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Chapter 4Chapter 4 Results: Analysis of Autosomal...
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Chapter 4Chapter 4Chapter 4Chapter 4 Results: Analysis of Autosomal Results: Analysis of Autosomal Results: Analysis of Autosomal Results: Analysis of Autosomal
MarkersMarkersMarkersMarkers
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 94
ANALYSIS OF AUTOSOMAL MARKERS
4.1. Analysis of Autosomal Markers
The biparently inherited autosomal DNA represents the larger portion of the genome. Of
the estimated 32,000 genes present in the human genome, the majority are located on the
autosomes, while the X chromosome has approximately 1,500 genes, and the Y contains
approximately 78 genes (Venter et al., 2001; Skaletsky et al., 2003). Although these
regions are under functional constraints but the large portion of autosomal DNA contain
neutral variants. Various classes of autosomal markers such as Single Nucleotide
Polymorphism (SNP), Variable Number Tandem Repeats (VNTR), Restriction Fragment
Length Polymorphism (RFLP), Amplified Fragment Length Polymorphism (AFLP),
Retroelements etc., having characteristic features are known which are widely used to
investigate the human population structure and history. In the present investigation Alu
elements belonging to Short Interspersed Nuclear Element (SINE) family of retroelement
class of autosomal markers and SNPs that happens to be located within restriction sites
were used to determine the Chaudhari population structure and its relation to other Indian
populations. The current section highlights the results obtained from the laboratory analysis
and statistical analysis of autosomal markers in the four study groups. The autosomal
markers screened were seven Alu Insertion Deletion (InDel) polymorphisms and seven
unlinked RFLP loci. The detailed description of the markers employed has been given in
the material and method section. Because of technical reasons, numbers of samples
analyzed were different for different markers. Results have been presented in two parts in
the present chapter. The first section deals with findings from the Chaudhari subpopulations
and the second section deals with their analysis with other population groups.
4.2. Findings from the Four Chaudhari Populations
4.2.1. Genotype and Allele Frequency
4.2.1.1. Alu InDel Polymorphisms
4.2.1.1.1. PV92
Table 4.1 presents the genotype and allele frequency data for PV92 locus in the four
Chaudhari subpopulations. Barring Mota Chaudhari, the frequency of heterozygous
4
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
genotype was found to be highest
frequency of genotype homozygous for deletion allele.
homozygous for deletion allele genotype, the homozygous for insertion allele was
found in low frequency except in Pavagadhi Chaudhari in which both homozygo
genotypes were observed in similar
similar distribution pattern of alleles with deletion allele
frequency levels than insertion
insertion allele (+) was in Pavagadhi Chaudhari
Chaudhari (0.430). Both Nana and Mota Chaudhari exhibited
of insertion allele. Figure 4.1 displays the
Table 4.1. Genotype and allele frequency distribution at PV92 locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count
VC NC MC PC
+ + 10 07 06
+ – 23 24 18
– – 17 20 26
Total 50 51 50
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudharib ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, c+ Insertion allele, – Deletion allele
Figure 4.1. Gel photograph showing polymorphism at PV92 locus
Analysis of Autosomal Markers
Structured Chaudhari Tribe of Southern Gujarat
be highest in all the other Chaudhari subgroups, followed by the
homozygous for deletion allele. In comparison to the
homozygous for deletion allele genotype, the homozygous for insertion allele was
y except in Pavagadhi Chaudhari in which both homozygo
observed in similar frequencies. The study populations exhibited
of alleles with deletion allele (–), displaying higher
n insertion allele (+). It was observed that the highest frequency
insertion allele (+) was in Pavagadhi Chaudhari (0.500), followed by that in
. Both Nana and Mota Chaudhari exhibited almost similar proportion
displays the polymorphism at PV92 locus.
Genotype and allele frequency distribution at PV92 locus among the Chaudhari
Frequency (%) Allelec Frequency
PC VC NC MC PC VC NC
10 20.0 13.7 12.0 24.4 + 0.430 0.373
21 46.0 47.1 36.0 51.2 – 0.570 0.627
10 34.0 39.2 52.0 24.4
41 100.0 100.0 100.0 100.0 1.000 1.000
VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari
Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele
Gel photograph showing polymorphism at PV92 locus
Autosomal Markers
95
, followed by the
In comparison to the
homozygous for deletion allele genotype, the homozygous for insertion allele was
y except in Pavagadhi Chaudhari in which both homozygous
. The study populations exhibited a
displaying higher
the highest frequency of
, followed by that in Valvi
similar proportion
Genotype and allele frequency distribution at PV92 locus among the Chaudhari
Frequency
MC PC
0.300 0.500
0.700 0.500
1.000 1.000
Homozygous for deletion allele
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 96
4.2.1.1.2. FXIIIB
Table 4.2 presents the genotype and allele frequency data for FXIIIB locus in the four
Chaudhari subpopulations. In all the groups heterozygous genotype were found in low
frequency compared to the homozygote genotypes. The maximum and minimum
frequency of genotype homozygous for insertion allele was observed in Nana
Chaudhari (51.00%) and Mota Chaudhari (16.00%) respectively. However, the trend
was found to be reversed in the case of genotype homozygous for deletion allele. Its
highest frequency was observed in Mota Chaudhari (72.00%) in contrast to its least
frequency in Nana Chaudhari (25.50%). Frequency of the insertion allele (+) was found
to be higher than the frequency of the deletion allele in all the populations except Mota
Chaudhari. Figure 4.2 displays the polymorphism at FXIIIB locus.
Table 4.2. Genotype and allele frequency distribution at FXIIIB locus among the
Chaudhari subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 20 26 08 19 40.0 51.0 16.0 46.3 + 0.550 0.627 0.220 0.573
+ – 15 12 06 09 30.0 23.5 12.0 22.0 – 0.450 0.373 0.780 0.427
– – 15 13 36 13 30.0 25.5 72.0 31.7
Total 50 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Insertion allele, – Deletion allele
Figure 4.2. Gel photograph showing polymorphism at FXIIIB locus
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
4.2.1.1.3. D1
Genotype and allele frequency dist
The frequency of genotype homozygous
proportion in all the four populations. The highest frequency of
for insertion allele was found in Valvi Chaudhari
than frequency observed in Nana Chaudhari
lowest frequency of the genotype
genotype distribution, frequency of the deletion allele (
proportion than insertion allele
polymorphism at D1 locus.
Table 4.3. Genotype and allele frequency distribution at D1
subgroups
Populationa
Genotypeb
Count
VC NC MC PC
+ + 15 15 05
+ – 15 10 21
– – 19 26 24
Total 49 51 50
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudharib ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, c+ Insertion allele, – Deletion allele
Figure 4.3. Gel photograph showing polymorphism at D1 locus
650bp 333bp +
Analysis of Autosomal Markers
Structured Chaudhari Tribe of Southern Gujarat
allele frequency distribution pattern at D1 locus is presented in Table 4.3.
genotype homozygous for deletion allele was observed in
all the four populations. The highest frequency of genotype homozygous
was found in Valvi Chaudhari (30.60%), which was slightly higher
frequency observed in Nana Chaudhari (29.40%). Mota Chaudhari displayed the
the genotype homozygous for insertion allele. Similar to
frequency of the deletion allele (–) was noticed in higher
proportion than insertion allele (+) in all the populations. Figure 4.3
e frequency distribution at D1 locus among the
Frequency (%) Allelec Frequency
PC VC NC MC PC VC NC
07 30.6 29.4 10.0 17.1 + 0.459 0.329
15 30.6 19.6 42.0 36.6 – 0.541 0.608
19 38.8 51.0 48.0 46.3
41 100.0 100.0 100.0 100.0 1.000 1.000
VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari
Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele
Gel photograph showing polymorphism at D1 locus
650bp 333bp + – – – ++
Autosomal Markers
97
sented in Table 4.3.
observed in higher
genotype homozygous
which was slightly higher
Chaudhari displayed the
. Similar to the
) was noticed in higher
Figure 4.3 displays
locus among the Chaudhari
Frequency
MC PC
0.310 0.354
0.690 0.646
1.000 1.000
Homozygous for deletion allele
L
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 98
4.2.1.1.4. APO
Table 4.4 presents the genotype and allele frequency data at APO locus in the study
populations. The distribution pattern showed the highest frequency of genotype
homozygous for insertion allele followed by the heterozygous genotype and the
genotype homozygous for deletion allele. However, in Valvi Chaudhari heterozygote
genotypes outnumbered genotype homozygous for insertion allele by 10.00%.
Similarly, the frequency for insertion allele was found in higher proportions in all the
populations as compared to the deletion allele. The frequency of insertion allele was
found to vary between 0.650 among Valvi Chaudhari and 0.775 among Nana
Chaudhari. Figure 4.4 shows polymorphism at APO locus.
Table 4.4. Genotype and allele frequency distribution at APO locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 20 30 27 26 40.0 58.5 54.0 63.41 + 0.650 0.775 0.700 0.768
+ – 25 19 16 11 50.0 37.3 32.0 26.83 – 0.350 0.225 0.300 0.232
– – 05 02 07 04 10.0 3.92 14.0 9.76
Total 50 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Insertion allele, – Deletion allele
Figure 4.4. Gel photograph showing polymorphism at APO locus
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
4.2.1.1.5. ACE
Table 4.5 presents data pertaining to genotype and allele frequ
populations at ACE locus. Out of the two
genotype homozygous for insertion
genotype homozygous for deletion allele. However, in comparison to
genotype, the frequencies of homozygous genotypes were
frequency distribution showed
allele. Out of the four Chaudhari sub
to be highest in Nana Chaudhari (0.618
Pavagadhi Chaudhari and Valvi Chaudhari which
insertion allele. Figure 4.5 shows polymorphism at ACE locus.
Table 4.5. Genotype and allele frequency distribution
subgroups
Populationa
Genotypeb
Count
VC NC MC PC
+ + 19 20 19
+ – 17 23 20
– – 14 08 11
Total 50 51 50
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudharib ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, c+ Insertion allele, – Deletion allele
Figure 4.5. Gel photograph showing polymorphism at ACE locus
190bp 490bp – –
Analysis of Autosomal Markers
Structured Chaudhari Tribe of Southern Gujarat
Table 4.5 presents data pertaining to genotype and allele frequency among study
Out of the two homozygous combinations, the frequency of
insertion was observed in higher proportion than that of
for deletion allele. However, in comparison to the heterozygous
homozygous genotypes were found to be less.
frequency distribution showed a higher frequency of insertion allele than the
allele. Out of the four Chaudhari subgroups, the frequency of insertion allele was found
highest in Nana Chaudhari (0.618) followed by that in Mota Chaudhari,
Pavagadhi Chaudhari and Valvi Chaudhari which showed almost similar proportion
shows polymorphism at ACE locus.
Genotype and allele frequency distribution at ACE locus among the
Frequency (%) Allelec Frequency
PC VC NC MC PC VC NC
15 38.0 39.2 38.0 36.6 + 0.550 0.618
16 34.0 45.1 40.0 39.0 – 0.450 0.382
10 28.0 15.7 22.0 24.4
41 100.0 100.0 100.0 100.0 1.000 1.000
VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele
Gel photograph showing polymorphism at ACE locus
– + – + +
Autosomal Markers
99
ency among study
frequency of
observed in higher proportion than that of
the heterozygous
found to be less. The allele
than the deletion
the frequency of insertion allele was found
Mota Chaudhari,
almost similar proportion of
ACE locus among the Chaudhari
Frequency
MC PC
0.580 0.561
0.420 0.439
1.000 1.000
Homozygous for deletion allele
L
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 100
4.2.1.1.6. CD4
Genotype and allele frequency distribution for CD4 locus among populations under
study is given in Table 4.6. In all the populations genotype homozygous for insertion
allele was present in overwhelming frequencies than the other genotypes. Genotype
homozygous for deletion allele was found to be absent in Nana and Pavagadhi
Chaudhari populations. The deletion allele (–) in decreasing order of frequency was
observed in Mota Chaudhari, Valvi Chaudhari, Pavagadhi Chaudhari and Nana
Chaudhari. Figure 4.6 shows polymorphism at CD4 locus.
Table 4.6. Genotype and allele frequency distribution at CD4 locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 43 46 41 35 86.0 90.2 82.0 85.4 + 0.920 0.951 0.900 0.927
+ – 06 05 08 06 12.0 09.8 16.0 14.6 – 0.080 0.049 0.100 0.073
– – 01 00 01 00 02.0 00.0 02.0 00.0
Total 50 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Insertion allele, – Deletion allele
Figure 4.6. Gel photograph showing polymorphism at CD4 locus
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 101
4.2.1.1.7. PLAT
Data on the genotype and allele frequencies at PLAT locus is given in Table 4.7. It was
observed that heterozygous genotype was most frequent compared to homozygous
genotypes in all the populations. The minimum frequency of (+–) genotype was
observed in Mota Chaudhari (40.00%) and its maximum frequency was seen in Valvi
Chaudhari (60.00%). In case of genotype homozygous for deletion allele, the opposite
trend was seen, with higher frequency in Mota Chaudhari (24.00%) and lowest in Valvi
Chaudhari (6.00%). The allele frequency distribution pattern revealed that Pavagadhi,
Valvi and Nana Chaudhari showed almost similar frequency of insertion allele (0.622-
0.640) which was slightly higher than the frequency observed in Mota Chaudhari
(0.560). Figure 4.7 shows polymorphism at the PLAT locus.
Table 4.7. Genotype and allele frequency distribution at PLAT locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 17 20 18 16.0 34.0 40.0 36.0 39.0 + 0.640 0.640 0.560 0.622
+ – 30 24 20 19.0 60.0 48.0 40.0 46.4 – 0.360 0.360 0.440 0.378
– – 03 06 12 06.0 06.0 12.0 24.0 14.6
Total 50 50 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Insertion allele, – Deletion allele
Figure 4.7. Gel photograph showing polymorphism at PLAT locus
- - ++ + - L
260bp 570bp
A Genomic Study on the Sub
The overall allele frequency distribution
markers in the study populations is presented in Figure 4.8. The comparison revealed
slight variation in the allele
CD4 and PLAT loci in the Chaudhari subgroups.
Figure 4.8. Frequency distribution of derived (mutant) allele
except CD4} at
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
PV92 FXIII B
Fe
wq
ue
ncy
of
de
riv
ed
all
ele
Analysis of
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
allele frequency distribution pattern observed at the
markers in the study populations is presented in Figure 4.8. The comparison revealed
slight variation in the allele frequency distribution at the loci examined, except
PLAT loci in the Chaudhari subgroups.
Frequency distribution of derived (mutant) alleles {Insertion (+) for all,
except CD4} at Alu InDel loci among the four study groups
FXIII B DI APO ACE CD4 PLAT
Loci analysed
Valvi Chaudhari
Nana Chaudhari
Mota Chaudhari
Pavagadhi Chaudhari
Analysis of Autosomal Markers
102
the seven Alu InDel
markers in the study populations is presented in Figure 4.8. The comparison revealed
loci examined, except ACE,
{Insertion (+) for all,
InDel loci among the four study groups
Valvi Chaudhari
Nana Chaudhari
Mota Chaudhari
Pavagadhi Chaudhari
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 103
4.2.1.2. Restriction Fragment Length Polymorphisms (RFLPs)
4.2.1.2.1. ESR
Table 4.8 presents the allele and genotype frequency distribution data for ESR locus in
four Chaudhari subpopulations. Barring Mota Chaudhari, all other Chaudhari
subpopulations showed a similar trend of the distribution of genotypes with higher
frequency of genotype heterozygous for the presence and absence of restriction site
followed by that of genotype homozygous for presence of restriction site. Except in
Nana Chaudhari (0.373), the allele for presence of restriction site (+) was observed in
higher frequency than the allele for the absence of restriction site (–) in all the
populations. Figure 4.9 shows polymorphism at ESR locus.
Table 4.8. Genotype and allele frequency distribution at ESR locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 21 16 18 14 42.0 32.0 36.0 34.2 + 0.650 0.373 0.520 0.573
+ – 23 22 16 19 46.0 44.0 32.0 46.3 – 0.350 0.627 0.480 0.427
– – 06 12 16 08 12.0 24.0 32.0 19.5
Total 50 50 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Restriction site present, – Restriction site absent
Figure 4.9. Gel photograph showing polymorphism at ESR locus
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 104
4.2.1.2.2. NAT
Table 4.9 presents the genotype and allele frequency data at NAT locus observed in the
study populations. The genotype pattern showed that three out of the four groups had a
higher frequency of (++) genotype, followed by that of (+–) genotype. Genotype
homozygous for the absence of restriction site showed the least frequency in all the
groups. The allele frequency for presence of restriction site in Valvi, Mota and
Pavagadhi Chaudhari was found to range from 0.650–0.695 whereas, it lagged behind
in Nana Chaudhari (0.529). Likewise, the frequency of allele for absence of a restriction
site in Nana Chaudhari was found to stand apart from the other Chaudhari groups which
showed almost the similar proportions of (–) allele. Figure 4.10 shows polymorphism
at NAT locus.
Table 4.9. Genotype and allele frequency distribution at NAT locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 23 14 24 20 46.0 27.0 48.0 49.0 + 0.650 0.529 0.650 0.695
+ – 19 26 17 17 38.0 51.0 34.0 41.2 – 0.350 0.471 0.350 0.304
– – 08 11 09 04 16.0 22.0 18.0 09.8
Total 50 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Restriction site present, – Restriction site absent
Figure 4.10. Gel photograph showing polymorphism at NAT locus
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 105
4.2.1.2.3. T2
Genotype and allele frequency data for T2 locus is given in Table 4.10. From the table
it is evident that the heterozygous genotype dominated the genotype distribution pattern
in all the four groups. Out of the two homozygous genotypes, all Chaudhari subgroups
showed higher frequency of (++) genotype than (– –) genotype. Similarly, allele for
presence of restriction site was found in higher frequency than the allele for the absence
of a restriction site. Figure 4.11 shows polymorphism at T2 locus.
Table 4.10. Genotype and allele frequency distribution at T2 locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 14 20 14 13 28.0 39.2 28.0 31.7 + 0.530 0.647 0.570 0.610
+ – 25 26 29 24 50.0 51.0 58.0 58.5 – 0.470 0.353 0.430 0.390
– – 11 05 07 04.0 22.0 09.8 14.0 09.8
Total 50 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Restriction site present, – Restriction site absent
Figure 4.11. Gel photograph showing polymorphism at T2 locus
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 106
4.2.1.2.4. LPL
Table 4.11 illustrates the genotype and allele distribution data at LPL locus in the study
populations. It was observed that the heterozygous genotype occurred with greater
frequency than both homozygous genotypic combinations in all the groups. Where the
frequency of genotype homozygous for presence of restriction site was found to be
more frequent than the genotype homozygous for absence of restriction site in Valvi
and Pavagadhi Chaudhari, it was the other way round in Nana and Mota Chaudhari. In
terms of allele frequency distribution, both Valvi and Nana Chaudhari displayed similar
allele frequencies on one hand and Mota and Pavagadhi Chaudhari on the other. Figure
4.12 shows polymorphism at LPL locus.
Table 4.11. Genotype and allele frequency distribution at LPL locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 20 07 15 12 40.8 13.7 30.0 29.3 + 0.643 0.647 0.500 0.561
+ – 23 22 20 22 47.0 43.1 40.0 53.7 – 0.357 0.353 0.500 0.439
– – 06 22 15 07 12.2 43.2 30.0 17.0
Total 49 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Restriction site present, – Restriction site absent
Figure 4.12. Gel photograph showing polymorphism at LPL locus
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 107
4.1.1.2.5. PSCR
Data on genotype and allele frequency for PSCR locus in populations under study is
presented in Table 4.12. Genotype with two copies of the allele for presence of
restriction site was present in least frequency in all the groups ranging between 6.00%
in Valvi Chaudhari and 24.00% in Mota Chaudhari. Genotype with both alleles, one for
the presence of restriction site and one for the absence of restriction site, was most
frequent genotype in all the groups. The frequency distribution of the two alleles was
found to be similar in all the groups, with higher frequencies observed for the deletion
allele. Figure 4.13 shows polymorphism at PSCR locus.
Table 4.12. Genotype and allele frequency distribution at PSCR locus among the Chaudhari
subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 03 09 12 04 06.0 17.7 24.0 09.8 + 0.440 0.431 0.490 0.378
+ – 38 26 25 23 76.0 51.0 50.0 56.1 – 0.560 0.569 0.510 0.622
– – 09 16 13 14 18.0 31.3 26.0 34.1
Total 50 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Restriction site present, – Restriction site absent
Figure 4.13. Gel photograph showing polymorphism at PSCR locus
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 108
4.2.1.2.6. ADH2
Table 4.13 illustrates the genotype and allele frequency data observed at ADH2 locus in
four Chaudhari subgroups. (++) genotype occurred more frequently in Valvi and Nana
Chaudhari as compared to Mota and Pavagadhi Chaudhari. (+–) genotype frequency
was found to range from 31.40% in Nana Chaudhari to 56.10% in Pavagadhi
Chaudhari. The allele for absence of restriction site was present in higher frequency
than the allele for presence of restriction site in all the groups. Figure 4.14 shows
polymorphism at ADH2 locus.
Table 4.13. Genotype and allele frequency distribution at ADH2 locus among the
Chaudhari subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 08 08 03 04 16.0 15.6 06.0 09.8 + 0.370 0.314 0.240 0.378
+ – 21 16 18 23 42.0 31.4 36.0 56.1 – 0.630 0.686 0.76 0.622
– – 21 27 29 14 42.0 53.0 58.0 34.1
Total 50 51 50 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Restriction site present, – Restriction site absent
Figure 4.14. Gel photograph showing polymorphism at ADH2 locus
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 109
4.2.1.2.7. ALAD
Data on the genotype and allele frequencies at ALAD locus in Chaudhari subgroups is
presented in Table 4.14. Barring Valve Chaudhari, all other Chaudhari subgroups
showed the high frequency of (– –) genotype followed by that of (+ –) genotype. The
frequency of genotype with two copies of the allele for presence of restriction site was
observed to be least in all the groups. The allele frequency distribution pattern showed
that the allele for absence of restriction site was more frequent ranging from 0.633 to
0.847 compared to the allele for presence of restriction site which was found to be
ranging from 0.153 to 0.367. Figure 4.15 shows polymorphism at ALAD locus.
Table 4.14. Genotype and allele frequency distribution at ALAD locus among the
Chaudhari subgroups
Populationa
Genotypeb
Count Frequency (%) Allelec Frequency
VC NC MC PC VC NC MC PC VC NC MC PC
+ + 03 03 01 02 06.2 05.9 2.04 4.88 + 0.367 0.206 0.153 0.171
+ – 30 15 13 10 61.2 29.4 26.53 24.39 – 0.633 0.794 0.847 0.829
– – 16 33 35 29 32.6 64.7 71.43 70.73
Total 49 51 49 41 100.0 100.0 100.0 100.0 1.000 1.000 1.000 1.000
a VC=Valvi Chaudhari; NC=Nana Chaudhari; MC=Mota Chaudhari; PC=Pavagadhi Chaudhari b ++ Homozygous for insertion allele, +– Heterozygous for insertion and deletion alleles, – – Homozygous for deletion allele c+ Restriction site present, – Restriction site absent
Figure 4.15. Gel photograph showing polymorphism at ALAD locus
A Genomic Study on the Sub
Figure 4.16 presents the comparison of allele frequencies observed
loci in the four study groups
distribution at almost all the loci among the
Figure 4.16. Frequency distribution of allele
RFLP loci among the four study groups
4.2.2. Hardy–Weinberg
The allele frequency estimates
goodness–of–fit test to determine if the observed genotype frequencies in the study
populations deviate from the Hardy
statistical tests were being performed
correction, an adjustment made to
After applying Bonferroni’s correction for multiple
data, the observed genotype frequencies were found to be in
expected Hardy–Weinberg proportions for all the loci except
Mota and Pavagadhi Chaudha
Valvi Chaudhari. The overall pattern
the Hardy–Weinberg expectations.
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
ESR NAT
Fre
qu
en
cy a
f a
lle
le f
or
the
pre
sen
ce o
f
Re
stri
ctio
n s
ite
Analysis of
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
Figure 4.16 presents the comparison of allele frequencies observed
loci in the four study groups. The figure indicated the differences in allele frequency
almost all the loci among the four Chaudhari subgroup.
Frequency distribution of alleles for presence of restriction site at the
RFLP loci among the four study groups
Weinberg Equilibrium
The allele frequency estimates at the examined loci were subjected to chi
fit test to determine if the observed genotype frequencies in the study
populations deviate from the Hardy–Weinberg proportions (Table 4.15)
statistical tests were being performed simultaneously on each population
an adjustment made to p value, was applied to avoid false positive results
applying Bonferroni’s correction for multiple comparisons on
data, the observed genotype frequencies were found to be in agreement with their
Weinberg proportions for all the loci except at FXIII
and Pavagadhi Chaudhari, at D1 locus in Nana Chaudhari and at PSCR
he overall pattern of genotype distribution was in accordance with
Weinberg expectations.
NAT T2 LPL PSCR ADH2 ALAD
Loci analysed
Valvi Chaudhari
Nana Chaudhari
Mota Chaudhari
Pavagadhi Chaudhari
Analysis of Autosomal Markers
110
at the seven RFLP
differences in allele frequency
subgroup.
for presence of restriction site at the
at the examined loci were subjected to chi–square
fit test to determine if the observed genotype frequencies in the study
(Table 4.15). Since multiple
population, Bonferroni’s
to avoid false positive results.
on Alu and RFLP loci
agreement with their
at FXIIIB locus in Nana,
and at PSCR locus in
of genotype distribution was in accordance with
Valvi Chaudhari
Nana Chaudhari
Mota Chaudhari
Pavagadhi Chaudhari
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 111
Table 4.15. Chi square (χ2) test for estimation of Hardy–Weinberg Equilibrium at Alu
InDel and RFLP loci among the four subdivisions of Chaudhari population
Locus χ2
Estimates
Valvi
Chaudhari
Nana
Chaudhari
Mota
Chaudhari
Pavagadhi
Chaudhari
PV92 0.189 0.002 1.021 0.024
FXIIIB 7.759 12.582* 21.147* 12.464*
D1 7.211 17.675* 0.016 1.635
APO 0.489 0.226 2.834 2.490
ACE 4.902 0.104 1.601 1.769
CD4 1.707 0.135 0.617 0.255
PLAT 4.562 0.086 1.773 0.008
ESR 0.006 0.653 6.443 0.114
NAT 1.358 0.027 3.194 0.019
PSCR 14.699* 0.078 0.000 1.525
ALAD 4.930 0.515 0.026 0.788
T2 0.001 0.688 1.677 2.168
LPL 0.024 0.157 2.000 0.327
ADH2 0.491 3.757 0.008 1.525
* χ2 statistically significant at pcorrected <0.0035, df=1, after applying Bonferroni’s correction.
4.2.3. Heterozygosity
Table 4.16 illustrates the heterozygosity levels observed at 14 studied loci in thr four
Chaudhari subgroups. The heterozygosity analysis revealed overall high heterozygosity
level in all the four groups, ranging from 0.421 in Mota Chaudhari to 0.457 in Valvi
Chaudhari. Examination of heterozygosity at individual loci revealed variation between
the study groups. Minimum heterozygosity level was observed at CD4 locus in all the
populations. Whereas, maximum heterozygosity value (0.500) was seen at various loci
in the study populations. Loci FXIIIB, D1, ACE and T2 exhibited highest
heterozygosity in Valvi Chaudhari. Nana Chaudhari showed similar values at ESR and
NAT loci. Although, Mota Chaudhari had the lowest average heterozygosity compared
to the other subgroups, three loci namely, ESR, PSCR and LPL were found to harbor
the maximum heterozygosity in Mota Chaudhari. Only one locus namely, PV92 was
observed to show highest heterozygosity value in Pavagadhi Chaudhari.
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 112
Table 4.16. Heterozygosity estimates and their Standard Errors for Alu InDel and RFLP
among the four subdivisions of Chaudhari population
Locus Heterozygosity ± Standard Error
Valvi
Chaudhari
Nana
Chaudhari
Mota
Chaudhari
Pavagadhi
Chaudhari
PV92 0.495±0.015 0.473±0.025 0.424±0.037 0.500±0.009
FXIIIB 0.500±0.012 0.473±0.025 0.347±0.047 0.495±0.018
D1 0.500±0.011 0.481±0.022 0.432±0.036 0.463±0.032
APO 0.460±0.029 0.353±0.046 0.424±0.037 0.360±0.050
ACE 0.500±0.012 0.477±0.024 0.492±0.017 0.499±0.016
CD4 0.149±0.045 0.094±0.039 0.182±0.048 0.137±0.049
PLAT 0.465±0.027 0.465±0.028 0.498±0.014 0.476±0.027
ESR 0.460±0.029 0.500±0.011 0.500±0.008 0.495±0.018
NAT 0.460±0.029 0.500±0.009 0.460±0.029 0.429±0.040
PSCR 0.498±0.014 0.495±0.015 0.500±0.007 0.476±0.027
ALAD 0.469±0.026 0.330±0.047 0.262±0.051 0.287±0.055
T2 0.500±0.009 0.461±0.029 0.495±0.016 0.482±0.025
LPL 0.464±0.028 0.461±0.029 0.500±0.007 0.499±0.016
ADH2 0.471±0.026 0.435±0.035 0.368±0.045 0.476±0.027
Average
Heterozygosity 0.457±0.023 0.429±0.027 0.421±0.028 0.434±0.029
4.2.4. Genetic Differentiation among Populations
4.2.4.1. Gene Diversity Estimate
Table 4.17 presents the gene diversity estimates based on examined loci in Chaudhari
subgroups. Gene diversity analysis in the four subgroups revealed an overall high levels
of heterozygosity (HT=0.441). It was observed that on an average each subgroup
harbored significant amount of heterozygosity (HS=0.431). Estimate of inter population
difference (GST) was found to be 2.30%. The four populations seemed to differ most at
FXIIIB locus (GST=10.20%) and least at ACE locus (0.30%).
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 113
Table 4.17. Gene diversity estimates at the studied Alu InDel and RFLP loci among the
four subdivisions of Chaudhari population
Locus HT HS GST
PV92 0.480 0.469 0.023
FXIIIB 0.500 0.449 0.102
D1 0.471 0.465 0.013
APO 0.400 0.395 0.013
ACE 0.488 0.487 0.003
CD4 0.140 0.139 0.005
PLAT 0.473 0.471 0.005
ESR 0.490 0.485 0.010
NAT 0.466 0.458 0.016
PSCR 0.491 0.488 0.006
ALAD 0.348 0.334 0.041
T2 0.484 0.480 0.008
LPL 0.500 0.477 0.045
ADH2 0.439 0.433 0.014
All Loci 0.441 0.431 0.023
4.2.4.2. Genetic Differentiation using Wright’s F–Statistics
Table 4.18 presents results of fixation–index–based measures of departure from expected
heterozygosity, commonly used to quantify population structure. At the first level, FIS
was estimated which compared average observed heterozygosity of individuals in each
subpopulation and the average Hardy–Weinberg expected heterozygosity for all
subpopulations. From the table it was observed that the subpopulations on average had
7.92% deficiency of heterozygotes as expected if there was nonrandom mating taking
place. The next level in the hierarchy was the average expected heterozygosity for
subpopulations compared with expected heterozygosity for the total population i.e. FST.
The result indicated that there was 2.29% less heterozygosity on average for the four
subpopulations compared with the heterozygosity expected in case of panmixia. The
final level in the hierarchy was FIT. The Level of FIT indicated that the homozygosity was
10.04% greater than would be expected in a randomly mating, panmictic population with
the same allele frequencies.
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 114
Table 4.18. Estimates of F–Statistics at the studied Alu InDel and RFLP loci among the
four subdivisions of Chaudhari population
Locus FIS FST FIT
PV92 0.0399 0.0225 0.0615
FXIIIB 0.5126 0.1023 0.5625
D1 0.3069 0.0128 0.3157
APO 0.0756 0.0132 0.0878
ACE 0.1879 0.0027 0.1901
CD4 0.0570 0.0048 0.0615
PLAT –0.0358 0.0044 –0.0312
ESR 0.1324 0.0100 0.1411
NAT 0.1024 0.0163 0.1170
PSCR –0.1932 0.0064 –0.1855
ALAD –0.0468 0.0462 0.0016
T2 –0.1323 0.0079 –0.1233
LPL 0.0373 0.045 0.0806
ADH2 0.0446 0.0139 0.0578
All loci 0.0792 0.0229 0.1004
4.2.4.3. Analysis of Molecular Variance (AMOVA)
The analysis of molecular variance across the four populations on the basis of allele
frequency data on 14 autosomal loci showed 98.39% of variability due to within
population differences and 1.61% (p<0.05) due to differences among the Chaudhari
subpopulations. The results have been presented with other AMOVA results in
Table 4.23 at the end of the chapter.
4.2.4.4. Genetic Distance and Neighbor Joining Tree
To find out the genetic relation among the study groups, genetic distances were
computed based on the allele frequencies observed at 14 autosomal loci. From the Table
4.19, it is evident that the highest genetic proximity i.e least genetic distance was
between Nana Chaudhari and Mota Chaudhari (0.003) followed by that between
Pavagadhi and Nana Chaudhari (0.005). Mota Chaudhari showed the highest genetic
distance with Valvi Chaudhari. The dendrogram (Figure 4.17) generated using the data
indicated the genetic proximity between Nana and Mota Chaudhari by clustering the
two populations in one group.
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 115
Table 4.19. Genetic distance matrixa based on 14 autosomal loci among the four
Chaudhari subgroups
Valvi
Chaudhari
Nana
Chaudhari
Mota
Chaudhari
Pavagadhi
Chaudhari
Valvi Chaudhari 0 0.0106 0.0137 0.0047
Nana Chaudhari 0.0161 0 0.0204 0.0060
Mota Chaudhari 0.0254 0.0030 0 0.0157
Pavagadhi Chaudhari 0.0237 0.0050 0.0190 0
aStandard genetic distance values are in 10¯
1 codon difference per locus along with standard error above
the diagonal.
Figure 4.17. Neighbor–Joining tree showing genetic relation between the Chaudhari
subdivisions
4.3. Comparison of Study Populations with Other Population Groups
The following section presents the result obtained from the analysis of the study
populations along with other Indian populations. Based on the ethno-historical
information and availability of comparable data from the secondary sources two data
sets were created. Dataset 1 included allele frequency data at autosomal loci among the
nine Indo–European speaking tribes of Gujarat, including the study populations. The
allele frequency data used for the analysis was compiled from Kshatriya et al. (2011).
Dataset 2 included allele frequency data at autosomal loci among Indo–European
speaking groups of Gujarat and other populations of India, compiled from various
published studies. These datasets were subjected to diverse analytical tools to examine
firstly, the genetic structure of Indo–European speaking tribes of Gujarat and secondly,
to understand the genetic affinities of these Indo–European speaking tribal populations
of Gujarat with other Indian populations.
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 116
4.3.1. Dataset 1: Genetic Relation between Neighbouring Indo–European (IE)
Speaking Tribal Populations of Gujarat
The first comparison was based on the allele frequency data of 14 biallelic autosomal
markers in the four study groups and five neighbouring Indo–European speaking tribal
groups namely, Dhodia, Dubla, Konkana, Vasava and Gamit of Gujarat. The allele
frequency data used for the analysis was compiled from Kshatriya et al. (2011). Allele
frequency data used for this analysis is given in Appendix XIII.
4.3.1.1. Heterozygosity
Table 4.20 presents the heterozygosity estimates among the nine Indo–European
speaking tribal populations of Gujarat based on the allele frequencies of 14 autosomal
markers. Although, the heterozygosity values of the majority of the loci were found to
be high in most of the populations, certain loci such as APO, CD4, ALAD and ADH2
showed low heterozygosity in some of the populations. Overall, the average
heterozygosity was found to be substantially high in all the groups, which varied from
0.404 in Konkana to 0.457 in Valvi Chaudhari.
Table 4.20. Heterozygosity estimates at the studied 14 autosomal loci among the nine
Indo–European speaking tribal groups of Gujarat
Locus Valvi
Chaudhari
Nana
Chaudhari
Mota
Chaudhari
Pavagadhi
Chaudhari
Dhodia Dubla Konkana Vasava Gamit
PV92 0.495 0.473 0.424 0.500 0.499 0.500 0.500 0.498 0.485
FXIIIB 0.500 0.473 0.347 0.495 0.484 0.484 0.495 0.497 0.481
D1 0.500 0.481 0.432 0.463 0.456 0.433 0.437 0.431 0.423
APO 0.460 0.353 0.424 0.360 0.280 0.305 0.339 0.318 0.394
ACE 0.500 0.477 0.492 0.499 0.462 0.400 0.498 0.375 0.428
CD4 0.149 0.094 0.182 0.137 0.091 0.116 0.204 0.208 0.095
PLAT 0.465 0.465 0.498 0.476 0.456 0.479 0.496 0.451 0.495
ESR 0.460 0.500 0.500 0.495 0.480 0.476 0.495 0.497 0.492
NAT 0.460 0.500 0.460 0.429 0.456 0.466 0.461 0.460 0.431
PSCR 0.498 0.495 0.500 0.476 0.500 0.492 0.478 0.497 0.496
ALAD 0.469 0.330 0.262 0.287 0.353 0.229 0.309 0.436 0.196
T2 0.500 0.461 0.495 0.482 0.500 0.487 0.485 0.455 0.485
LPL 0.464 0.461 0.500 0.499 0.497 0.499 0.463 0.500 0.487
ADH2 0.471 0.435 0.368 0.476 0.458 0.416 0.000 0.436 0.438
All loci 0.457 0.429 0.421 0.434 0.427 0.413 0.404 0.433 0.416
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 117
4.3.1.2. Genetic Differentiation among Populations
4.3.1.2.1. Gene Diversity Estimate
Table 4.21 presents data on genomic diversity analysis for 14 loci among the Indo-
European speaking tribal populations from Gujarat. From the table it was observed that
the total average heterozygosity among the tribes of Gujarat was high (0.433). Most of
this genomic diversity could be attributed to individual variations within the population as
reflected by high HS value (0.423). Whereas, 2.20% of the total genetic diversity
accounted for variation between the populations (GST). Maximum genetic differentiation
between the populations was observed with respect to FXIIIB and ADH2 loci (5.80%).
At loci ESR and PSCR minimum differentiation between the populations was seen.
Table 4.21. Gene diversity analysis at the studied 14 autosomal loci among the nine Indo–
European speaking tribal groups of Gujarat
4.3.1.2.2. Analysis of Molecular Variance (AMOVA)
Considering all the Indo–European speaking tribes of Gujarat as one group, the analysis
of molecular variance across the populations on the basis of allele frequency data on 14
autosomal loci showed 99.21% of variability due to within population differences and
HT HS GST
PV92 0.494 0.484 0.020
FXIIIB 0.500 0.471 0.058
D1 0.453 0.449 0.010
APO 0.363 0.357 0.017
ACE 0.471 0.457 0.031
CD4 0.143 0.141 0.010
PLAT 0.477 0.473 0.007
ESR 0.490 0.487 0.006
NAT 0.460 0.456 0.009
PSCR 0.494 0.491 0.006
ALAD 0.331 0.317 0.039
T2 0.486 0.481 0.010
LPL 0.497 0.484 0.027
ADH2 0.411 0.387 0.058
All loci 0.433 0.423 0.022
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 118
0.79% (p<0.05) due to differences among Gujarat populations. The results have been
presented with other AMOVA results in Table 4.23 at the end of the chapter.
4.3.1.3. Population Structure and Gene Flow
The Harpending and Ward (1982) model for population structure and gene flow was
employed to understand the population structure and the level of gene flow among the
Indo–European speaking tribal groups of Gujarat. The model is based on regression of
heterozygosity on genetic distance from the gene frequency centroid. Data on average
heterozygosity (Hi) and the genetic distances from the centroid (rii) in the studied
groups is given in Table 4.22. It was seen that average heterozygosity in the pooled
population (0.432) did not differ significantly from the regression coefficient (0.434),
signifying that these populations have received a similar proportion of gene flow. The
plot (Figure 4.18) made between observed heterozygosity (Hi) and the distance from the
gene frequency centroid (rii) made it possible to understand the population structure of
the populations in a better way. The grouping of majority of populations near the
theoretical line of regression coupled with moderate distance from the centroid signifies
that Indo–European speaking tribal groups of Gujarat have neither received a large
amount of gene flow nor experienced absolute isolation.
Table 4.22. Genetic heterozygosity (Hi) and genetic distances from the centroid (rii)
among the nine Indo–European speaking tribal groups of Gujarat
rii±SE Hi±SE
Valvi Chaudhari (VC) 0.032±0.012 0.452±0.024
Nana Chaudhari (NC) 0.025±0.011 0.425±0.028
Mota Chaudhari (MC) 0.036±0.020 0.417±0.026
Pavagadhi Chaudhari (PC) 0.011±0.003 0.429±0.027
Vasava (Vas) 0.019±0.006 0.433±0.022
Gamit (Gam) 0.012±0.004 0.416±0.032
Konkana (Kon) 0.047±0.030 0.404±0.039
Dhodia (Dho) 0.009±0.003 0.427±0.030
Dubla (Kon) 0.010±0.004 0.413±0.031
Regression analysis: Hi = b (1 − rii); Hi plotted against 1 − rii through the origins has t = 0.804,
7 df, p > 0.05. Regression coefficient through origin: b = 0.434 ± 0.014; H = 0.432 ± 0.0270
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
Figure 4.18. Regression of genetic heterozygosity (
among the nine Indo
4.3.2. Dataset 2: Genetic Affinities o
Populations of Gujarat
Dataset 2 included the allele frequency data on 14
population groups of India. The allele frequency data for the
populations considered for analysis of molecular variance
XIV. The analysis was carried out between different combinations of populations,
grouped on the basis of language and
considered in different categories were
4.3.2.1. Analysis of Molecular
The results of the analysis have been presented in T
results of previous sections.
influence in determining the population clustering as
was observed between the groups classified on the basis of their lingui
Least among groups variance was seen between the Indo
linguistic groups of India (0.1
population groups (0.51%). Indo
Gam
Dho
Dub
PC
0.30
0.32
0.34
0.36
0.38
0.40
0.42
0.44
0.46
0.48
0.50
0.00 0.01
Analysis of Autosomal Markers
Structured Chaudhari Tribe of Southern Gujarat
Regression of genetic heterozygosity (Hi) on distance from centroid (
Indo–European speaking tribal groups of Gujarat
Genetic Affinities of Indo–European (IE) Speaking Tribal
e frequency data on 14 autosomal loci among different
. The allele frequency data for the autosomal loci and the
for analysis of molecular variance has been given in
The analysis was carried out between different combinations of populations,
anguage and ethnicity. Number of populations and markers
dered in different categories were different, depending on the availability of data.
olecular Variance (AMOVA)
ave been presented in Table 4.23 along with
. In comparison to ethnicity, language showed more
influence in determining the population clustering as 1.71% of among group variance
was observed between the groups classified on the basis of their linguistic affiliation.
Least among groups variance was seen between the Indo–European and Dravidian
linguistic groups of India (0.11%) followed by that between the castes an
%). Indo–European speaking tribes of Gujarat showed
Vas
Kon
VC
NCMC
0.02 0.03 0.04 0.05 0.06
Autosomal Markers
119
) on distance from centroid (rii)
European speaking tribal groups of Gujarat
European (IE) Speaking Tribal
l loci among different
autosomal loci and the
been given in Appendix
The analysis was carried out between different combinations of populations,
. Number of populations and markers
different, depending on the availability of data.
along with AMOVA
In comparison to ethnicity, language showed more
% of among group variance
stic affiliation.
European and Dravidian
%) followed by that between the castes and tribal
European speaking tribes of Gujarat showed
0.07
Analysis of Autosomal Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 120
minimum between group variance with Dravidian speaking groups of India (1.44%),
followed by higher variance with other Indo–European speaking groups of India
(2.83%). In all comparisons, within the population component of variance was found to
explain the major component of variance. All the comparison values were found to be
statistically significant.
Table 4.23. Extent of genetic differentiation estimated by AMOVA among the Indo–
European speaking tribes of Gujarat and other Indian populations on the
basis of autosomal loci allele frequencies
Category
Among groups
variance
(In %)b
Among
population
within groups
variance
(In %)b
Within
population
variance
(In %)b
Chaudhari subgroups as one group 1.61 98.39
IE speaking tribes of Gujarat as one
group 0.79 99.21
Castes and Tribal groups of India 0.51 5.02 94.48
4 linguistic groups of Indiaa 1.71 3.69 94.6
IE and DR linguistic groups of India
0.11 3.60 96.29
IE speaking tribes of Gujarat and DR
speaking groups of India 1.44 2.65 95.91
IE speaking tribes of Gujarat and IE
speaking groups of India 2.83 1.63 95.54
a IE:Indo–European; DR:Dravidian; AA:Austro–Asiatic; TB:Tibeto–Burman
b All the values are significant, p < 0.05