Table S2.

Number of observed alleles and locus diversities of 19 single copy Y-STR loci in 270

Pathan samples. Loci were ranked in order of diversity.

Y-STR No. of alleles Diversity

DYS449 12 0.8339

DYS458 9 0.8031

DYS447 11 0.7714

DYS446 9 0.7672

DYS390 8 0.7260

DYS635 9 0.7015

DYS19 5 0.6706

DYS439 5 0.6561

DYS448 6 0.6503

Y-GATA-H4 5 0.5969
a
DYS389b 5 0.5852

DYS437 4 0.5714

DYS438 5 0.5648

DYS391 4 0.5200

DYS456 8 0.5120

DYS393 5 0.4860

DYS389I 4 0.4262

DYS392 7 0.4080

DYS388 7 0.2506
a
DYS389b = DYS389II – DYS389I

1
Table S3. Number of observed haplotypes and diversities of 2 multi-copy Y-STRs in 270 Pathan

samples.

Y-STR No. of haplotypes Diversity

DYS385a/b 40 0.8538

DYS464 46 0.8258

2
Table S4. Change in haplotype distribution after the addition of additional Y-STRs to the Yfiler loci.

The shared haplotypes in the Yfiler system were separated to more specific haplotypes by adding the

mentioned key marker. The resolution pattern indicates the number of haplotypes generated by the

key marker and the number of individuals who belonged to the newly generated haplotype.

17 Yfiler loci 22 Y-STRs

Shared haplotypes No. of samples Resolution pattern Key marker
Haplotype 1 2 1-1 DYS449, DYS464
Haplotype 2 2 -a
Haplotype 3 2 -
Haplotype 4 2 1-1 DYS447
Haplotype 5 2 -
Haplotype 6 2 1-1 DYS388, DYS449
Haplotype 7 2 1-1 DYS446, DYS464
Haplotype 8 2 1-1 DYS449
Haplotype 9 2 1-1 DYS449, DYS464
Haplotype 10 2 1-1 DYS447
Haplotype 11 2 -
Haplotype 12 2 -
Haplotype 13 2 1-1 DYS447, DYS449
Haplotype 14 2 -
Haplotype 15 2 1-1 DYS446
Haplotype 16 2 -
Haplotype 17 2 -
Haplotype 18 2 1-1 DYS464
Haplotype 19 2 1-1 DYS446, DYS449, DYS464
Haplotype 20 2 1-1 DYS446, DYS449
Haplotype 21 2 -
Haplotype 22 2 1-1 DYS446
Haplotype 23 3 -
Haplotype 24 3 1-1-1 DYS446, DYS449, DYS464
Haplotype 25 3 1-2 DYS449
Haplotype 26 5 -
Haplotype 27 6 1-5 DYS449
Haplotype 28 7 1-1-1-1-3 DYS446, DYS449, DYS464
Haplotype 29 7 1-1-5 DYS446, DYS464
Haplotype 30 23 1-1-1-1-1-2-2-2-12 DYS446, DYS447, DYS449, DYS464
Total
30 haplotypes 101 samples 61 haplotypes
a
Individuals belonging to the same haplotype were not separated by any Y-STR combination.

3
Table S5. Haplotype diversities and discriminatory capacities in each haplogroup observed in the Pathans from Pakistan.

Haplogroup C G H J2 K L O3 Q R1a1a R2 R2a T Total

No. of samples 2 38 14 26 1 16 2 14 133 1 19 4 270

Frequency 0.7% 14.1% 5.2% 9.6% 0.4% 5.9% 0.7% 5.2% 49.3% 0.4% 7.0% 1.5% 100.0%

DCa 100.0% 71.1% 100.0% 80.8% - 75.0% 100.0% 85.7% 65.4% - 89.5% 75.0%
17 Yfiler loci
hb 1.0000 0.9616 1.0000 0.9815 - 0.9583 1.0000 0.9780 0.9649 - 0.9883 0.8333

DC 100.0% 84.2%c 100.0% 80.8% - 93.8% 100.0% 92.9% 79.7% - 100.0% 100.0%
22 Y-STRs
h 1.0000 0.9829 1.0000 0.9815 - 0.9917 1.0000 0.9890 0.9892 - 1.0000 1.0000
a
DC, discriminatory capacity.
b
h, haplotype diversity.
c
The increased DC and h by using 22 Y-STRs were written in bold.

4
 Table S6. Pair-wise comparison between the Pathans and neighboring populations.a

Khyber
Pakhtunkhwa, North South Uttar Pradesh,
Afghanistan
Population Pakistan Afghanistan Afghanistan India [Afridi Afghanistan7,13,14 India7,10,17-19 Iran7,20 Pakistan7 Pakistan [Pathan]
[Pathan]7,14
[Yousafzai [Pathan]7,13 [Pathan]7,13 Pathan]7
Pathan]7
Afghanistan
- 0 0.0005 0 0 0.0001 0 0 0 0
[Pathan]
Khyber
Pakhtunkhwa,
Pakistan 0.0493 - 0.0001 0 0 0 0 0 0 0
[Yousafzai
Pathan]
North
Afghanistan 0.0154 0.0364 - 0.0349 0.0001 0.2318 0 0 0.0016 0.0033
[Pathan]
South
Afghanistan 0.0206 0.0469 0.0055 - 0 0.0007 0 0 0 0
[Pathan]
Uttar Pradesh,
India [Afridi 0.0281 0.0445 0.0197 0.0238 - 0 0 0 0.0001 0.0003
Pathan]

Afghanistan 0.0055 0.0381 0.0009 0.0028 0.0183 - 0 0 0 0

India 0.013 0.035 0.0048 0.0108 0.0166 0.0035 - 0 0 0

Iran 0.0132 0.0356 0.0049 0.0108 0.0181 0.0035 0.0006 - 0 0

Pakistan 0.0147 0.021 0.0054 0.0124 0.0173 0.005 0.0019 0.0021 - 0.0005

Pakistan [Pathan] 0.0171 0.0166 0.0075 0.0136 0.0168 0.0075 0.0064 0.0066 0.0029 -
a
P-values are shown above the diagonal and Φst values below the diagonal. References for compared populations were indicated in superscript.

5
Figure S1. MDS plot based on the pair-wise genetic distances between neighboring populations.