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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