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Forensic and Genetic Characterization of mtDNA Lineages of Shin, a Unique Ethnic Group in Pakistan

PJZ_53_1_133-141

Forensic and Genetic Characterization of mtDNA Lineages of Shin, a Unique Ethnic Group in Pakistan

Muhammad Umer Khan1,2*, Muhammad Farooq Sabar1, Atif Amin Baig3, Arif-un-Nisa Naqvi4 and Muhammad Usman Ghani1

1Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan

2Faculty of Allied Health Sciences, The University of Lahore, Lahore, Pakistan

3Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia

4Karakoram International University, Gilgit-Baltistan, Pakistan

ABSTRACT

Mitochondrial DNA has been adopted as a versatile genetic marker all over the globe and provides a unique maternal ancestry portrait of a person’s genetic pin code. Overall knowledge of mtDNA profiles of worldwide populations can benefit population genetics and forensic sciences. Consequently, this study was designed to establish the mtDNA profiles of the Shin ethnic group in Gilgit-Baltistan, the northern most territory of Pakistan. Phlebotomy was performed for a total of 79 maternally unrelated Shin volunteers. Genomic DNA was extracted from whole blood samples and subjected to PCR amplification using specific primers for the control region of mtDNA (covering positions 16024–16569 and 1–576), including the three hypervariable segments (HVS1, HVS2, HVS3). The PCR products were subjected to cycle sequencing and further evaluated through computational analysis. A total of 75 different haplotypes were identified in Shin people; among them, 72 were unique and 3 were shared by more than one individual. This study revealed the predominance of West Eurasian lineages in the Shin population (59.49%), followed by South Asian lineages (25.32%) and then East and Southeast Asian lineages (15.19%). Shin population presented a high genetic diversity of 0.9996 and a low random match probability of 0.0129. To the best of our knowledge, this is the first report of mtDNA profiles of the Shin population, providing a complementing dataset for curative generation of future mtDNA databases in Pakistan.


Article Information

Received 24 October 2019

Revised 11 February 2020

Accepted 09 March 2020

Available online 11 December 2020

Authors’ Contribution

MUK and MUG wrote the manuscript. MFS supervised the whole project and also helped in sequencing analysis. AAB provided the technical assistance regarding genetic and statistical analysis. ANN provided the facility for sampling.

Key words

Mitochondrial DNA, Shin population, Haplotypes, Haplogroups, Control region

DOI: https://dx.doi.org/10.17582/journal.pjz/20191024091047

* Corresponding author: umer.khan685@gmail.com

0030-9923/2021/0001-0133 $ 9.00/0

Copyright 2021 Zoological Society of Pakistan



INTRODUCTION

Mitochondrial DNA has emerged as one of the most popular genetic markers to investigate the genetic diversity of human populations (Pugach and Stoneking, 2015). In forensic practice, mtDNA analysis functions as a pivotal tool for human identity testing, population genetics, phylogenetics, anthropology, archaeology, human evolution and migration studies (Gupta et al., 2015).

MtDNA typing provides a unique maternal genealogical portrait of a person’s genetic code. Its remarkable characteristics, which include a high copy number within the cells, an exclusive maternal inheritance, a high level of variation in its control regions, its size, and a neutral mode of evolution, make it a marker of choice in those circumstantial forensic caseworks where routine nuclear markers are not applicable (Conrad et al., 1968; Legros et al., 2004; Nilsson et al., 2008; Khan, 2013; O’Neill, 2013). Specifically, due to its significantly high copy number per cell, it has an advantage and provides valuable data in the legal scenarios where only degraded DNA is available (Gupta et al., 2015). Moreover, its absolute maternal inheritance pattern and absenteeism of recombination events allow specific mtDNA sequences to be well reserved in all maternally-related family members of a family (Conrad et al., 1968). This has led to an extraordinary evolutionary consistency of genetic factors across multiple generations through the entire four billion spectrum of years since the birth of Adam and Eve (Zenil, 2017). Consequently, forensic comparisons can be made using a reference sample from multiple generations (Conrad et al., 1968).

All these benefits of mtDNA analysis are employed by forensic scientists for multiple purposes such as recognition of the relics of missing persons in disasters or matching evidential DNA recovered from a crime scene to those available in a database (of, e.g., convicted criminal profiles or the database for probable relatives) (Ziętkiewicz et al., 2012). Hence an overall knowledge of mtDNA profiles of worldwide populations is imperative to take advantage of mtDNA in a plethora of applications including forensic genetics and phylogenetic studies (Butler, 2009). Population specificity of mitochondrial genome (mtgenome) is widely reported in literature. MtDNA has been found to be very informative for inference of ethnicity (Prieto et al., 2011, Ladoukakis and Zouros, 2017).

Through historical perspective of human population migrations, South Asia comes next to Africa in holding heterogeneity and genetic diversity of populaces. Pakistan is situated in the core region of South Asia and probably was inhabited during primitive human movements (Shi et al., 2008). This zone is thus considered as the cradle of multiple civilizations. Currently a number of racial groups and minority units reside in Pakistan (Ayub and Tyler-Smith, 2009).

Gilgit-Baltistan is an important independent territory of Pakistan (Afzal, 2017). It is situated in the northern zone of Pakistan and consists of sight worthy valleys disjointed by some of the globe’s highest mountain ranges including Hindu Kush, the Himalayas, Karakoram and the Pamir Mountains. Thus, it embraces a mixture of dynamic cultures and civilizations. Hence it is well-intentioned to study the ethnicity of people residing there (Khan, 2013).

One of the dominant populations of Gilgit-Baltistan is Shin, a Dardic tribe, whose mother tongue is Shina (Radloff, 1992; O’Neill, 2013). Unfortunately, this smaller but significant ethnic group of Pakistan has remained neglected and understudied. Understanding the genetic structure of this population is important, not only from a historic standpoint, but also for effective implementation and interpretation of forensic genetics.

In this regard, the current study was aimed to establish the mitochondrial DNA profiles of the Shin population, residing in Gilgit-Baltistan. The entire mtDNA control region of Shin individuals was sequenced and analyzed (as per recommendations) (Parson et al., 2014). This is the first study to report the mtDNA profiles of the Shin population. The main target of this work was to establish the predominant mtDNA lineages of this population to infer their ethnicity and history of their settlements in Pakistan and to compare them with other relevant races. The outcomes of this study will be useful for generating a genetic database of these areas which may be utilized for multipurpose future forensic implications.

 

MATERIALS AND METHODS

Samples

Blood samples were collected from 79 maternally unrelated Shin individuals, both males and females, living in different regions of Gilgit-Baltistan, Pakistan (Fig. 1). Only individuals who confirmed their Shin origin of at least last three generations on the maternal side were included in the study. Scripted informed consent was taken from all the volunteer participants according to the declarations of Helsinki. Sample collection was performed in different towns and cities of Gilgit-Baltistan to achieve a reliable and complete representation of Shin population. A bioethical clearance certificate was obtained by the Bioethics committee of University of the Punjab. All procedures performed in this study were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.


 

DNA extraction, amplification and sequencing

Whole blood samples collected in EDTA vials were subjected to DNA extraction via QIAamp DNA Mini Kit as per manufacturer instructions (Qiagen, Hilden, Germany. Cat No./ID: 51304). The quality and purity of extracted DNA samples were determined and adjusted (Nano Drop TM 1000 Spectrophotometer). The amplification of the desired sequences was done by Polymerase Chain Reaction (GeneAmp PCR System 9700, Applied Biosystems, Foster City, CA, USA), using specific primers as mentioned in Table I. PCR cyclic reactions were performed in 50µl of reaction mixture containing a total of 25µl 2x PCR hotstart master mix (abm, Canada, Cat. No. G906), a total of 21µl nuclease free H 2 O (Ambion, ThermoFisher Scientific, USA) a total of 2µl forward (10µM) and reverse primers (10µM) and a 2µl of DNA template. The PCR (30 cycles) was engineered to be; initial denaturation at 94°C for 10 min; second denaturation at 94°C for 30 seconds, annealing

 

Table I. Primers used in this study to amplify the control region of mitochondrial DNA in Shin ethinic group in Pakistan.

Sr. No.

Primer name (Control region)

Primer sequences (5´→3´)

PCR

Sequencing

1

F15975

CTC CAC CAT TAG CAC CCA AA

Yes

Yes

2

F16327

CCG TAC ATA GCA CAT TAC AGT C

No

Yes

3

F155

TAT TTA TCG CAC CTA CGT TC

No

Yes

4

R16419

GAG GAT GGT GGT CAA GGG A

No

Yes

5

R042

AGA GCT CCC GTG AGT GGT TA

No

Yes

6

R635

GAT GTG AGC CCG TCT AAA CA

Yes

Yes

7

F403

CCG CTT CTG GCC ACA GCA CT

No

Yes

8

R389

CTG GTT AGG CTG GTG TTA GG

No

Yes

9

F16524

AAG CCT AAA TAG CCC ACA CG

No

Yes

 

at 60 C for 30 seconds and extension at 72 °C for 1.5 min. followed by a final extension 72 °C for 5 min.. The amplified PCR products were analyzed for their quality and purity (Nano Drop TM 1000 Spectrophotometer, USA) to be subjected further to cycle sequencing (BigDye Terminator v3.1 Cycle Sequencing Kit, Thermo Fisher Scientific, USA) using manufacturer instructions, followed by DNA sequencing readout through Applied Biosystems 3730xl Genetic Analyzer (Thermo Fisher Scientific, USA).

Data analysis

The mtDNA control region forward and reverse sequences were aligned through the sequence analysis tool Geneious (Version 7.0.3, Biomatters Ltd, New Zealand) (Drummond, 2009) and were then compared to the revised Cambridge Reference Sequence (Andrews et al., 1999) using mtDNA profiler (Yang et al., 2013). To ensure high quality, two independence evaluations of the raw data were performed as per recommendations (Parson and Bandelt, 2007). The haplogroup assignments were carried out using previously published data (Metspalu et al., 2004; Behar et al., 2008; van Oven et al., 2011; Elmadawy et al., 2013), and by using Mitotool (www.mitotool.org) (Fan and Yao, 2011) and Haplogrep (www.haplogrep.uibk.ac.at) online tools (Kloss-Brandstätter et al., 2011), based on PhyloTree Build 17 (http://www.phylotree.org) (Van Oven and Kayser, 2009) as classification tree.

Indices of forensics and population genetics; e.g., genetic diversity, random match probability and power of discrimination were analyzed as explained previously (Tajima, 1989; Prieto et al., 2011). The current study strictly adhered to the guidelines and recommendations from the International Society for Forensic Genetics (ISFG) (Parson and Bandelt, 2007).


 

RESULTS AND DISCUSSION

The present study generated population data for the complete mtDNA control region (16,024–576) of 79 subjects from the Shin ethnic group. A total of 75 haplotypes were observed including 72 unique and 3 shared haplotypes. The most frequent haplotype (16129A 16223T 16298C 16327T 16519C 73G 249d 263G 315.1C 315.2C 489C) was found in 3.79 % of the sampled population (Table II). In 1122 positions analyzed, 174 variable sites were found in the mtDNA control region of the Shin population.

MtDNA analysis of the subjects revealed that the Shin population exhibited mtDNA genetic diversity of 0.9996, random match probability of 0.0129 and

 

Table II. Polymorphism in control region of mitochondrial DNA in Shin ethnicity in Pakistan.

Sr. no.

Sample ID

Sampling area

Haplotypes

Haplogroups

1

SHN-009

Ghizer

16114A 16192T 16256T 16270T 16294T 16526A 73G 263G 309.1C 361d

U5a2a

2

SHN-010

Ghizer

16129A 16242T 16356C 73G 200G 263G 309.1C 315.1C550.1C

H3b6

3

SHN-011

Astore

16166d 16309G 16318T 16519C 73G 151T 152C 263G 315.1C 523d 524d 550.1C 573.1C

U7a

4

SHN-012

Astore

16126C 16223T 16519C 73G 263G 315.1C 482C 489C 523d 524d 550.1C 573.1C

M3

5

SHN-013

Sultan Abad

16224C 16311C 16320T 16519C 73G 89C 146C 195C 263G 309.1C 315.1C 524.1A 524.2C 524.3A 524.4C 573.1C

K1b2

6

SHN-014

Haramosh

16150T 16166d 16223T 16519C 73G 146C 152C 195A 263G 315.1C 489C 523d 524d 549T 573.1C

M30c1

7

SHN-015

Astore

16223T 16304C 16519C 73G 151T 199C 204C 263G 309.1C 315.1C 489C 550.1C 573.1C

M35b1

8

SHN-016

Astore

16223T 16519C 73G 152C 195A 263G 272G 309.1C 315.1C489C 523d 524d 573.1C

M30

9

SHN-017

Astore

152C 200G 235G 263G 315.1C 523d 524d 573.1C

H1+152

10

SHN-018

Astore

73G 152C 263G 315.1C 523d 524d 573.1C

H32

11

SHN-019

Danyor

16126C 16163G 16186T 16189C 16294T 16519C 73G 152C 263G 315.1C 573.1C 573.2C 573.3C573.4C

T1a+152

12

SHN-020

Gilgit City

16223T 16234T 16274A 16519C 73G 195A 263G 309.1C 309.2C 315.1C 489C 523d 524d 573.1C

M30+16234

13

SHN-021

Gunji

263G 315.1C 573.1C

H29

14

SHN-022

Danyor

16129A 16223T 16298C 16327T 16519C 73G 249d263G 315.1C 315.2C 489C

C

15

SHN-023

Gultari

16344T 16519C 73G 263G 315.1C 482C 489C 523d 524d549.1C 550.1C 573.1C

M3d

16

SHN-024

Gilgit City

16126C 16294T 16296T 16519C 73G 263G 309.1C315.1C 550.1C 573.1C

T2b5a1

17

SHN-025

Gilgit City

16049.1G 16182C 16183C 16189C 16194C 16195A 16196.1G 16197G 205.1G 206G 220A 221T 230G 237T 240T 250A 253T 256G 257C 260A

H2a2a1g

18

SHN-026

Jalalabad

16145A 16192T 16256T 16270T 16304C 16311C 16399G 73G 263G

U5a1f1

19

SHN-027

Gilgit City

16111T 16223T 16391A 16519C 73G 195A 263G

N5

20

SHN-028

Gilgit City

16223T 16519C 73G 152C 195A 263G 272G 309.1C315.1C 489C 523d 524d 573.1C

M30

21

SHN-029

Gilgit City

73G 152C 263G 315.1C 573.1C

H32

22

SHN-030

Jager Basen

16086C 16185T 16223T 16260T 16519C 73G 152C 249d 263G 309.1C 315.1C 489C 573.1C

Z+152

23

SHN-031

Astore

16166G 16256T 16352C 16519C 200G 263G 309.1C309.2C 315.1C 573.1C

H14a

24

SHN-032

Haramosh

16126C 16294T 16296T 16325C 16519C 16527T 73G 263G 315.1C 523d 524d 573.1C

T2

25

SHN-033

Chilas

63C 64T 73G 105G 114T 141T 146C 151T 167T 186G 194T 242T 253T 263G 295T 309.1C 315.1C 462T 489C 552.1T 573.1C

J1

26

SHN-034

Gilgit City

16309G 16318T 16519C 73G 152C 263G 309.1C315.1C 523d 524d 573.1C

U7

27

SHN-035

Diamir

16223T 16304C 16519C 73G 146T 199C 263G 309.1C 309.2C 315.1C 489C 573.1C

M35b+16304

28

SHN-036

Jaglot

16309G 16318T 16343G 16519C 73G 151T 152C 185A 263G 315.1C 368.1A 368.2G 368.3A 368.4A 573.1C

U7a

29

SHN-037

Ganj Skrdu

16092C 16223T 16290T 16319A 16362C 73G 152C 235G 263G 309.1C 315.1C 573.1C

A+152+16362

30

SHN-038

Naltar

16126C 16294T 16296T 16325C 16519C 16527T 73G 263G 315.1C 523d 524d 550.1C 573.1C

T2

31

SHN-039

Gilgit City

16309G 16318T 16519C 73G 152C 263G 309.1C315.1C 523d 524d 573.1C

U7

32

SHN-040

Haramosh

73G 194T 263G 315.1C

P2

33

SHN-041

Gulmit

16223T 16289G 16290T 16360T 16519C 73G 198T 263G 315.1C 489C 511T 524.1A 524.2C 573.1C

M65a+@16311

34

SHN-042

Nagar

16309G 16318T 16519C 64T 73G 151T 152C 263G 309.1C 315.1C 523d 524d 573.1C

U7a

35

SHN-043

Jaglot

16266T 16304C 16311C 16356C 16524G 73G 146C 152C 263G 315.1C 523d 524d 549.1C 550.1C

R5a2

36

SHN-044

Baseen

16309G 16318C 16368C 16519C 73G 152C 200G 263G 315.1C 523d 524d 573.1C

H32

37

SHN-045

Bunji

16086C 16311C 263G 309.1C 315.1C 480C 573.1C

HV14

39

SHN-047

Danyor

93G 152C 263G 309.1C 309.2C 315.1C 524.1A 524.2C

H1e1a1

40

SHN-048

Ghizer

16189C 150T 263G 315.1C 550.1C 573.1C

H1e1a6

41

SHN-049

Gilgit City

73G 152C 235G 263G 309.1C 315.1C 573.1C

F2d

42

SHN-050

Baseen

16037G 16039.1G 16266T 16304C 16311C 16356C 16524G 16526A 73G 150T 152C 263G 309.1C 315.1C 523d 524d 573.1C

R5a2

43

SHN-052

Ghizer

16126C 16163G 16186T 16189C 16294T 16519C 73G 152C 195C 263G 309.1C 309.2C 315.1C 524.1A 524.2C 573.1C

T1a1'3

44

SHN-053

Jalal abad

16136C 16356C 73G 195C 263G 309.1C 315.1C 499A 524.1A 524.2C 524.3A 524.4C 573.1C

U4b2

45

SHN-054

Ghizer

16069T 16126C 16145A 16172C 16222T 16261T 16519C 73G 242T 263G 295T 315.1C 462T 489C 550.1C 573.1C

J1b1a1

46

SHN-055

Ghizer

16519C 143A 263G 309.1C 309.2C 315.1C 572.1G

H3ak

47

SHN-056

Gilgit City

73G 150T 200G 263G 309.1C 315.1C 550.1C

U5b2a1a2

48

SHN-057

Danyor

16209C 16239T 16311C 16352C 16353T 73G 146C 152C 153G 234G 263G 309.1C 315.1C 573.1C

U2b2

49

SHN-058

Danyor

16126C 16147T 16223T 16519C 73G 195C 263G 309.1C 315.1C482C 489C

M3

50

SHN-059

Astore

16223T 16274A 16362C 16519C 73G 263G 298T 309.1C 309.2C 315.1C 489C 550.1C

D4g2a

51

SHN-060

Ghizer

16069T 16126C 16193T 16278T 16519C 73G 150T 152C 235G 263G 295T 315.1C 489C 550.1C

J2b1a

52

SHN-061

Danyor

16111T 16239T 16362C 16482G 239C 263G 309.1C 309.2C315.1C 549.1C

H6

53

SHN-062

Danyor

16183C 16189C 16304C 16519C 73G 249d 263G 309.1C 315.1C 523d 524d

F1+16189

54

SHN-063

Momin abad

16129A 16223T 16298C 16327T 16519C 73G 249d263G 315.1C 315.2C 489C

C

55

SHN-064

Gilgit City

16360T 16519C 73G 198T 263G 315.1C 489C 511T 524.1A524.2C

M65

56

SHN-065

Gilgit City

16093C 16223T 16519C 73G 195A 263G 315.1C 352C 489C 523d 524d

M30

57

SHN-066

Ghizer

16311C 16354T 263G 315.1C 550.1C

HV8

58

SHN-067

Gilgit City

16124C 16184T 16311C 44.1C 55C 57C 146C 263G 309.1C 315.1C 550.1C

H15a1b

59

SHN-068

Diamer

16311C 16354T 263G 315.1C

HV8

60

SHN-069

Yasin

16209C 16239T 16311C 16352C 16353T 73G 146C 152C 153G 234G 263G 309.1C 315.1C

U2b2

61

SHN-070

Hunza

263G 309.1C 315.1C

H2a2a

62

SHN-071

Gujal

16049.1G 16183d 16189d 16194d 16195C 16196C 16519C 73G 153G 195C 263G 309.1C 315.1C 550.1C

R8

63

SHN-072

Juglot

16049.1G 16183C 16189C 16277C 16304C 16519C 73G 249d 263G 309.1C 315.1C 523d 524d

F1+16189

64

SHN-073

Astore

16183C 16189C

H2a2a1g

65

SHN-074

Astore

16179T 16223T 16292T 16295T 16519C 73G 146C 189G 194T 195C 204C 207A 263G 309.1C 315.1C 550.1C

W+194

66

SHN-075

Gilgit City

16519C 72C 73G 146C 152C 195C 263G 315.1C 550.1C

HV2a

67

SHN-076

Danyor

16129A 16223T 16298C 16327T 16519C 73G 249d263G 315.1C 315.2C 489C

C

68

SHN-077

Astore

16223T 16302G 16519C 73G 143A 195A 263G 315.1C 489C 523d 524d 550.1C

M30

69

SHN-078

Jalal abad

16311C 152C 263G 309.1C 315.1C 548.1A 550.1C

H2a+152 16311

70

SHN-079

Gilgit

16223T 16289G 16519C 73G 263G 315.1C 489C 511T

M65a+@16311

71

SHN-080

Juglot

16245T 16309G 16318T 16356C 16519C 73G 151T 152C 263G 315.1C 523d 524d

U7a

72

SHN-081

Diamer

16223T 16245T 103A 235G 263G 309.1C 315.1C

H106

73

SHN-082

Yasin

16270T 16343G 73G 150T 200G 263G 309.1C 315.1C550.1C

U3a2a

74

SHN-083

Hunza

16093C 16145A 16223T 16362C 73G 152C 195C 263G 309.1C 315.1C 489C

G2c

75

SHN-084

Gujal

194T 200G 263G 309.1C 309.2C 315.1C 550.1C

H3s

76

SHN-085

Duglot

73G 152C 263G 309.1C 315.1C 524.1A 524.2C

H32

77

SHN-086

Astore

16223T 16362C 16519C 73G 263G 309.1C 315.1C489C

M9

78

SHN-087

Astore

16183d 16189d 16194d 16195C 16196C 16519C 73G 249d 263G 309.1C 315.1C 523d 524d

F

79

SHN-088

Gilgit City

16111T 16239T 16362C 239T263G 309.1C 315.1C 523d 524d

A2v

 

Table III. Forensic and genetics parameter indices in Shin population.

Total number of samples

79

No. of haplotypes

75

Unique haplotypes

72

Polymorphic positions

178

Random match probability

0.0129

Power of discrimination

0.9871

Genetic diversity

0.9996


 

power of discrimination of 0.9871, as presented in Table III. We compared the forensic and population genetics parameters including no. of haplotypes, unique haplotypes, genetic diversity, random match probability and power of discrimination of the Shin population with the other reported indigenous populations of Pakistan such as Saraiki, Sindhi, Makrani, Pathan, Kashmiri and Hazara, and found that the Shin population had the highest proportion of unique haplotypes reflecting high population heterogeneity in Shins. The large proportion of unique haplotypes in Shin population also corresponded well with their greatest genetic diversity (0.9996) when compared to other ethnic groups of Pakistan, i.e. Pathan (0.9978), Kashmiri (0.9977) Hazara (0.9945), Sindhi (0.9924), Makrani (0.9905) and Saraiki (0.9570) (Rakha et al., 2011, 2016, 2017; Hayat et al., 2015; Siddiqi et al., 2015; Yasmin et al., 2017) (Table IV).

Haplogroup affiliations

The haplogroups observed in the Shin population showed affiliations with different phylogenetic lineages. They were mainly assigned into three continental groups, namely the West Eurasian (59.41%), South Asian (25.32%) and East and Southeast Asian (15.19%) groups. Thus, a high degree of genetic association with West Eurasian lineage was observed as compared to South Asian and South East Asian lineages. The most frequent haplogroups identified in the Shin population were U7a (5.06%), M30 (5.06%) and H32 (5.06%), carried by 15.19% of the population. The rest of the haplogroups observed in the Shin population were C (3.79%), U5a2a (1.27%), H3b6 (1.27%), M3 (2.53%), K1b2 (1.27%), M30c1 (1.27%), M35b1 (1.27%), H1+152(1.27%), T1a+152 (1.27%), M30+16234 (1.27%), H29 (1.27%), M3d (1.27%), T2b5a1 (1.27%), U5a1f1 (1.27%), N5 (1.27%), Z+152 (1.27%), H14a (1.27%), T2 (1.27%), U7 (2.53%), M35b+16304 (1.27%), A+152+16362 (1.27%), P2 (1.27%), M65a+@16311 (2.53%), R5a2 (2.53%), HV14 (1.27%), F2d (2.53%), H1e1a1 (1.27%), H1e1a6 (1.27%), T1a1’3 (1.27%), U4b2 (1.27%), J1b1a1 (1.27%), H3ak (1.27%), U5b2a1a2 (1.27%), U2b2 (2.53%), D4g2a (1.27%), J2b1a (1.27%), H6 (1.27%), F1+16189 (2.53%), M65 (1.27%), HV8 (2.53%), H15a1b (1.27%), H2a2a (1.27%), R8 (1.27%), W+194 (1.27%), HV2a (1.27%), H2a+152 16311 (1.27%), H106 (1.27%), U3a2a (1.27%), G2c (1.27%), H3s (1.27%), M9 (1.27%), F (1.27%) and A2v (1.27%) (Fig. 2, Table V).

The current study revealed that the majority of the haplogroups of the Shin population indicated affiliation with West Eurasian lineage. A similar pattern was observed in other studies conducted on other Pakistani ethnic groups such as the Pathan, Hazara and Kashmiri, Bugti and Laghari, where maximum frequencies of West Eurassian haplogroups were reported. However, the rest of the Pakistani ethnic groups, such as the Gujjar, Araiyn, Bijrani, Chandio, Ghallu, Khosu, Nasrani, Solangi, Laghari, Lashari, Makrani, Saraiki and Sindhi, represented quite contrasting genetic structure and affiliations (Rakha et al., 2011, 2016, 2017; Hayat et al., 2015; Siddiqi et al., 2015; Yasmin et al., 2017; Bhatti et al., 2017, 2018a, b) (Fig. 3). The pronounced prevalence of West Eurasian matrilineal lineages may root back to great historical movements from Europe and Central Asia such as the invasion by the soldiers of Alexander the Great, the Arab and Muslim takeovers, and the era of the British Indian Empire (McElreavey and Quintana-Murci, 2005).

 

CONCLUSION

To the best of our knowledge, this is the first report regarding a forensic dataset of the Shin population including entire mtDNA control region sequences. The results reveal high genetic diversity and low random match probability, predicting the worth of mtDNA profiles of the Shin population for exploring maternal genetic lineages and routine forensic investigations in Pakistan. The outcomes of this study show the West Eurasian

 

Table IV. Comparison of forensic and genetic diversity indices of mtDNA control region of main ethnic groups of Pakistan.

Parameters

Shin

Saraiki

Sindhi

Makrani

Pathan

Kashmiri

Hazara

No. of samples

79

85

88

99

230

317

319

No. of haplotypes

75

63

66

71

192

251

189

No. of unique haplotypes

72

58

50

54

128

201

124

Genetic diversity

0.9996

0.957

0.9924

0.9905

0.9978

0.9977

0.9945

Power of discrimination

0.9871

0.9458

0.9811

0.7172

0.8348

0.7918

0.5925

Random match probability

0.0129

0.0542

0.0188

0.0195

0.0066

0.0054

0.0085

 

haplogroups to be predominant in the Shin population. The data reported in this study will contribute in generation of mtDNA databases in Pakistan and will be beneficial for multipurpose future forensic implications.

 

Table V. Haplogroup frequencies of 79 Shins from Gilgit Baltistan, Pakistan.

Broad haplogroup

Number

Proportion

%

Haplogroup

Number

Proportion %

Possible origin

A

2

3.4

A+152+

16362

1

1.27

East Asia

A2v

1

1.27

East Asia

C

1

1.7

C

3

3.79

East Asia

D

1

1.7

D4g2a

1

1.27

East Asia

F

3

5.2

F

1

1.27

East Asia

F1+16189

2

2.53

East Asia

F2d

2

2.53

East Asia

G

1

1.7

G2c

1

1.27

East Asia

H

15

25.7

H1+152

1

1.27

West Eurasian

H106

1

1.27

West Eurasian

H14a

1

1.27

West Eurasian

H15a1b

1

1.27

West Eurasian

H1e1a1

1

1.27

West Eurasian

H1e1a6

1

1.27

West Eurasian

H29

1

1.27

West Eurasian

H2a+152 16311

1

1.27

West Eurasian

H2a2a

1

1.27

West Eurasian

H2a2a1g

2

2.53

West Eurasian

H32

4

5.06

West Eurasian

H3ak

1

1.27

West Eurasian

H3b6

1

1.27

West Eurasian

H3s

1

1.27

West Eurasian

H6

1

1.27

West Eurasian

HV

3

5.2

HV14

1

1.27

West Eurasian

HV2a

1

1.27

West Eurasian

HV8

2

2.53

West Eurasian

Continued on next column.....

Broad haplogroup

Number

Proportion

%

Haplogroup

Number

Proportion %

Possible origin

J

3

5.2

J1

1

1.27

West Eurasian

J1b1a1

1

1.27

West Eurasian

J2b1a

1

1.27

West Eurasian

K

1

1.7

K1b2

1

1.27

West Eurasian

M

10

17.2

M3

2

2.53

South Asian

M30

4

5.06

South Asian

M30+

16234

1

1.27

South Asian

M30c1

1

1.27

South Asian

M35b+

16304

1

1.27

South Asian

M35b1

1

1.27

South Asian

M3d

1

1.27

South Asian

M65

1

1.27

South Asian

M65a+

@16311

2

2.53

South Asian

M9

1

1.27

South Asian

N

1

1.7

N5

1

1.27

West Eurasian

P

1

1.7

P2

1

1.27

East Asian

R

2

3.4

R5a2

2

2.53

West Eurasian

R8

1

1.27

West Eurasian

T

4

6.9

T1a+152

1

1.27

West Eurasian

T1a1'3

1

1.27

West Eurasian

T2

2

2.53

West Eurasian

T2b5a1

1

1.27

West Eurasian

U

8

13.79

U2b2

2

2.53

South Asian

U3a2a

1

1.27

West Eurasian

U4b2

1

1.27

South Asian

U5a1f1

1

1.27

West Eurasian

U5a2a

1

1.27

West Eurasian

U5b2a1a2

1

1.27

West Eurasian

U7

2

2.53

West Eurasian

U7a

4

5.06

West Eurasian

W

1

1.7

W+194

1

1.27

West Eurasian

Z

1

1.7

Z+152

1

1.27

East Asian

 

ACKNOWLEDGEMENTS

We are grateful to Dr. Muhammad Hassan Siddiqui for his support in sample collection and Dr. Emmanuel William Smith for English language editing.

 

Accession number

The mtDNA control region sequences of Shin population reported in the current study have been submitted to GenBank and are available under MK032930 to MK033007 accession number.

 

Statement of conflict of interest

The authors have declared no conflict of interests regarding the publication of this article.

 

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