represents an “invader” origin, specifically in post Roman times it is most likely associated with Angles, Saxons, Jutes and maybe Normans. S21 has been geographically associated with the so-called “Frisian” R1b STR cluster. L1 appears to be somewhat different from that STR cluster. However, it shares characteristics with its distribution within Britain. Its age and diversity (predating the Anglosaxon invasions) also suggest that it has originated from a larger population that has yet been unsampled or only poorly sampled from Europe. On a speculative note it may indicate French or Norman origins as distinct from Northern European.

 

Summary

The L1 SNP is likely to be a subclade of the S21 positive group. It has a different STR profile that the majority of S21 positive individuals identified to date, which belong to the R1bSTR22Frisian group. However, its distribution in England shows some similarities to the expected historic spread of Angles and Saxons although further work is required. Its age is estimated as being after S21 and before the age of the Roman empire. Its diversity and age suggest that this grouping may be present on the continent in some as yet unsampled geographical location.

 

Table 1. List of L1 haplotypes used and modal values. Note by convention DYS439=12

Ysearch Database Configuration - DNA Results Comparison

ID

D
Y
S
3
9
3

D
Y
S
3
9
0

D
Y
S
1
9
/
3
9
4

D
Y
S
3
9
1

D
Y
S
3
8
5
a

D
Y
S
3
8
5
b

D
Y
S
4
2
6

D
Y
S
3
8
8

D
Y
S
4
3
9

D
Y
S
3
8
9
-
1

D
Y
S
3
9
2

D
Y
S
3
8
9
-
2

D
Y
S
4
5
8

D
Y
S
4
5
9
a

D
Y
S
4
5
9
b

D
Y
S
4
5
5

D
Y
S
4
5
4

D
Y
S
4
4
7

D
Y
S
4
3
7

D
Y
S
4
4
8

D
Y
S
4
4
9

D
Y
S
4
6
4
a

D
Y
S
4
6
4
b

D
Y
S
4
6
4
c

D
Y
S
4
6
4
d

D
Y
S
4
6
0

G
A
T
A
-
H
4

Y
C
A
-
I
I
a

Y
C
A
-
I
I
b

D
Y
S
4
5
6

D
Y
S
6
0
7

D
Y
S
5
7
6

D
Y
S
5
7
0

C
D
Y
a

C
D
Y
b

D
Y
S
4
4
2

D
Y
S
4
3
8

modal

13

24

14

11

11

14

12

12

12

13

13

29

17

9

9

11

11

25

15

19

29

15

16

16

17

10

11

19

23

16

16

17

17

37

38

12

12

Adams

14

23

14

11

11

14

12

12

12

13

13

29

16

9

10

11

11

25

15

19

32

15

15

15

15

10

11

19

23

16

15

16

17

36

37

12

12

Atkins1

13

24

14

11

11

14

12

12

12

13

13

29

17

9

9

11

11

25

15

19

29

14

15

16

18

10

11

19

23

15

16

18

16

37

38

12

12

Atkins2

13

24

14

11

12

14

12

12

12

13

13

29

18

9

10

11

11

25

15

20

29

15

15

16

17

10

12

19

23

16

15

17

17

39

39

12

12

Brown

13

24

14

11

12

14

12

12

12

13

13

29

16

9

10

11

11

25

15

19

29

15

15

15

16

11

11

19

22

15

15

17

17

37

38

12

12

Cotton1

13

24

14

10

11

14

12

12

12

13

13

29

17

9

9

11

11

25

15

20

29

15

16

16

17

10

11

19

23

16

15

18

17

38

38

12

12

Davison

13

24

14

12

11

14

12

12

12

13

13

29

18

9

10

11

11

26

15

19

30

15

15

17

17

11

11

19

23

17

15

17

17

37

38

12

12

Fox1

13

24

14

11

11

15

12

12

12

13

13

29

17

9

9

11

11

25

15

19

29

14

14

16

16

10

11

19

23

16

16

18

17

38

38

13

12

Fox3

13

24

14

11

11

15

12

12

12

13

13

29

17

9

9

11

11

26

15

19

29

14

16

16

16

10

11

19

23

16

16

19

17

38

39

13

12

Glass

13

24

14

11

11

14

12

12

12

13

13

31

16

9

9

11

11

25

15

19

29

15

16

16

17

12

11

19

23

15

16

17

16

38

38

12

12

Goodwin

13

24

14

10

11

15

12

12

12

14

13

30

17

9

9

11

11

25

15

19

29

14

14

16

16

10

11

19

23

15

16

16

16

37

37

12

12

Hazelwood1

13

24

14

11

11

14

12

12

12

13

13

29

16

9

9

11

11

25

15

19

29

15

15

16

16

10

11

19

23

16

16

17

17

37

39

12

12

Holt3

13

25

14

11

12

14

12

12

12

13

13

29

16

9

10

11

11

25

15

19

28

15

15

15

16

11

11

19

23

15

15

16

17

37

38

11

12

Holt4

13

25

14

11

12

14

12

12

12

13

13

29

16

9

10

11

11

25

15

19

28

15

15

15

16

11

11

19

22

15

15

17

17

36

39

11

12

Jardine

13

24

14

12

11

14

12

12

12

13

13

29

18

9

10

11

11

25

15

19

31

15

15

17

17

11

11

19

23

16

15

17

17

37

38

12

12

King

13

24

14

11

11

14

12

12

12

13

13

29

17

9

9

11

11

24

15

19

29

16

16

16

17

10

11

19

23

17

15

17

17

37

39

12

12

Little1

13

24

14

10

11

14

12

12

12

13

13

30

17

9

9

11

11

25

15

19

30

15

16

16

17

11

11

19

23

16

16

17

16

37

38

12

12

Little4

13

24

14

10

11

15

12

12

12

13

13

29

17

9

9

11

11

25

15

19

29

14

16

16

17

10

11

19

23

16

16

17

16

39

39

12

12

Little5

13

24

14

10

11

14

12

12

12

13

13

29

17

9

9

11

11

24

15

19

29

16

16

17

17

10

11

19

23

17

16

17

17

36

36

12

12

Smith

13

24

14

10

12

14

12

12

12

13

13

29

18

9

10

11

11

25

15

19

29

15

16

17

18

11

10

19

23

17

16

17

17

36

36

11

12

Vines

13

24

14

11

11

14

12

12

12

13

13

29

16

9

9

11

11

24

15

19

30

15

16

16

17

10

10

19

23

16

16

17

17

35

37

12

12

Webb

13

24

14

10

11

14

12

12

12

13

13

29

17

9

9

11

11

25

15

19

29

15

16

16

17

10

11

19

23

16

16

18

17

38

38

12

12

Distance from reference:

Zero

One

Two

Three+

 

Table 2. Genetic distance using the infinite alleles model

Genetic Distance

ID

m
o
d
a
l

A
d
a
m
s

A
t
k
i
n
s
1

A
t
k
i
n
s
2

B
r
o
w
n

C
o
t
t
o
n
1

D
a
v
i
s
o
n

F
o
x
1

F
o
x
3

G
l
a
s
s

G
o
o
d
w
i
n

H
a
z
e
l
w
o
o
d
1

H
o
l
t
3

H
o
l
t
4

J
a
r
d
i
n
e

K
i
n
g

L
i
t
t
l
e
1

L
i
t
t
l
e
4

L
i
t
t
l
e
5

S
m
i
t
h

V
i
n
e
s

W
e
b
b

 

modal

37

12

5

9

9

5

10

6

8

6

9

3

12

14

8

5

5

6

6

11

6

3

 

Adams

12

37

14

12

11

13

13

15

16

15

16

10

10

11

11

14

16

16

15

16

12

13

 

Atkins1

5

14

37

13

10

8

13

7

10

7

7

7

12

15

12

9

8

8

10

13

11

6

 

Atkins2

9

12

13

37

9

9

11

14

14

13

17

8

12

11

9

10

14

11

13

10

11

11

 

Brown

9

11

10

9

37

12

9

14

16

10

15

8

5

5

8

11

12

15

14

11

13

12

 

Cotton1

5

13

8

9

12

37

12

7

10

9

11

8

14

16

10

8

8

8

8

13

10

2

 

Davison

10

13

13

11

9

12

37

16

16

13

17

11

11

13

3

10

10

15

11

11

12

12

 

Fox1

6

15

7

14

14

7

16

37

4

10

8

8

15

17

14

10

11

7

10

15

11

5

 

Fox3

8

16

10

14

16

10

16

4

37

12

10

8

17

17

16

8

13

7

10

16

11

8

 

Glass

6

15

7

13

10

9

13

10

12

37

11

7

13

14

12

10

7

9

10

13

9

7

 

Goodwin

9

16

7

17

15

11

17

8

10

11

37

10

16

19

16

11

10

6

10

16

13

9

 

Hazelwood1

3

10

7

8

8

8

11

8

8

7

10

37

11

11

9

6

8

7

8

12

6

6

 

Holt3

12

10

12

12

5

14

11

15

17

13

16

11

37

4

10

14

14

18

17

12

15

14

 

Holt4

14

11

15

11

5

16

13

17

17

14

19

11

4

37

12

14

16

17

16

11

15

16

 

Jardine

8

11

12

9

8

10

3

14

16

12

16

9

10

12

37

11

9

13

12

11

12

10

 

King

5

14

9

10

11

8

10

10

8

10

11

6

14

14

11

37

10

8

5

13

8

8

 

Little1

5

16

8

14

12

8

10

11

13

7

10

8

14

16

9

10

37

7

9

12

9

6

 

Little4

6

16

8

11

15

8

15

7

7

9

6

7

18

17

13

8

7

37

7

13

10

6

 

Little5

6

15

10

13

14

8

11

10

10

10

10

8

17

16

12

5

9

7

37

9

8

6

 

Smith

11

16

13

10

11

13

11

15

16

13

16

12

12

11

11

13

12

13

9

37

12

11

 

Vines

6

12

11

11

13

10

12

11

11

9

13

6

15

15

12

8

9

10

8

12

37

8

 

Webb

3

13

6

11

12

2

12

5

8

7

9

6

14

16

10

8

6

6

6

11

8

37

 

Related

Probably Related

Possibly Related

FTDNA's Interpreting Genetic Distance for 12 Markers

FTDNA's Interpreting Genetic Distance for 25 Markers

FTDNA's Interpreting Genetic Distance for 37 Markers

- Infinite allele mutation model is used
- Values on the diagonal indicate number of markers tested