Information on the Native American Metapopulation

The Native American Metapopulation (Native American) consists of 7,484 haplotypes (at least minimal) which were published in 22 population studies and were additionally submitted via personal communication (11 submissions) .

Most common haplotypes

Count DYS19 DYS389I DYS389II DYS390 DYS391 DYS392 DYS393 DYS385
145 14 13 29 24 11 13 13 11,14
86 14 12 28 25 10 14 14 16,17
82 13 12 29 23 10 15 13 15,17
80 15 13 29 23 9 11 12 15,15
74 13 13 30 24 10 14 13 14,15
61 14 13 29 24 10 13 13 11,14
53 13 13 31 23 10 14 13 14,17
50 13 14 32 23 10 15 13 15,18
50 14 13 29 23 11 13 13 11,14
42 13 12 29 24 11 16 13 14,14
Count DYS391 DYS389I DYS439 DYS389II DYS438 DYS437 DYS19 DYS392 DYS393 DYS390 DYS385
71 9 13 11 29 10 14 15 11 12 23 15,15
63 10 12 12 28 11 14 14 14 14 25 16,17
54 11 13 12 29 12 15 14 13 13 24 11,14
51 10 12 13 29 11 14 13 15 13 23 15,17
50 10 14 10 32 12 15 13 15 13 23 15,18
47 10 13 11 31 11 14 13 14 13 23 14,17
39 11 12 12 29 11 14 13 16 13 24 14,14
38 10 13 11 30 11 14 13 14 13 24 14,15
36 10 13 11 28 10 14 16 11 13 23 13,13
32 10 13 10 28 11 14 13 14 13 23 15,15
Count DYS456 DYS389I DYS390 DYS389II DYS458 DYS19 DYS385 DYS393 DYS391 DYS439 DYS635 DYS392 YGATAH4 DYS437 DYS438 DYS448
28 15 14 23 32 15 13 15,18 13 10 10 22 15 13 15 12 20
23 15 12 25 28 15 14 16,17 14 10 12 22 14 12 14 11 20
23 15 13 24 30 16 13 14,15 13 10 12 22 14 11 15 11 20
22 15 13 23 31 17 13 15,18 13 11 11 22 14 13 14 11 19
21 15 13 23 28 16 13 15,15 13 10 10 24 14 12 14 11 20
21 15 13 23 29 18 15 15,15 12 9 11 22 11 11 14 10 21
21 16 13 24 29 17 13 13,14 13 10 12 23 14 11 14 11 20
20 16 14 26 31 15 13 12,20 14 10 12 22 14 11 14 11 20
19 17 13 24 30 15 13 14,15 13 10 11 23 14 11 14 11 19
18 15 12 23 30 17 13 16,17 13 10 13 23 15 12 14 11 20
Count DYS576 DYS389I DYS448 DYS389II DYS19 DYS391 DYS481 DYS549 DYS533 DYS438 DYS437 DYS570 DYS635 DYS390 DYS439 DYS392 DYS643 DYS393 DYS458 DYS385 DYS456 YGATAH4
20 16 14 20 32 13 10 26 14 11 12 15 19 22 23 10 15 10 13 15 15,18 15 13
14 17 13 19 30 13 10 23 12 12 11 14 20 23 24 11 14 10 13 15 14,15 17 11
12 16 13 19 30 14 10 25 12 11 11 14 19 22 25 11 16 10 13 15 12,18 15 12
10 18 13 21 29 14 9 25 12 13 10 14 17 22 23 11 11 9 12 18 15,15 15 11
9 14 13 21 30 15 10 26 11 12 11 14 19 21 21 11 11 14 13 18 15,15 15 12
9 18 12 20 28 14 10 25 13 10 11 14 17 22 25 11 15 10 14 15 16,17 15 12
9 18 12 20 28 14 10 25 13 11 11 14 17 22 25 12 14 10 14 15 16,17 15 12
8 17 13 21 29 15 9 25 12 13 10 14 16 22 23 11 11 9 12 18 15,15 14 11
8 17 13 21 29 15 9 26 12 13 10 14 16 22 23 11 11 9 12 18 15,15 15 11
7 17 14 21 30 13 10 25 13 12 11 14 17 22 23 14 14 10 13 15 16,17 15 12
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
14 16 14 22 32 22 10 15 13 13 20 10 15 23 12 15 36 19 15 15,18 31 13 10 26 35,40 11
13 16 14 22 31 20 10 15 13 11 20 10 16 26 11 14 35 17 14 12,20 31 14 12 24 36,39 12
8 17 13 22 29 21 11 18 15 11 21 9 15 23 10 11 40 16 14 15,15 28 12 11 26 37,38 13
8 18 13 23 31 21 10 16 13 12 0 10 16 23 11 14 39 18 14 14,17 27 13 11 23 35,40 11
7 17 13 22 29 21 11 18 15 11 21 9 14 23 10 11 40 16 14 15,15 28 12 11 25 37,38 13
6 16 12 22 28 18.2 11 16 14 11 20 10 14 22 10 11 41 19 15 13,14 30 13 11 25 38,38 11
6 16 13 22 29 18 11 15 14 12 19 10 15 25 11 14 39 20 14 12,18 27 13 11 25 36,38 11
6 16 13 22 30 18 11 15 14 12 19 10 15 25 11 16 39 19 14 12,18 27 13 11 25 36,38 11
6 17 13 23 30 20 11 15 13 11 19 10 17 24 11 14 40 20 14 14,15 29 13 11 23 34,40 12
6 18 13 22 29 21 11 18 14 11 21 9 15 23 10 11 39 17 14 15,15 29 12 11 25 37,38 13
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
13 13 14 32 23 10 15 13 15,18 10 12 15 15 15 22 13 20 16 26 14 11 19 10 22 10 36 31 35,40
8 15 13 29 23 9 11 12 15,15 11 10 14 15 18 22 11 21 17 26 12 13 16 9 21 11 40 28 37,38
6 13 13 30 24 10 14 13 14,15 11 11 14 17 15 23 11 19 17 23 12 12 20 10 20 11 40 29 34,40
6 13 13 31 23 10 14 13 14,17 11 11 14 16 16 23 12 0 18 23 14 11 18 10 21 10 39 27 35,40
6 14 13 30 25 10 16 13 12,18 11 11 14 15 15 22 12 19 16 25 12 11 19 10 18 11 39 27 36,38
6 15 13 29 23 9 11 12 15,15 11 10 14 14 18 22 11 21 17 25 12 13 16 9 21 11 40 28 37,38
5 13 12 28 24 10 16 13 14,17 12 11 14 15 16 23 13 20 19 25 12 11 19 10 18 11 37 30 37,42
5 13 13 28 24 10 14 13 15,16 11 11 14 17 15 23 11 19 17 24 11 12 19 10 20 11 38 29 35,40
5 13 14 33 24 10 13 13 16,17 13 11 14 15 17 23 13 20 18 25 11 11 15 10 21 10 37 29 36,37
5 14 13 29 23 9 11 12 15,15 11 10 14 15 18 22 11 21 18 25 12 13 17 9 21 11 39 29 37,38

Discrete-Laplace frequency estimation (Minimal)

Release
R69
Loci included
DYS19, DYS389I, DYS389II*, DYS390, DYS391, DYS392, DYS393
Central haplotypes
42
EM converged
true
EM iterations
49
GLM method
internal_coef
Init method
pam
Threshold frequency
1 in 181,064
Per locus details
DL centers distribution (download PDF)
Table of haplotype centers (click to show/hide)
DYS19 DYS389I DYS389II* DYS390 DYS391 DYS392 DYS393
1 13 13 17 24 10 15 13
2 13 13 17 23 10 14 13
3 13 13 18 23 10 14 13
4 14 13 17 23 10 14 13
5 13 14 17 24 11 14 11
6 13 13 18 25 10 14 13
7 14 13 17 24 10 14 13
8 13 13 16 24 10 14 13
9 13 12 18 24 10 14 13
10 13 13 17 24 10 14 13
11 13 13 18 24 10 14 13
12 13 14 18 23 10 14 13
13 13 13 19 24 10 14 13
14 13 14 17 23 10 16 14
15 13 13 16 23 10 14 13
16 14 12 16 23 10 11 13
17 16 13 17 21 10 11 14
18 14 13 16 24 11 13 13
19 14 14 16 24 10 15 13
20 14 14 16 24 11 13 13
21 13 13 17 24 10 11 13
22 13 14 16 23 10 14 13
23 13 13 17 24 11 16 13
24 13 14 17 23 10 13 14
25 13 13 16 25 10 14 13
26 13 14 16 24 9 11 13
27 13 14 17 25 10 14 14
28 13 12 17 23 10 15 13
29 14 13 16 24 10 13 13
30 14 13 17 23 10 11 12
31 14 13 17 24 11 13 13
32 16 13 15 23 10 11 13
33 13 13 17 24 10 16 13
34 16 13 17 24 10 11 13
35 14 13 16 23 11 13 13
36 14 12 16 22 10 11 13
37 14 12 16 25 10 14 14
38 14 13 16 25 11 13 13
39 15 12 17 22 10 11 14
40 15 13 17 23 10 12 14
41 15 13 16 23 9 11 12
42 15 13 18 21 10 11 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
27
EM converged
true
EM iterations
146
GLM method
internal_coef
Init method
pam
Threshold frequency
1 in 298,928,818
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 13 13 17 24 10 14 13 14 11 12 20 15 16 22 11
2 13 13 18 23 11 14 13 14 11 11 19 15 17 22 13
3 13 13 18 24 10 14 13 14 11 12 20 16 17 22 11
4 13 13 17 24 10 14 13 14 11 12 20 15 17 22 12
5 13 13 17 23 10 14 13 14 11 12 21 15 15 22 12
6 13 14 17 23 10 16 14 14 11 13 20 15 16 22 12
7 14 12 16 22 10 11 13 16 10 11 20 14 15 21 11
8 13 13 17 24 10 11 13 14 10 12 20 16 17 22 12
9 15 13 17 21 10 11 13 14 11 12 21 15 17 21 12
10 13 13 18 24 10 14 13 15 11 12 20 16 17 23 12
11 14 13 17 23 10 14 13 14 11 11 19 15 15 22 12
12 14 13 16 24 11 13 13 15 12 12 19 15 17 23 12
13 13 14 17 26 10 14 14 14 11 12 20 16 15 22 11
14 13 13 17 24 10 14 13 14 11 11 19 17 15 23 11
15 13 13 17 24 10 14 13 14 11 11 19 15 16 22 12
16 13 12 17 24 10 16 13 14 11 12 20 15 17 23 12
17 13 13 16 23 10 14 13 14 12 12 19 17 15 22 12
18 15 13 16 23 9 11 12 14 10 11 21 15 18 22 11
19 14 13 16 24 11 13 13 15 12 12 19 16 17 23 12
20 16 13 17 21 10 11 14 14 11 12 21 15 16 21 11
21 14 13 16 24 11 13 13 14 12 12 18 16 17 23 11
22 14 14 16 24 10 15 13 14 11 13 19 14 17 22 12
23 14 12 16 25 10 14 14 14 11 12 20 15 15 22 12
24 15 13 16 23 10 11 13 14 10 11 20 15 16 21 11
25 13 13 16 23 11 16 13 14 11 12 19 15 16 25 10
26 16 13 17 25 10 11 13 14 11 10 20 16 15 23 12
27 13 14 18 23 10 15 13 15 12 10 20 15 15 22 13

* Please note that DYS389I was substracted from DYS389II

Population studies

  • Roewer L., Nothnagel M., Gusmão L., Gomes V., González M., Corach D., Sala A., Alechine E., Palha T., Santos N., Ribeiro-Dos-Santos A., Geppert M., Willuweit S., Nagy M., Zweynert S., Baeta M., Núñez C., Martínez-Jarreta B., González-Andrade F., De F., Silva D., Builes JJ., Turbón D., Parra L., Arroyo-Pardo E., Toscanini U., Borjas L., Barletta C., Ewart E., Santos S. and Krawczak M. (2013), 'Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans.', PLoS Genet 9(4):e1003460 [PubMed] [DOI]
  • Roewer L., Nagy M., Schmidt P., Epplen JT. and Herzog-Schröder G. (1993), 'Microsatellite and HLA class II oligonucleotide typing in a population of Yanomami Indians.', EXS 67:221-30 [PubMed]
  • González-Andrade F., Roewer L., Willuweit S., Sánchez D. and Martínez-Jarreta B. (2009), 'Y-STR variation among ethnic groups from Ecuador: Mestizos, Kichwas, Afro-Ecuadorians and Waoranis.', Forensic Sci Int Genet 3(3):e83-91 [PubMed] [DOI]
  • Tirado M., López-Parra AM., Baeza C., Bert F., Corella A., Pérez-Pérez A., Turbón D. and Arroyo-Pardo E. (2009), 'Y-chromosome haplotypes defined by 17 STRs included in AmpFlSTR Yfiler PCR Amplification Kit in a multi ethnical population from El Beni Department (North Bolivia).', Leg Med (Tokyo) 11(2):101-3 [PubMed] [DOI]
  • Palha TJ., Rodrigues EM. and Santos D. (2010), 'Y-STR haplotypes of Native American populations from the Brazilian Amazon region.', Forensic Sci Int Genet 4(5):e121-3 [PubMed] [DOI]
  • Geppert M., Baeta M., Núñez C., Martínez-Jarreta B., Zweynert S., Cruz OW., González-Andrade F., González-Solorzano J., Nagy M. and Roewer L. (2011), 'Hierarchical Y-SNP assay to study the hidden diversity and phylogenetic relationship of native populations in South America.', Forensic Sci Int Genet 5(2):100-4 [PubMed] [DOI]
  • Blanco-Verea A., Jaime JC., Brión M. and Carracedo A. (2010), 'Y-chromosome lineages in native South American population.', Forensic Sci Int Genet 4(3):187-93 [PubMed] [DOI]
  • Ascunce MS., González-Oliver A. and Mulligan CJ. (2008), 'Y-chromosome variability in four Native American populations from Panama.', Hum Biol 80(3):287-302 [PubMed]
  • Bolnick DA., Bolnick DI. and Smith DG. (2006), 'Asymmetric male and female genetic histories among Native Americans from Eastern North America.', Mol Biol Evol 23(11):2161-74 [PubMed] [DOI]
  • Martínez-González LJ., Saiz M., Alvarez-Cubero MJ., Gómez-Martín A., Alvarez JC., Martínez-Labarga C. and Lorente JA. (2012), 'Distribution of Y chromosomal STRs loci in Mayan and Mestizo populations from Guatemala.', Forensic Sci Int Genet 6(1):136-42 [PubMed] [DOI]
  • Davis C., Ge J., Chidambaram A., King J., Turnbough M., Collins M., Dym O., Chakraborty R., Eisenberg AJ. and Budowle B. (2011), 'Y-STR loci diversity in native Alaskan populations.', Int J Legal Med 125(4):559-63 [PubMed] [DOI]
  • Toscanini U., Gusmão L., Berardi G., Amorim A., Carracedo A., Salas A. and Raimondi E. (2008), 'Y chromosome microsatellite genetic variation in two Native American populations from Argentina: population stratification and mutation data.', Forensic Sci Int Genet 2(4):274-80 [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]
  • Neyra-Rivera CD., Mamani R., Ramos D., Reinoso V. and Budowle B. (2023), 'Analysis of 27 STR markers of the chromosome Y in the population of the jungle from Peru', preprint [Link] [DOI]
  • Neyra-Rivera CD., Arenas T., Ramos D., Reinoso V., Rey C. and Budowle B. (2021), 'Population data of 27 Y-chromosome STRS in Aymara population from Peru', Australian Journal of Forensic Sciences 54(5):596-610 [DOI]
  • Cardoso S., Sevillano R., Illescas MJ. and Pancorbo D. (2016), 'Analysis of 16 autosomal STRs and 17 Y-STRs in an indigenous Maya population from Guatemala', Int J Legal Med 130(2):365-6 [DOI]
  • Guevara EK., Palo JU., Guillén S. and Sajantila A. (2016), 'MtDNA and Y-chromosomal diversity in the Chachapoya, a population from the northeast Peruvian Andes-Amazon divide', Am J Hum Biol. 28(6):857-67 [DOI]
  • Perez-Benedico D., Salvia L., Zeng Z., Herrera GA., Garcia-Bertrand R. and Herrera RJ. (2016), 'Mayans: a Y chromosome perspective', Eur J Hum Genet 24(9):1352-8 [DOI]
  • Sala A., Caputo M., Ginart S., Theiler G., Parolin ML., Carnese RF., Fainboim L. and Corach D. (2018), 'Historical records under the genetic evidence: "Chiriguano" tribe genesis as a test case.', Mol Biol Rep 45(5):987-1000 [PubMed] [DOI]
  • Villaescusa P., Seidel M., Nothnagel M., Pinotti T., González-Andrade F., Alvarez-Gila O., dePancorbo MM. and Roewer L. (2021), 'A Y-chromosomal survey of Ecuador’s multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373', For Sci Int Genet 51:102427 [DOI]
  • Pignone ML., Manzella AM., Galusha M., Le J. and Moreno LI. (2022), 'Y-STR Sample Haplotypes From Five United States of America Population Groups', Forensic Science International: Reports 5:100274 [DOI]
  • Sala A., Caputo M. and Corach D. (2019), 'Genetic structure of Mataco-Guaycurú speakers from Argentina and the extent of their genetic admixture with neighbouring urban populations.', Sci Rep 9(1):17559 [PubMed] [DOI]

Personal communications

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