Study of 17 X-STRs in Native American and Mestizo populations of Central America for forensic and population purposes


In the present work, an extensive analysis of the X-chromosomal pool of Native American and Mestizo groups of Central America (Guatemala, El Salvador, Nicaragua, and Panama) has been carried out. Allele and haplotype frequency databases, as well as other forensic parameters for these populations, are presented. The admixture analysis supports the tri-hybrid composition in terms of ancestry in the Mestizo populations, with a predominant Native American contribution (54–69%), followed by European (19–28%) and African contributions (12–19%). Pairwise FST genetic distances highlight the genetic proximity between the northernmost Central American populations, especially among admixed populations. The unique and complex nature of this area, where populations from different origins intercrossed, as well as the informativity of X-STR data, highpoint the great interest of this genetic study. Furthermore, the X-chromosome databases for Central American populations here provided will be not only useful for forensic and population purposes not only in the target countries but also in the host countries.

This is a preview of subscription content, access via your institution.


  1. 1.

    Loue S, Sajatovic M (2012) Encyclopedia of immigrant health. Springer, New York; London

    Google Scholar 

  2. 2.

    The World Factbook. Central Intelligence Agency. Accessed: July 2020

  3. 3.

    Canales AI (2009) Current view of international migration in Latin America. XXVI IUSSP Int. Popul. Conf

  4. 4.

    Gómez-Ramírez E (2018) Migration from Central America. Accessed: July 2020

  5. 5.

    Cardoso S, Sevillano R, Illescas MJ, de Pancorbo MM (2016) Analysis of 16 autosomal STRs and 17 Y-STRs in an indigenous Maya population from Guatemala. Int J Legal Med 130:365–366.

    Article  PubMed  Google Scholar 

  6. 6.

    Söchtig J, Álvarez-Iglesias V, Mosquera-Miguel A, Gelabert-Besada M, Gómez-Carballa A, Salas A (2015) Genomic insights on the ethno-history of the Maya and the ‘Ladinos’ from Guatemala. BMC Genomics 16:131.

    Article  PubMed  PubMed Central  Google Scholar 

  7. 7.

    Salas A, Lovo-Gómez J, Álvarez-Iglesias V, Cerezo M, Lareu MV, Macaulay V, Richards MB, Carracedo Á (2009) Mitochondrial echoes of first settlement and genetic continuity in El Salvador. PLoS One 4:e6882.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  8. 8.

    Lovo-Gómez J, Blanco-Verea A, Lareu M et al (2007) The genetic male legacy from El Salvador. Forensic Sci Int 171:198–203.

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Núñez C, Geppert M, Baeta M, Roewer L, Martínez-Jarreta B (2012) Y chromosome haplogroup diversity in a Mestizo population of Nicaragua. Forensic Sci Int Genet 6:6–e195.

    CAS  Article  Google Scholar 

  10. 10.

    Núñez C, Baeta M, Sosa C et al (2010) Reconstructing the population history of Nicaragua by means of mtDNA, Y-chromosome STRs, and autosomal STR markers. Am J Phys Anthropol 143:591–560.

    Article  PubMed  Google Scholar 

  11. 11.

    Núñez C, Baeta M, Aznar JM, Sosa C, Casalod Y, Bolea M, de Pancorbo MM, Martínez Jarreta B (2013) Genetic diversity of 10 X chromosome STRs in an admixed population of Nicaragua. Forensic Sci Int Genet 7:e95–e96.

    CAS  Article  PubMed  Google Scholar 

  12. 12.

    Bourgeois S, Yotova V, Wang S, Bourtoumieu S, Moreau C, Michalski R, Moisan JP, Hill K, Hurtado AM, Ruiz-Linares A, Labuda D (2009) X-chromosome lineages and the settlement of the Americas. Am J Phys Anthropol 140:417–428.

    Article  PubMed  Google Scholar 

  13. 13.

    Gusmão L, Sánchez-Diz P, Alves C, Gomes I, Zarrabeitia MT, Abovich M, Atmetlla I, Bobillo C, Bravo L, Builes J, Cainé L, Calvo R, Carvalho E, Carvalho M, Cicarelli R, Catelli L, Corach D, Espinoza M, García Ó, Malaghini M, Martins J, Pinheiro F, João Porto M, Raimondi E, Riancho JA, Rodríguez A, Rodríguez A, Rodríguez Cardozo B, Schneider V, Silva S, Tavares C, Toscanini U, Vullo C, Whittle M, Yurrebaso I, Carracedo Á, Amorim A (2009) A GEP-ISFG collaborative study on the optimization of an X-STR decaplex: data on 15 Iberian and Latin American populations. Int J Legal Med 123:227–234.

    Article  PubMed  Google Scholar 

  14. 14.

    Pinto N, Gusmão L, Egeland T, Amorim A (2013) Paternity exclusion power: comparative behaviour of autosomal and X-chromosomal markers in standard and deficient cases with inbreeding. Forensic Sci Int Genet 7:290–295.

    Article  PubMed  Google Scholar 

  15. 15.

    Walsh PS, Metzger DA, Higuchi R (1991) Chelex-100 as a medium for simple extraction of DNA for PCR- based typing from forensic material. Biotechniques 10:506–513.

    Article  Google Scholar 

  16. 16.

    Prieto-Fernández E, Baeta M, Núñez C, Zarrabeitia MT, Herrera RJ, Builes JJ, de Pancorbo MM (2016) Development of a new highly efficient 17 X-STR multiplex for forensic purposes. Electrophoresis 37:1651–1658.

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Prieto-Fernández E, Núñez C, Baeta M, Jiménez-Moreno S, Martínez-Jarreta B, de Pancorbo MM (2016) Forensic Spanish allele and haplotype database for a 17 X-STR panel. Forensic Sci Int Genet 24:120–123.

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinformatics Online 1:47–50.

    CAS  Article  Google Scholar 

  19. 19.

    Desmarais D, Zhong Y, Chakraborty R, Perreault C, Busque L (1998) Development of a highly polymorphic STR marker for identity testing purposes at the human androgen receptor gene (HUMARA). J Forensic Sci 43:1046–1049.

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. 21.

    Ibarra A, Restrepo T, Rojas W, Castillo A, Amorim A, Martínez B, Burgos G, Ostos H, Álvarez K, Camacho M, Suarez Z, Pereira R, Gusmão L (2014) Evaluating the X chromosome-specific diversity of colombian populations using insertion/deletion polymorphisms. PLoS One 9:e87202.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  22. 22.

    Messoussi M, Prieto-Fernández E, Baeta M, Núñez C, Gaaied ABAE, de Pancorbo MM, Fadhlaoui-Zid K (2018) Genetic variation of 17 X-chromosome STR loci in Tunisian population of Nabeul. Int J Legal Med 133:85–88.

    Article  PubMed  Google Scholar 

  23. 23.

    Prieto-Fernández E, Díaz-de Usera A, Baeta M, Núñez C, Chbel F, Nadifi S, Rouault K, Férec C, Hardiman O, Pinheiro F, de Pancorbo MM (2017) A genetic overview of Atlantic coastal populations from Europe and North-West Africa based on a 17 X-STR panel. Forensic Sci Int Genet 27:167–171.

    CAS  Article  PubMed  Google Scholar 

  24. 24.

    Ruiz-Linares A, Adhikari K, Acuña-Alonzo V, Quinto-Sanchez M, Jaramillo C, Arias W, Fuentes M, Pizarro M, Everardo P, de Avila F, Gómez-Valdés J, León-Mimila P, Hunemeier T, Ramallo V, Silva de Cerqueira CC, Burley MW, Konca E, de Oliveira MZ, Veronez MR, Rubio-Codina M, Attanasio O, Gibbon S, Ray N, Gallo C, Poletti G, Rosique J, Schuler-Faccini L, Salzano FM, Bortolini MC, Canizales-Quinteros S, Rothhammer F, Bedoya G, Balding D, Gonzalez-José R (2014) Admixture in Latin America: geographic structure, phenotypic diversity and self-perception of ancestry based on 7,342 Individuals. PLoS Genet 10:e1004572.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. 25.

    Salzano FM, Sans M (2014) Interethnic admixture and the evolution of Latin American populations. Genet Mol Biol 37:151–170.

    Article  PubMed  Google Scholar 

Download references


The authors are grateful to PhD Maite Alvarez for her technical and human support provided by the DNA Bank Service (SGIker) of the University of the Basque Country (UPV/EHU, European funding: ERDF and ESF).


Funds were provided by the Basque Government (Grupo Consolidado IT998-16 and IT1271-19).

Author information



Corresponding author

Correspondence to Marian M. de Pancorbo.

Ethics declarations

Ethics declarations

All procedures performed in the study were in accordance with the Declaration of Helsinki.

Consent to participate

All participants provided signed informed consent.

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Fig. S1.

Individual admixture estimation based on 17 X-STRs in Mestizo populations from El Salvador, Guatemala, Nicaragua, and Panama, using STRUCTURE v2.3.4 (K=3). Native American, European, and African components are indicated in blue, red, and green, respectively. (PNG 174 kb).

Fig. S2.

A 3D-Non-Metric Multidimensional Scaling (3D-NMDS) representation of FST distances. Populations here studied: Native American (GUA_NA) and Mestizo (GUA_ME) from Guatemala; Native American (SAL_NA) and Mestizo (SAL_ME) from El Salvador; Mestizo from Nicaragua (NIC_ME) and Mestizo from Panama (PAN_ME). Other populations: Hispanics from Colombia (COL); Europeans from Spain (SPA), northern Portugal (POR), Brittany from France (BRF) and Ireland (IRE); Africans from Morocco (MOR), Tunisia (TUN), and Equatorial Guinea and Malawi (SAF). (PNG 199 kb).

High Resolution Image (TIF 1818 kb).

High Resolution Image (TIF 2486 kb).


(DOCX 252 kb).


(DOCX 101 kb).


(DOCX 38 kb).


(DOCX 24 kb).


(DOCX 13 kb).


(DOCX 18 kb).

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Baeta, M., Prieto-Fernández, E., Núñez, C. et al. Study of 17 X-STRs in Native American and Mestizo populations of Central America for forensic and population purposes. Int J Legal Med (2021).

Download citation


  • Central America
  • Native American
  • Mestizo
  • Admixed ancestry
  • X-STRs database
  • Guatemala
  • El Salvador
  • Nicaragua
  • Panama