Forensic parameters of 10 Y-STR markers in the Nigerian Hausa, Igbo, and Yoruba populations
DOI:
https://doi.org/10.56919/usci.2431.012Keywords:
Y chromosome STRs, discrimination capacity, haplotypes, private alleles, NigeriaAbstract
Y chromosome short tandem repeats, or Y-STRs, are interesting genetic markers suitable for identifying male offenders in forensic investigations because of the haploid nature of the human male determining chromosome. Furthermore, due to the non-recombining nature of the Y chromosome, Y-STRs are choice markers in paternity or kinship analysis, human evolutionary investigations, and population studies. The lack of reference Y-haplotype data for the populace currently hampers the use of these markers in forensic applications in Nigeria. In this study, the 10 Y-STR loci in the UniQTyperTM Y-10 system including DYS385ab, DYS447, DYS449, DYS481, DYS504, DYS518, DYS612, DYS626, DYS644 and DYS710 were studied in 461 males comprising 139 Hausa, 96 Igbo and 226 Yoruba ethnic populations. Sixty alleles were recorded for the pooled dataset across the 10 loci, with allele frequencies ranging from 0.0022 to 0.6052. There were 430 haplotypes detected, 403 unique (singletons), and 27 were shared. The discrimination capacity and haplotype diversity were 0.9330 and 0.9770, respectively. Allelic richness was highest in the locus DYS626 and lowest in DYS504. Private alleles were found in each group, with the Hausa population having the highest number. Duplications and microvariant alleles were also reported. These findings may be helpful for paternal lineage investigations, population genetics, and forensic applications among the Nigerian populations.
References
Akpan, U. U. (2022). Multiplex PCR and forensic potentials of nine short tandem repeats in the Hausa, Yoruba, Igbo, Ibibio and Tiv populations of Nigeria. PhD Thesis. University of Lagos, Nigeria.
Ballantyne, K. N., Ralf, A., Aboukhalid, R., Achakzai, N. M., Anjos, M. J., Ayub, Q., Balažic, J., Ballantyne, J., Ballard, J. D., Berger, B., Bobillo, C., Bouabdellah, M., Burri, H., Capal, T., Caratti, S., Cárdenas, J., Cartault, F., Carvalho, E. F., Carvalho, M., … Kayser, M. (2014). Toward male individualization with rapidly mutating y‐chromosomal short tandem repeats. Human Mutation, 35(8), 1021-1032. https://doi.org/10.1002/humu.22599
Batini, C., Hallast, P., Zadik, D., Delser, P. M., Benazzo, A., Ghirotto, S., Arroyo-Pardo, E., Cavalleri, G. L., De Knijff, P., Dupuy, B. M., & Eriksen, H. A. (2015). Large-scale recent expansion of European patrilineages shown by population resequencing. Nature Communications, 6(1), 1-8. https://doi.org/10.1038/ncomms8152
Budowle, B., Aranda, X. G., Lagace, R. E., Hennessy, L. K., Planz, J. V., Rodriguez, M., & Eisenberg, A. J. (2008). Null allele sequence structure at the DYS448 locus and implications for profile interpretation. International Journal of Legal Medicine, 122, 421-427. https://doi.org/10.1007/s00414-008-0258-y
Burrows, A. M. Kasu, M., & D’Amato, M. E. (2019). Preservation of DNA integrity in biological material. Forensic Science International Genetics: Supplemental Series, 7(1), 416-418. https://doi.org/10.1016/j.fsigss.2019.10.034
Campbell, M. C., & Tishkoff, S. A. (2010). The evolution of human genetic and phenotypic variation in Africa. Current Biology, 20(4), 166-173. https://doi.org/10.1146/annurev.genom.9.081307.164258
Castric, V., & Bernatchez, L. (2003). The rise and fall of isolation by distance in the anadromous brook charr (Salvelinus fontinalis Mitchill). Genetics, 163(3), 983-996. https://doi.org/10.1093/genetics/163.3.983
Chakravarti, A. (2015). Perspectives on human variation through the lens of diversity and race. Cold Spring Harbor Perspectives in Biology, 7(9), a023358. https://doi.org/10.1101%2Fcshperspect.a023358
Chiaroni, J., Underhill, P. A., & Cavalli-Sforza, L. L. (2009). Y chromosome diversity, human expansion, drift, and cultural evolution. Proceedings of the National Academy of Sciences, 106(48), 20174-20179. https://doi.org/10.1073/pnas.0910803106
D’Amato, M. E., Bajic, V. B., & Davison, S. (2011). Design and validation of a highly discriminatory 10-locus Y-chromosome STR multiplex system. Forensic Science International: Genetics, 5(2), 122-125. https://doi.org/10.1016/j.fsigen.2010.08.015
D’Amato, M. E., Bodner, M., Butler, J. M., Gusmão, L., Linacre, A., Parson, W., ... & Carracedo, A. (2020). Ethical publication of research on genetics and genomics of biological material: guidelines and recommendations. Forensic Science International: Genetics, 48, 102299. https://doi.org/10.1016/j.fsigen.2020.102299
D’Atanasio, E., Iacovacci, G., Pistillo, R., Bonito, M., Dugoujon, J. M., Moral, P., ... & Cruciani, F. (2019). Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa. Forensic Science International: Genetics, 38, 185-194. https://doi.org/10.1016/j.fsigen.2018.11.002
de Filippo, C., Barbieri, C., Whitten, M., Mpoloka, S. W., Gunnarsdóttir, E. D., Bostoen, K., ... & Pakendorf, B. (2011). Y-chromosomal variation in sub-Saharan Africa: insights into the history of Niger-Congo groups. Molecular Biology and Evolution, 28(3), 1255-1269. https://doi.org/10.1093/molbev/msq312
Della Rocca, C., Cannone, F., D'Atanasio, E., Bonito, M., Anagnostou, P., Russo, G., ... & Cruciani, F. (2020). Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel. Forensic Science International: Genetics, 49, 102374. https://doi.org/10.1016/j.fsigen.2020.102374
Dooley, K. B., Madisha, M. T., Strümpher, S., & Ehlers, K. (2022). Forensic genetic value of 27 Y-STR loci (Y-Filer® Plus) in the South African population. Science & Justice, 62(3), 358-364. https://doi.org/10.1016/j.scijus.2022.03.009
Duello, T. M., Rivedal, S., Wickland, C., & Weller, A. (2021). Race and genetics versus ‘race’in genetics: a systematic review of the use of African ancestry in genetic studies. Evolution, Medicine, and Public Health, 9(1), 232-245. https://doi.org/10.1093%2Femph%2Feoab018
Fakorede, S. T., Adekoya, K. O., Akpan, U. U., & Ogunlusi, O. V. (2019). Allele frequencies and haplotype diversities of five Y-chromosome short tandem repeat loci in a random sample of Yoruba population in Lagos, Nigeria. FUW Trends in Science & Technology Journal, 4(2), 577-581
Fan, H., & Chu, J. Y. (2007). A brief review of short tandem repeat mutation. Genomics, Proteomics and Bioinformatics, 5(1), 7-14. https://doi.org/10.1016/s1672-0229(07)60009-6
Gharesouran, J., Hosseinzadeh, H., Ghafouri-Fard, S., Taheri, M., & Rezazadeh, M. (2021). STRs: ancient architectures of the genome beyond the Sequence. Journal of Molecular Neuroscience, 71(12), 2441-2455. https://doi.org/10.1007/s12031-021-01850-6
Goudet, J. 2003. Fstat (ver. 2.9.4), a program to estimate and test population genetics parameters. Available from http://www.unil.ch/izea/softwares/fstat.html
Gouy, A., & Zieger, M. (2017). STRAF—a convenient online tool for STR data evaluation in forensic genetics. Forensic Science International: Genetics, 30, 148-151. https://doi.org/10.1016/J.FSIGEN.2017.07.007
Greenberg, J. H. (1947). Islam and clan organization among the Hausa. Southwestern Journal of Anthropology, 3(3), 193-211. https://doi.org/10.1086/soutjanth.3.3.3628775
Hammer, M., & Redd, A. J. (2006). Forensic applications of Y chromosome STRs and SNPs. Forensics in Law Enforcement, 133.
Jobling, M. A., & Tyler-Smith, C. (2003). The human Y chromosome: an evolutionary marker comes of age. Nature Reviews Genetics, 4(8), 598-612. https://doi.org/10.1038/nrg1124
Kasu, M., Cloete, K. W., Pitere, R., Tsiana, K. J., & D’Amato, M. E. (2022). The genetic landscape of South African males: A Y-STR perspective. Forensic Science International: Genetics, 58, 102677. https://doi.org/10.1016/j.fsigen.2022.102677
Kayser, M. (2007). Uni-parental markers in human identity testing including forensic DNA analysis. Biotechniques, 43(6), S16-S21. https://doi.org/10.2144/000112580
Khubrani, Y. M., Wetton, J. H., & Jobling, M. A. (2018). Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs. Forensic Science International: Genetics, 33, 98-105. https://doi.org/10.1016/j.fsigen.2017.11.015
Lesaoana, M., Kasu, M., & D’Amato, M. E. (2019). Forensic parameters and genetic structure based on Y-chromosome short tandem repeats in Lesotho populations. Forensic Science International: Genetics Supplement Series, 7(1), 414-415. https://doi.org/10.1016/J.FSIGSS.2019.10.033
Lewontin, R. C., & Hartl, D. L. (1991). Population genetics in forensic DNA typing. Science, 254(5039), 1745-1750. https://doi.org/10.1126/science.1845040
Martinez, B., Catelli, L., Romero, M., Okolie, V. O., Keshinro, S. O., Carvalho, E. F., ... & 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. https://doi.org/10.1016/j.fsigss.2017.09.138
Medrano, J. F., Aasen, E., & Sharrow, L. (1990). DNA extraction from nucleated red blood cells. Biotechniques, 8(1), 43-43.
Nei, M., & Tajima, F. (1981). Genetic drift and estimation of effective population size. Genetics, 98(3), 625-640.
Niederstätter, H., Berger, B., Kayser, M., & Parson, W. (2016). Differences in urbanization degree and consequences on the diversity of conventional vs. rapidly mutating Y-STRs in five municipalities from a small region of the Tyrolean Alps in Austria. Forensic Science International: Genetics, 24, 180-193. https://doi.org/10.1016/j.fsigen.2016.07.009
Okolie, V. O., Cisana, S., Schanfield, M. S., Adekoya, K. O., Oyedeji, O. A., & Podini, D. (2018). opulation data of 21 autosomal STR loci in the Hausa, Igbo and Yoruba people of Nigeria. International Journal of Legal Medicine, 132, 735-737. ttps://doi.org/10.1007/s00414-017-1722-3
Ollivier, L., & Foulley, J. L. (2005). Aggregate diversity: new approach combining within-and between-breed genetic diversity. Livestock Production Science, 95(3), 247-254. https://doi.org/10.1016/j.livprodsci.2005.01.005
Purps, J., Siegert, S., Willuweit, S., Nagy, M., Alves, C., Salazar, R., ... & Turrina, S. (2014). A global analysis of Y-chromosomal haplotype diversity for 23 STR loci. Forensic Science International: Genetics, 12, 12-23. https://doi.org/10.1016/j.fsigen.2014.04.008
Roewer, L. (2019). Y‐chromosome short tandem repeats in forensics—Sexing, profiling, and matching male DNA. Wiley Interdisciplinary Reviews: Forensic Science, 1(4), e1336. https://doi.org/10.1002/wfs2.1336
Swanson, E. C., & Lagace, R. O. (1997). Hausa: Ethnographic Atlas. Centre for Social Anthropology and Computing, University of Kent at Canterbury.
Syndercombe-Court, D. (2021). The Y chromosome and its use in forensic DNA analysis. Emerging Topics in Life Sciences, 5(3), 427-441. https://doi.org/10.1042%2FETLS20200339
Turrina, S., Caratti, S., Ferrian, M., & De Leo, D. (2015). Deletion and duplication at DYS448 and DYS626 loci: unexpected patterns within the AZFc region of the Y-chromosome. International Journal of Legal Medicine, 129, 449-455. https://doi.org/10.1007/s00414-015-1178-2
Usman, H. (1997). Reproductive health and rights: The case of Northern Nigerian Hausa women. Africa Development/Afrique et Développement, 22(1), 79-94
Veeramah, K. R., Connell, B. A., Pour, N. A., Powell, A., Plaster, C. A., Zeitlyn, D., ... & Thomas, M. G. (2010). Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria. BMC Evolutionary Biology, 10(1), 1-17. https://doi.org/10.1186/1471-2148-10-92/FIGURES/6
Willems, T., Gymrek, M., Highnam, G., Mittelman, D., Erlich, Y., & 1000 Genomes Project Consortium. (2014). The landscape of human STR variation. Genome research, 24(11), 1894-1904. https://doi.org/10.1101/gr.177774.114
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