Information on the African - Sub-Saharan African Metapopulation

The Sub-Saharan African Metapopulation (African - Sub-Saharan African) consists of 6,976 haplotypes (at least minimal) which were published in 26 population studies and were additionally submitted via personal communication (20 submissions) .

Most common haplotypes

Count DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS385
104 15 13 31 21 10 11 13 16,17
92 15 14 32 24 10 11 13 11,11
67 15 13 30 21 10 11 13 16,17
64 15 14 33 21 10 11 13 16,17
52 14 12 28 26 10 11 13 15,20
52 15 13 31 21 11 11 13 16,17
47 16 13 30 21 10 11 15 17,18
44 17 13 30 21 10 11 14 17,17
44 17 13 30 21 10 11 14 17,18
43 17 13 30 21 10 11 15 17,18
Count DYS391 DYS389I DYS439 DYS389II DYS438 DYS437 DYS19 DYS392 DYS393 DYS390 DYS385
51 10 14 12 32 10 14 15 11 13 24 11,11
49 10 14 11 33 11 14 15 11 13 21 16,17
44 10 13 11 31 11 14 15 11 13 21 16,17
36 11 13 11 31 11 14 15 11 13 21 16,17
33 10 12 11 28 11 14 14 11 13 26 15,20
30 10 13 11 31 11 14 15 11 14 21 15,15
23 10 13 12 31 11 14 15 11 13 21 16,17
21 10 13 11 30 11 14 15 11 13 21 16,17
21 10 13 12 30 11 14 16 11 14 21 16,17
20 10 13 12 30 11 14 17 11 14 21 17,18
Count DYS456 DYS389I DYS390 DYS389II DYS458 DYS19 DYS385 DYS393 DYS391 DYS439 DYS635 DYS392 YGATAH4 DYS437 DYS438 DYS448
31 15 14 21 33 17 15 16,17 13 10 11 21 11 12 14 11 21
19 15 12 26 28 18 14 15,20 13 10 11 24 11 11 14 11 19
14 15 13 21 31 17 15 16,18 13 10 13 21 10 12 14 11 21
13 13 14 24 33 18 15 11,11 14 10 12 17 11 14 14 10 23
10 15 13 21 31 16 15 16,17 13 11 11 21 11 12 14 11 21
10 15 13 25 31 15 14 19,20 13 11 13 21 11 12 14 10 20
10 15 14 21 30 17 15 15,17 13 10 12 21 11 12 14 11 21
9 13 14 24 32 18 15 11,11 13 10 12 17 11 13 14 10 23
9 15 14 21 31 16 16 16,20 15 10 12 21 11 11 14 11 21
9 15 14 21 32 17 15 16,17 13 10 11 21 11 12 14 11 21
Count DYS576 DYS389I DYS448 DYS389II DYS19 DYS391 DYS481 DYS549 DYS533 DYS438 DYS437 DYS570 DYS635 DYS390 DYS439 DYS392 DYS643 DYS393 DYS458 DYS385 DYS456 YGATAH4
16 16 14 21 33 15 10 28 11 11 11 14 19 21 21 11 11 14 13 17 16,17 15 12
10 15 12 19 28 14 10 25 13 12 11 14 18 24 26 11 11 11 13 18 15,20 15 11
10 17 14 23 33 15 10 25 11 11 10 14 17 17 24 12 11 13 14 18 11,11 13 14
8 15 14 21 30 15 10 26 12 11 11 14 19 21 21 12 11 15 13 17 15,17 15 12
8 17 13 20 31 14 11 22 13 12 10 14 17 21 25 13 11 12 13 15 19,20 15 12
8 17 14 21 31 16 10 27 11 11 11 14 18 21 21 12 11 13 15 16 16,20 15 11
6 19 14 23 32 15 10 24 11 11 10 14 17 17 24 12 12 12 13 18 11,12 13 12
5 16 13 21 30 16 9 26 11 11 10 16 17 19 21 11 11 9 13 17 12,12 15 12
5 16 14 21 32 15 10 28 11 11 11 14 19 21 21 11 11 14 13 17 16,17 15 12
5 18 10 19 27 13 11 25 12 12 10 14 19 21 24 11 11 14 13 16 16,16 18 11
Count DYS576 DYS389I DYS635 DYS389II DYS627 DYS460 DYS458 DYS19 YGATAH4 DYS448 DYS391 DYS456 DYS390 DYS438 DYS392 DYS518 DYS570 DYS437 DYS385 DYS449 DYS393 DYS439 DYS481 DYF387S1 DYS533
8 16 14 21 33 21 10 17 15 12 21 10 15 21 11 11 39 19 14 16,17 28 13 11 28 36,39 11
8 18 12 22 30 18 10 15 15 11 19,20 9 17 22 10 12 37 19 16 16,16 32 13 13 27 37,37 12
6 17 13 23 29 20 11 18 15 11 18 10 15 24 12 14 38 18 14 13,15 30 13 11 22 37,39 11
4 15 12 24 28 21 10 18 14 11 19 11 15 25 12 11 41 18 14 13,18 27 13 12 25 37,39 12
4 15 13 23 30 22 11 18 15 11 20 10 15 21 11 11 40 20 14 16,17 31 13 13 26 37,38 13
4 19 13 21 30 20 10 16 17 11 21 10 17 21 11 11 41 17 14 18,18 26 14 12 24 40,41 11
3 15 12 20 30 20 10 17 17 11 21 10 15 21 11 11 38 19 14 16,18 31 13 12 28 35,38 11
3 15 13 21 29 19 10 16 14 12 21 10 14 21 11 11 39 19 14 16,18 28 13 12 23 35,38 11
3 15 13 22 30 19 11 15 16 11 20 10 16 21 11 11 39 18 14 16,17 31 15 12 26 38,38 12
3 16 13 19 30 20 10 18 16 12 21 9 15 21 10 11 40 17 16 12,12 35 13 11 25 36,37 11
Count DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS385 DYS439 DYS438 DYS437 DYS456 DYS458 DYS635 YGATAH4 DYS448 DYS576 DYS481 DYS549 DYS533 DYS570 DYS643 DYS627 DYS460 DYS518 DYS449 DYF387S1
6 15 14 33 21 10 11 13 16,17 11 11 14 15 17 21 12 21 16 28 11 11 19 14 21 10 39 28 36,39
3 15 14 32 21 10 11 13 16,17 11 11 14 15 17 21 12 21 16 28 11 11 19 14 21 10 39 28 36,39
3 15 14 33 21 10 11 13 16,17 11 11 14 15 17 21 12 21 16 28 11 11 19 14 22 10 39 28 36,39
2 15 13 32 21 10 11 13 16,17 11 11 14 15 17 21 12 21 16 28 11 11 19 14 21 10 39 28 36,39
2 15 14 33 21 10 11 13 16,17 11 11 14 15 17 21 12 21 17 28 11 11 20 14 21 10 40 28 36,39
2 15 14 33 21 10 11 13 16,17 11 11 14 15 18 21 12 21 16 28 11 11 19 14 21 10 39 28 36,39
2 15 14 33 21 10 11 13 16,17 12 11 14 15 17 21 12 21 16 28 11 11 19 14 21 10 39 28 36,39

Discrete-Laplace frequency estimation (Minimal)

Release
R69
Loci included
DYS19, DYS389I, DYS389II*, DYS390, DYS391, DYS392, DYS393
Central haplotypes
33
EM converged
true
EM iterations
53
GLM method
internal_coef
Init method
pam
Threshold frequency
1 in 593,546
Per locus details
DL centers distribution (download PDF)
Table of haplotype centers (click to show/hide)
DYS19 DYS389I DYS389II* DYS390 DYS391 DYS392 DYS393
1 15 14 18 24 10 11 13
2 14 12 16 25 11 11 13
3 14 13 17 23 10 11 13
4 14 13 16 24 10 13 13
5 15 13 17 21 10 11 14
6 15 13 18 21 10 11 13
7 15 13 19 21 10 11 13
8 14 12 16 25 10 11 13
9 15 13 18 21 10 11 14
10 15 12 17 22 10 11 13
11 15 13 17 21 10 11 13
12 15 13 17 21 10 11 15
13 15 13 17 21 11 11 13
14 16 14 17 21 10 11 15
15 15 14 18 21 10 11 13
16 15 14 19 21 10 11 13
17 16 13 17 21 10 11 14
18 16 13 18 21 10 11 13
19 16 13 17 21 10 11 15
20 16 13 17 21 10 11 13
21 16 14 17 21 10 11 14
22 17 13 17 21 10 11 14
23 16 12 18 22 9 12 13
24 17 14 17 21 10 11 14
25 15 13 18 24 10 11 13
26 15 14 17 21 10 11 13
27 15 14 17 21 10 11 14
28 17 13 17 21 10 11 15
29 15 13 18 21 11 11 13
30 15 14 16 24 11 13 13
31 13 10 17 24 11 11 14
32 13 14 17 24 11 11 14
33 11 13 17 24 10 12 13

Discrete-Laplace frequency estimation (Y17)

Release
R69
Loci included
DYS19, DYS389I, DYS389II*, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, YGATAH4
Central haplotypes
32
EM converged
true
EM iterations
156
GLM method
internal_coef
Init method
pam
Threshold frequency
1 in 103,277,139
Per locus details
DL centers distribution (download PDF)
Table of haplotype centers (click to show/hide)
DYS19 DYS389I DYS389II* DYS390 DYS391 DYS392 DYS393 DYS437 DYS438 DYS439 DYS448 DYS456 DYS458 DYS635 YGATAH4
1 14 12 16 25 10 11 13 14 11 11 19 15 18 24 11
2 15 13 18 21 10 11 13 14 11 12 21 15 17 21 12
3 17 13 17 21 10 11 15 14 11 12 21 15 15 21 11
4 15 13 16 24 11 13 13 14 12 12 19 15 17 23 12
5 16 13 17 21 10 11 15 14 11 12 21 15 16 21 11
6 16 13 17 21 10 11 14 14 11 12 21 15 16 21 11
7 15 13 18 21 11 11 13 14 11 11 21 15 16 21 12
8 15 14 18 24 10 11 13 14 10 12 23 13 18 17 13
9 17 13 17 21 10 11 14 14 11 12 21 17 16 21 11
10 15 14 19 21 10 11 13 14 11 11 21 15 17 21 12
11 16 13 17 21 10 11 15 14 11 12 21 16 16 21 11
12 15 13 18 21 10 11 13 14 11 13 21 15 17 21 12
13 14 13 17 24 10 11 13 14 10 12 20 15 16 21 11
14 15 13 17 21 10 11 13 14 11 12 21 15 16 21 12
15 15 13 18 21 10 11 13 14 11 12 21 15 17 22 12
16 17 13 17 21 10 11 14 14 11 12 21 15 17 21 11
17 13 10 17 24 11 11 14 14 10 11 20 17 16 21 11
18 15 13 17 21 10 11 14 14 11 12 20 15 18 22 11
19 16 13 18 24 10 11 13 15 10 12 21 13 17 17 12
20 15 13 17 21 10 11 14 14 11 12 20 15 16 21 11
21 16 13 17 21 10 11 14 14 11 12 21 16 16 21 11
22 15 13 17 21 10 11 14 14 11 12 21 15 17 23 11
23 15 12 17 22 10 11 13 17 10 12 20 15 15 20 11
24 15 13 17 21 9 11 15 16 10 11 21 17 18 20 12
25 11 13 17 24 10 12 13 14 11 12 21 16 14 22 12
26 15 13 17 21 9 11 13 16 10 11 21 15 17 19 12
27 15 14 18 21 10 11 13 14 11 12 21 14 17 21 11
28 13 14 17 24 11 11 14 14 10 11 20 15 17 21 11
29 15 13 17 21 11 11 13 14 11 12 21 15 17 21 11
30 14 14 17 20 11 11 13 14 11 12 15 12 15 17 10
31 16 14 17 22 10 11 13 14 11 11 21 15 16 21 10
32 15 13 18 21 10 11 14 14 11 11 20 17 19 22 11

* Please note that DYS389I was substracted from DYS389II

Population studies

  • Alves C., Gusmão L., Barbosa J. and Amorim A. (2003), 'Evaluating the informative power of Y-STRs: a comparative study using European and new African haplotype data.', Forensic Sci Int 134(2-3):126-33 [PubMed]
  • Rocca D., Cannone F., D'Atanasio E., Bonito M., Anagnostou P., Russo G., Barni F., Alladio E., Destro-Bisol G., Trombetta B., Berti A. and Cruciani F. (2020), 'Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel', For Sci Int Genet 49:102374 [DOI]
  • Leat N., Ehrenreich L., Benjeddou M., Cloete K. and Davison S. (2007), 'Properties of novel and widely studied Y-STR loci in three South African populations.', Forensic Sci Int 168(2-3):154-61 [PubMed] [DOI]
  • Arroyo-Pardo E., Gusmão L., López-Parra AM., Baeza C., Mesa MS. and Amorim A. (2005), 'Genetic variability of 16 Y-chromosome STRs in a sample from Equatorial Guinea (Central Africa).', Forensic Sci Int 149(1):109-13 [PubMed] [DOI]
  • Rosa A., Ornelas C., Brehm A. and Villems R. (2006), 'Population data on 11 Y-chromosome STRs from Guiné-Bissau.', Forensic Sci Int 157(2-3):210-7 [PubMed] [DOI]
  • Carvalho M., Brito P., Bento AM., Gomes V., Antunes H., Costa A., Lopes V., Serra A., Balsa F., Andrade L., Anjos MJ., Corte-Real F. and Gusma˜o L. (2011), 'Paternal and maternal lineages in Guinea-Bissau population', For Sci Int Genet 5:114-6 [DOI]
  • Pereira L., Gusmão L., Alves C., Amorim A. and Prata MJ. (2002), 'Bantu and European Y-lineages in Sub-Saharan Africa.', Ann Hum Genet 66(Pt 5-6):369-78 [PubMed] [DOI]
  • Fujihara J., Yuasa I., Muro T., Iida R., Tsubota E., Nakamura H., Imamura S., Yasuda T. and Takeshita H. (2009), 'Allele frequencies and haplotypes for 28 Y-STRs in Ovambo population.', Leg Med (Tokyo) 11(4):205-8 [PubMed] [DOI]
  • Gomes V., Alves C., Amorim A., Carracedo A., Sánchez-Diz P. and Gusmão L. (2010), 'Nilotes from Karamoja, Uganda: haplotype data defined by 17 Y-chromosome STRs.', Forensic Sci Int Genet 4(4):e83-6 [PubMed] [DOI]
  • Fortes-Lima C., Brucato N., Croze M., Bellis G., Schiavinato S., Massougbodji A., Migot-Nabias F. and Dugoujon J. (2015), 'Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups', Forensic Science International: Genetics 19:232–237 [Link] [DOI]
  • Brucato N., Cassar O., Tonasso L., Tortevoye P., Migot-Nabias F., Plancoulaine S., Guitard E., Larrouy G., Gessain A. and Dugoujon JM. (2010), 'The imprint of the Slave Trade in an African American population: mitochondrial DNA, Y chromosome and HTLV-1 analysis in the Noir Marron of French Guiana.', BMC Evol Biol 10:314 [PubMed] [DOI]
  • Melo MM., Carvalho M., Lopes V., Anjos MJ., Serra A., Vieira DN., Sequeiros J. and Corte-Real F. (2011), 'Y-STR haplotypes in three ethnic linguistic groups of Angola population.', Forensic Sci Int Genet 5(3):e83-8 [PubMed] [DOI]
  • Purps J., Siegert S., Willuweit S., Nagy M., Alves C., Salazar R., Angustia SM., Santos LH., Anslinger K., Bayer B., Ayub Q., Wei W., Xue Y., Tyler-Smith C., Bafalluy MB., Martínez-Jarreta B., Egyed B., Balitzki B., Tschumi S., Ballard D., Court DS., Barrantes X., Bäßler G., Wiest T., Berger B., Niederstätter H., Parson W., Davis C., Budowle B., Burri H., Borer U., Koller C., Carvalho EF., Domingues PM., Chamoun WT., Coble MD., Hill CR., Corach D., Caputo M., D'Amato ME., Davison S., Decorte R., Larmuseau MH., Ottoni C., Rickards O., Lu D., Jiang C., Dobosz T., Jonkisz A., Frank WE., Furac I., Gehrig C., Castella V., Grskovic B., Haas C., Wobst J., Hadzic G., Drobnic K., Honda K., Hou Y., Zhou D., Li Y., Hu S., Chen S., Immel UD., Lessig R., Jakovski Z., Ilievska T., Klann AE., García CC., Knijff D., Kraaijenbrink T., Kondili A., Miniati P., Vouropoulou M., Kovacevic L., Marjanovic D., Lindner I., Mansour I., Al-Azem M., Andari AE., Marino M., Furfuro S., Locarno L., Martín P., Luque GM., Alonso A., Miranda LS., Moreira H., Mizuno N., Iwashima Y., Neto RS., Nogueira TL., Silva R., Nastainczyk-Wulf M., Edelmann J., Kohl M., Nie S., Wang X., Cheng B., Núñez C., Pancorbo MM., Olofsson JK., Morling N., Onofri V., Tagliabracci A., Pamjav H., Volgyi A., Barany G., Pawlowski R., Maciejewska A., Pelotti S., Pepinski W., Abreu-Glowacka M., Phillips C., Cárdenas J., Rey-Gonzalez D., Salas A., Brisighelli F., Capelli C., Toscanini U., Piccinini A., Piglionica M., Baldassarra SL., Ploski R., Konarzewska M., Jastrzebska E., Robino C., Sajantila A., Palo JU., Guevara E., Salvador J., Ungria MC., Rodriguez JJ., Schmidt U., Schlauderer N., Saukko P., Schneider PM., Sirker M., Shin KJ., Oh YN., Skitsa I., Ampati A., Smith TG., Calvit LS., Stenzl V., Capal T., Tillmar A., Nilsson H., Turrina S., Leo D., Verzeletti A., Cortellini V., Wetton JH., Gwynne GM., Jobling MA., Whittle MR., Sumita DR., Wolańska-Nowak P., Yong RY., Krawczak M., Nothnagel M. and Roewer L. (2014), 'A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.', Forensic Sci Int Genet 12:12-23 [PubMed] [DOI]
  • Xu H., Wang CC., Shrestha R., Wang LX., Zhang M., He Y., Kidd JR., Kidd KK., Jin L. and Li H. (2015), 'Inferring population structure and demographic history using Y‐STR data from worldwide populations', Mol Genet Genomics 290(1):141-50 [DOI]
  • Larmuseau MHD., Vessi A., Jobling MA., Geystelen A., Primativo G., Biondi G., Martínez-Labarga C., Ottoni C., Decorte R. and Rickards O. (2015), 'The Paternal Landscape along the Bight of Benin - Testing Regional Representativeness of West-African Population Samples Using Y-Chromosomal Markers', PLoS ONE 10(11):e0141510 [Link] [DOI]
  • Tau T., Davison S. and Eugenia M. (2015), 'Polymorphisms at 17 Y-STR loci in Botswana populations', Forensic Science International: Genetics 17:47-52 [Link] [DOI]
  • Rowold DJ., Perez-Benedico D., Stojkovic O., Alfonso-Sanchez MA., Garcia-Bertrand R. and Herrera RJ. (2016), 'On the Bantu expansion', Gene 593(1):48-57 [DOI]
  • Charles F., Mulima E. and Misinzo G. (2018), 'Analysis of Mutation Rate of 17 Y-Chromosome Short Tandem Repeats Loci Using Tanzanian Father-Son Paired Samples', Genetics Research International Article ID 8090469: [Link] [DOI]
  • Iacovacci G., D’Atanasio E., Marini O., Coppa A., Sellitto D., Trombetta B., Berti A. and Cruciani F. (2017), 'Forensic data and microvariant sequence characterization of 27 Y-STR loci analyzed in four Eastern African countries', Forensic Science International: Genetics 27:123-31 [DOI]
  • Barbieri C., Hübner A., Macholdt E., Ni S., Lippold S., Schröder R., Mpoloka SW., Purps J., Roewer L., Stoneking M. and Pakendorf B. (2016), 'Refining the Y chromosome phylogeny with southern African sequences', Hum Genet. 135(5):541-53 [DOI]
  • Martinez B., Catelli L., Romero M., Okolie VO., Keshinro SO., Carvalho EF., Vullo C. and Gusmão L. (2017), 'Forensic evaluation of 27 Y-STR haplotypes in a population sample from Nigeria', Forensic Science International: Genetics Supplement Series 6:e289-e291 [DOI]
  • Kofi AE., Hakim HM., Khan HO., Ismail SA., Ghansah A., David AA., Mat NFC., Chambers GK. and Edinur HA. (2020), 'Population data of 23 Y chromosome STR loci for the five major human subpopulations of Ghana', Int J Legal Med 134:1313-1315 [DOI]
  • Reid KM. and Heathfield LJ. (2020), 'Allele frequency data for 23 Y-chromosome short tandem repeats (STRs) for the South African population', For Sci Int Genet 46:102270 [DOI]
  • Shonhai M., Nhiwatiwa T., Nangammbi T. and Mazando S. (2020), 'Genetic analysis of 27 Y-chromosomal STR loci in a Zimbabwean Shona ethnic group', Legal Medicine 43:101660 [Link] [DOI]
  • Bini C., Sarno S., Tangorra E., Iuvaro A., DeFanti S., Tseghereda YG., Pelotti S. and Luiselli D. (2021), 'Haplotype data and forensic evaluation of 23 Y-STR and 12 X-STR loci in eight ethnic groups from Eritrea', Int J Legal Med 135(2):449-453 [DOI]
  • Zeye MMJ., Li J., Ouedraogo SY., Zha L., Simpore J. and Jifeng C. (2021), 'Population data and genetic structure analysis based on 29 Y-STR loci among the ethnolinguistic groups in Burkina Faso', Int J Legal Med 135:1767–9 [DOI]

Personal communications

YA005191, YA002959, YA005618, YA004765, YA005009, YA005705, YA005434, YA005476, YA005614, YA005247, YA005942, YA005167, YA006036, YA006037, YA006038, YA006039, YA006040, YA006041, YA006042, YA006043, YA006044
* See FAQ/Glossary (http://yhrd.org/pages/faq) for further explanations of abbreviated terms used here
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