Scientific African 7 (2020) e00310

Contents lists available at ScienceDirect

Scientific African
journal homepage: www.elsevier.com/locate/sciaf

Preliminary investigation of distinguishing between

Zimbabwean Shona brother pairs using the health gene sure
ID 27Y human STR identification kit
Mandipa Shonhai a,∗, Tamuka Nhiwatiwa a, Tshifhiwa Nangammbi b,
Sungai Mazando a
a
The university of Zimbabwe (UZ), Department of Biological Sciences, 630 Churchill Avenue, Harare, Zimbabwe
b
Tshwane university of technology, Department of Nature Conservation, Staatsartillerie Road, Private Bag X680, Pretoria West, 0001,
South Africa

a r t i c l e i n f o a b s t r a c t

Article history: Objectives: Preliminary investigation of individualizing capacity of the SureID

R
27Y Human
Received 17 October 2019 STR Identification Kit with Shona male brother participants.
Revised 5 December 2019
Accepted 3 February 2020 Materials and Methods: Thirty-six buccal swabs were collected from 18 brother pairs and
subsequently used to generate Y-STR haplotype profiles with the use of the SureIDR
27Y
Human STR Identification Kit.
Editor: Dr. B. Gyampoh
Results: Of the 18 brother pairs analysed, 22.2% (four brother pairs) were distinguishable
Keywords: from each other at one maker, namely DYS481, DYS393, DYS458 or DYS518. One Y-STR
Zimbabwean
haplotype profile was reported in four of the 18 brother pairs (22.2%) studied.
Shona
Brothers Discussion: Maker DYS518, considered a RM Y-STR followed the expected outcome of be-
SureIDR
27Y human STR ing one of the discriminating markers between brothers. In addition, makers DYS518 and
Y-STR DYS481 are reported to have high genetic diversity for Shona unrelated males so it would
Rapidly mutating Y-STRs (RM Y-STRs) follow that they would have a more notable discriminatory capacity even between related
males of the same ethnic group. Whereas the variation between brothers at mini Y-STR
makers DYS393 and DYS458 may be attested to small or single point mutations which
upon analysis result in detection of variant alleles. These mini Y-STR marker produce rela-
tively smaller polymerase chain reaction (PCR) products and as such micro changes in the
DNA sequence could have a greater effect on the allele observed.
The shared Y-STR haplotype profile observed between brother P14, P15, P17 and P18 sug-
gested relatedness between the brother pair and probable common ancestry. Brother pair
P17 and P18 shared the same totems or clan “Moyo” while P15 with the “Shava” totem
might be explained by the common ancestry from the “Mbire” lineage.
© 2020 The Author(s). Published by Elsevier B.V. on behalf of African Institute of
Mathematical Sciences / Next Einstein Initiative.
This is an open access article under the CC BY license.
(http://creativecommons.org/licenses/by/4.0/)

∗
Corresponding author: The university of Zimbabwe (uz), Department of Biological Sciences, 630 Churchill Avenue, Harare, Zimbabwe.
E-mail addresses: m.shonz1@gmail.com (M. Shonhai), drtnhiwatiwa@gmail.com (T. Nhiwatiwa), NangammbiTC@tut.ac.za (T. Nangammbi),
sungimazando@gmail.com (S. Mazando).

https://doi.org/10.1016/j.sciaf.2020.e00310
2468-2276/© 2020 The Author(s). Published by Elsevier B.V. on behalf of African Institute of Mathematical Sciences / Next Einstein Initiative. This is an
open access article under the CC BY license. (http://creativecommons.org/licenses/by/4.0/)
2 M. Shonhai, T. Nhiwatiwa and T. Nangammbi et al. / Scientific African 7 (2020) e00310

Introduction

Human identification with the use of deoxyribose nucleic acids (DNA) analysis is fast growing in the fields of forensic, ge-
nealogical, anthropological, and population genetic studies. Y chromosomal short tandem repeats (Y-STRs) have been found
to be invaluable particularly when coupled with autosomal short tandem repeat (STR) analysis [1]. While still considerably
useful when tracing relatedness in cases such as mass disasters [2], or isolating male DNA from mixtures with female DNA
[3].
Rapidly mutating Y chromosomal short tandem repeats (RM Y-STRs) have become more popular in commercial Y-STR
human identification kits over the years [4]. Ballantyne et al., 2012 reported a 13 RM Y-STR panel with high discriminatory
capabilities to distinguish closely related males; “approximately 50% of the father and sons, and 60% of brothers” [5]. A later
study revealed that differentiation between related males was increased by 23.5% as compared to with tht Yfiler kit which
targets 17Y-STRs none of which are RM Y-STRs [6]. Well established kits on the market which have since incorporated RM
Y-STR loci include the PromegaPowerPlex R
Y23, as well as Applied BiosystemsAmpFLSTR R
Yfiler
R
Plus [7,8]. In fact, two out
of five brother pairs analysed from Upper Austria and Salzburg with the Yfiler R
Plus kit were distinguishable at RM Y-STR
markers DYS449 and DYF387S1 as well as DYS570 [9]. The SureID R
27Y Human STR Identification Kit, another commercial
Y-STR kit on the market is no exception and targets six RM Y-STR similar to those targeted by the Yfiler R
Plus (HEALTH Gene
Technologies, Ningbo, China).
For this preliminary study, buccal swabs from 36 male volunteers (18 brother pairs) belonging to the Shona ethnic group
were sampled. The kit of interest, the SureID R
27Y Human STR Identification Kit, was used to generate Y-STR profiles and
the generated profiles compared.
The Shona people are one of several ethnic groups under the Bantu lineage. These people are the majority indigenous
population of the sub-Saharan country of Zimbabwe, while also found in minority particularly in the neighbouring countries
Botswana, South Africa, Zambia, Mozambique, and Namibia.

Materials and methods

DNA samples

This study was approved by the Medical Research Council of Zimbabwe (Approval numbers MCRZ/B/852 and
MCRZ/B/1323). Written and oral consent were obtained from each participant after the principle investigator had exam-
pled research aims and procedure in compliance with research ethical requirements. A buccal swab was taken from each
participant with the FG-4N6FLOQSWAB (Applied Biosystems). Following the manufactures instructions, DNA extraction was
performed with the use of the Qiagen blood and tissue kit (Qiagen, Hilden, Germany). Quantification of the extracted DNA
was done using the NanodropTM 20 0 0/20 0 0c Spectrophotometer by ThermoFisher Scientific.

Genotyping multiplex Y-STR

The extracted DNA samples were amplified using the SureID R

27Y Human STR Identification Kit which genotyped the
following loci: DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYF387S1, DYS437, DYS438, DYS439,
DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627, DYS635 and GATA_H4
(HEALTH Gene Technologies, Ningbo, China). Each reaction had a total volume of 12.5 μL, half the stated reaction volume on
the kit. To do so the manufacturers’ volumes for the various reagents were halved (6.25 μL of Master Mix, 3.125 μL of Primer
Mix and 3.125 μL of diluted DNA template). The Gene Amp PCR System 2400 by Applied Biosystems set at the manufactures
recommended amplification condition for 30 cycles run the polymerase chain reaction (PCR). For fragment analysis the am-
plicons were run on the Applied Biosystems R
3500 Genetic Analyzer and the data processed utilizing GeneMapper ID-X R

software v5.0. Before sample analysis, a spectral calibration file was created using the HGT 5-Dye Matrix Standard. Before
the plate was run on the auto sampler a denaturation step was conducted at 95 °C for 3 min and an immediate chill step
on ice for 3 min (or use PCR program 3 min at 95 °C → 3 min at 4 °C).

Quality control

To comply with quality control requirements, we took part in the Twelfth Asian DNA Proficiency Test for 2018 and
were certified upon successful completion. In addition, the raw data produced by the Applied Biosystems R
3500 Genetic

R 
R
Analyzer was initially processed with GeneMapper ID-X software v5.0. subsequently with GeneMarker HID STR Human
Identification Software (Soft Genetics, Oakwood, PA) to check for allele calling consistency. Each genetic profile was checked
by the researchers for wrong entries, missing entries, duplicate entries, incomplete entries and other errors furthermore
appropriately edited.

Results

Only four out of the 18 brother pairs (22.2%) that were analysed showed a variation of allele numbers on just one of the
27 markers studied in each case. Brother pair samples ZHID410 and ZHID411 had alleles 26 and 27 respectively at maker
Table 1
Haplotypes observed in 18 Brother Pair, Zimbabwean Shona males of Harare Province, based on 27 Y-STR loci.

Marker
Sample ID

DYF387S1

GATA_H4
DYS389II
Brother

DYS389I
DYS449

DYS448
DYS481
DYS456

DYS458

DYS439

DYS392

DYS385

DYS393

DYS438
DYS460

DYS390

DYS635

DYS533
DYS627

DYS437

DYS391
DYS570
DYS576

DYS518
DYS19
Pair

P1 ZHID400 15 15 19 27 36, 40 20 16 9 14 11 11 16, 16 13 10 21 21 29 11 11 13 21 30 15 12 38

M. Shonhai, T. Nhiwatiwa and T. Nangammbi et al. / Scientific African 7 (2020) e00310

P1 ZHID401 15 15 19 27 36, 40 20 16 9 14 11 11 16, 16 13 10 21 21 29 11 11 13 21 30 15 12 38
P2 ZHID402 15 15 20 27 37, 39 21 16 10 14 11 11 16, 17 13 10 21 21 28 11 11 12 21 30 15 12 36
P2 ZHID403 15 15 20 27 37, 39 21 16 10 14 11 11 16, 17 13 10 21 21 28 11 11 12 21 30 15 12 36
P3 ZHID404 14 15 20 29 38, 39 20 16 10 14 11 11 16, 18 13 10 21 21 28 12 11 13 21 30 15 13 39
P3 ZHID405 14 15 20 29 38, 39 20 16 10 14 11 11 16, 18 13 10 21 21 28 12 11 13 21 30 15 13 39
P4 ZHID406 17 16 17 24 39, 39 20 16 10 14 12 9 16, 16 14 10 21 20 30 11 11 14 21 31 17 11 41
P4 ZHID407 17 16 17 24 39, 39 20 16 10 14 12 9 16, 16 14 10 21 20 30 11 11 14 21 31 17 11 41
P5 ZHID408 15 16 20 27 37, 39 20 15 10 14 11 11 17, 17 13 11 21 21 30 11 11 13 21 31 15 12 38
P5 ZHID409 15 16 20 27 37, 39 20 15 10 14 11 11 17, 17 13 11 21 21 30 11 11 13 21 31 15 12 38
P6 ZHID410 16 16 20 26∗ 38, 39 19 17 10 14 11 11 16, 19 13 11 20 21 27 11 11 13 21 32 15 12 39
P6 ZHID411 16 16 20 27∗ 38, 39 19 17 10 14 11 11 16, 19 13 11 20 21 27 11 11 13 21 32 15 12 39
P7 ZHID412 15 15 20 28 38, 38 20 16 10 14 11 11 16, 17 14 11 21 21 27 11 11 13 21 30 15 12 39
P7 ZHID413 15 15 20 28 38, 38 20 16 10 14 11 11 16, 17 14 11 21 21 27 11 11 13 21 30 15 12 39
P8 ZHID418 15 16 17 24 38, 38 20 17 10 14 10 11 17, 19 14 10 21 21 30 11 11 13 21 29 16 11 41
P8 ZHID419 15 16 17 24 38, 38 20 17 10 14 10 11 17, 19 14 10 21 21 30 11 11 13 21 29 15 11 41
P9 ZHID420 15 16 18 26 36, 39 21 16 10 14 12 11 15, 17 13 10 21 21 28 11 11 13 21 30 15 11 38
P9 ZHID421 15 16 18 26 36, 39 21 16 10 14 12 11 15, 17 13 10 21 21 28 11 11 13 21 30 15 11 38
P10 ZHID428 15 17 18 26 38, 39 19 16 11 14 12 11 18, 18 15∗ 10 20 20 32 11 11 13 21 31 15 11 40
P10 ZHID429 15 17 18 26 38, 39 19 16 11 14 12 11 18, 18 16∗ 10 20 20 32 11 11 13 21 31 15 11 40
P11 ZHID430 15 16 19 29 38, 39 20 16∗ 11 14 12 11 16, 18 13 11 21 21 29 11 11 13 21 31 15 12 38
P11 ZHID431 15 16 19 29 38, 39 20 17∗ 11 14 12 11 16, 18 13 11 21 21 29 11 11 13 21 31 15 12 38
P12 ZHID432 15 16 18 29 38, 38 20 16 9 14 11 11 16, 18 13 11 21 21 28 11 11 13 20 31 15 13 39
P12 ZHID433 15 16 18 29 38, 38 20 16 9 14 11 11 16, 18 13 11 21 21 28 11 11 13 20 31 15 13 39
P13 ZHID434 15 17 18 25 38, 39 24 17 11 14 13 11 16, 18 14 10 21 20 32 11 11 13 21 31 16 11 41
P13 ZHID435 15 17 18 25 38, 39 24 17 11 14 13 11 16, 18 14 10 21 20 32 11 11 13 21 31 16 11 41
P14 ZHID436 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
P14 ZHID437 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
P15 ZHID438 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
P15 ZHID439 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
P16 ZHID011 15 15 19 27 36, 39 19 16 10 14 11 11 16, 19 13 10 21 23 30 11 11 13 21 31 15 12 39∗
P16 ZHID440 15 15 19 27 36, 39 19 16 10 14 11 11 16, 19 13 10 21 23 30 11 11 13 21 31 15 12 38∗
P17 ZHID300 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
P17 ZHID441 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
P18 ZHID442 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
P18 ZHID443 17 19 17 24 40, 41 20 16 10 14 12 11 18, 18 14 10 21 21 26 11 11 13 21 30 17 11 41
∗
Distinguished allele between brother pair.

3
4 M. Shonhai, T. Nhiwatiwa and T. Nangammbi et al. / Scientific African 7 (2020) e00310

Table 2
Y-STR Profile for P14, P15, P17 and P18.

DYS456 DYS576 DYS570 DYS481 DYF387S1 DYF387S1 DYS627 DYS458

17 19 17 24 40 41 20 16
DYS460 DYS437 DYS439 DYS392 DYS385 DYS385 DYS393 DYS391
10 14 12 11 18 18 14 10
DYS390 DYS635 DYS449 DYS533 DYS438 DYS389I DYS448 DYS389II
21 21 26 11 11 13 21 30
DYS19 GATA_H4 DYS518
17 11 41

Table 3
Summary of brother pair preliminary data.

Brother Pair Totem or clan (Mutupo) Rural Home Stead Province

P14 Buffalo (Nyati) Murewa Mashonaland East

P15 Eland (Shava) Karoi Mashonaland West
P17 Heart (MoyoNdizvo) Masvingo Masvingo
P18 Heart (MoyoChirundu) Hwedza Mashonaland East

DYS481; ZHID428 and ZHID429 had alleles 15 and 16 respectively at maker DYS393; ZHID430 and ZHID431 had alleles 16
and 17 respectively at maker DYS458; ZHID440 and ZHID011 had alleles 38 and 39 respectively at marker DYS518 (Table 1).
Eight Y-STR profiles generated out of the 36 Y-STR profiles where identical, which means eight people or four pairs of
brother pair where indistinguishable from each other (Table 2). Based on preliminary data collected about the individuals,
the brother pairs do not come off as related individuals given their different family names and details (omitted to protect
the identity of the participants), totem or clan and rural home stead (Table 3). These brother pairs comprise of ZHID436 and
ZHID437 (P14); ZHID438 andZHID439 (P15); ZHID300 and ZHID441 (P17); ZHID442 and ZHID443 (P18).

Discussion

Unexpectedly only one of the markers which showed variation between brother profiles is a RM Y-STR, namely marker
DYS518, and has been found in other populations to have a mutation rate that is typically above 1 × 10−2 [5]. While the
other markers DYS481, DYS393, and DYS458 are not considered to be RM Y-STR markers. However, it is interesting to note
that in previous studies marker DYS458 has been recorded to have a mutation rate of 0.0071, the highest out of the 17 core
Y-STR makers [10].
In addition, a new kit aimed for use among eight South African ethnic groups, the UniQTyper Y-10, which targets 10
Y-STR markers namely DYS710, DYS518, DYS385, DYS644, DYS612, DYS626, DYS504, DYS481, DYS447 and DYS449, has been
specifically designed to target makers found to be of significant discriminatory capacity by thier study [11]. Four of the
markers appear in currently available Y-STR commercial kits whereas the rest are not as popular in these commercial kits.
It again is interesting to note that of the 4 markers found in both the UniQTyper Y-10 and the SureID R
27Y Human STR
Identification Kits, DYS481 was one of the markers which detected variation between brothers in addition to RM Y-STR
DYS518 [12].
Given that makers DYS518 and DYS481 showed high Genetic Diversity (GD > 0.8) with data from unrelated Shona males
(GD = 0.8504 and 0.8252 respectively) it further explains why genetic differences between brothers was detected at these
markers [13,16]. On the other hand, the reason behind the variations observed between the brothers at markers DYS393
(GD = 0.5590) and DYS458 (GD = 0.6613) is not as clear. However, DYS393 and DYS458 are considered mini Y-STR markers
which might possibly make them more prone to easily detectable mutations due to their relatively miniature PCR product
nature.
In Shona culture the people are separated into various clans corresponding to “mutupo” or “totems”. The totem also re-
ferred to as “clan name” of an individual is passed down from their father and thus a child’s identity is sealed to their pater-
nal heritage. The totems used in this culture are generally that of an animal or part of an animal for example “Tembo/Mbizi”
which means zebra, with the exception of the “Dziva” which means pool of water. Conferringto A.E. Chigwedere’s theory
in the book “From Mutapa to Rhodes” the Shona people can be split into two distinct lineages; the Hungwe linage and the
Mbire linage [7] This author explains the origins of the two empires in detail and in summary he states that as a general
rule the land animals or animal parts totems belong to the Mbire/Soko Family lineage while the water related animals, plants
or objects are of the Hungwe/Dziva Family lineage [14]. Moreover, theNyati (water buffalo) due to its relation to water is re-
garded as part of the Hungwe lineage. To take it a step further, each mutupo can be subdivided into such “chidavo”(zvidavo,
pl), as for the mutupo “Tembo,” there is “TemboWakapiwa”, “TemboMazvimbakupa”, and “TemboShumbaSamaita”. Such divisions
made the families within a clan more set apart and helped overcome some challenges associated with marriage customs.
It was and to an extent still is considered taboo for a man and a woman of the same family (same totem) to marry thus
pointing out the un-relatedness of individuals was imperative. There has been years and years of intermarrying between
 M. Shonhai, T. Nhiwatiwa and T. Nangammbi et al. / Scientific African 7 (2020) e00310 5

families with different Shona totems, as a result the genetics of the Shona people at this stage should be well diversified.
Suffice to say regardless of the chidavo all people belonging to a specific totem are said to be related with the exception of
the some Shumba and Sokochidavo.
Considering the above information, the production of the same Y-STR profile for P17 and P18 could be inline with the
theory presented that all families of the same totems regardless of the subdivision are the one family or related. Whereas
the similarity between the “Moyo” totem (P17 and P18) and the “Shava” totem (P15) could suggest a common ancestry
indicated as the “Mbire” lineage. Unexpectedly, P14 profiles might also suggest the same common ancestor which would not
be inline with the above, that the “Nyati” being associated with water would fall under the “Hungwe” lingeage.

Conclusion

In summation, there is need for further research regarding the discriminatory power of commercial kits such SureID R

27Y Human STR Identification Kit to detect the differences between related members in the Shona ethnic group. From pop-
ulation data on unrelated Shona males, high level of genetic diversity were found with Haplotype Diversity, HD = 0.9994,
Haplotype Match Probability, HMP = 0.0069 and overall Discriminatory Capacity, DC = 0.9686 [16]. Which suggests the
usage of this and similar kits for HID to distinguish between unrelated Shona male, however these kits may not be of as
significant use for distinguishing between related Shona males. The findings in this pilot study did not follow the expected
trend that RM Y-STRs would be the predominant distinguishing markers. On the contrary, these findings did however sup-
port that the use of markers DYS518 and DYS481 and possibly other not commonly used Y-STRs may be of better power of
discrimination in Southern African ethnic groups like the Shona people.

Declaration of Competing Interest

Mandipa Shonhai has received a research grant from Organization for Women in Science for the Developing World
(OWSD) and the Swedish International Development Cooperation Agency (Sida).

Acknowledgements

This study was supported by the Organization for Women in Science for the Developing World (OWSD) and the Swedish
International Development Cooperation Agency (Sida).

Funding

This study was funded by Organization for Women in Science for the Developing World (OWSD) and the Swedish In-
ternational Development Cooperation Agency (Sida). (Fund Reservation No. 3240287305). OWSD and Sida provided financial
support to cover travel, visa, medical aid, accommodation and general living expenses for the grantee to undertake a re-
search visit to a host institute and carry out laboratory work.

Ethical approval

All procedures performed in studies involving human participants were in accordance with the ethical standards of the
Medical Research Council of Zimbabwe (Approval numbers MCRZ/B/852 and MCRZ/B/1323) and with the 1964 Helsinki dec-
laration and its later amendments or comparable ethical standards.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Other Remarks

The data that support the findings of this study are available from the corresponding author upon reasonable request.

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