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 Table of Contents  
REVIEW ARTICLE
Year : 2022  |  Volume : 8  |  Issue : 3  |  Page : 104-113

Y-STR Kits and Y-STR diversity in the South African population: A review


Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa

Date of Submission22-Sep-2021
Date of Decision19-Jun-2022
Date of Acceptance22-Jun-2022
Date of Web Publication02-Sep-2022

Correspondence Address:
Meenu Ghai
Westville Campus,University of KwaZulu Natal, University Road, Durban, KwaZulu Natal
South Africa
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/jfsm.jfsm_67_21

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  Abstract 


The South African population consists of four ethnic groups, i.e., Blacks, Coloreds, Indians, and Whites, and is considered the most diverse conglomeration of humans. In addition to autosomal short tandem repeat (STR) variation, an important tool to study population diversity is Y-chromosome (Y)-STR analysis. Y-STRs aid in forensic investigations and provide essential data about paternal lineage origins. Y-STR kits consisting of an array of stable and rapidly mutating markers offer crucial information on a given population's genetic and haplotype diversity. This review discusses the development of Y-STR kits over the years and highlights some prominent Y-STR studies conducted on the South African population. The earliest Y-STR kit developed was the Y-PLEX™6, with the most recent being the UniQTyper™ Y-10 Multiplex. The South African population studies show varying data, with the “minimal haplotype” having low discrimination capacity among the ethnic groups and the UniQTyper™ Y-10 showing high genetic diversity among the ethnic groups of the country. There is a dearth of Y-STR studies on the South African population. With the advent of new Y-STR kits with increased discriminatory markers, additional studies are required to represent the South African population in the Y-STR databases. Considering the diversity of the South African population, establishment of a local/regional population database would be beneficial. In addition, data on the origins and prevalence of mutations and silent alleles should be obtained from STR datasets generated during kinship investigations (specifically, parentage tests) so that detailed information about the frequencies of mutations, silent alleles, and uniparental disomy in the South African population at Y STR loci can be estimated.

Keywords: DNA analysis, ethnicity, genetic diversity, population diversity, South Africa, Y-chromosome short tandem repeat diversity, Y-chromosome short tandem repeat kits, Y-chromosome short tandem repeats


How to cite this article:
Shabalala S, Ghai M, Okpeku M. Y-STR Kits and Y-STR diversity in the South African population: A review. J Forensic Sci Med 2022;8:104-13

How to cite this URL:
Shabalala S, Ghai M, Okpeku M. Y-STR Kits and Y-STR diversity in the South African population: A review. J Forensic Sci Med [serial online] 2022 [cited 2022 Sep 27];8:104-13. Available from: https://www.jfsmonline.com/text.asp?2022/8/3/104/355568




  Background Top


The population structure of South Africa consists of Blacks (natives), Asians/Indians, Coloreds and Whites [Figure 1]. The mid-year population estimates for 2021 showed a distribution of 80.9% Black, 2.6% Asian/Indian, 8.8% Colored, and 7.8% White males in South Africa.[1] The Black population can be further subdivided based on language, into Zulu, Xhosa, Ndebele, Swazi, Sotho, Tswana, Pedi, Venda, and Tsonga.[2] The earliest Indian communities developed from the immigration of Indian people in the mid-1900s to work in the sugarcane fields.[2] The Colored population is considered the most genetically diverse group compared to Asian/Indian, Blacks, and Whites due to an admixture of Asian, Black, European, and Khoisan.[3],[4],[5] The genetic diversity of the South African White population is attributed to several European ancestries such as British, French, German, and Portuguese.[2] Because of colonization, migration/immigration, and the slave trade in Southern Africa, it is safe to suggest that the population is genetically diverse.[6] Population diversity is aptly studied using autosomal and Y-chromosome short tandem repeats (Y-STRs). However,[7] noted insufficient data on Y-STRs for the South African population because the commercially available kits have a low discrimination capacity.
Figure 1: The population structure of South Africa based on the mid-year 2021 population statistics consists of: Black (80.9%), Coloured (8.8%), Indian/Asian (2.8%), and White (7.8%). Nine official languages further divide the Black population into the subgroups: Zulu, Xhosa, Pedi, Tswana, Sotho, Tsonga, Swati, Venda, and Ndebele

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  Application of Y-chromosome Short Tandem Repeats Top


The Y-STRs have been extensively used[8],[9] for forensic investigations in sexual assault cases,[10] mixture analysis,[11] familial searching,[12] kinship analysis[13] and paternity testing.[14]

Sexual assault cases

It is quite common in sexual assault cases for the amount of the victim's DNA to be higher than the low amounts of the perpetrator/s DNA present.[15],[16],[17] Y-STR analysis has made it possible to identify and amplify male DNA in sexual assault cases.[18] Use of both autosomal STRs and Y-STRs also allow effective detection of the likely ethnic group of the suspect/s.[19],[20] When Y-STRs are used in the investigation of sexual offences, mixed profiles from two or more men can also be observed. If the haplotype of a person of interest is fully represented in the mixed profile, then that male cannot be excluded as a contributor to that mixture. In such cases, mixture deconvolution is required to deduce the most likely DNA profiles from the contributors.[21]

Commercially available multiplex kits consist of the sex-identifier gene Amelogenin, which has been significant in sexual assault cases.[17] There has been a suggestion for the number of sex-identifier markers in commercial kits to be increased to more than one. The limited number of mutations occurring on the markers has resulted in males' misidentification as females.[18] In a study by,[22] the authors reported that using the sex-identifier gene Amelogenin and the Y-STR locus DSY391 was more effective and significant at identifying the sex of an individual. DNA analysis for sexual assault cases encounters various challenges, such as identifying the number of donors against the high quantity of the victim's DNA.[23] Thus, increasing the number of highly informative loci used during DNA analysis in sexual assault cases improves the outcome by either excluding or including the suspected perpetrator/s.[24]

Kinship analysis

In kinship analyses, individuals of a paternal lineage are tested against each other, where Y-STRs are normally used with other genetic markers such as mitochondrial DNA.[24] The Y-chromosome does not undergo DNA recombination, which means that the Y-chromosome remains unchanged and is passed down from father to child.[25],[26] Thus, distinguishing between paternally related individuals is possible if the Y-STR loci selected have a high mutation rate[27],[28] and, currently, there are 13 (DYF387S1, DYF399S1, DYF403S1, DYF404S1, DYS449, DYS518, DYS526, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) rapidly mutating Y-STRs loci.[18],[29] Furthermore,[16] suggested the inclusion of more rapidly mutating Y-STR loci to improve current Y-STR kits' discrimination capacity, for example, in a scenario, where the suspected perpetrators in a sexual assault case are genetically related individuals; or for paternity testing and human identification in the case of discovering unknown skeletal remains. Rapidly mutating Y-STRs have a mutation rate of 10− 2 per generation, more specifically the mutation rate values range from 1.19 × 10− 2 to 7.73 × 10− 2.[29] Estimating the mutation rates in Y-STRs arose by assessing fathers' and their sons' Y-haplotypes and the variations in the Y-STRs.[13] Rapidly-mutating Y-STRs, have the potential to minimize the intra-population haplotype similarities whilst maximizing the inter-population haplotype differences.[27] The Y-chromosome requires mutations to ensure variation in haplotypes while also analyzing the source of such variations.[30]

Familial searching

In familial searching, finding a DNA match is dependent upon the use of Y-STR databases; that is, if the DNA profiles of relatives of a suspect or victim are present in the database, they can be used as reference samples,[29],[31],[32] especially in missing person cases and human identification.[24] The Y-STR Haplotype Reference Database (YHRD) currently allows the user to run kinship analyses by comparing fathers and sons and two brothers.[19] However, familial searching in some countries may be controversial due to privacy issues and ethics.[12] Most importantly, the mutation rates of the Y-STRs used for familial searching and paternal analyses are different, and should have low to medium mutation rates per generation.[18] The low to medium mutation rate of some Y-STRs is more suitable for familial searching of distant relatives.[13]

Paternity testing

Y-STRs have been implemented in paternity cases to test whether the alleged father and child share the same Y-chromosome.[33],[34] Although variations in the Y-STRs allow for distinguishing between individuals, it should be noted that sons and their fathers share the same short tandem repeats (STRs) unless mutations occur.[35] Paternity testing can show variations in alleles, such as deletions, duplication, and mutations, which may be conserved in lineages.[34] Paternal lineages constitute the same Y-chromosome due to nonrecombination, resulting in an obstacle in distinguishing between closely related males.[26] Therefore, most Y-STR analysis kits contain several rapidly mutating loci, thus increasing the power of discrimination and maximizing sensitivity. However, rapidly mutating Y-STRs are not necessarily recommended for paternity testing because the presence of three or more mutations could exclude the alleged father.[36] Furthermore,[37] suggested the need for a better understanding in explaining results from the use of rapidly mutating Y-STRs in terms of the haplotype variations caused by mutations.

The Y-chromosome application for forensic investigations in South Africa has been minimal because not much information has been acquired for the South African population.[38] Several commercial kits have been developed to obtain genetic diversity at Y-STR loci among different populations. Earlier studies have reported high genetic diversity between Afrikaner, Asian/Indian, Colored and Zulu males.[4] The locus DSY710 has been one of the most useful for studying genetic diversity in the South African population.[4],[39] Thus far, from the studies conducted, the genetic diversity observed varies according to the markers used and the population group used.[38] The present review aims to discuss Y-STR markers, the development of commercially available Y-STR-based kits and Y-STR diversity in the South African population.


  The History of Y-chromosome Short Tandem Repeat Analyses and the Development of Y-chromosome Short Tandem Repeat Kits Top


The development of DNA applications has revolutionized forensic analysis systems by minimizing the number of steps taken to analyze DNA, allowing time-saving and improved efficiency without compromising the results.[40] Since the identification of Y-STRs by,[41] this polymorphic DNA type has played an essential role in genetic analyses focusing on males, such as paternity testing and determining the genetic relatedness of different individuals.[14],[17],[18]

The minimal haplotype can be explained as a set of nine Y-STRs designed to assess and analyze the European population, and these loci are also present in the earliest known Y-STR kits.[15],[42],[43] The initial Y-STR kits developed were made for the European and American populations.[44] The minimal haplotype set became quite valuable, given the limited amount of information about Y-STR at the time.[29]

As of 2018, South Africa launched its Y-STR kit called UniQ Typer™ Y-10 genotyping kit, a collaboration between the University of Western Cape and Inqaba Biotechnical Industries (Pty) Ltd.[7] Using the UniQ Typer™ on 957 South African individuals (Afrikaner, Black, Colored, English and Indian), the kit was able to identify 870 distinct haplotypes, and on average, the discrimination capacity was 0.91.[7] The UniQ Typer™ kit is relatively less costly than most commercially available kits, and although it has fewer loci than the other commercially available Y-STR kits, it can be considered significantly informative for the South African population. [Table 1] summarizes the commercially available Y-STR kits developed to date, from the latest (HomyGene RM Y32 Kit in 2021) to the earliest (Y-PLEX™6 PCR kit in 2001).
Table 1: The differences between the types of Y-short tandem repeat kits commercially available worldwide, from the most recent, HomyGene RM Y32 Kit (2021), to the earliest, Y-PLEX™6 PCR kit (2001)

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  The Y-chromosome Short Tandem Repeat DNA Databases Top


DNA databases can be easily accessed online or can be restricted for criminal and forensic investigations.[62] DNA databases are only effective and efficient at identifying suspects if the DNA profiles are uploaded onto the database.[63] It becomes quite time-consuming and challenging to compare DNA evidence to unknown suspects.[64] Notably, the United Kingdom was the pioneering nation in establishing a DNA database for criminal investigations in 1995, namely, the United Kingdom National DNA Database.[65]

South Africa has had a fully operational DNA database called the National Forensic DNA Database of South Africa since January 2015. The South African Police Service uses autosomal STRs for DNA evidence from crime scenes in forensic investigations. Establishing an efficient DNA database in developing countries can become an enormous challenge as running a fully operational database requires constant financial support and ethical considerations, factors which influence the acquisition of DNA profiles. Without a substantial number of profiles on the database, a backlog of unsolved cases will ensue.[64]

The YHRD established by the Institute of Legal Medicine in Berlin, Germany,[24],[66] has the most extensive collection of different Y-STR haplotypes generated from different male DNA profiles (from various population groups around the world) through the use of several commercially available Y-STR kits.[4],[18] The database initially contained the Y-STR markers known as the Minimal Haplotype (DYS19, DYS385 a/b, DYS389 I/II, DYS390, DYS391, DYS392 and DYS393)[67],[68] which have been genotyped and used to analyze DNA profiles from different geographic regions and ethnic groups from different parts of the world.[69]

Currently, the database has statistics for the commercially available Y-STR kits, i.e., PowerPlex Y12, Yfiler Kit, PowerPlex Y23, and Yfiler Plus Kit; the database also has statistics for Ymax, which is the set of all the markers available on YHRD.

The amount of data available for the South African population on the YHRD is quite limited [Figure 2], and the population is relatively under-represented.[38] A haplotype diversity study of three South African population groups (Afrikaner-Caucasian, Asian-Indian and Colored) by[54] compared the findings to data available on the YHRD. Notably, more data is available for the Afrikaner-Caucasian, and matches were obtained with European haplotype available on the database.[54] The Colored population had several haplotypes that matched European populations, such as the Dutch, German, and Spanish; however, data on the Indians was unavailable at the time of writing this review.
Figure 2: The number of South African haplotypes from different Y-STR kits available on YHRD (https://www.yhrd.org) (date accessed: 13 March 2022). Y-STR: Y-chromosome short tandem repeat, YHRD: Y-STR Haplotype Reference Database

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  Y-chromosome Short Tandem Repeat Diversity in the African Population Top


Many factors influence genetic diversity, such as migration patterns, geographic isolation, natural selection, culture, and language barriers.[70] There are about 2000 distinct languages and cultures on the continent. There is a significant relationship between language and the Y-chromosome genetic variation observed in Africa.[71] It has been noted that Y-STR studies on the sub-Saharan populations show the highest genetic diversity within individuals, especially for the marker, DYS19.[72] The genetic diversity in Africa can be considered one of the most diverse based on ethnic groups, tribes and languages.[71],[73] However, African studies on Y-STR diversity have heavily relied upon American or European Y-STR kits due to the unavailability of kits designed for the continent's population genetic diversity. Researchers may opt to select significantly informative loci or rapidly mutating loci, in some cases. For example, seven Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) were selected to analyze 66 individuals from Mozambique. The average haplotype diversity was 0.692 ± 0.004 and genetic diversity of 0.442 ± 0.069,[74] with the authors noting a 5.9% genetic variation influence on the Mozambican population resulting from European males. Y-STR population studies conducted in African countries have been summarized in [Table 2].
Table 2: Summarised Y-short tandem repeat population diversity studies done on the African population

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The data obtained from the various populations across Africa is quite robust and could suggest that it is time for a kit developed, designed, and refined specifically for the African continent. Through many years of research on Y-STR diversity in Africa, there is sufficient information about the gene diversity (GD) of various Y-STR loci such as DYS385, DYS449, DYS481, DYS518, DYS612, DYS626 and DYS710. Additionally, with the development of the UniQTyper™Y-10, South Africa is well-positioned to fully understand the genetic diversity in Africa, instead of being reliant upon European or American Y-STR kits to study the population.


  Y-chromosome Short Tandem Repeat Studies on the Population Diversity of the South African Population Top


For South Africa, the genetic diversity is linked to colonization, apartheid, immigration of Indians and geographic isolation in the case of KhoiSan.[70] The use of “minimal haplotype” loci to conduct forensic genetic studies in South Africa is inadequate in providing meaningful information, so more research is needed to refine and obtain effective Y-STR loci.[39] [Figure 3] shows Y-STR diversity studies conducted on the diverse South African population.
Figure 3: Y-STR studies conducted on the South African population between the years 2005 and 2019, using different Y-STR multiplexes and kits. Y-STR: Y-chromosome short tandem repeat

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The locus DYS711 showed the most genetic diversity among the three population groups.[54] The minimal haplotypes showed low haplotype diversity in the Asian/Indian and Xhosa populations, and successfully profiled all the Afrikaner individuals. For the Asian/Indian population group, the locus DYS385 had a high genetic diversity compared to the other population groups, with a value of 0.935. On average, the genetic diversity values obtained for the population were at least 0.5.

Varying values were observed by[84] for genetic diversity across the population groups, with locus DYS714 showing the most significant variation compared to the other loci. Similarly,[3] used the minimal haplotype loci to study the genetic diversity in Cape Town (South Africa) among Asian/Indian, Afrikaner, Colored, English and Xhosa. The sampled population groups yielded over 390 haplotypes and haplotype diversity, ranging from 0.56 for Xhosa to 0.69 for Coloreds. However, there was a low haplotype diversity in the sampled population groups, and this may be due to the minimal haplotype loci being initially developed for the European populations. Thus, this set of loci may be less informative for other people from different continents. Based on their study in Cape Town,[85] also observed higher discrimination capacity in Admixture individuals than in Afrikaner individuals. The Colored individuals showed a higher genetic diversity as compared to the Afrikaners.

To recommend which loci are suitable for the various forensic genetic applications and research studies;[86] analyzed 21 Y-STR loci (DYS437, DYS447, DYS448, DYS449, DYS456, DYS481, DYS504, DYS510, DYS518, DYS532, DYS536, DYS542, DYS552, DYS562, DYS576, DYS587, DYS612, DYS626, DYS644, DYS710, and Y-GATA-H4) for 260 Asian/Indians, European-English and Xhosa individuals. The Indian population showed higher genetic diversity than other populations, while the Xhosa group had low genetic diversity. In another study,[39] selected the loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710 to study the genetic diversity of 279 individuals from the same three population groups. The locus DYS710 was highly polymorphic and can be used for size homoplasy because of polymorphism on three sections of the locus.[39] Overall, the selected loci exhibited high genetic diversity and suggested a better than average discrimination power among the sampled population groups. The Cape Muslim population showed higher genetic diversity than the Asian/Indian, English, and Xhosa population groups, and the population group is more genetically related to the Asian/Indian population.[6]

The Bantu-speaking population can be explained as a group of languages descended from the Niger-Congo language family,[87] which came from West Africa and expanded to Sub-Saharan Africa.[77],[88] In South Africa, the Bantu-speaking population is divided into Nguni (IsiNdebele, Siswati, IsiXhosa and IsiZulu) and Sotho-Tswana (Sesotho, Setswana, Sepedi).[89],[90] To explore the Y-chromosome haplotype diversity in Bantu-speaking populations in Southern Africa,[91] sampled 411 individuals, 108 of them being Xhosa and Zulu from Cape Town, and observed about 70 haplotypes from the sampled populations. The Xhosa and Zulu population showed a haplotype diversity of 0.990 and 0.994, respectively, whereas,[52] obtained at least 18 000 haplotypes. Most notably, the PowerPlex®Y23 was able to identify a commonly shared haplotype between individuals from Kenyan Maasai and South African Xhosa populations [Figure 3].

The UniQTyper™ Y-10 was significantly informative while studying males from four population groups (Asian/Indian, Afrikaner, Colored and Zulu).[4] The loci DYS504 and DSY710 provided important information regarding the Afrikaner population revealing high genetic diversity. Similarly,[7] used the UniQTyper™ Y-10 to analyze the genetic diversity in the Afrikaner, Colored, English, Indian and Bantu (namely Pedi, Venda, Xhosa, and Zulu) population. The Indian population had a higher haplotype diversity and discriminatory power, with values of 0.9991 and 0.9579, respectively, compared to the Zulu population, which had 0.9956 and 0.8646, respectively. The Colored population consisted of paternal lineages of European descent.

The loci DYS449, DYS518, DYS612, and DYS626, were reported as the four highly mutable Y-STR markers among 2201 individuals across 15 different population groups (Afrikaner (161); English (111); Indian (104); Colored (500); Griequa [68]; Nama [47]; Pedi (198); Venda (122); Southern Sotho [70]; Tswana (99); Tsonga (118); Swazi (104); Ndebele [16]; Zulu (180) and Xhosa (303)).[47] The South African population showed size homogeneity in the alleles of rapidly mutating loci of the UniQTyper™ Y-10. The kit is said to have the highest discriminative power and is significantly informative among the South African population. Additionally,[48] assessed the applicability of the UniQTyper™ Y-10 amongst 2201 individuals (i.e., Afrikaner, English, Colored, Zulu, and Xhosa) and its applicability in the South African population. They found that the locus DYS644 had seven unique alleles and was exclusive to the Black and Colored population groups.

In a study by,[92] the PowerPlex® Y23 system (Promega Corp, Madison, WI, USA) was used to obtain the allele frequencies of the South African population: South African-African (n = 200), South African-Admixed (n = 175), South African-Indian/Asian (n = 112) and South African– European (n = 165). The DYS385a/b combined marker exhibited the greatest GD across all population groups, while DYS391 showed the lowest GD in the overall population group.

Data acquired throughout the years for the South African population show that the population is relatively genetically diverse. However, population dynamics are continually changing through immigration, emigration,[93] and interbreeding between the different ethnic groups or foreign nationals.[94] These factors should be considered when researching the genetic and haplotype diversity of a population.

More Y-STR analysis research studies have been opting to use the UniQTyper™Y-10 [Figure 3] developed specifically for the South African population. The studies conducted in the early 2000s on the South African ethnic groups provided essential data to refine informative and suitable loci selection. Such data can be used for Y-STR analyses and the development of kits, such as the locally manufactured UniQTyper™ Y-10.

Each Y-STR kit has its pros and cons; thus, it is challenging to recommend one kit exclusively. Researchers should assess and analyze data on the kit before using it and should examine the advantages and limitations. It would be best for researchers to use locally developed Y-STR kits that reflect the genetic diversity of the South African population.


  Future Characterization of Y-chromosome Short Tandem Repeat Markers for the South African Population Top


It is important to note that a population's haplotype diversity relies on the markers used to study it.[95] The commercially available Y-STR kits are not as informative for the South African population as for European and American populations.[47],[96] Thus, it becomes a challenge when analyzing and studying such a diverse population of people when the tools required to conduct population and genetic studies fail to provide informative and significant data.

To date, there is little to no research reported on the occurrences of mutations, silent alleles and uniparental disomy (UPD) at Y-STR loci in the South African population groups. Most of the studies report population diversity analysis on non-related males. As there were no close biological relationships between the individuals included in these studies, it is not possible to study occurrences such as mutations, silent alleles, and instances of UPD in detail. In future, data on the origins and prevalence of mutations and silent alleles can be obtained from STR datasets generated during kinship investigations (specifically parentage tests). As a result, the inheritance patterns between related individuals can be directly observed, and detailed information about the frequencies of mutations, silent alleles and UPD at the different Y-STR loci can be estimated.

For Y-STR applications to be fully effective and efficient for forensic investigations and population studies, a well-established DNA database enhances the labor-intensive Y-STR analysis processes.[97] Considering the diversity of the South African population, establishment of a local/regional population database would be beneficial.

It is suggested that the designated loci set could be chosen depending on the type of study.[24] Slow mutating Y-STRs can be used to study gene evolution; Intermediate mutating Y-STRs can be used to study population genetics or family genetic histories, whereas rapidly mutating Y-STRs can distinguish between paternally related individuals. Also, it is crucial to consider that, before using these rapidly mutating Y-STRs, there should be significant data on the distribution of haplotypes from these loci in a given population.[29]

Additionally, with advances in massive parallel sequencing on the rise, Y-STRs can be interrogated along with microhaplotypes (MHs, generally < 200 bp and consisting of two or more closely linked single nucleotide polymorphisms (SNPs) with three or more allelic combinations). This would further facilitate the deconvolution of DNA mixtures.[45]


  Conclusion Top


Based on studies on the genetically diverse South African population, we may be much closer to understanding the population's genetic distributions and dynamics. Furthermore, kits must be individualized to accommodate different populations as some haplotypes and loci are not present in specific population groups. Also, increasing the number of Y-STR loci and rapidly mutating loci in the kits could be more beneficial and significant in expanding our current knowledge of population genetic structures. Inclusion of MPS technology is the recommended approach to complement Y-STR with SNP and microhaplotype data.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.



 
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