Resolving the Placement of Haplogroup I-M223 in the Y-Chromosome Phylogenetic Tree

 

T. Whit Athey and Kenneth Nordtvedt

 

 

Evidence from four case studies is presented demonstrating that Y Haplogroup I-M223 should properly be considered a subgroup of Haplogroup I1, rather than as a separate Haplogroup I2 as recently proposed.  Haplogroup I-M223 had not been discovered when the 2002 Y phylogenetic tree was published by the Y-Chromosome Consortium (YCC).  The first study of Haplogroup I-M223 designated it as a subgroup of I1 and named it I1c.  A later proposed revision of the Y phylogenetic tree, however, showed I1a and I1b as P38+ and I1c with P38-, which required Haplogroup I-M223 to be renamed as Haplogroup I2.  The present study presents four cases in which M223+ men were shown to be also P38+, which reunites Haplogroup I-M223 with I1a and I1b within Haplogroup I1.

  

 

 

Received:  November 7, 2005, accepted November 29, 2005

 

Address for correspondence:  wathey@hprg.com

 

 

 


Introduction

 

Y-chromosome Haplogroup I includes about a quarter of all northwest European men.  Its largest subgroup, I1a, is common in Scandinavia and Germany and occurs in Britain at a frequency of about 15%.  Haplogroup I1b is common in the Balkans and parts of Eastern Europe.  The third major subgroup of Haplogroup I is defined by the single nucleotide polymorphism (SNP) M223, as reported by Rootsi et al (2004).  Rootsi placed I-M223 as a subgroup of I1, parallel to I1a and I1b, and named it Haplogroup I1c (see Figure 1).

 

 

 

 

Figure 1  Phylogenetic Chart for Haplogroup I according to Rootsi et al. (2004) (simplified for clarity).

 

 

 

The SNP M223 had not been discovered in 2002 when the Y-Chromosome Consortium (YCC) issued the latest official version of the Y phylogenetic tree.  Family Tree DNA (FTDNA) in late 2004 published a revision of the YCC-2002 structure.  In this new tree, Haplogroup I-M223 was apparently assumed to be P38- and, as such, it was renamed as Haplogroup I2, as shown in Figure 2.

 

 

Figure 2  Haplogroup I According to FTDNA’s Proposed Revision of the Y Phylogenetic Tree (simplified for clarity).

 

 

The current study presents the results of testing of SNPs in four men who were known or suspected to be members of I-M223.  In all cases, they were found to be both M223+ and P38+, demonstrating that the phylogenetic structure of Haplogroup I as presented in Rootsi et al (2004) (see Figure 1) is correct.

 

Methods

 

Table 1 – Y-STR Values* for All Subjects

ID

3
9
3

3
9
0

1
9

3
9
1

3
8
5
a

3
8
5
b

4
2
6

3
8
8

4
3
9

3
8
9
|
1

3
9
2

3
8
9
|
2

4
5
8

4
5
9
a

4
5
9
b

4
5
5

4
5
4

4
4
7

4
3
7

4
4
8

4
4
9

 

 

 

4
6
4
a

 

 

 

4
6
4
b

4
6
4
c

4
6
4
d

4
6
4
e

4
6
4
f

4
6
0

G
A
T
A

H
4

Y
C
A
I
I

a

Y
C
A
I
I

b

4
5
6

6
0
7

5
7
6

5
7
0

C
D
Y

a

C
D
Y

b

4
4
2

4
3
8

101

15

24

15

10

15

15

11

13

13

14

12

31

15

8

10

11

11

25

14

21

27

11

14

14

15

 

 

 

 

 

 

 

 

 

 

 

 

 

 

102

14

22

15

10

15

15

11

13

11

13

12

29

15

8

10

11

11

25

15

20

28

11

14

15

15

 

 

12

10

19

19

17

16

16

20

34

36

12

11

103

14

23

15

10

14

15

11

13

11

14

12

32

14

8

10

11

11

25

14

19

27

11

14

15

15

 

 

 

 

 

 

 

 

 

 

 

 

 

 

104

14

24

15

10

15

17

11

13

11

13

12

29

16

8

9

11

11

26

15

23

27

11

11

11

11

14

15

11

10

19

21

15

 

 

 

 

 

12

10

*  Results are presented in the same order as in an FTDNA report.

 


Four subjects were chosen from four different surname projects where the Y-STR values suggested strongly that they were members of I-M223.  Three subjects had results from testing either 25 or 37 Y-STR values carried out at Family Tree DNA (FTDNA, Houston, TX), and one from testing 45 markers at Relative Genetics (Salt Lake City, UT).  The Y-STR values, shown in Table 1, were used with the permission of the participants, and were known prior to the present study.

 

Participants in the present study were designated as Subjects 101-104.  The subjects displayed a diverse set of Y-STR haplotypes and (where known) geographic origin.  Subject 101 has an uncertain geographic origin, but his Y-STR values are similar to I-M223 haplotypes from northwest continental Europe as described by Nordtvedt (2005).  Subject 102’s lineage is from Spain and Subject 103’s lineage is from Germany.  Subject 104 has Y-STR values similar to those found in Britain for this haplogroup (Nordtvedt 2005).  Thus, each subject in the study represents one of the major European populations in which the haplogroup is found. 

 

For the present study, SNP testing was carried out on all subjects by Ethnoancestry (Cyprus, CA) for SNPs M223 and P38.  At Ethnoancestry, Y chromosome SNPs were amplified by PCR with standard primers giving products from 200 to 500 bp in length.  PCR products were then sequenced using dye terminator chemistry with electrophoresis on a capillary ABI sequencer.  Alleles were called in the software package, Sequencher, by alignment with chromosomes of known allelic state (positive and negative controls).

 

 

Results

 

The results for all of the SNP tests from the present study are shown in Table 2.  All subjects were found to be derived (positive) for both P38 and M223.  Where additional SNP testing was done, these results are also included in Table 2 for completeness.

 

 

Table 2  SNP Results for All Subjects, This Study*

ID

SNP Status (+ or -)

101

M170+

P38+

M223+

M253-

P37-

 

102

P19+*

P38+

M223+*

 

 

M284-

103

M170+

P38+

M223+

M253-

P37-

 

104

M170+

P38+

M223+

M253-

P37-

M284+

*  All results are from Ethnoancestry except those marked with

an asterisk.  The P19 test was carried out at FTDNA, and one

M223 test was carried out at Trace Genetics.

 

 

Conclusion

 

Since all subjects were P38+ and M223+, the correct phylogenetic structure of Haplogroup I is shown in the chart published by Rootsi (see Figure 1).  Thus, the alternate structure shown in Figure 2 is incorrect.  Since Haplogroups I-M253, I-P37, and I-M223 are parallel sub-clades of Haplogroup I1-P38, they are properly named I1a, I1b, and I1c.

 

Electronic-Database Information

 

http://www.northwestanalysis.net/

Haplogroup I Information

 

References

 

Nordtvedt K (2005)  Population Varieties within Y-Haplogroup I and their Extended Modal Haplotypes.  Web site, URL = http://www.northwestanalysis.net/.

 

Rootsi S, Magri C, Kivisild T, Benuzzi G, Help H, Bermisheva M, Kutuev I, Barac L, Pericic M, Balanovsky O, Pshenichnov A, Dion D, Grobei M, Zhivotovsky LA, Battaglia V, Achilli A,  Al-Zahery N, Parik J, King R, Cinnioglu C, Khusnutdinova E, Rudan P, Balanovska E, Scheffrahn W, Simonescu M, Brehm A, Goncalves R, Rosa A, Moisan JP, Chaventre A, Ferak V, Furedi S, Oefner PJ, Shen P, Beckman L, Mikerezi I, Terzic R, Primorac D, Cambon-Thomsen A, Krumina A, Torroni A, Underhill PA, Santachiara-Benerecetti AS, Villems R, Semino O (2004)  Phylogeography of Y-chromosome haplogroup I reveals distinct domains of prehistoric gene flow in Europe.  Am J Hum Genet 75:128-137.