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Table 2 Shared mtDNA polymorphisms per hierBAPS groupa

From: Evolution and dispersal of mitochondrial DNA haplogroup U5 in Northern Europe: insights from an unsupervised learning approach to phylogeography

 

hierBAPS Group

I

II

III

IV

V

VI

VII

 

IX

X

XI

XII

XIII

XIV

U5a2, U5a2b, U5a2c, U5a2d

U5a2e

U5a1,U5a1g, U5a1i

U5b1, U5b1a, U5b1d, U5b1f, U5b1i, U5b3

U5b1 + T16189C! U5b1b, U5b1c

U5a1a2

U5a1h

RSRS (Ancestral)

U5a1d

U5a1c

U5a1a1

U5b2a

U5b2, U5b2c

U5b2a2

Number of shared mitochondrial polymorphisms within each U5 hierBAP group (n)

 

19

21

16

18

19

29

45

1

20

28

21

27

33

35

Nucleotide Position

Location

              

146

HVS-II

 

T

    

T

T

 

T

 

T

T

T

150

HVS-II

  

T

   

T

C

   

T

T

T

151

HVS-II

 

T

     

C

      

152

HVS-II

 

C!

T

  

T

T

T

     

T

195

HVS-II

 

T

   

T

T

T

     

T

247

HVS-II

G

G

G

  

G

G

G

 

G

G

G

G

G

523

HVS-III

      

A

A

    

A

 

524

HVS-III

      

C

C

    

C

 

769

12S_rRNA

G

G

G

G

G

G

G

G

G

G

G

 

G

G

1303

12S_rRNA

      

A

G

      

1700

16S_rRNA

     

C

 

T

  

C

   

1721

16S_rRNA

       

C

   

T

T

T

2757

16S_rRNA

       

A

      

3027

16S_rRNA

       

T

C

     

3107

preserves historical genome annotation numbering

     

d

d

-

     

d

3192

16S_rRNA

      

T

C

      

3197

16S_rRNA

C

C

 

C

C

C

C

T

C

C

C

C

C

C

3212

16S_rRNA

       

C

     

T

3552

ND1 (Ala—3rd position in codon)

       

T

C

     

3591

ND1 (Leu—3rd position in codon)

      

A

G

      

3768

ND1 (Leu—3rd position in codon)

 

G

     

A

      

4592

ND2 (Ser—3rd position in codon)

      

C

T

      

4732

ND2 (Asn—2nd position in codon)

       

A

   

G

 

G

5452

ND2 (Thr—2nd position in codon)

       

C

      

5495

ND2 (Phe—3nd position in codon)

       

T

  

C

   

5656

position between tRNA-Ala and tRNA-Asn

    

G

  

A

      

7146

CO1 (Ala—1st position in codon)

A

A

A

A

A

A

A

A

 

A

A

 

A

A

7256

CO1 (Asn—3rd position in codon)

C

C

C

C

C

C

C

C

C

C

C

C

C

 

7521

tRNA-Asp

G

G

 

G

G

G

G

G

G

G

G

G

G

G

7768

CO2 (Met—3rd position in codon)

   

G

G

  

A

   

G

G

G

7853

CO2 (Val—1st position in codon)

       

G

      

8337

tRNA-Lys

       

T

      

8701

ATP6 (Ala—1st position codon)

A

A

A

 

A

A

A

A

A

A

A

A

A

A

8705

ATP6 (Met—2nd position codon)

       

T

      

9477

CO3 (Val—1st position codon)

A

A

A

A

A

A

A

G

A

A

 

A

A

A

9540

CO3 (Leu—1st position codon)

T

T

T

T

T

T

T

T

T

T

T

T

T

T

10,283

ND3 (Leu—3rd position codon)

       

A

      

10,398

ND3 (Ala—1st position codon)

A

A

A

A

A

A

A

A

A

A

 

A

A

A

10,810

ND4 (Leu—3rd position codon)

T

T

T

T

T

 

T

T

T

T

T

T

T

T

10,873

ND4 (Pro—3rd position codon)

T

T

 

T

T

T

T

T

T

T

T

T

T

T

10,915

ND4 (Cys—3rd position codon)

 

T

T

T

T

T

T

C

T

T

T

T

T

T

10,927

ND4 (Phe—3rd position codon)

       

T

      

11,296

ND4 (Leu—3rd position codon)

      

T

C

      

11,653

ND4 (Val—3rd position codon)

       

A

      

11,914

ND4 (Thr—3rd position codon)

G

G

 

G

 

G

G

G

G

G

 

G

G

G

11,938

ND4 (Leu—3rd position codon)

      

T

C

      

12,308

tRNA-Leu

 

G

G

 

G

G

G

A

G

G

G

G

G

G

12,346

ND5 (His—1st position codon)

     

T

 

C

      

12,372

ND5 (Leu—3rd position codon)

A

A

A

 

A

A

A

G

A

A

A

A

A

A

12,406

ND5 (Val—1st position codon)

       

G

      

12,616

ND5 (Leu—1st position codon)

       

T

      

12,618

ND5 (Leu—3rd position codon)

      

A

G

      

12,634

ND5 (Ile—1st position codon)

       

A

      

12,705

ND5 (Ile—3rd position codon)

       

C

      

13,105

ND5 (Val—1st position codon)

A

 

A

A

A

 

A

A

A

A

A

A

A

A

13,145

ND5 (Ser—2nd position codon)

       

G

      

13,276

ND5 (Val—2nd position codon)

       

A

      

13,617

ND5 (Ile—3rd position codon)

 

C

C

 

C

C

C

T

C

C

C

C

C

C

13,630

ND5 (Thr—1st position codon)

       

A

      

13,637

ND5 (Gln—2nd position codon)

       

A

   

G

C

G

14,182

ND6 (Val—1st position codon)

    

C

  

T

   

C

 

C

14,518

ND6 (Gly—1st position codon)

       

A

      

14,793

CYB (His—2nd position codon)

G

G

   

G

G

A

G

G

    

15,218

CYB (Thr—1st position codon)

     

G

G

A

G

G

    

15,497

CYB (Gly—1st position codon)

       

G

      

15,511

CYB (Asn—3rd position codon)

       

T

      

15,924

tRNA-Thr

       

A

      

16,114

HVS-I

       

C

      

16,129

HVS-I

   

G

  

G

G

  

G

G

G

G

16,187

HVS-I

C

C

 

C

 

C

C

C

    

C

 

16,189

HVS-I

     

T

 

T

  

C!

T!!

  

16,192

HVS-I

 

T

    

T

C

  

T

 

T

 

16,223

HVS-I

C

C

 

C

 

C

C

T

 

C

  

C

C

16,230

HVS-I

A

  

A

 

A

A

G

 

A

A

A

A

A

16,239

HVS-I

      

T

C

      

16,256

HVS-I

 

T

    

T

C

 

T

    

16,270

HVS-I

       

C

    

T

T

16,278

HVS-I

 

C

   

C

C

C

 

C

 

C

C

C

16,294

HVS-I

       

C

      

16,311

HVS-I

 

C!

    

T

T

 

T

  

T

T

16,320

HVS-I

       

C

 

T

    

16,362

HVS-I

       

T

      

16,398

HVS-I

       

G

     

A

16,399

HVS-I

     

G

G

A

 

G

    

16,465

HVS-I

       

C

      

16,519

HVS-I

      

T

T

      
 

hierBAPS Group

XV

XVI

XVII

XVIII

XIX

XX

XXI

XXII

XXIII

XXIV

U5b2b

U5b2b1

U5b1b1a

U5b1b1

U5b2a1a + C16311T!

U5b2a1a2

U5a2a

U5a2a2a

U5b1e1

U5b1e1 (+ T8337C)

Number of shared mitochondrial polymorphisms within each U5 hierBAP group (n)

33

36

20

32

32

41

18

40

33

38

Nucleotide Position

          

146

T

T

 

T

T

T

 

T

T

T

150

T

T

 

T

T

T

  

T

T

151

          

152

     

T

 

T

  

195

T

T

  

T

T

 

T

  

247

G

G

 

G

 

G

 

G

G

G

523

 

A

 

A

 

A

 

A

  

524

 

C

 

C

 

C

 

C

d

d

769

G

G

G

G

G

G

G

G

G

G

1303

          

1700

          

1721

T

T

  

T

T

    

2757

        

G

G

3027

          

3107

     

d

 

d

 

d

3192

          

3197

C

C

 

C

C

C

C

C

C

C

3212

          

3552

          

3591

          

3768

          

4592

          

4732

    

G

G

    

5452

     

T

    

5495

          

5656

  

G

G

    

G

G

7146

A

A

A

A

A

A

A

A

A

A

7256

C

C

C

C

C

C

C

C

C

C

7521

 

G

G

G

G

G

G

G

G

G

7768

G

G

G

G

G

G

  

G

G

7853

       

A

  

8337

         

C

8701

A

A

A

A

A

A

A

A

A

A

8705

     

C

    

9477

A

 

A

A

A

A

A

 

A

A

9540

T

T

T

T

T

T

 

T

T

T

10,283

        

G

G

10,398

A

A

A

A

A

A

A

A

A

A

10,810

T

T

T

T

T

T

T

T

T

T

10,873

T

T

T

T

T

T

T

T

T

T

10,915

T

T

T

T

T

T

T

T

T

T

10,927

   

C

      

11,296

          

11,653

G

G

        

11,914

G

G

G

G

G

G

 

G

G

G

11,938

          

12,308

G

G

G

G

G

G

G

G

G

G

12,346

          

12,372

A

A

A

A

A

A

A

A

A

A

12,406

       

A

  

12,616

        

C

C

12,618

  

A

A

      

12,634

G

         

12,705

      

C

   

13,105

A

A

A

A

A

A

A

A

A

A

13,145

       

A

  

13,276

      

A

   

13,617

C

C

C

C

C

C

C

C

C

C

13,630

G

G

        

13,637

G

 

C

 

G

G

    

14,182

C

C

 

C

C

C

  

C

C

14,518

       

G

  

14,793

      

G

G

  

15,218

          

15,497

 

A

        

15,511

    

C

C

    

15,924

     

G

    

16,114

       

A

  

16,129

G

G

   

G

 

G

G

G

16,187

C

C

 

C

C

C

 

C

C

C

16,189

 

T

  

T!!

T

 

T

  

16,192

 

C!

   

C!

  

C!

C!

16,223

C

C

 

C

C

C

 

C

C

C

16,230

A

A

 

A

A

A

 

A

A

A

16,239

          

16,256

       

T

  

16,270

 

T

     

T

T

T

16,278

C

C

 

C

C

C

 

C

C

C

16,294

       

T

  

16,311

T

  

T

C!

  

T

 

T

16,320

          

16,362

          

16,398

          

16,399

          

16,465

       

T

 

T

16,519

         

T

  1. a The Ancestral state is represented by the RSRS sequence. Blank cells indicate that the nucleotide position was not a factor in determining the hierBAPS group. All BAPS groups also contain the following mutations: 825 T,1018G,2758G,2885 T,3594C,4104A,4312C,8468C,8655C,10664C,10688G,11467G,12705C,13276A,13506C,13650C. Mutations are reckoned in forward evolutionary time direction in reference to the RSRS sequence. In case of a transversion, the derived allele is shown in lowercase instead of uppercase. Exclamation mark signifies back mutation to the ancestral sequence RSRS. (!) for single mutation and (!!) for double back mutation. Yellow-colored boxes indicate mutations that are diagnostic for particular haplogroup or subclade as per Phylotree. ATP ATP synthase, CO Cytochrome c oxidase, CYB Cytochrome b