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					TableS3. Domestic chicken and wild fowl mitochondrial DNA genomes information.

Code in    Sample Name
                        Source       GenBank ID Haplogroup
Fig. 1     (Other Name)
                          domestic
1                                  AB086102      A
                          chicken

                          domestic
2          yp20085                 GU261684      A
                          chicken


3          YP19289 (H5)   wild fowl GU261695     A


4          Man1           wild fowl GU261700     A

5                        wild fowl   NC_007235   B
6          YP19902 (H8)  wild fowl   GU261704    B
                         domestic
7          yp20081                   GU261705    B
                         chicken
                         domestic
8          J37                       GU261714    B
                         chicken
                         domestic
9          YP20190 (W56)             GU261699    B
                         chicken

10         1210-1         wild fowl GU261674     Z


11         YP20736        wild fowl GU261696     Z


12         DHZ1           wild fowl GU261693     Y


                          domestic
13         HD38                    GU261701      C1
                          chicken


                          domestic
14         yp18793                 GU261675      C1
                          chicken



                          domestic
15         HH131                   GU261681      C1
                          chicken
                   domestic
16   yp20332                GU261718     C1
                   chicken


                   domestic
17   YP20523                GU261679     C1
                   chicken



                   domestic
18   YP63                   GU261680     C2
                   chicken




19   YP19903 (sp4) wild fowl GU261716    C3




20   GGM7          wild fowl GU261707    C3



21                 wild fowl NC_007236   D1



22                 wild fowl NC_007237   D1


                   domestic
23   yp20477                GU261687     D1
                   chicken

                   domestic
24   yp20463                GU261682     D1
                   chicken


                   domestic
25   YP20697                GU261683     D2
                   chicken


                   domestic
26   yp19263                GU261677     D3
                   chicken


                   domestic
27   YP66                   GU261697     D3
                   chicken
               domestic
28   yin12              GU261685   D3
               chicken


               domestic
29   yp20488            GU261686   E1
               chicken


               domestic
30   J41                GU261713   E1
               chicken


               domestic
31                      AP003317   E1
               chicken


               domestic
32                      AY235571   E1
               chicken


               domestic
33                      AP003318   E1
               chicken


               domestic
34   YP20320            GU261712   E1
               chicken


               domestic
35   ggm1               GU261709   E1
               chicken


               domestic
36                      AY235570   E1
               chicken


               domestic
37                      AP003580   E1
               chicken


     YP20648   domestic
38                      GU261694   E1
     (CD60)    chicken
                     domestic
39                            AP003319    E1
                     chicken


                     domestic
40   yin109                   HQ857210    E1
                     chicken



                     domestic
41   yin100                   HQ857209    E2
                     chicken




42   GGM4            wild fowl GU261708   E3



                     domestic
43   yin46                    HQ857212    E3
                     chicken



                     domestic
44   yin125                   HQ857211    E3
                     chicken




45   MAN2            wild fowl GU261691   F




46   YP19915 (H20) wild fowl GU261702     F



     YP20069         domestic
47                            GU261688    F
     (TC48)          chicken


                     domestic
48   YP20266 (N10)            GU261711    F
                     chicken


     YP20051         domestic
49                            GU261689    F
     (TC30)          chicken
50   YP19906 (H11) wild fowl GU261703     F




                     domestic
51   YP20123                  GU261717    F
                     chicken


                     domestic
52                            DQ648776    F
                     chicken


                     domestic
53   YP19315                  GU261678    G
                     chicken



                     domestic
54   YP20307 (N51)            GU261710    G
                     chicken



                     domestic
55   YP18844                  GU261676    G
                     chicken


                     domestic
56   YP20092                  GU261719    G
                     chicken



57   DH40 (nD40)     wild fowl GU261690   G



                     domestic
58   YP20112 (D32)            GU261715    H
                     chicken




59   YP19297 (H6)    wild fowl GU261706   W




60   DHZ2            wild fowl GU261692   X
                              domestic
61           yin21                     GU261698          I
                              chicken


                                         NC_001323
                                         (previous
X
                                         reference
                                         sequence)

References
1. Wada Y, Yamada Y, Nishibori M, Yasue H (2004) Complete nucleotide sequence of mitochondrial genome in silki
2. This work.
3. Nishibori M, Shimogiri T, Hayashi T, Yasue H (2005) Molecular evidence for hybridization of species in the genus
4. Nishibori M, Hanazono M, Yamamoto Y, Tsudzuki M, & Yasue H (2003) Complete nucleotide sequence of mitoch
5. Froman DP, Kirby JD (2005) Sperm mobility: phenotype in roosters (Gallus domesticus) determined by mitochond
6. Tong XM, et al. (2006) Complete sequence and gene organization of the Tibetan chicken mitochondrial genome.He
7. Desjardins P, Morais R (1990) Sequence and gene organization of the chicken mitochondrial genome. A novel gen
al DNA genomes information.

          Variation                                                           Location
          167 212 225 246 315 355 686 859d 1215 1699C 2071 2209 5106 5688G
          5832 9806 10270 10447 12104 12689 12961 13229 13884 15693T 15875    Japan: Hiroshima
          16263 16371
          167 212 225 246 315 859d 1215 1699C 2071 2209 3125 5106 5832 8612
          9484 9806 10270 10447 12054 12104 12689 12961 13884 14232T          China: Yunnan
          15693T 15875 16263 16356 16371
          167 212 225 246 315 396 859d 1215 1699C 2071 2209 2295 5106 5832
          9806 10270 10447 12104 12689 12961 13884 15693T 15875 15958A        China: Yunnan
          16263 16356 16371
          167 212 225 246 256 315 391A 859d 1215 1699C 2071 2209 3125 5106
          5832 8612 9806 10270 10447 11103 12054 12104 12689 12961 13884      Myanmar
          14232T 15088 15693T 15875 16263 16356 16371 @256!
          new reference sequence                                              Laos: Vientiane
          223 296 859d 2792A 10669 15693T 15875                               China: Yunnan
          686 792 3098 10669 15652Y 15693T 15875                              China: Yunnan

          296 792 10669 15693T 15875                                          China: Yunnan

          256 792 4805 9313 10669 15693T 15875 @256!                          China: Yunnan
          212 246 256 306 310 315 391A 859d 889 1215 1385 1699C 2209 4451
          4829 5106 5832 7370 10270 10300 10833 11007 11684 11979 13884       China: Hainan
          15030 15693T 15875 15976 16269 16356 16596
          199 212 246 256 291 306 310 315 889 1215 1385 1699C 2209 3514+C
          4451 4829 5106 5832 8358 10270 10300 11007 11684 11979 12429        China: Hainan
          13884 15693T 15875 15976 16269 16356 16596
          197 212 243 246 256 261 270 281 310 315 391A 1215 1587 1699C 2209
          3514 3898A 5106 5832 6252 6965 7370 7868 7964A 8597 10270 11007     China: Yunnan
          12491 12557 12593 13884 14301 14331 15292 15693T 15875 16596
          242 243 246 256 281 310 315 363 367 859d 1215 1699C 2209 2885+C
          3269A 3837 3900 5106 5700T 5724G 5832 5960 6236 7214 7886 8223
                                                                              China: Henan
          9042 9440 9602 10270 11007 13884 14208 14399 15211 15331 15391
          15400 15409 15693T 15706 15875 16257 16596 No261! No212! No342!
          212 242 243 246 256 281 310 315 363 367 859d 1215 1699C 2209
          2885+C 3269A 3837 3900 5106 5700T 5724G 5832 5960 6236 7214
                                                                              China: Hunan
          7886 8223 9042 9440 9602 9848 10270 11007 13884 14399 15211 15331
          15391 15400 15409 15693T 15706 15875 16257 16596 No261! No342!
          212 242 243 246 248 256 310 315 342 363 367 859d 1215 1699C 2209
          2885+C 3269A 3837 3900 5106 5700T 5724G 5832 5960 6112 6236
          6890 7214 7886 8223 9042 9440 9602 9848 10270 11007 11531 12057     China: Hunan
          13884 14399 15211 15331 15391 15400 15409 15693T 15706 15875
          16257 16596 No261! No281!
212 242 243 246 256 281 310 315 342 363 367 1215 1699C 2209
2885+C 3157 3269A 3837 3900 5106 5700T 5724G 5832 5960 6236
                                                                     China: Yunnan
7214 7715 7886 8223 9042 9440 9602 10270 11007 13884 14399 15211
15331 15391 15400 15409 15693T 15706 15875 16257 16596 No261!
212 242 243 246 256 281 310 315 342 363 367 391 1215 1699C 2209
2885+C 3269A 3837 3900 5106 5700T 5724G 5832 5960 6236 7214
                                                                     China: Henan
7886 8223 9042 9440 9602 10270 11007 13783R 13884 14399 15211
15331 15391 15400 15409 15693T 15706 15875 16257 16596 No261!
212 243 246 256 261 306 310 315 342 362 363 1215 1264 1588 1699C
2209 2876 3514+C 3837 3900 5106 5724G 5832 7268 7886 8059 8223
9042 9440 9556 9602 10270 11007 11064 11695 12135 12644 12864        Southern India
13884 14399 15211 15331 15400 15409 15693T 15706 15875 16257
16596 No281!
177T 212 243 246 256 261 265 281 306 310 315 342 363 686 859d 1215
1699C 2209 2385 3837 3838 3900 5106 5724G 5832 7101 7589 7886
8223 9042 9407T 9440 9602 10270 10279 11007 11023 12557 13884        Myanmar
14010 14399 14734 15211 15331 15400 15409 15693T 15706 15875
16257 16596
177T 212 243 246 256 261 265 281 306 310 315 363 859d 1215 1699C
1786 2209 2830 2963 3837 3900 4382 5106 5724G 5832 7886 8223 9042
                                                                     India
9440 9602 10270 10279 11007 11422T 12557 13884 14010 14399 14734
15211 15331 15400 15409 15693T 15706 15875 16257 16596 No342!
212 243 246 256 261 281 296 306 310 315 342 686 1215 1699C 2209
2595 3837 4291 4772 5106 5724G 5832 8642 9602 10270 11007 11381G     Philippine: Manila
11447 11693 12215 13884 15409 15693T 16596 No15875!
212 243 246 256 261 281 306 310 315 342 1215 1699C 2209 2595 3837
4291 4772 5106 5724G 5832 8192 8642 9602 10107 10270 11007
                                                                     Indonesia: Bali
11381G 11465 11636 11693 13884 14514 15409 15615 15693T 15875
16466 16596
212 243 246 256 261 281 306 310 315 342 859d 1215 1699C 2209 2595
3837 4291 4772 5106 5724G 5832 6236 8642 9602 10270 11007 11693      Laos
13884 15409 15693T 15875 16596
212 220 243 246 256 261 281 306 310 315 344 859d 1215 1699C 2209
2595 3837 4291 4772 5106 5724G 5832 8642 9550 9602 10270 11007       Laos
11693 13884 15409 15693T 15875 16596 16674A
212 243 246 256 261 281 306 310 315 859d 1215 1699C 1762 2209 2595
2942 3480 3837 5106 5724G 5832 6758 7031 7155 9602 10270 10697
                                                                     China: Xinjiang
11007 11693 12539 13722 13884 15229A 15409 15545 15693T 15875
16447 16596 No342!
212 220 243 246 256 261 302 306 310 315 391A 859d 1215 1699C 2209
2595 3837 5106 5381 5724G 5832 9602 10170 10270 11007 11260
                                                                     China: Zhejiang
11693 12678 13884 14468 15235 15403 15409 15693T 15875 16596
@281!
212 243 246 256 261 306 310 315 1215 1699C 2209 2595 3837 4572
5106 5724G 5832 6738 9461A 9602 10270 11007 11693 13737 13884        Southern India
15235 15391 15409 15693T 15875 16356 16596 @281!
210 212 221 243 246 256 261 281 306 310 315 342 859d 1215 1699C
2209 2361+C 2595 3837 4572 4586 5106 5557 5690 5724G 5832 9461A
                                                                     Northeast India
9602 10270 10620 11007 11693 12143 13737 13884 15235 15391 15409
15606Y 15693T 15875 16356 16596
212 217 243 256 261 310 315 446 859d 1214 1215 1699C 2209 3837
3941 3946+C 4586 5106 5375 5832 6764 6806 6905 8079 8339 8473
                                                                     China: Henan
8618 9542 9602 10081 10270 10978 11007 11388 11973 12464 13884
15445 15505 15693T 15875 16131 16596 No246!
199 212 217 243 246 256 261 310 315 446 859d 1214 1215 1699C 2209
3837 3941 4586 5106 5832 6236 6764 6806 6905 8079 8339 8473 8618
                                                                     China: Yunnan
9542 9602 10081 10270 10978 11007 11388 11973 12464 13884 15445
15693T 15875 16131 16596
212 217 243 246 256 261 310 315 446 859d 1214 1215 1699C 2027 2209
2361+C 3837 3946+CCC 4586 5106 5832 6764 6806 6905 8079 8339
                                                                     Commercial Line
8473 8618 9542 9602 10081 10270 10978 11007 11388 11973 12464
13884 15445 15693T 15875 16131 16596 No3941!
212 217 222 243 246 256 261 310 315 330 446 859d 1214 1215 1297
1699C 2209 3837 3945-3946d 4586 5106 5832 6764 6806 6905 8079
                                                                     Commercial Lines
8339 8473 8618 9542 9602 10081 10270 10978 11007 11388 11973
12464 13227 13884 15445 15693T 15875 16131 16596 No3941!
212 217 243 246 256 261 310 315 446 859d 1214 1215 1699C 2209 3837
3941 3946+C 4586 5106 5832 6764 6806 6905 8079 8339 8473 8618
                                                                     Commercial Line
9542 9602 10081 10270 10978 11007 11388 11973 12464 12690 13569
13884 15445 15693T 15875 16131 16596
212 217 243 246 256 261 310 315 446 859d 1214 1215 1699C 2209 3837
3941 3946+C 4586 5106 5832 6764 6806 6905 8079 8339 8473 8618
                                                                     China: Yunnan
9542 9602 10081 10270 10978 11007 11388 11973 12464 13569 13884
15445 15693T 15875 16131 16596
212 217 243 246 256 261 310 315 446 859d 1214 1215 1699C 2209 3837
3941 3946d 4586 5106 5832 6764 6806 6905 8079 8339 8473 8618 9542
                                                                     India
9602 10081 10270 10814 10978 10996 11007 11388 11797 11973 12464
13542 13884 15445 15693T 15875 16131 16596
212 217 243 246 256 261 310 315 446 1214 1215 1699C 2022 2209 3837
3941 3946d 4586 5106 5832 6764 6806 6905 8079 8339 8473 8618 9542
                                                                     Commercial Line
9602 10081 10270 10978 11007 11187 11388 11973 12464 13884 15362
15445 15693T 15875 16131 16596
212 217 243 246 256 261 310 315 446 1214 1215 1699C 2209 3837 3941
3946+CCC 4586 5106 5832 6437 6764 6806 6905 8079 8339 8473 8618
                                                                     Commercial Line
9542 9602 10081 10270 10978 11007 11388 11973 12464 13257 13884
15445 15693T 15875 16131 16596
212 217 246 256 261 310 315 446 686 1214 1215 1525+A 1699C 2209
3837 3941 4586 5106 5832 6764 6806 6905 8079 8339 8473 8618 8783
                                                                     China: Hebei
9542 9602 10081 10270 10978 11007 11388 11973 12008 12464 13884
15445 15693T 15835 15875 16131 16596 No243!
212 217 243 246 256 261 310 315 342 446 686 859d 1214 1215 1699C
2209 3837 3941 4586 5106 5832 6764 6806 6905 8079 8339 8473 8618
                                                                     Laos: Vientiane
9542 9602 10081 10270 10978 11007 11388 11973 12464 13884 14220
15445 15693T 15875 16131 16596
207 212 217 238 243 256 261 310 315 330 446 859d 1214 1215 1699C
2209 3837 3941 3946d 4586 5106 5832 6764 6806 6905 8079 8339 8473
                                                                     Northeast India
8618 9542 9602 10081 10270 10978 11007 11388 11973 12464 12705
13884 14046 15445 15693T 15875 16131 16596 No246!
212 217 224 243 256 261 310 315 446 859d 1174 1214 1215 1699C
2209 2886 2890+CC 3837 3941 3946+CCC 4586 5106 5832 6905 8079
8339 8618 9542 9602 9870C 10081 10270 10978 11007 11040 11388        Northeast India
11973 12200 13884 14712 14871 15445 15693T 15875 16131 16356
16596 No246!
212 217 243 249 256 261 310 315 344 355 446 859d 1214 1215 1699C
2209 3099 3837 3941 4586 5106 5832 6905 8079 8339 8618 8796 9014
                                                                     India
9542 9587 9602 9794T 10081 10255 10270 10978 11007 11388 11973
12224 13884 15445 15545 15693T 15875 16131 16596 No246!
212 217 222 243 246 249 256 261 310 315 355 446 1214 1215 1699C
2209 3050 3837 3941 3946d 4586 5106 5749 5832 6905 8079 8339 8618
                                                                     Northeast India
8796 9014 9542 9602 9794T 10081 10270 10978 11007 11388 11973
13884 15445 15545 15693T 15875 16131 16596
212 217 222 243 246 249 256 261 281 310 315 355 446 686 1214 1215
1699C 2209 3837 3941 3946+CC 4586 5106 5832 6905 8079 8137 8339
8618 8796 9014 9542 9602 9794T 10081 10270 10978 11007 11388         Northeast India
11973 12819 13884 14468 15445 15545 15693T 15875 15951 16131
16596
212 234 236 243 246 254 256 261 310 317C 396 446 859d 904 1214
1215 1699C 2209 3837 3941 4586 5106 5832 6905 7385 7463 8618 9542
                                                                     Myanmar
9602 10081 10115 10270 11007 11573 11973 13884 14034G 15693T
15875 16131 16339 16596 No315!
212 234 236 243 246 254 256 261 310 317C 347 396 446 904 1214 1215
1699C 2209 3837 3945-3946d 4586 5106 5832 6905 7385 7463 8618
                                                                     China: Yunnan
9542 9602 10081 10115 10270 10300 11007 11573 11973 13884 14034G
15693T 15875 16131 16339 16596 No315! No3941!
212 234 236 243 246 254 256 261 265 310 317C 446 859d 904 1214
1215 1699C 2209 3837 3941 3946+CCC 4586 5106 5832 6905 7385
                                                                     China: Yunnan
7463 8618 9542 9602 10081 10115 10270 11007 11573 11973 13884
14034G 15693T 15875 15992A 16131 16339 16596 No315!
212 234 236 243 246 254 256 261 310 317C 446 859d 904 1214 1215
1699C 2209 3837 3941 3946+C 4325 4586 5106 5832 6905 7385 7463
                                                                     China: Yunnan
8618 9542 9602 10081 10115 10270 11007 11024 11573 11973 13884
13949 14034G 14847C 15693T 15875 16131 16339 16596 No315!
212 234 236 243 246 254 256 261 310 317C 342 446 859d 904 1214
1215 1699C 2209 3837 3941 3946+C 4586 5106 5832 6905 7385 7463
                                                                     China: Yunnan
8618 9542 9602 10081 10115 10270 11007 11531 11573 11973 12247
12830 13884 14034G 15693T 15734 15875 16131 16339 16596 No315!
212 234 236 243 246 254 256 261 310 317C 446 859d 904 1214 1215
1699C 2209 3837 3941 3946d 4586 5106 5299 5832 6000 6905 7385
7463 8618 9542 9602 10081 10115 10229 10270 11007 11531 11573        Myanmar
11973 13884 14034G 15443 15471 15693T 15875 16131 16339 16596
No315!
212 234 236 243 254 256 261 310 317C 446 686 859d 904 1214 1215
1699C 2209 3837 3941 4586 5106 5832 6905 7385 7463 8618 9542 9602
                                                                     China: Yunnan
10081 10115 10270 11007 11573 11973 12167T 13509 13884 14034G
15693T 15875 16131 16339 16596 No246! No315!
212 234 236 243 254 256 261 310 317C 446 686 859d 904 1214 1215
1699C 2209 3837 3941 3946d 4586 5106 5832 6799 6905 7385 7463
                                                                     China: Yunnan
8618 8903T 9542 9602 10081 10115 10270 11007 11573 11973 13884
14034G 15693T 15875 16131 16339 16596 No246! No315!
243 246 256 261 296A 302 310 322 347 446 859d 1214 1215 1699C
1988 2209 3837 3941 3946+C 4229 4586 5106 5832 6236 6905 7031
                                                                     China: Henan
7475 8618 9542 9602 10081 10270 11007 11504 11973 13328 13884
15017 15232 15693T 15875 16339 16596 No212! No315!
243 246 256 261 281 296A 302 310 317C 391A 446 686 1214 1215
1699C 2209 3837 3941 3946+CCC 4586 5106 5832 6236 6536 6905
7031 7475 8618 9542 9602 10081 10270 11007 11504 11656 11973         China: Yunnan
13884 15017 15232 15693T 15875 16339 16556 16596 No212! No315!
No322!
243 246 256 261 296A 302 310 446 1214 1215 1699C 2209 3837 3941
3946+CCC 4586 5106 5832 6236 6536 6905 7031 7475 8618 9542 9602
                                                                     China: Yunnan
10081 10270 11007 11504 11973 13706A 13884 15017 15232 15693T
15875 16339 16596 No212! No315! No322!
243 246 256 261 296A 302 310 322 446 859d 1214 1215 1699C 2209
3837 3941 3946+C 4586 5106 5832 6236 6536 6905 7031 7475 8618
                                                                     China: Yunnan
9542 9602 9914 10081 10270 11007 11504 11973 13884 15017 15232
15693T 15875 16339 16596 No212! No315!
243 246 256 261 296A 302 310 322 362 446 1214 1215 1699C 2209
3837 3941 3946+CC 4395 4586 5106 5832 6236 6536 6905 7031 7475
                                                                     China: Yunnan
8618 9542 9602 10081 10270 11007 11504 11973 13884 15017 15232
15693T 15875 16339 No16596! No212! No315!
198 199 212 243 246 256 261 281 306 310 315 363 391 446 1215 1699C
2209 2799 3837 4586 5106 5832 5875 6041 6095 6905 7292 8618 9542
                                                                     China: Yunnan
9602 10081 10270 11007 11973 13884 14802 15693T 15875 16356
16397 16596 No1214!
133 167 212 243 246 256 261 315 363 391 417 446 521 859d 1214 1215
1699C 2209 3837 4095 4457 4586 5106 5832 7181 7577 7715 7739 8618
9542 9602 10081 10270 10432 11007 11603 11708 11732 11973 12003T     China: Yunnan
12191 12725T 13884 15693T 15835 15875 16596 16665 No310!
No6905!
212 242 243 246 256 261 310 315 326 363 417 446 859d 1214 1215
1699C 2209 3837 4526 4586 4613 5106 5832 6905 8618 8681 9542 9602
                                                                     China: Yunnan
10081 10270 11007 11744 11773 11973 12218 12383 12410 13884
14877 14957 15277 15693T 15875 15943 16356 16442 16596
            171 207 221 229 243 256 261 310 315 322A 354 362 363 391 446 521
            686 859d 1215 1699C 2209 2275 2768 3837 4598 4607 4874A 5106
            5832 5840C 6011 6194 7022 7364 7769 7979 8141 8192 8444 9184 9347 Northeast India
            9542 9602 10270 11007 11024 13779 13884 14208 15403 15693T 15875
            16103 16257 16676 No16596! No212! No246!
            52-54d 167 210 212 225 246 315 686 707d 859d 1215 1699C 2071 2209
            2678 3842-3843d 3952+G 5106 5832 5934C 7098d 7105-7106d 7539C
                                                                              Commercial Line
            9806 10270 10447 10958d 12104 12689 13884 14393+C 14406d 14853
            15445 15693T 15875 16131


ete nucleotide sequence of mitochondrial genome in silkie fowl (Gallus gallus var. domesticus). J Poult Sci 41(1):76-82.

ecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim Genet 36(5):367-375.
Yasue H (2003) Complete nucleotide sequence of mitochondrial DNA in White Leghorn and White Plymouth Rock chickens. Ani
n roosters (Gallus domesticus) determined by mitochondrial function. Biol Reprod 72(3):562-567.
nization of the Tibetan chicken mitochondrial genome.Hereditas (Beijing) 28(7):769-777.
 ation of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J Mol Biol 212(4):599-634.
Reference


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 m Genet 36(5):367-375.
White Plymouth Rock chickens. Anim Sci J 74(5):437-439.


 ol 212(4):599-634.

				
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