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Chapter 5Chapter 5Chapter 5Chapter 5 Results: Analysis of Mitochondrial Results: Analysis of Mitochondrial Results: Analysis of Mitochondrial Results: Analysis of Mitochondrial
DNADNADNADNA
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 121
ANALYSIS OF MITOCHONDRIAL DNA
5.1. Analysis of Mitochondrial DNA Hypervariable Regions (HVRs)
The human mitochondrial DNA (mtDNA) is a circular, double-stranded molecule,
16,569 base pairs (bp) in length. mtDNA consists predominantly of coding DNA,
barring a ~1100 bp long DNA stretch that has mainly regulatory functions and therefore
termed as control region. The mutation rate of mtDNA is several orders of magnitude
higher than that of nuclear genes. However, in the two hypervariable regions HVR-I
and HVR-II (each ~400bp) of the non coding control region, the rate are even higher,
making them efficient tool for searching mtDNA variation. This property of mtDNA,
along with other features such as high copy number, maternal inheritance and lack of
recombination, make mtDNA useful for studies of human evolution, migrations,
population histories and affinities.
It is assumed that all mtDNA types in the human gene pool can ultimately be traced
back to a common matrilineal ancestor that lived approximately 200,000 years ago in
Africa (Mishmar et al., 2003; Macaulay et al., 2005; Behar et al., 2008). mtDNA
sequence variations thus, evolved as a result of the sequential accumulation of
mutations along maternally inherited lineages, which can be represented in a tree,
reflecting the phylogenetic relationships of known mtDNA variants. The commonly
referred mtDNA phylogenetic tree employed to identify the diverse mtDNA lineages
(also known as haplogroups) is Phylotree (latest version 15, maintained and updated by
van Oven and Kayser, 2008) which represents a comprehensive phylogeny of global
human mtDNA variation, based on both coding- and control region mutations.
In the present chapter results obtained from the laboratory and statistical analysis of
HVR I and HVR II regions of mtDNA among the four Chaudhari populations have
been given. The first section deals with the findings from the four study populations and
the second section deals with the comparative analysis with other population groups.
5
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 122
5.2. Findings from the Four Chaudhari Populations
5.2.1. Haplogroup Distribution Patterns
A total of 193 samples were analyzed for variation in HVR I within nucleotide position
(np) 15904 to np 16544 and HVR II within np 70 to 300 np of mtDNA. The
differentiation of samples in haplogrous M or N was done by screening coding region
mutations at 10398 and 10400 np. The samples bearing G substitution in place of A at
position 10398 and having T mutation in place of C at position 10400 were classified
under haplogroup M while others were classified under N haplogroup (Phylotree v15,
van Oven and Kayser, 2008). The haplotypic motifs observed in each Chaudhari sample
has been given in Appendix XV. These motifs were used to classify samples to different
haplogroups.
Figures 5.1 to 5.3 display the sequencing results of mtDNA coding region (15F) and
control region (HVR I and HVR II).
The results for the various variable sites within HVR I and II were recorded in the same
manner and used to identify mtDNA lineages.
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
Figure 5.1. Sequencing result showing C>T mutation at nucleotide position 10400 characteristic of haplogroup M
Analysis of Mitochondrial DNA Markers
Tribe of Southern Gujarat
Figure 5.1. Sequencing result showing C>T mutation at nucleotide position 10400 characteristic of haplogroup M
Analysis of Mitochondrial DNA Markers
123
Figure 5.1. Sequencing result showing C>T mutation at nucleotide position 10400 characteristic of haplogroup M
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 124
Figure 5.2. Sequencing result showing mutation in Hypervariable region I of mtDNA
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 125
Figure 5.3. Sequencing result showing mutation in Hypervariable region II of mtDNA
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 126
Overall 69.000% of individuals from the studied populations were found to belong to
haplogroup M lineages. Haplogroup N lineages accounted for 23.000% of the total
haplogroup distribution. 15 out of 193 samples could not be classified into any
haplogroup on the basis of the examined mtDNA segments (Appendix XV). However,
these samples were retained for other genetic analyses. The frequency distribution of
the haplogroups is presented in Figure 5.4. The frequency distribution of putative M
and N lineages, assigned on the basis of control region and coding region’s haplotypic
in motifs in 178 samples have been given in Table 5.1. From the Table , it is evident
that lineage M3 constituted the most frequent haplogroup (11.00%). Its highest
frequency was observed in Pavagadhi Chaudhari (16.00%) and minimum frequency
in Mota Chaudhari (6.00%). Apart from M3, lineages M2 (inclusive of M2a and M2b,
10.00%) and M57 (8.00%) were found to be the other frequent lineages. Although
some of haplogroups had overall low frequency levels, they displayed significant
frequency levels in individual populations such as M35 in Valvi Chaudhari (13.00%),
M39 and M5 in Mota Chaudhari (13.00% each) and M30 in Pavagadhi Chaudhari
(11.00%). Among N lineages, only U7 lineage was observed in relatively higher
frequency (7.00%). Its highest frequency was observed in Nana Chaudhari (11.00%)
whereas it was found to be absent in Valvi Chaudhari. Figures 5.5 and 5.6 present the
distribution of the diverse lineages belonging to M and N haplogroups among the four
Chaudhari subgroups. From the figures, it was evident that most of the haplogroups
were shared between different Chaudhari subgroups. However, there were a number
of haplogroups, which were exclusively noticed among one particular Chaudhari
subtribe. Valvi Chaudhari had the highest number of private haplogroups not shared
by any other Chaudhari subgroups. Whereas, Pavagadhi Chaudhari had less number
of diverse M and N lineages, occurring in low frequencies, compared to other study
groups.
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 127
Table 5.1. mtDNA haplogroup frequencies among the Chaudhari subgroups
Populationa VC NC MC PC Total
Haplogroup M
Sub
haplogroups
Count
(n)
Frequencyb Count
Frequency Count
Frequency Count Frequency Count Frequency
D4m2 3 0.06 0 0.00 0 0.00 0 0.00 3 0.02
M10a1 2 0.04 0 0.00 0 0.00 0 0.00 2 0.01
M18'38 1 0.02 1 0.02 0 0.00 0 0.00 2 0.01
M25 0 0.00 1 0.02 4 0.08 0 0.00 5 0.03
M2a 6 0.13 0 0.00 3 0.06 0 0.00 9 0.05
M2b 0 0.00 2 0.04 1 0.02 6 0.16 9 0.05
M3 6 0.13 4 0.09 3 0.06 6 0.16 19 0.11
M30 1 0.02 4 0.09 3 0.06 4 0.11 12 0.07
M33a2 0 0.00 1 0.02 2 0.04 0 0.00 3 0.02
M35 6 0.13 1 0.02 0 0.00 0 0.00 7 0.04
M37 3 0.06 3 0.07 3 0.06 1 0.03 10 0.06
M38c 1 0.02 4 0.09 1 0.02 2 0.05 8 0.04
M39 3 0.06 2 0.04 6 0.13 1 0.03 12 0.07
M4 0 0.00 1 0.02 0 0.00 0 0.00 1 0.01
M40a 0 0.00 0 0.00 1 0.02 0 0.00 1 0.01
M5 0 0.00 4 0.09 6 0.13 1 0.03 11 0.06
M57 4 0.09 4 0.09 3 0.06 3 0.08 14 0.08
M61 0 0.00 0 0.00 2 0.04 0 0.00 2 0.01
M66 1 0.02 0 0.00 0 0.00 0 0.00 1 0.01
M9a'b 0 0.00 1 0.02 0 0.00 2 0.05 3 0.02
Total (M) 37 0.78 33 0.73 38 0.78 26 0.71 134 0.76
Haplogroup N
Population VC NC MC PC Total
Sub
haplogroups
Count
(n)
Frequency Count Frequency Count Frequency Count Frequency Count Frequency
A4a1 3 0.06 1 0.02 0 0.00 1 0.03 5 0.03
H1a3c 1 0.02 0 0.00 0 0.00 0 0.00 1 0.01
J1 1 0.02 0 0.00 1 0.02 0 0.00 2 0.01
JT 1 0.02 0 0.00 0 0.00 0 0.00 1 0.01
N1a'd'e'I 0 0.00 0 0.00 1 0.02 0 0.00 1 0.01
R30b1 0 0.00 1 0.02 0 0.00 1 0.03 2 0.01
R5a2 2 0.04 2 0.04 0 0.00 3 0.08 7 0.04
U1a'c 0 0.00 0 0.00 0 0.00 2 0.05 2 0.01
U2 0 0.00 2 0.04 2 0.04 0 0.00 4 0.02
U4 1 0.02 0 0.00 0 0.00 0 0.00 1 0.01
U5 0 0.00 1 0.02 1 0.02 0 0.00 2 0.01
U7 0 0.00 5 0.11 5 0.10 2 0.05 12 0.07
U9a 0 0.00 0 0.00 0 0.00 2 0.05 2 0.01
W 1 0.02 1 0.02 0 0.00 0 0.00 2 0.01
Total (N) 10 0.22 13 0.27 10 0.22 11 0.29 44 0.24
Total: T (M+N) 47 1.00 46 1.00 48 1.00 37 1.00 178 1.00
a VC: Valvi Chaudhari; NC: Nana Chaudhari; MC: Mota Chaudhari: PC: Pavagadhi Chaudhari bn/T
A Genomic Study on the Sub–Structured Chaudhari
Figure 5.4. Percentage distribution of major mtDNA
Chaudhari subgroups
VC: Valvi Chaudhari; NC: Nana Chaudhari; MC: Mota Chaudhari; PC: Pavagadhi Chaudhari
Figure 5.5. Frequency distribution
N
23%
0
0.02
0.04
0.06
0.08
0.1
0.12
0.14
0.16
0.18
Ha
plo
gro
up
Fre
qu
en
cy
Analysis of Mitochondrial DNA Markers
Structured Chaudhari Tribe of Southern Gujarat
ercentage distribution of major mtDNA haplogroups (M and N)
groups
; MC: Mota Chaudhari; PC: Pavagadhi Chaudhari
requency distribution of diverse M lineages among the Chaudhari
M
69%
ND
8%
Haplogroup M Lineages
VC NC MC PC
Analysis of Mitochondrial DNA Markers
128
(M and N) among the
udhari subgroups
A Genomic Study on the Sub
VC: Valvi Chaudhari; NC: Nana Chaudhari; MC: Mota Chaudhari; PC: Pavagadhi Chaudhari
Figure 5.6. Frequency distribution of di
5.2.2. mtDNA Diversity
Using the HVR I and HVR
of mismatch, nucleotide diversity, raggedness statistic value
Tajima’s D value, of all the studied population groups were calculated and are given in
Table 5.2. In total, 114 polymorphic sites
Haplotypes diversity (h
ranging from 0.967 in Pavagadhi Chaudhari to
number of pairwise difference
DNA sequences in each
Mota Chaudhari to 9.14
similar in the four groups
of the groups.
0
0.02
0.04
0.06
0.08
0.1
0.12H
ap
log
rou
p F
req
ue
ncy
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat
; NC: Nana Chaudhari; MC: Mota Chaudhari; PC: Pavagadhi Chaudhari
requency distribution of diverse N lineages among the Chaudhari
Diversity and Populations’ Demographic Histories based on HVR I
HVR II sequence data, number of polymorphic site
match, nucleotide diversity, raggedness statistic value, Fu’s Fs statistic value,
of all the studied population groups were calculated and are given in
114 polymorphic sites were identified in pooled Chaudhari samples
h) was found to be high and similar in the studied populations,
ranging from 0.967 in Pavagadhi Chaudhari to 0.988 in Valvi Chaudhari
pairwise differences, also called as mean number of mismatches
DNA sequences in each Chaudhari subgroup were found to be ranging from 8.02
to 9.141 in Valvi Chaudhari. Nucleotide diversity (
similar in the four groups varying between 0.009 in Mota Chaudhari
Haplogroup N lineages
VC NC MC PC
Analysis of Mitochondrial DNA Markers
129
Chaudhari subgroups
based on HVR I, II
umber of polymorphic site, mean number
, Fu’s Fs statistic value,
of all the studied population groups were calculated and are given in
in pooled Chaudhari samples.
lar in the studied populations,
in Valvi Chaudhari. The mean
also called as mean number of mismatches (k) in the
found to be ranging from 8.022 in
(π) was also almost
Chaudhari to 0.010 in the rest
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 130
Table 5.2. Descriptive statistics based on HVR I and HVR II among the Chaudhari subgroups
Population
group
Number of
sequences
(Na)
Number of
polymorphic
sites
(Nb)
Number of
haplotypes
(Nc)
Haplotype (gene)
diversity ±S.D
(h)
Nucleotide
diversity ±S.D
(π)
Mean number
of mismatches
(k)
Raggedness
(r)
Fu’s Fs
statistic
(Fs)
Tajima’s
D
(D)
Valvi
Chaudhari 50 67 31 0.988±0.008 0.010±0.0006 9.141 0.009 -11.553* -1.422*
Nana
Chaudhari 52 83 39 0.986±0.007 0.010±0.0006 8.813 0.008 -23.949* -1.849*
Mota
Chaudhari 50 64 37 0.985±0.007 0.009±0.0006 8.022 0.012 -23.170* -1.564*
Pavagadhi
Chaudhari 41 61 25 0.967±0.013 0.010±0.0007 9.058 0.094 -6.516 -1.381
Total 193 114 95 0.982±0.002 0.010±0.0003 8.826 0.0039 -83.071* -1.764*
*Statistically significant at p<0.05
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 131
Figures 5.7 (a-d) depict the mismatch distribution patterns and respective genealogies
for the studied population groups. The shape of the distribution curves and length of the
branches in genealogy has been used to infer the population history. The mismatch
distribution plots appeared to be unimodal in all the groups except Pavagadhi
Chaudhari. Apart from Pavagadhi Chaudhari, all other Chaudhari subgroups’s
mismatch distribution plots showed a high frequency of low pairwise mismatches. The
mismatch distribution curves were observed to be smooth as revealed by the small
values of the raggedness index (r<0.03) barring Pavagadhi Chaudhari. The plots also
displayed good fit between the expected and observed mismatch distributions in all the
groups except Pavagadhi Chaudhari. Thus, the smooth, unimodal mismatch in case of
Valvi, Nana and Mota Chaudhari, indicated a period of rapid population growth for
them whereas, the ragged, multimodal mismatch distribution of Pavagadhi Chaudhari,
suggested Pavagadhi Chaudhari as a population whose size has been constant over a
long period.
The respective Neighbor-Joining trees also depicted longer external than internal
branches, a hallmark for population growth in all Chaudhari subgroups other than
Pavagadhi Chaudhari. Similarly, the significantly large negative values of Fu’s Fs
statistics, and the significant negative values of Tajima’s D for Valvi, Nana and Mota
Chaudhari clearly indicated that there were significant population expansions in the
studied population groups. On the other hand, relatively small negative values of Fu’s
Fs and statistically nonsignificant Tajima’s D value supported the constant population
size for Pavagadhi Chaudhari.
Figures 5.8 (a-b) display the median joining tree constructed separately for HVR I and
II regions among the Chaudhari Subgroups. The figure showed considerable sharing of
haplotypes, possibly suggesting the possibility of their common maternal gene pool.
The star like topology of the tree, an indicator of population expansion also
corroborated the other evidence of rapid population growth for the majority of
Chaudhari subgroups.
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 132
(a) Valvi Chaudhari
Fre
qu
en
cy
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 133
(b) Nana Chaudhari
Fre
qu
en
cy
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 134
(c) Mota Chaudhari
Fre
qu
en
cy
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 135
(d) Pavagadhi Chaudhari
Figure 5.7. Observed (dashed line) and expected (solid line) mismatch distribution curves
and respective Neighbor-Joining trees showing population expansion patterns
based on mtDNA HVR I and HVR II data among the Chaudhari subgroups
Fre
qu
en
cy
A Genomic Study on the Sub–Structured Chaudhari
(a) HVR I
(b) HVR II
Figure 5.8. Median-Joining tree
Valvi Chaudhari; Nana Chaudhari; Mota Chaudhari;
Analysis of Mitochondrial DNA Markers
Structured Chaudhari Tribe of Southern Gujarat
ree of the studied populations based on mtDNA HVR
Valvi Chaudhari; Nana Chaudhari; Mota Chaudhari; Pavagadhi Chaudhari
Analysis of Mitochondrial DNA Markers
136
of the studied populations based on mtDNA HVR I and II
Pavagadhi Chaudhari
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 137
5.2.3. Genetic Differentiation among Populations
The preceding analysis indicated the possibility of underlying uniformity between the
four Chaudhari subgroups. However, to assess the extent of similarity or differentiation
within the Chaudhari subgroups following analyses were performed.
5.2.3.1. Analysis of Molecular Variance (AMOVA)
AMOVA showed the existence of 1.19% of variation among Chaudhari subgroups
while the large percentage of variation (98.91%) was attributable to variation within
populations. Thus, the results indicated the existence of less differentiation among
populations. The results have been presented with other AMOVA results in Table 5.6 at
the end of the chapter.
5.2.3.2. Exact Test
Table 5.3 (above the diagonal) presents an Exact Test of population differentiation
based on haplogroup frequencies (Raymond and Rousset, 1995) with significance
estimation using Markov chain Monte Carlo procedure (100,000 iterations). From the
analysis, it was found that both Valvi Chaudhari and Pavagadhi Chaudhari differ
significantly with each other and with Mota and Nana Chaudhari subgroups. Whereas,
the latter two showed nonsignificant difference with each other.
Table 5.3. Non-differentiation Exact p values to test population differentiation (above the
diagonal) and Slatkin’s linearized FST distance (below the diagonal) based on
mtDNA sequence polymorphisms among the Chaudhari subgroups
Valvi
Chaudhari
Nana
Chaudhari
Mota
Chaudhari
Pavagadhi
Chaudhari
Valvi Chaudhari 0 0.00064±0.0000 0.00000±0.0000 0.00000±0.0000
Nana Chaudhari 0.0108* 0 0.66916±0.0032 0.01549±0.0032
Mota Chaudhari 0.0152* 0.0000 0 0.00249±0.0008
Pavagadhi Chaudhari 0.0237* 0.0117* 0.0156* 0
*FST (p<0.05)
5.2.3.3. Genetic Distance and Neighbor Joining Tree
Table 5.3 (below the diagonal) demonstrated the Slatkin’s linearized FST values
between the pairs of Chaudhari subpopulations. The Neighbor-Joining Tree (Figure 5.9)
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 138
based on the genetic distance (Slatkin’s linearized FST values) revealed that the
population groups Nana Chaudhari and Mota Chaudhari formed a cluster, supporting
the genetic affinity between them as compared to Valvi and Pavagadhi Chaudhari.
Figure 5.9. Neighbor-Joining tree of the studied population groups based on the genetic
distances of Slatkin’s linearized FST values obtained from HVR I and II data
5.3. Comparison of Study Populations with Other Population Groups
The following section presents the results obtained from the comparative analysis of
study groups, with other Indian populations to understand their genetic affinities and
relationships. First of all, analysis was undertaken among the nine Indo-European
speaking tribes of Gujarat, including the Chaudhari subgroups, in order to decipher the
genetic affinities between them. For this comparison mtDNA sequence data from five
other Indo-European speaking tribes namely, Dhodia, Dubla, Konkana, Vasava and
Gamit from Gujarat, was compiled from the unpublished work by Kshatriya et al.
Second, comparison was based on the mtDNA haplogroup frequencies data between
Indo-European speaking groups of Gujarat and other populations of India to understand
the genetic affinities of Indo-European speaking tribes of Gujarat with other Indian
populations for which the data was compiled from other published works.
5.3.1. Dataset 1: Genetic Relation between Neighbouring Indo-European (IE)
Speaking Tribal Populations of Gujarat
The first analysis was conducted among nine Indo-European speaking tribes of Gujarat
including the Chaudhari subgroups. The analysis was based on the mtDNA HVR I and
HVR II sequence polymorphisms. Sequence data corresponding to nucleotide positions
70-299 (HVR II) and 15904-16520 (HVR I) were analyzed from 447 individuals from
the nine IE speaking tribes of Gujarat.
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 139
Table 5.4. Descriptive statistics based on HVR I and HVR II among the nine Indo-European speaking tribes of Gujarat
Population
group
Number
of
sequences
(Na)
Number of
polymorphic
sites
(Nb)
Number of
haplotypes
(Nc)
Haplotype (gene)
diversity ±S.D
(h)
Nucleotide
diversity
±S.D
(π)
Mean
number of
mismatches
(k)
Raggedness
(r)
Fu’s Fs
statistic
(Fs)
Tajima’s
D
(D)
Reference
Valvi
Chaudhari 50 67 31 0.988±0.008 0.010±0.0006 9.141 0.009 -11.553* -1.422* Present Study
Nana
Chaudhari 52 83 39 0.986±0.007 0.010± 0.0006 8.813 0.008 -23.949* -1.849* Present Study
Mota
Chaudhari 50 64 37 0.985±0.007 0.009±0.0006 8.022 0.012 -23.170* -1.564* Present Study
Pavagadhi
Chaudhari 41 61 25 0.967±0.013 0.010±0.0007 9.058 0.094 -6.516 -1.381 Present Study
Dhodia 74 105 57 0.987±0.006 0.011±0.0004 9.416 0.005 -46.851* -1.929* Kshatriya et al.,
(unpublished data)
Dubla 64 71 42 0.975±0.009 0.010±0.0004 8.657 0.015 -23.413* -1.525* Kshatriya et al.,
(unpublished data)
Gamit 34 67 33 0.998±0.008 0.010±0.0008 8.904 0.009 -25.512* -1.720* Kshatriya et al.,
(unpublished data)
Vasava 47 68 35 0.986±0.008 0.010±0.0007 8.540 0.005 -19.877* -1.659* Kshatriya et al.,
(unpublished data)
Konkana 37 80 31 0.988±0.0001 0.012±0.0007 10.063 0.009 -16.714* -1.794* Kshatriya et al.,
(unpublished data)
Total 449 184 225 0.995±0.001 0.011±0.0002 9.111 0.004 -436.925* -2.076*
*Statistically significant at p<0.05
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 140
5.3.1.1. mtDNA Diversity and Populations’ Demographic Histories
The diversity indices and other demographic parameters among the nine Indo-European
speaking groups of Gujarat have been given in Table 5.4. Overall, haplotype diversity
was found to be similar among the tribes of Gujarat, ranging from 0.967 in Pavagadhi
Chaudhari to 0.998 in Gamit. The nucleotide diversity also showed the similar values
~0.01 in all the groups. Mean pairwise difference values were found to be varying from
8.022 in Mota Chaudhari to10.063 in Konkana.
The mismatch distribution of the tribes of Gujarat as a single unit has been presented
in Figure 5.10. The distribution was observed to be unimodal. As mentioned earlier,
unimodal distributions are interpreted as signs of demographic expansion while
multimodal distributions are interpreted as signs of constant population size over time,
thus, the observed distributions supported the possibility of population expansion. In
parallel, the raggedness index (r) was found to be considerably lower than 0.030,
which again is an indicator of population expansion. The significant lower and
negative values of Fu’s Fs and Tajima’s D also supported demographic expansion in
these populations.
Figure 5.10. Observed (dashed line) and expected (solid line) mismatch distribution curves
showing population expansion patterns based on mtDNA HVR I and HVR II
data of combined nine Indo-European speaking tribes of Gujarat
Fre
qu
en
cy
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 141
Thus, the overall high gene diversity, nucleotide diversity along with significant,
negative Fu’s Fs and Tajima’s D values as well as a low raggedness index and
mismatch distribution supported similar pattern of demographic history for the Indo-
European speaking tribes of Gujarat.
5.3.1.2. Genetic Differentiation among Populations
5.3.1.2.1. Analysis of Molecular Variance (AMOVA)
The AMOVA, employed to investigate the genetic structure of the tribes of Gujarat,
showed considerably lower percentage of variance among the populations (1.60%) and
the large percentage of variance within populations (98.40%) indicating uniformity of
their maternal gene pool. The results have been presented with other AMOVA results in
Table 5.6 at the end of the chapter.
5.3.1.2.2. GST and NST Analysis
The pairwise genetic differentiation estimates, computed on the basis of haplotype data
(GST) and nucleotide data (NST) are given in Table 5.5. Mota Chaudhari showed no
differences with Nana Chaudhari (GST and NST=0%) and Gamit (NST= 0%). The highest
differentiation was observed between Dubla and Pavagadhi Chaudhari (GST=1.41% and
NST=5.97%). Overall, the level of differentiation was not found to be high (GST=0.013
and NST=0.024) among the tribes of Gujarat.
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 142
Table 5.5. Pairwise estimate of genetic differentiation based on mtDNA HVR I and II sequence data (GST: below the diagonal and NST: above
the diagonal) among the Indo-European speaking tribes of Gujarat
Dubla Dhodia Gamit Konkana Vasava Mota
Chaudhari
Nana
Chaudhari
Pavagadhi
Chaudhari
Valvi
Chaudhari
Average
NST
Dubla 0 0.053 0.008 0.030 0.026 0.016 0.030 0.060 0.035
0.024
Dhodia 0.009 0 0.045 0.027 0.041 0.045 0.041 0.055 0.053
Gamit 0.008 0.005 0 0.008 0.002 0.000 0.003 0.028 0.011
Konkana 0.009 0.005 0.004 0 0.016 0.013 0.004 0.019 0.010
Vasava 0.007 0.006 0.004 0.006 0 0.009 0.008 0.030 0.026
Mota Chaudhari 0.007 0.007 0.004 0.006 0.005 0 0.000 0.026 0.008
Nana Chaudhari 0.010 0.007 0.004 0.006 0.006 0.000 0 0.007 0.014
Pavagadhi Chaudhari 0.014 0.011 0.008 0.011 0.009 0.008 0.006 0 0.025
Valvi Chaudhari 0.010 0.009 0.006 0.008 0.009 0.008 0.005 0.012 0
Average GST 0.013
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 143
5.3.2. Dataset 2: Genetic Affinities of Indo-European (IE) Speaking Tribal
Populations of Gujarat
Dataset 2 included the mtDNA haplogroup frequencies data among different population
groups of India. The frequencies of six major haplogroups considered for the analysis
were compiled and have been given in Appendix XVI. The data set was used for the
analysis of molecular variance and for multidimensional scaling analysis (Given in
chapter 7).
5.3.2.1. Analysis of Molecular Variance (AMOVA)
The AMOVA was carried out between different combinations of populations, grouped
on the basis of language and ethnicity. Numbers of populations considered in different
categories were different, depending on the availability of data. Table 5.6 presents the
results of AMOVA analysis. The highest among group variance was observed between
the four linguistic families (3.66%) whereas, the same was observed to be considerably
low on the basis of ethnicity (0.09%), implying the major role of language over
ethnicity in determining the clustering of Indian maternal gene pools. Hence, the further
categories were formed keeping in view the significant role of language. On comparing
Indo-European (IE) speaking populations with the Dravidian (DR) speaking groups,
among group variance was observed to be low (0.66%). Further comparison of the IE
speaking tribes of Gujarat with IE and DR speaking population of India showed least
among group variance between tribes of Gujarat and DR speaking groups of India
(0.08%) as compared to variance with IE speaking groups of India (1.62%). In all
comparisons, within population component of variance was found to explain the major
component of variance. All the comparison values were found to be highly significant.
The table also presents results of AMOVA from previous sections.
Analysis of Mitochondrial DNA Markers
A Genomic Study on the Sub–Structured Chaudhari Tribe of Southern Gujarat 144
Table 5.6. Extent of genetic differentiation estimated by AMOVA among the Indo-
European speaking tribes of Gujarat and other Indian populations on the
basis of mtDNA haplogroup frequencies
Category
Among groups
variance
(In %)b
Among
population within
groups variance
(In %)b
Within population
variance
(In %)b
Chaudhari Subgroups as one group 1.19 98.81
IE speaking tribes of Gujarat as one
group 1.60 98.40
4 Linguistic groups of Indiaa 3.66 5.10 91.24
Castes and Tribal groups of India 0.09 7.44 92.48
IE and DR linguistic groups of India 0.66 5.12 94.21
IE speaking tribes of Gujarat and DR
speaking groups of India 0.08 4.42 95.50
IE speaking tribes of Gujarat and IE
speaking groups of India 1.62 3.13 95.25
a IE:Indo–European; DR:Dravidian; AA:Austro–Asiatic; TB:Tibeto–Burman
b All the values are significant, p < 0.05
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