CASTES AND GENES

CASTES AND GENES

5.1. Indian caste system and gene pool

It is a well established observation that each caste is endogamous consisting of

many (mostly) exogamous, patrilineal clans: their clan systems many times were

animistic or totemic in tribal populations. Almost all forms of marriages and family

systems have been tested in India, age immemorial, but as on date monogamy has

prevailed in most of the ‘modern’ populations. Nonetheless, there is very little difference

between castes and tribes, the tribes being primitive in their life style; live with nature on

simple domicile and food but mostly with good ethical and moral values of a well

organised ancient society. These tribes as on date in Tamil Nadu account for <10% of the

population.

A large chunk of Tamil Nadu populations live in the plains. Many of them do not

have well organised social structure like that of the modern castes. The questions of

societal formation and origin of caste system were the most attempted ones, though

without any definite conclusion. These are further discussed below and in latter chapters.

5.2. Gotra and Brahmin populations

I studied various endogamous Brahmin populations of Tamil Nadu such as

Iyengar, Telugu Brahmin, Brahacharnam-Iyers and Vadama-Iyers to test the hypothesis

whether they were drawn from the same stock. Brahmins, with their Vedic tradition were

the highly evolved social structure, with strict rules and regulations of life style, adopted

as a religious fervor. Under the Vedic pantheon there were many gotras (patrilineal

clans) and the name of these gotras were all the same all through the Brahmin caste-

clusters. It was of interest to see whether each Brahmin caste or gotra of each Brahmin

castes were derived from same stock or various Brahmin caste or gotras were derived

84
from various stocks. Figure 41 shows the distribution of various NRY haplogroups in

various gotras of the study population. The following observations were made from the

figure:

1. Each Brahmin population was composed of varied number of gotras: not all the gotras

were present in all the populations.

2. Each gotra of different Brahmin populations (castes) were composed of varying

frequencies of different NRY haplogroups.

3. The NRY HG composition of each gotra was unique in each population studied;

though all of them had HG R1a1-M17 but not HG R2-M124.

4. HG R-M207 was commonest in many gotras of Vadama and Brahacharanam while

sparse in Iyengar and Telugu Brahmins.

5. HG L-M20 was found in few gotras of Vadama and Telugu Brahmin.

6. Bhartwaja gotra in three or four population studied, have significant HG L-M20.

Thus Brahmin caste-clusters were not derived from a single source. It is clear

from the figures that these Brahmins were distinct from one another, as on date of these

gotras might have been drawn from a single source. It is possible that a predominant HG

R1a1-M17 population from Southern Russia migrated to south Tamil Nadu from Andhra

Pradesh as Nilakanda Shastri proposed (1975), might have amalgamated enroute other

HG’s identified in these populations. Large scale conversions were not uncommon those

days and this could be confirmed by simply looking at the Thurston’s photographs

(1909) of various Brahmin populations of India (Appendix XI). Various Brahmin

populations may not thus be “ethnically pure” descendents of any one “Aryan”. There

are ample evidences available in Tamil literature of religious conversions and believes of

yester years.

85
5.3. The Clans and villages of Kotas

Kota was the only Nilgiri tribe with a very high proportion of R-M207 clades

along with HG H-M69 and negligible other HGs. The clan system in Kota is interesting.

The clan is designated by their street (‘Kher’) and hence many Kota villages possess the

same pattern of longitudinal rows of houses forming streets and street exogamy is the

order. However, a groom from Keelkher of one village has a liberty to marry a bride

from Keelkher of another – thus street exogamy among villages is not a taboo. This was

a more pragmatic approach to avoid inbreeding or selecting spouses from a limited

number of mates available.

The distribution of various NRY HGs in various clans of different villages was

interesting. Not all the villages had the same ‘Kher’, not all the Kher had all the NRY

HGs and various Kher of each village consisted of different proportions of various NRY

HGs (Fig. 42). The data showed that not all the Kher’s were derived from the same

ancestral populations: in Trichigady village 70% samples in Akkher were made of R-

M207 clade (both R2-M124 and R1a1-M17), whereas as in Pibherkher of the same

village 90% of samples were HGs F*-M89* and H-M69. This has proved Karve’s model

of different clans drawn from various stock/migrations (caste-clusters). The caste system

is thus a dynamic social institution adapting and amalgamating the contemporary

changes through ages, as proposed earlier (Pitchappan et al., 1997). In another settlement

Solur, samples HG R-M207 clade was absent, and in Pudukothagiri HG L-M20 was

absent but the latter possessed a good proportion of HG H-M69. Kollimalai settlement

had appreciable R-M207 clades but very little HG H-M69 and HG L-M20. This showed

the real diversity of Kota gene pool and the risk of misinterpreting their origin.

86
5.4. Various settlements of a tribe had different NRY HG composition

Five primitive tribes of Nilgiris included in Groups I and II of Table 10 were

further studied for NRY HGs distribution based on their settlement. Not all the

settlements had the same composition of NRY HGs (Fig. 43). For example, HGs C-

M130 and F*-M89* were present in only some of the settlements of Paniya not in others.

Similarly HG L-M20 was identified in only in Kargudy in Bettakurumba settlements

(70%). In Kamaraj Nagar, a recent settlement, there was an HG R1a1-M17. Among

Mullukurumba settlements HG L-M20 was present in three settlements, but not in the

fourth. Among Kurumbas most of the settlements were of only HG H-M69. The data on

Irula settlements also showed a high diversity of NRY HGs in various settlements. Thus

no two settlements had similar frequencies of various NRY HGs except Kurumba. This

reiterated the point that sampling in one or two settlements of a tribe or caste might

present a misleading picture as in the case of many Nilgiri tribes studied (Fig. 43). The

diversity of gene pool between various settlements were thus minimal in Kurumba

indicating it to be more isolated, but HG H-M69 showed Irula to be the most ancient,

though they possessed many other HGs.

87
 HG J-M304
HG O-M175

HG H-M69

HG R-M207

HG L-M20
MDU

Figure 15a. Neighbour Joining tree from MEGA for haplogroup frequency with group

VII of Wells et al. (2001).

 NadarMDU(19)
Vanniyar(32)
Maniyani(18)
TeluguBrahmin(10) HG L-M20
NadarTNV(70)
Vannan(14)
Kammalar(19)
Bettakurmba(24)
Pallar(100)
Mappilla(58)
Maravar(90)
NadarCape(25)
Nair(57)
KeralaBrahmin(9)
Vadama(76)
HG R1A1-M17
Brahacharanam(25)
Thiyya(123)
Iyengar(14)
Moopanar(12)
Naidu(13)
Mukkuvar(20) HGJ-304
Parayar(36)
Paravar(55)
Thoda(29)
Vellala(14)
Kota(68)
Pulaya(23)
Kanikaran(18)
Agamudaiyar(21)
Sakkiliyar(10) HGH-M69
Mollukurumba(34)
Paniya(80)
Irula(102)
Kattunaickan(50)
Kurumba(38)
Saliya(11)
Koya(98)
Bondo(88)
Gadaba(87)

0.02

Figure 15b. Neighbour Joining tree from MEGA for Haplogroup frequency without

Group VII of Wells et al. (2001). Note: Negative Fst values forced to ‘0’.
 Principal Coordinates (1 vs 2)

K ur umba

K at t unai c kan

I r ul a

P ani ya
Axis 2

A gamudai yar
Sakk i l i yar M ul l ukur umba K oya

K ot a
V elKl al
ania k ar an
B etPtar
akur mba
ayar
P ar avar
I yengar
PNadar
ul aya
SalTi yNV
a
B ondo
MMoopanar
uk kuvar
Nai du P al l ar
Nai r
M appi lla
K ammal ar M ar avar
Nadar Cape
K er al a B r ahmi n
B r ahac ahr
T hi anam
yya
Gadaba

T el ugu B r ahmi
Nadar M DUn
T hoda
V annan
V adama

M aniVy ani
anni yar

Axis 1

Figure 16. Principal component analysis for HG Frequencies.

 HG C-M130
HG F*-M89
HG H-M69
Figure 17. Torso of all STRs studied without the HG context. HG HG J -304
HG L-M20
colours superimposed. HG O-M175
HG R2-M124
HG R1a1-M17
Cluster II

Cluster I
Middle
Cluster

Figure 18. Network of all STRs studied without the HG context. HG colours

superimposed.
Figure 19. Network of cluster I in all STRs studied without the HG context. HG colours superimposed.

Note: The colour codes as per legend in Figure 17.

Figure 20. Network of cluster II in all STRs studied without the HG context. HG colours superimposed.
Note: The colour codes as per legend in Figure 17.
Figure 21. Network of middle cluster joining clusters I and II in all STRs studied without the HG context. The mutated positions are shown in red.

HG colours superimposed.

Note: The colour codes as per legend in Figure 17.

 BettaKurumba(12)
Paniya(47)
TeluguBrahmin(3)
Paravar(26)
MulluKurumba(21)
Thoda(18)
Irula(64)
Koya(31)
Kattunaickan(38)
Kurumba(27)
TNVNadar(52)
Thiyya(32)
Pallar(11)
Battar(5)
Iyengar(7)
Kota(52)
Brahacharnam(12)
Vadama(52)
Parayar(4)
Bondo(35)
Gadaba(25)

0.02

Figure 22. Neighbour Joining dendrogram using Fst values obtained by Distance Method

for Y-STRs without the HG context.

Note: Each Y-STR allele variance was considered as independent entity. Data in bracket

denotes the sample size studied. Homoplasy will not be discriminating in the analysis.
 Parayar(4)
TeluguBrahmin(3)
Battar(5)
Iyengar(7)
Pallar(11)
Brahacharnam(12)
Vadama(52)
Bondo(35)
Gadaba(25)
Paravar(26)
Thoda(18)
Paniya(47)
BettaKurumba(12)
MulluKurumba(21)
Irula(64)
Kurumba(27)
Kattunaickan(38)
Kota(52)
Thiyya(32)
TNVNadar(52)
Koya(31)

0.005

Figure 23. Neighbour Joining dendrogram using Fst values obtained by 16 loci Y-STR

haplotype frequency method for Y-STRs without the HG context.

Note: Data in bracket denotes the sample size studied.

 Principal Coordinates (1 vs 2)

BettaKurumba

Paniya

Battar
Brahacharnam
Telugu Brahmin Pallar
Thoda
Paravar

Axis 2
TNV Nadar Thiyya Vadama

Irula
MooluKurumba
Iyengar
Bondo Kota
Parayar

Kattunaickan

Gadaba

Kurumba

Koya

Axis 1
Figure 24. Principal Component Analysis of all STR studied without HG context.

Note: PCA Y-STR is not informative than PCA for HG frequency in discriminating the population.
 Paniya
Irula
Vadama

Figure 25. Network of HG C-M130. Note: Population colour codes superimposed.

 Out Group
Paniya
Irula
Mullukurumba
Kattunaickan
Bettakurumba
Nadar TNV
Bondo
Koya

Figure 26. Network of HG F*-M89*.

Note: Population colour codes superimposed.

 Kota(3)
MulluKurumba(3)
NadarTNV(6)
Irula(6)
Kattunaickan(7)
BettaKurumba(5)
Paniya(12)
Bondo(9)
Koya(11)

0.05

Figure 27. Neighbour Joining dendrogram using Fst values obtained by Distance method

for HG F*-M89 Y-STRs.

Note: Data in bracket denotes the sample size studied.

 Out Group
Paniya
Irula
Mullukurumba
Kattunaickan
Bettakurumba
Kurumba
Thoda
Paravar
Nadar TNV
Koya
Bondo
Kota
Thiyya
Vadama
Brahacharanam
Iyengar

Figure 28. Network of HG H-M69.

Note: Population colour codes superimposed

 Bondo(3)
Vadama(7)
Iyengar(3)
Brahacharanam(3)
NadarTNV(14)
Irula(40)
BettaKurumba(4)
Paniya(21)
Paravar(5)
Thoda(3)
Thiyya(7)
Kattunaickan(26)
Kurumba(19)
Koya(16)
Kota(20)
MulluKurumba(8)

0.05

Figure 29. Neighbour Joining dendrogram using Fst values obtained by Distance method

for HG H-M69 Y-STRs.

Note : Data in bracket denotes the sample size studied.

 Out Group
Paravar
Thoda
Nadar-TNV
Thiya
Vadama

Figure 30. Network of HG J-M304.

Note: Population colour codes superimposed.

 Paravar(9)
NadarTNV(3)
Thiyya(4)
Kattunaickan(3)
Vadama(3)
Kota(3)
Thoda(9)

0.05

Figure 31. Neighbour joining dendrogram using Fst values obtained by Distance method

for HG J-M304 Y-STRs.

Note: Data in bracket denotes the sample size studied.

 Out Group
Irula
Mullukurumba
Paravar
Nadar TNV
Thiyya
Vadama

Figure 32a. Network of HG L-M20.

Note: Population colour codes superimposed.

 Out Group
Irula
Mullukurumba
Paravar
Nadar TNV
Thiyya
Vadama

Figure 32b. Network of HG L-M20.

Note: Population colour codes superimposed

 Thiyya(6)
TNVNadar(13)
Vadama(10)
Paravar(5)
Irula(9)
Mullukurumba(6)

0.02

Figure 33. Neighbour Joining dendrogram using Fst values obtained by Distance method

for HG L-M20 Y-STRs.

Note: Data in bracket denotes the sample size studied.

 Out Group
Koya
Gadaba
Bondo

Figure 34. Network of HG O-M175.

Note: Population colour codes superimposed.
 Out Group
Mullukurumba
Nadar TNV
Vadama

Figure 35. Network of HG R2-M124.

Note: Population colour codes superimposed.

 Out Group
Kota
Thiyya
Vadama
Pallar
Iyengar
Brahacharanam
Nadar TNV

Figure 36a. Network of HG R1a1-M17.

Note: Population colour codes superimposed.

Figure 36b. Network of HG R1a1-M17 showing 17 mutations between 7lVad and 6cTNVN.
 Iyengar(4)
Brahacharanam(5)
Pallar(5)
NadarTNV(4)
Vadama(21)
Thiyya(11)
Kota(12)

0.02

Figure 37. Neighbour Joining dendrogram using Fst values obtained by Distance method

for HG R1a1-M17 Y-STRs.

Note: Data in bracket denotes the sample size studied.

 Irula
Mullukurmba
Kattunaickan
Koya
Kota

Figure 38. Network of Modal haplogroups.

Note: Population colour codes superimposed.

 0.6
y = 3.1554x -0.7568
R2 = 0.8702

0.4

0.2

0.0
0 20 40 60 80 100 120 140

Figure 39. Correlation between the samples studied (X axis) and the ‘Discrimination

capacity’ (Y axis) based on haplogroups identified.

 y = 5.3145e0.2379x
140
R2 = 0.4221

120

100
Sample Size

80

60

40

20

0
0 2 4 6 8 10 12 14
Haplogroups Identified

Figure 40a. Haplogroups identified Vs sample size.

Note: As the sample size increases, the chances of identifying more HGs increase. This is
however influenced by the number of HGs present in the population respective of larger
sample size alone.

y = 0.2995Ln(x) + 0.5344
R2 = 0.7121
1.0

0.8
HG diversity

0.6

0.4
0.0 1.0 2.0 3.0 4.0
Mean Pairwise Differences

Figure 40b. Mean Pairwise differences Vs HG diversity.

Note: As Mean Pair wise differences increase the HG diversity also increases.
 y = 0.0224e0.3291x
R2 = 0.2438
0.20
Rag gedness In dex

0.15

0.10

0.05

0.00
0 1 2 3 4 5 6
Tau

Figure 40c. Tau values Vs Raggedness index.

Note: Larger values of Tau give significant radeggness index.

y = -1636.7x + 68703
120,000 2
R = 0.0101
Expansion Age

80,000

40,000

0
0 1 2 3 4 5 6 7
Tau

Figure 40d. Tau Vs Expansion age.

Note: When Tau increases there should be an increase in expansion age. But this was not
observed because of recent origin of human populations. Lower effective population size
for Y chromosome may also give lesser age estimates.
 3.0
y = 1.2678x - 0.6595
2
R = 0.5555
2.0

1.0
Fs

0.0
-1.5 -1.0 -0.5 0.0 0.5 1.0 1.5 2.0

-1.0

-2.0

-3.0
Tajima's D

Figure 40e. Tajima’s D Vs Fs

Note: Negative Tajima's D and negative Fs correlate irrespective of no molecular
diversity

60,000 -0.2833x
y = 21635e
2
R = 0.4752
Expansion Age

40,000

20,000

0
-3 -2 -1 0 1 2 3
Fs

Figure 40f. Fs Vs Expansion Age.

Note: Negative Fs increased the expansion age
 Total

Figure 41: HG frequencies in various gotras of Brahmin populations.

 Total

Figure 42. NRY HG frequencies in various clans of Kota tribe.

 T

Figure 43. NRY HG frequencies in various settlements of Nilgiri tribes.

Table 8. Details of the Populations studied

Tamil Language Language/

N
Population Place of Living Sampled At Subsistance
Nadu Family Dialect

Caste
Tribe /
studied
Group I Dravidian Paniya 82 Tribe Paniya Hill Nilgiris Basketry and trappers
Kurumba with
Dravidian Kattunaickar 52 Tribe Tamil and Hill Nilgiris Hunter Gatherer Hill
Malayalam
Dravidian Kurumba 38 Tribe Kurumba Hill Nilgiris Food Gathering
Group
Dravidian Irula 105 Tribe Irula Hill Nilgiris Hunter Gatherer Hill
II
Dravidian Bettakurumba 24 Tribe Kurumba Hill Nilgiris Hunter Gatherer Hill
Dravidian Mullukurumba 34 Tribe Kurumba Hill TN, Kerala Hunter Gatherer Hill
Kanikarar with
Group
Dravidian Kanikarar 18 Tribe Tamil and Hill Thirunelveli Hunter Gatherer Hill
III
Malayalam
Dravidian Paravar 57 Tribe Tamil Coastal Thirunelveli Fishing, Pearl Mining
Dravidian Thoda 33 Tribe Thoda Hill Nilgiris Pastorals, Domestication
Group
Dravidian Parayar 37 Caste Tamil Inland Thirunelveli Agriculture
IV
Dravidian Pallar 105 Caste Tamil Inland Thirunelveli Agriculture
Dravidian Nadar-TNV 73 Caste Tamil Inland Thirunelveli Pastorals, Toddy tappers
Dravidian Maravar 92 Caste Tamil Inland Ramnad Warrior
Dravidian Nadar-MDU 19 Caste Tamil Inland Madurai Pastorals, Toddy tappers
Dravidian Vanniyar 32 Caste Tamil Inland North TN Agriculture, Warrior
Dravidian Nadar-Cape 25 Caste Tamil Inland Cape Pastorals, Toddy tappers
Dravidian Mukuvar 21 Caste Tamil coast Kanyakurai Fishing
Dravidian Agamudaiyar 22 Caste Tamil Inland Madurai Agriculture
Dravidian Sakkiliyar 11 Caste Tamil Inland Madurai Artisan
Group Indo-
Telugu Brahmin 11 Caste Sanskrit Inland Thirunelveli Artisan
V European
Indo-
Vadama 78 Caste Sanskrit Inland Thirunelveli Agriculture
European
Contd….Table 8.
Groups Indo-
Brahacahranam 25 Caste Sanskrit Inland Thirunelveli Agriculture
VI European
Indo-
Iyengar 14 Caste Sanskrit Inland Thirunelveli Agriculture
European
Dravidian Moopanar 14 Caste Tamil Inland Madurai Agriculture
Dravidian Naidu 14 Caste Telugu Inland Madurai Agriculture
Dravidian Kota 69 Caste Kota Hill Nilgiris Artisan
Dravidian Vellala 14 Caste Tamil Inland Madurai Agriculture
Group Indo-
Sourashtra 46 Caste Sourashtra Plains Madurai Artisan, Weavers
VII European
(Wells
Agriculture, Dry land
et al Dravidian Piramalai Kallar 84 Caste Tamil Plains Madurai
farming
2001)
Dravidian Yadhava 129 Caste Tamil Plains Madurai Pastorals
North
Dravidian Pulaya 23 Caste Malayalam Hill Kannur Hunter Gatherer
Kerala
Dravidian Saliya 11 Caste Malayalam Inland Kannur Hunter Gatherer
Agriculture,Toddy
Dravidian Thiyya 127 Caste Malayalam Inland Kannur
Tappers
Dravidian Vannar 15 Caste Malayalam Inland Kannur Pastoral, Domestication
Dravidian Nair 62 Caste Malayalam Inland Kannur Warrior, Agriculture
Indo-
Kerala Brahmin 9 Caste Sanskrit Inland Kannur Vedic tradition
European
Dravidian Kammalar 19 Caste Malayalam Inland Kannur Artisan
Indo-
Mapilla 60 Caste Urudu Inland Kannur Agriculture
European
Dravidian Maniyani 18 Caste Malayalam Inland Kannur Agriculture
Orissa Dravidian Koya 100 Tribe Koya Inland Malkangiri Agriculture
Austro Asiatic Bondo 92 Tribe Bondo Hill South Orissa Hunter Gatherer
Austro Asiatic Gadaba 91 Tribe Gadaba Hill South Orissa Hunter Gatherer
 ABI
Marker

Cultural
Distribution$

Characteristics
Estimated age*
Wells et al, 2001
NRY Haplogroup

Geographic Origin /

Common ancestor to all

Ethiopia /Sudan 31,000 - 79,000 M168
SNP

outside africa
Fr = Indel by Fragment Analysis
Fr

M139
A

Fr

Africa 55,000 M91

SNP = Characteristic biallelic polymorphism
B

Fr

50,000 - 60,000 M60

C

Coastal marker 50,000 M130

SSP
SNP

Hunter Gatherers Middle East 45,000 M89*

F*

SSP
SNP

* From Wells et al 2001, www.nationalgeographic.com/genographic

Change from Hunter

G

Gatherer to settled Middle East 10,000 -20,000 M201

SNP

agriculture
H

Middle East 20,000 - 30,000 M69

SNP

Indian 25,000 M52

H1

SSP
Table 9. Details of the NRY markers, their age and methods used in the present study

Gravettian Culture Central Europe 20,000 M170

J

Agriculture Middle East/South Europe 10,000 - 15,000 M304

SNP

Jews have 30% of combined

Middle East/South Europe 10,000 - 15,000 M172
J2

SSP

frequency of J and J2
K

Iran / Central Asia 40,000 M9*

SSP
SNP

$ = From Literature: Wells et al 2001, www.nationalgeographic.com/genographic, Sengupta et al., 2006, Sahoo et al., 2006
L

Indian 30,000 M20

SSP
SNP
Fr
M

M186
N

Uralic speakers Siberia 10,000 LLY22

SNP
O

Fr

Central / East Asia 35,000 M175

SSP

China M95
O2

SSP

Agricultural spread in China China 30,000 M122

O3

SSP

Ancestors to most Europeans

P

Central Asia 35,000 - 40,000 M45*

SSP
SNP

and native Americans

Q

Ist wave into Americas Siberia 15,000 - 20,000 M242

SNP
R

Central Asia 30,000 M207

SNP
1st large wave to reach
Central Asia 30,000 M173
R1

SSP
Europe
Central Asia / India / Pakistan ? 25,000 M124 R2

SSP
SNP
Fr
Indo European speakers ? Southern Russia / Ukraine / India ? 10,000 M17

SSP
R1a1
Table 10. NRY Haplogroup frequencies in selected castes and tribes from Tamilnadu, North Kerela and Orissa investigated in the present study

N
Group Population NRY haplogroup Frequencies (x100)

studie
A B C F G H H1 I J J2 K L M N O O2 O3 P Q R R1 R2 R1a1
y
y

Neg
M91
M60
M9*
M20
M17

M69
M52
M95

M130
M89*
M201
M170
M186
M45*
M242
M207
M124
Mean

M304
M172
M175
M122
M207
M173

M69 #
Group

LLY22

M304 $
Diversit
Diversit

M175 &
Group I Paniya 82 2 0 0 15 30 0 44 0 44 0 0 0 0 1 1 0 0 0 0 0 0 0 1 1 1 0 1 2 100 0.700
Kattunaickar 52 4 0 0 2 15 0 60 23 37 0 6 4 2 0 2 0 0 0 0 0 0 0 2 6 6 0 4 0 100 0.624
Kurumba 38 0 0 0 3 5 0 76 16 61 0 0 0 0 3 5 0 0 0 0 0 0 0 0 0 0 0 5 3 100 0.418 0.58

Group II Irula 105 3 0 0 5 10 0 57 24 33 0 3 0 3 1 17 0 0 0 0 0 0 0 1 1 1 0 2 0 100 0.635

Bettakurumba 24 0 0 0 0 38 0 29 8 21 0 0 0 0 0 21 0 0 0 0 0 0 0 0 4 4 0 4 4 100 0.757
Mullukurumba 34 0 0 0 0 21 0 41 41 0 0 0 0 0 3 21 0 0 0 0 0 0 0 0 0 0 0 15 0 100 0.745 0.71

Group III Kanikarar 18 0 0 0 0 11 6 33 6 28 0 11 0 11 0 17 0 0 0 0 0 0 0 6 11 11 0 6 0 100 0.863

Paravar 57 4 0 0 2 2 0 30 5 25 0 26 4 23 4 16 0 0 5 0 2 4 0 4 2 2 0 5 2 100 0.822
Thoda 33 12 0 0 9 3 0 9 6 3 0 39 33 6 0 12 0 0 3 3 0 0 3 0 0 0 0 9 0 100 0.828 0.84

Group IV Parayar 37 3 0 0 3 0 5 32 14 19 0 16 8 8 0 14 0 0 3 0 3 0 3 0 8 5 3 5 8 100 0.852

Pallar 105 5 0 0 0 9 9 19 14 5 0 11 7 5 1 21 0 0 0 0 0 1 4 4 0 7 14 100 0.874
Nadar-TNV 73 4 0 0 0 12 5 25 25 0 0 4 4 0 27 0 0 0 0 0 5 0 0 0 10 7 100 0.839
Maravar 92 2 0 0 1 17 9 12 12 0 0 12 12 1 10 0 0 1 1 0 3 4 4 0 12 15 100 0.893
Nadar-MDU 19 0 0 0 0 5 0 16 0 16 0 0 0 0 0 47 0 0 0 0 0 0 5 5 0 0 0 11 11 100 0.760
Vanniyar 32 0 0 0 6 9 3 3 3 0 0 13 13 0 44 0 0 0 0 0 0 0 0 0 9 13 100 0.778
Nadar-Cape 25 0 0 0 4 12 8 16 16 0 0 12 12 0 12 0 0 8 8 0 8 0 0 0 4 16 100 0.920
Mukuvar 21 5 0 0 0 0 0 24 24 0 0 19 19 0 5 0 0 0 0 0 0 14 14 0 19 14 100 0.869
Agamudaiyar 22 5 0 0 0 0 5 45 27 18 0 0 0 0 5 9 0 0 0 0 0 0 0 0 18 18 0 5 9 100 0.773
Sakkiliyar 11 9 0 0 0 0 0 45 27 18 0 0 0 0 0 36 0 0 0 0 0 0 0 0 0 0 0 9 0 100 0.718 0.83

Group V Telugu Brahmin 11 9 0 0 0 0 9 18 9 9 0 0 0 0 0 36 0 0 0 0 0 0 0 0 0 0 0 0 27 100 0.827

Vadama 78 3 0 0 4 3 3 12 0 12 0 6 0 6 1 17 0 0 3 0 1 1 0 0 5 4 1 0 45 100 0.757 0.79

Groups VI Brahacharanam 25 0 0 0 0 4 0 20 0 20 0 12 0 12 0 4 0 0 0 0 0 0 4 0 16 8 8 4 36 100 0.817

Iyengar 14 0 0 0 0 0 0 36 0 36 0 14 0 14 7 7 0 0 0 0 0 0 0 0 0 0 0 0 36 100 0.769
Moopanar 14 14 0 0 7 0 7 21 7 14 0 7 0 7 0 7 0 0 0 0 0 0 0 7 7 7 0 0 21 100 0.945
Naidu 14 7 0 0 7 0 0 21 7 14 0 14 7 7 0 7 0 0 0 0 0 0 0 0 21 21 0 7 14 100 0.918
Kota 69 1 0 0 0 6 0 35 23 12 0 7 3 4 1 1 0 0 0 0 0 0 0 4 4 4 0 17 22 100 0.800
Vellala 14 0 0 0 7 0 36 29 7 0 0 0 0 0 7 0 0 0 0 0 0 0 0 14 14 0 14 21 100 0.835 0.85
Total Tamil Nadu 1119
Group VII Sourashtra MDU 46 0 0 7 4 15 15 2 2 26 2 2 0 4 39 99 0.766
(Wells et al., 2001) Piramalai Kallar 84 0 0 7 18 15 15 1 1 48 1 1 1 5 4 100 0.714
Yadhava 129 0 0 3 12 19 19 20 20 19 2 1 1 3 9 13 100 0.853
Total Wells et al.
259
(2001)
North Kerala Pulaya 23 8 0 0 16 0 0 24 24 0 0 8 8 4 4 0 0 0 0 0 0 4 4 0 20 12 100 0.890
Saliya 11 0 0 0 0 18 0 27 27 0 0 0 0 0 18 0 0 9 9 0 0 9 9 0 9 9 100 0.909
Thiyya 127 3 0 0 4 7 0 14 14 0 0 9 9 1 16 0 0 2 2 1 1 4 4 0 6 31 100 0.841
Nair 62 8 0 0 2 3 3 18 18 0 0 6 6 0 16 0 0 0 0 2 5 2 2 0 15 21 100 0.882
Vannar 15 7 0 0 0 27 0 7 7 0 0 7 7 0 20 0 0 0 0 0 0 13 13 0 0 20 100 0.881
Kerala Brahmin 9 0 0 0 0 0 0 22 22 0 0 11 11 0 22 0 0 0 0 0 0 0 0 0 11 33 100 0.861
Mapilla 60 3 0 0 2 7 3 18 18 0 0 8 8 0 22 0 2 2 2 0 0 2 2 0 12 20 100 0.867
Kammalar 19 0 0 0 0 26 0 21 21 0 0 0 0 0 32 0 0 0 0 0 0 0 0 0 5 16 100 0.801
Maniyani 18 0 0 0 0 0 0 6 6 0 0 6 6 0 39 0 0 0 0 0 6 6 6 0 17 22 100 0.804 0.86
Total North Kerala 344

Orissa Koya 100 2 0 0 0 26 0 33 33 0 0 0 0 9 0 0 0 24 24 0 0 1 1 0 5 100 0.763

Bondo 92 4 0 0 3 27 0 10 10 0 0 0 0 18 1 0 0 36 36 0 0 0 0 0 0 100 0.761
Gadaba 91 4 0 0 1 3 0 3 3 0 0 3 3 15 0 0 0 68 68 0 0 0 0 0 1 99 0.515 0.68
Total Orissa 283
Total 1746

All the samples were tested for M168 and M139: All were positive
The data in italics are subsets: Not considered for further Analysis
# = All those M69 samples, tested for M52, answered for M52. (column H1): the samples not tested for 52 are presented in the previous column: The column next to M52 thus
denotes the sum of both the columns; i.e., M69
$ =M172 was phenotyped by SSP (column J2); all these samples answered for M304 in Taqman assay; Not all the Taqman assay tested M304 samples (column J) were tested for
M172; hence these two columns were added together and called as M304.

& =M95 (ColumnO2) and M122 (Column O3) were phenotyped by SSP; all these samples have answered for M175 by SSP and TaqMan; Not all the M175 tested samples (column
O) were tested for M95 and M122; hence these three columns were added together and called as M175
Hence only H, J, O were used along with other haplogoups for subsequent analyses
However since all the H1 were H and all the J2 were J in the subset of samples studied (SSP studied), It is possible that I have not lost any information. Still there is a possibility
that there are some markers which may be H and not H1 and also J and not J2 in some populations studied.
The negative (neg) samples were not used for diversity estimates considering it as a technical failure
The blanks are not studied: '0's are shaded in light colour
TNV = Thirunelveli
MDU = Madurai
Table 11. Hierarchial AMOVA results based on Y Haplogroup Frequencies

Total Variance %

Compared Groups Compared (Populations No of Within Between Between

Groups studied=39) Chromosomes Populations populations Groups

1 All Study Populations 1746 88.14 11.86 ----

2 Castes (28) and Tribes (11 ) 1746 85.83 8.8 5.37
Castes
2 Tamil Nadu (22) and Kerala (9) 1463 92.96 6.41 0.63
2 Dravidian (34) and IE speakers`(5) 1463 88.9 6.55 4.56
Tribes
2 Tamil Nadu and Orissa 761 76.48 8.49 14.93
2 Dravidian and Austro Asiatic 761 73.11 8.02 18.86
Tamil Nadu (Caste / Tibe), Kerala and Orissa
3 1746 86.13 5.33 8.55
Tribes
Table 12. Genetic distances (Fst ) between populations estimated from Y haplogroup frequencie

Hill tribes of Tamil Nadu Castes of the Plains of Tamil Nadu Brahmin castes Castes HT Caste Castes of Kerala Orissa Tribals

Nair

Irula
Kota
Koya

Pallar
Naidu
Saliya

Thoda
Bondo

Paniya
Pulaya

Vellala
Thiyya
Vannar

Iyengar
Gadaba

Paravar
Parayar
Vadama

Maravar
Mappilla

Vanniyar
Maniyani

Kurumba
Sakkiliyar

Kanikarar
Moopanar

Mukkuvar
Kammalar

Nadar-TNV
Nadar-Cape

Nadar-MDU

Bettakurmba

Kattunaickar
Agamudaiyar

Mullukurumba
Brahacharanam
Kerala Brahmin

Telugu Brahmin
Paniya 0.00
Kattunaickar 0.04 0.00
Kurumba 0.12 0.02 0.00
Irula 0.06 0.01 0.03 0.00
Bettakurmba 0.04 0.11 0.22 0.09 0.00
Mullukurumba 0.04 0.05 0.12 0.03 0.00 0.00
Kanikarar 0.05 0.05 0.14 0.04 0.01 -0.01 0.00
Paravar 0.12 0.10 0.17 0.09 0.09 0.06 0.00 0.00
Thoda 0.22 0.25 0.35 0.24 0.17 0.16 0.08 0.03 0.00
Parayar 0.10 0.07 0.14 0.06 0.07 0.04 -0.03 -0.01 0.06 0.00
Pallar 0.11 0.13 0.20 0.11 0.05 0.05 0.00 0.03 0.07 0.01 0.00
Nadar-TNV 0.10 0.12 0.18 0.08 0.02 0.01 -0.01 0.04 0.11 0.02 0.00 0.00
Maravar 0.11 0.15 0.23 0.15 0.04 0.06 0.02 0.05 0.07 0.03 0.01 0.03 0.00
Nadar-MDU 0.21 0.24 0.33 0.17 0.08 0.07 0.05 0.09 0.15 0.07 0.03 0.00 0.07 0.00
Vanniyar 0.23 0.28 0.37 0.23 0.10 0.12 0.08 0.09 0.10 0.09 0.03 0.03 0.06 -0.01 0.00
Nadar-Cape 0.10 0.14 0.24 0.13 0.04 0.05 0.00 0.02 0.06 0.01 -0.01 0.01 -0.01 0.05 0.04 0.00
Mukkuvar 0.14 0.13 0.22 0.14 0.10 0.07 0.00 0.02 0.05 -0.01 0.02 0.05 0.02 0.10 0.10 0.01 0.00
Agamudaiyar 0.08 0.03 0.08 0.03 0.09 0.04 -0.01 0.06 0.19 0.00 0.05 0.06 0.08 0.13 0.17 0.06 0.03 0.00
Sakkiliyar 0.13 0.09 0.13 0.01 0.08 0.00 0.00 0.05 0.19 0.03 0.05 0.01 0.11 0.02 0.10 0.08 0.09 0.03 0.00
Telugu Brahmin0.20 0.24 0.32 0.16 0.09 0.09 0.04 0.08 0.16 0.04 -0.01 0.01 0.05 -0.03 0.00 0.01 0.08 0.09 0.04 0.00
Vadama 0.22 0.26 0.32 0.24 0.17 0.18 0.13 0.14 0.19 0.10 0.06 0.11 0.07 0.12 0.11 0.05 0.09 0.14 0.19 0.01 0.00
Brahacharanam 0.16 0.18 0.27 0.19 0.12 0.13 0.06 0.08 0.13 0.04 0.03 0.09 0.03 0.13 0.12 0.02 0.00 0.06 0.16 0.04 0.01 0.00
Iyengar 0.13 0.13 0.20 0.12 0.12 0.10 0.04 0.05 0.13 0.01 0.03 0.07 0.05 0.12 0.14 0.01 0.02 0.04 0.10 0.02 0.02 -0.02 0.00
Moopanar 0.10 0.12 0.22 0.11 0.08 0.07 -0.01 0.02 0.09 -0.02 -0.01 0.02 0.00 0.07 0.08 -0.04 -0.02 0.00 0.07 -0.01 0.01 -0.03 -0.04 0.00
Naidu 0.11 0.12 0.23 0.13 0.08 0.07 -0.02 0.01 0.06 -0.02 0.00 0.04 0.01 0.09 0.08 0.00 -0.05 0.00 0.08 0.04 0.06 -0.02 0.00 -0.05 0.00
Kota 0.09 0.08 0.13 0.10 0.09 0.05 0.03 0.06 0.14 0.02 0.04 0.06 0.04 0.12 0.15 0.03 0.00 0.03 0.09 0.08 0.09 0.02 0.00 -0.01 0.01 0.00
Vellala 0.07 0.06 0.15 0.07 0.05 0.02 -0.01 0.05 0.14 -0.01 0.01 0.02 0.02 0.08 0.12 0.01 -0.02 -0.03 0.05 0.03 0.06 -0.01 -0.01 -0.04 -0.04 -0.03 0.00
Pulaya 0.10 0.12 0.20 0.12 0.10 0.06 0.02 0.04 0.08 0.01 0.03 0.05 0.03 0.10 0.10 0.02 -0.01 0.04 0.08 0.08 0.10 0.04 0.03 -0.01 -0.02 0.01 -0.01 0.00
Saliya 0.04 0.07 0.18 0.05 -0.03 -0.03 -0.05 0.02 0.10 -0.02 -0.02 -0.03 -0.01 0.01 0.04 -0.03 0.00 0.00 0.00 0.00 0.08 0.02 0.02 -0.03 -0.03 0.00 -0.05 0.00 0.00
Thiyya 0.15 0.18 0.24 0.17 0.09 0.10 0.06 0.08 0.11 0.05 0.02 0.05 0.02 0.07 0.06 0.00 0.03 0.09 0.12 0.00 0.01 0.00 0.00 -0.02 0.01 0.04 0.02 0.04 0.01 0.00
Nair 0.13 0.15 0.21 0.14 0.08 0.06 0.02 0.05 0.10 0.02 0.00 0.02 0.01 0.03 0.05 0.00 0.01 0.06 0.06 0.00 0.04 0.02 0.01 -0.02 0.00 0.02 -0.01 0.01 -0.01 0.00 0.00
Vannar 0.13 0.21 0.35 0.20 0.01 0.08 0.03 0.09 0.12 0.06 0.01 0.03 0.00 0.05 0.03 0.00 0.05 0.11 0.14 0.02 0.05 0.02 0.07 0.01 0.01 0.08 0.03 0.08 -0.03 0.01 0.03 0.00
Kerala Brahmin 0.15 0.17 0.27 0.14 0.08 0.06 0.01 0.02 0.08 -0.01 -0.03 0.00 0.00 0.01 0.02 -0.03 -0.02 0.04 0.05 -0.07 -0.03 -0.04 -0.06 -0.06 -0.03 -0.01 -0.04 -0.01 -0.03 -0.05 -0.05 0.00 0.00
Mappilla 0.13 0.15 0.22 0.13 0.06 0.05 0.01 0.04 0.09 0.02 -0.01 0.01 0.01 0.02 0.03 -0.01 0.01 0.06 0.05 -0.02 0.04 0.02 0.02 -0.01 0.00 0.03 0.00 0.02 -0.02 0.00 -0.01 0.01 -0.05 0.00
Kammalar 0.09 0.16 0.27 0.12 -0.02 0.02 0.02 0.08 0.15 0.05 0.01 -0.01 0.02 0.00 0.02 0.01 0.08 0.09 0.05 -0.01 0.09 0.08 0.07 0.03 0.06 0.07 0.03 0.07 -0.04 0.03 0.02 -0.03 -0.01 0.00 0.00
Maniyani 0.24 0.28 0.37 0.23 0.12 0.11 0.07 0.09 0.12 0.07 0.02 0.03 0.04 -0.02 -0.02 0.03 0.06 0.14 0.09 -0.03 0.06 0.07 0.09 0.03 0.04 0.10 0.06 0.07 0.02 0.02 0.00 0.03 -0.04 0.00 0.02 0.00
Koya 0.06 0.10 0.17 0.12 0.05
0.20 0.07 0.06 0.11 0.09 0.10 0.10 0.09 0.19 0.20 0.06
0.20 0.00 0.12 0.10 0.15 0.17 0.19 0.14 0.11 0.09 0.11 0.10 0.07 0.11 0.01 0.13 0.12 0.10 0.13 0.11 0.09
Bondo 0.15 0.22 0.30 0.22 0.12 0.15 0.13 0.15 0.21 0.15 0.15 0.15 0.12 0.21 0.21 0.09 0.17 0.18 0.23 0.21 0.22 0.19 0.19 0.15 0.16 0.17 0.15 0.16 0.07 0.16 0.16 0.13 0.18 0.15 0.14 0.22 0.03 0.00
Gadaba 0.40 0.46 0.53 0.44 0.40 0.40 0.37 0.33 0.38 0.35 0.32 0.35 0.30 0.42 0.40 0.29 0.38 0.41 0.47 0.43 0.37 0.39 0.41 0.37 0.37 0.36 0.39 0.37 0.32 0.31 0.34 0.38 0.40 0.33 0.40 0.41 0.22 0.11 0.00

Highest values in Bold

Negative values italised
Values < 0.05 are shaded
Table 13. Matrix of significant Fst P values for genetic distances between populations estimated from Y haplogroup frequencies

Nair

Irula
Kota
Koya

Pallar
Naidu
Saliya

Thoda
Bondo

Paniya
Pulaya
Thiyya

Vellala
Vannar

Iyengar
Gadaba

Paravar
Parayar
Vadama

Maravar
Mappilla

Vanniyar

Kurumba
Maniyani

Moopanar

Sakkiliyar

Kanikarar
Mukkuvar
Kammalar

Nadar-TNV
Nadar-Cape

Nadar-MDU

Bettakurmba
Agamudaiyar

Kattunaickar
Mullukurumba
Brahacharanam
Kerala Brahmin

Telugu Brahmin
Paniya
Kattunaickar +
Kurumba + -
Irula + - -
Bettakurmba - + + +
Mullukurumba + + + + -
Kanikarar + - + - - -
Paravar + + + + + + -
Thoda + + + + + + + +
Parayar + + + + + + - - +
Pallar + + + + + + - + + -
Nadar-TNV + + + + - - - + + + -
Maravar + + + + + + - + + + - +
Nadar-MDU + + + + + + + + + + - - +
Vanniyar + + + + + + + + + + + + + -
Nadar-Cape + + + + - + - - + - - - - + +
Mukkuvar + + + + + + - - + - - + - + + -
Agamudaiyar + - + - + - - + + - + + + + + + -
Sakkiliyar + + + - - - - - + - - - + - + + + -
Telugu Brahmin + + + + - + - + + - - - + - - - - - -
Vadama + + + + + + + + + + + + + + + + + + + -
Brahacharanam + + + + + + + + + - + + + + + - - + + - -
Iyengar + + + + + + - + + - - + + + + - - - + - - -
Moopanar + + + + + + - - + - - - - - + - - - - - - - -
Naidu + + + + + + - - - - - - - + + - - - - - + - - -
Kota + + + + + + - + + + + + + + + + - - + + + - - - -
Vellala + + + + - - - + + - - - - + + - - - - - - - - - - -
Pulaya + + + + + + - + + - + + + + + - - - - + + - - - - - -
Saliya - + + - - - - - + - - - - - - - - - - - + - - - - - - -
Thiyya + + + + + + + + + + + + + + + - + + + - - - - - - + - + -
Nair + + + + + + - + + - - + - - + - - + - - + - - - - - - - - -
Vannar + + + + - + - + + + - - - - - - - + + - - - - - - + - + - - -
Kerala Brahmin + + + + + - - - + - - - - - - - - - - - - - - - - - - - - - - -
Mappilla + + + + + + - + + - - - - - - - - + - - + - - - - + - - - - - - -
Kammalar + + + + - - - + + + - - - - - - + + - - + + - - - + - + - + - - - -
Maniyani + + + + + + + + + + - - + - - - + + + - + + + - - + - + - - - - - - -
Koya + + + + + + - + + + + + + + + + + + + + + + + + + + - + - + + + + + + +
Bondo + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + +
Gadaba + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

No. of Permutations = 110

+ = Significant
- = Not significant
Table 14. Demographic Parameters for SNP data

Discrimin Mean Haplogro Ne

No of W (sudden
ation number of up Expansion (Effective
SN Population haploty N expansion TK r** D*** Fs****
Capacity mismatche Diversity age in YBP Population
pes (k) model)
(k/N) s (p) (h) Size)
1 Paniya 9 82 0.110 1.519 0.700 0.292 2.398 0.0505 -0.6549 * -1.51528 2,355 967
2 Kattunaickar 8 52 0.154 1.479 0.624 5.055 2.442 0.0607 -0.9649 * -1.49036 40,766 985
3 Kurumba 7 38 0.184 1.306 0.418 6.000 2.251 0.2879 -1.1528 * -1.45033 48,387 908
4 Irula 9 105 0.086 1.574 0.635 3.712 2.195 0.1609 -0.4642 * -1.0532 29,935 885
5 BettaKurumba 6 24 0.250 1.862 0.757 3.129 2.236 0.0158 -0.0203 * -0.16348 25,234 902
6 MulluKurumba 6 34 0.176 2.098 0.745 4.404 1.373 0.0348 1.1899 * 1.6772 35,516 554
7 Kanikarar 8 18 0.444 2.471 0.863 3.232 4.948 0.0436 -0.1978 * -1.76098 26,065 1,995
8 Paravar 11 57 0.193 2.384 0.822 3.107 3.857 0.1225 -0.2650 -1.7614 25,056 1,555
9 Thoda 8 33 0.242 2.478 0.828 3.611 3.299 0.1719 -0.0859 -0.6316 29,121 1,330
10 Parayar 10 37 0.270 2.770 0.852 3.516 4.234 0.0948 -0.1347 -1.3184 28,355 1,707
11 Pallar 10 105 0.095 2.750 0.874 3.887 2.572 0.0450 1.0828 0.5229 31,347 1,037
12 Nadar-TNV 8 73 0.110 2.573 0.839 3.772 2.120 0.0534 0.6480 1.0229 30,419 855
13 Maravar 12 92 0.130 2.804 0.893 3.791 3.499 0.0406 0.2569 -0.7653 30,573 1,411
14 Nadar-MDU 7 19 0.368 2.468 0.760 3.905 3.543 0.1126 0.2674 -0.6834 31,492 1,428
15 Vanniyar 8 32 0.250 2.673 0.778 4.046 3.096 0.1073 -0.0674 * -0.1843 32,629 1,249
16 Nadar-Cape 10 25 0.400 2.973 0.920 3.408 5.678 0.0416 -0.4687 -2.0101 27,484 2,289
17 Mukkuvar 6 21 0.286 3.011 0.869 4.975 2.524 0.1624 1.1293 * 0.91489 40,121 1,018
18 Agamudaiyar 7 22 0.318 2.533 0.773 4.610 3.259 0.0769 0.4631 * -0.38988 37,177 1,314
19 Sakkiliyar 3 11 0.273 2.244 0.718 4.349 1.052 0.4632 0.2410 * 2.27778 35,073 424
20 Telugu Brahmin 4 11 0.364 2.956 0.827 4.493 1.956 0.1452 0.8236 * 1.51078 36,234 789
21 Vadama 10 78 0.128 2.802 0.757 4.934 2.861 0.0855 0.6758 0.1614 39,790 1,154
22 Brahacharanam 8 25 0.320 2.687 0.817 5.078 3.668 0.0930 0.8512 * -0.67571 40,952 1,479
23 Iyengar 5 14 0.357 2.923 0.769 5.184 2.330 0.3448 1.2102 * 1.05549 41,806 940
24 Moopanar 8 14 0.571 3.379 0.945 4.111 9.317 0.0684 -0.3013 * -2.18558 33,153 3,757
25 Naidu 7 14 0.500 3.179 0.918 4.269 5.425 0.0490 -0.0533 * -0.94731 34,427 2,188
Contd….Table 14.

26 Kota 9 69 0.130 2.875 0.800 5.224 2.558 0.1895 1.4057 0.7293 42,129 1,032
27 Vellala 6 14 0.429 2.868 0.835 4.990 3.429 0.1013 1.1181 -0.0225 40,242 1,383
28 Pulaya 8 23 0.348 3.368 0.890 4.810 3.919 0.1157 0.8191 -0.1381 38,790 1,580
29 Saliya 7 11 0.636 2.727 0.909 3.419 7.237 0.0400 -0.0062 * -1.93713 27,573 2,918
30 Thiyya 12 127 0.094 2.947 0.841 4.342 3.099 0.0515 0.8327 * -0.01664 35,016 1,250
31 Nair 11 62 0.177 3.075 0.882 4.073 3.786 0.0773 0.5257 -0.6095 32,847 1,526
32 Vannar 6 15 0.400 2.527 0.881 3.602 3.429 0.0571 0.5470 * -0.35381 29,048 1,383
33 Kerala Brahmin 5 9 0.556 3.333 0.861 4.602 3.829 0.1659 0.6011 * 0.27937 37,113 1,544
34 Mapilla 11 60 0.183 2.989 0.867 4.017 3.752 0.0615 0.1882 -0.6923 32,395 1,513
35 Kammala 5 19 0.263 2.421 0.801 3.947 1.864 0.0645 0.6971 * 1.14461 31,831 751
36 Maniyani 7 18 0.389 2.758 0.804 4.133 3.720 0.1307 0.1917 * -0.48008 33,331 1,500
37 Koya 6 100 0.060 1.635 0.763 2.191 1.242 0.0247 0.9132 1.2520 17,669 501
38 Bondo 6 92 0.065 1.354 0.761 1.570 1.284 0.0386 0.3192 * 0.4760 12,661 518
39 Gadaba 7 91 0.077 0.905 0.515 2.188 1.612 0.1128 -1.2584 * -1.6871 17,645 650

* = No molecular diversity within a sample while performing Fu's test

** = rageddeness index , significant below 0.05 indicates demographic expansion
*** = Tajima's D. Negative D values, P<0.05 indicate Population expansion. Positive D indicates bottleneck
**** = Fs, singnificant below 0.2%. Large negative Fs indicates population expansion
Table 15. Modal Haplotypes identified in various populations (in the context of various haplogroups)

Haplogroup

Sl.No
DYS19

DYS426
DYS391
DYS437
DYS392
DYS438
DYS393
DYS635
DYS439
DYS390
DYS448
DYS456
DYS458

DYS389a

DYS389b

Population
Y GATA H4

% frequency

N chromosome +
Irula 9 4 10 11 10 15 16 11 10 11 13 20 13 17 13 23 18 15 18
Irula 1 4 10 11 10 14 15 12 10 11 13 25 11 16 12 24 19 13 18
Irula 2 5 12.5 11 10 14 15 11 10 12 13 22 12 17 12 21 20 13 19
Irula 3 4 10 11 10 14 15 11 10 12 13 22 12 18 12 21 20 13 18
"H-M69" Kattunaickar 4 4 15.4 11 10 14 15 11 9 11 13 20 11 16 13 22 19 16 16
Mullukurumba 5 8 50 11 10 14 15 11 9 12 12 20 11 16 13 22 20 17 17
Kurumba 6 4 21.1 11 10 14 15 11 9 12 13 20 11 17 13 22 19 15 18
Kota 7 5 25 11 10 14 15 11 9 12 12 20 11 17 13 22 19 16 17
Koya 8 8 50 11 10 14 15 11 9 12 12 20 11 16 14 22 19 16 20

No. of alleles
10 1 1 2 2 2 2 2 2 3 3 3 3 4 4 4 5
identified

"R2-M124" Kota 11 5 41.7 12 10 16 14 10 11 11 14 24 10 15 13 23 20 16 18

"R1a1-M17" Kota 12 8 80 12 11 14 15 11 11 12 13 23 10 18 13 25 14 16 14

* = Marker seuquence Original 8 5 9 1 6 10 16 7 15 11 3 2 4 12 13 14

Table 16. Y-STR Gene diversity Estimates (Heterozygosity) for Individual Populations based on Y-STR data (estimates for sample size >2)

Heterozygosity & (N studied) in the context of various Haplogroups

Population All C** F* H J L O R2** R1a1
Paniya 0.513(47) 0.274 (10) 0.372 (12) 0.395 (21) *** ***
Kattunaickar 0.491 (38) 0.488 (7) 0.385 (26) 0.104 (3) ***
Kurumba 0.453 (27) *** *** 0.288 (19) *** 0.813 (2)
Irula 0.567(64) 0.167 (3) 0.300 (6) 0.501 (40) *** 0.342 (9) 0.125 (2)
BettaKurumba 0.424 (12) 0.175 (5) 0.479 (4) *** *
MulluKurumba 0.563 (21) 0.500 (3) 0.170 (8) 0.136 (6) 0.563 (3)
Paravar 0.634 (26) *** 0.550 (5) 0.375 (9) 0.225 (5) *** 0.250 (2) ***
Thoda 0.592 (18) *** 0.208 (3) 0.224 (9) *** *** 0.250 (2)
Parayar 0.646 (4) *** *** ***
Pallar 0.691 (11) *** *** *** *** 0.500 (5)
Nadar-TNV 0.650 (52) 0.496 (6) 0.615 (14) 0.458 (3) 0.420 (13) 0.573 (4) 0.646 (4)
Vadama 0.630 (52) 0.542 (3) *** 0.640 (7) 0.750 (3) 0.514 (10) *** 0.432 (21)
Brahacharnam 0.636 (12) 0.604 (3) *** 0.563 (5)
Iyengar 0.643 (7) 0.646 (3) 0.562 (4)
Battar$ 0.683 (6) *** *** ***
Kota 0.567 (52) 0.396 (3) 0.279 (20) 0.479 (3) 0.022 (10) 0.292 (12)
Thiyya 0.640 (32) *** *** 0.485 (7) 0.531 (4) 0.567 (6) 0.438 (2) 0.327 (11)
Koya 0.492 (31) 0.209 (11) 0.237 (16) 0.436 (3) ***
Bondo 0.452 (35) 0.125 (2) 0.212 (9) 0.563 (3) 0.259 (13)
Gadaba 0.492 (25) 0.443 (22)
** = estimates for more than 1 individual shown
*** = insufficient number of inviduals for reliable estimates of Variance
$ = Excluded from all futher analysis since insufficient number of individulas for reliable estimates of variance
Highest values in bold
Lowest values italised
Table 17. Variance in Repeat Numbers at 16 microsatellite Loci within HGs with sample sizes >2 in the Populations studied

Population
Mean

DYS19
DYS390
DYS391
DYS392
DYS393
DYS426
DYS437
DYS438
DYS439
DYS448
DYS456
DYS458
DYS635
Variance

DYS389a

N studied
DYS389b
Y GATA H4

All Populations studied

C 22 1.154 0.221 0.191 1.309 0.191 0.000 0.515 0.059 0.059 0.235 0.471 0.059 0.500 1.860 8.382 0.316 0.970
H 201 0.478 0.515 0.580 1.010 0.186 0.320 0.512 0.221 0.264 0.445 0.895 0.552 1.490 1.779 3.900 0.351 0.844
J 34 0.685 0.735 0.453 0.981 0.057 0.332 0.315 0.151 0.168 0.229 0.757 1.463 1.002 1.530 3.584 0.250 0.793
L 49 0.338 0.374 0.400 0.490 0.061 1.451 0.521 0.133 0.221 0.232 0.949 0.039 0.418 1.847 2.902 0.317 0.668
F* 56 1.068 0.413 0.440 0.741 0.137 0.016 0.635 0.016 0.351 0.049 0.880 0.888 0.899 1.519 1.256 0.629 0.621
R2 30 0.610 0.110 1.691 2.316 0.059 0.110 0.154 0.154 0.346 0.110 0.721 0.640 0.191 0.515 0.691 0.721 0.571
O 43 0.324 0.399 0.732 0.402 0.308 0.105 0.686 0.026 0.000 0.475 0.245 2.299 0.581 1.065 0.618 0.347 0.538
R1a1 62 0.437 0.226 0.620 0.865 0.253 0.616 0.133 0.203 0.286 0.145 0.569 0.268 0.484 1.716 0.338 0.609 0.486
Haplogroup C
Paniya 10 1.218 0.164 0.000 0.218 0.000 0.000 0.473 0.000 0.000 0.000 0.618 0.000 0.255 0.091 1.073 0.000 0.257
Vadama 3 0.000 0.000 0.333 0.333 0.333 0.000 1.333 0.333 0.333 1.333 0.333 0.333 0.333 0.333 0.333 1.333 0.458
Irula 3 0.000 0.000 0.333 0.000 0.333 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 3.000 40.333 0.000 2.750
Haplogroup F*
Koya 11 0.164 0.000 0.255 0.000 0.255 0.000 0.000 0.000 0.000 0.000 0.873 0.000 0.000 0.164 0.218 0.273 0.137
Bettakurumba 5 0.000 0.000 0.300 0.000 0.000 0.000 0.200 0.000 0.000 0.000 0.700 0.800 0.000 0.300 0.000 0.000 0.144
Bondo 9 1.000 0.000 0.194 0.000 0.111 0.000 0.194 0.000 0.000 0.000 0.694 0.111 0.278 0.111 0.111 1.000 0.238
Irula 6 0.267 0.267 0.167 0.000 0.000 0.000 0.267 0.000 0.267 0.000 0.000 1.067 1.067 0.967 0.000 0.267 0.287
Paniya 12 0.750 0.000 0.265 0.424 0.083 0.000 0.545 0.083 0.000 0.083 0.811 0.636 0.750 0.992 0.265 0.000 0.356
Kota 3 4.333 0.000 0.333 3.000 0.000 0.000 0.000 0.000 0.333 0.000 0.333 0.333 0.333 0.000 0.333 0.333 0.604
Nadar-TNV 6 1.067 0.267 0.267 0.267 0.000 0.000 0.400 0.000 0.300 0.167 0.267 0.267 1.367 2.827 3.500 0.667 0.727
Kattunaickan 7 0.286 0.476 0.333 2.476 0.143 0.143 0.286 0.000 0.286 0.143 2.571 0.619 0.810 4.143 2.333 0.143 0.949
Mullukurumba 3 1.333 0.000 3.000 1.333 0.000 0.000 0.333 0.000 1.333 0.000 0.333 1.333 3.000 1.333 1.000 4.000 1.146
Haplogroup H
Thoda 3 0.163 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.333 0.333 0.333 0.333 0.094
Mullukurumba 8 0.000 0.000 0.000 0.000 0.214 0.000 0.000 0.000 0.214 0.000 0.000 0.286 1.929 0.000 0.214 0.857 0.232
Koya 16 0.000 0.783 0.000 0.383 0.000 0.383 0.133 0.000 0.063 0.117 0.296 0.063 0.250 1.600 0.117 0.117 0.269
Kota 20 0.934 0.274 0.576 0.450 0.200 0.000 0.221 0.050 0.095 0.168 0.463 0.050 0.450 0.175 0.134 0.095 0.271
Bettakurumba 4 0.250 0.000 0.250 1.000 0.000 0.000 0.667 0.000 0.250 0.250 0.667 0.917 0.250 0.917 0.667 0.250 0.396
Kurumba 19 0.099 0.287 0.468 0.275 0.053 0.099 0.164 0.053 0.053 0.140 0.099 0.164 0.333 2.667 1.813 0.140 0.432
Paniya 21 1.133 0.048 0.490 0.762 0.433 0.000 0.462 0.648 0.000 0.190 0.190 0.748 1.757 1.348 0.214 0.000 0.526
Brahacharanam 3 0.333 0.333 0.333 0.333 0.000 0.000 1.333 0.333 0.333 0.333 0.333 1.000 0.333 2.333 0.000 1.000 0.542
Thiyya 7 0.476 0.143 1.476 1.286 0.238 0.000 0.905 0.000 0.143 0.286 1.333 0.238 1.143 0.476 1.286 0.000 0.589
Kattunaickar 26 0.455 0.535 0.215 0.295 0.106 0.215 0.106 0.000 0.265 0.326 0.266 0.154 1.386 1.284 5.458 0.215 0.705
Paravar 5 0.700 0.300 0.200 0.300 0.500 0.200 0.800 0.200 0.000 0.200 2.200 0.700 1.700 0.200 3.000 0.200 0.712
Iyengar 3 0.333 1.000 1.333 0.333 0.000 0.000 4.333 0.333 1.333 0.333 1.000 1.000 0.333 2.333 0.333 0.000 0.896
 Irula 40 0.244 0.563 0.661 1.446 0.164 0.677 0.297 0.100 0.179 0.128 0.563 0.743 1.208 1.037 8.131 0.336 1.030
Nadar-TNV 14 0.729 0.629 0.896 1.863 0.250 0.800 0.917 0.000 0.200 0.333 1.467 1.000 1.067 1.850 5.067 0.396 1.091
Vadama 7 0.143 0.619 0.810 4.143 0.333 0.810 0.333 0.333 1.000 1.286 2.667 0.619 0.571 1.143 3.238 0.476 1.158
Bondo 3 0.333 3.000 0.333 8.333 0.333 1.333 0.333 0.000 0.333 0.333 0.333 5.333 0.000 1.000 3.000 0.000 1.521
Haplogroup J
Paravar 9 0.361 1.111 0.250 0.361 0.000 0.000 0.000 0.194 0.111 0.111 0.361 0.944 0.250 0.861 0.778 0.000 0.356
Thoda 9 0.000 0.111 0.500 0.000 0.111 0.444 0.000 0.000 0.000 0.250 0.444 0.000 0.000 0.111 4.000 0.278 0.391
Kattunacikar 3 0.000 0.000 0.000 0.000 0.000 0.333 0.000 0.000 0.000 0.000 0.000 0.000 0.000 6.333 0.000 0.000 0.417
Kota 3 0.333 0.333 0.333 0.333 0.000 0.000 0.333 0.333 0.333 0.000 1.000 1.333 0.333 0.000 5.333 0.000 0.646
Nadar-TNV 3 2.333 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.333 0.000 0.333 2.333 1.000 2.333 1.000 0.000 0.667
Vadama 3 0.333 0.333 1.000 0.333 0.000 2.333 1.000 1.000 0.333 1.000 1.000 0.333 1.000 1.333 4.333 0.000 0.979
Thiyya 4 1.000 0.250 0.333 3.583 0.250 0.250 0.250 0.000 0.250 0.000 0.250 1.667 0.917 5.583 1.583 0.000 1.010
Haplogroup L
Mullukurumba 6 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.267 0.000 0.267 0.267 1.767 0.000 0.160
Paravar 5 0.000 0.000 0.000 0.300 0.200 0.000 0.000 0.800 0.000 0.000 0.200 0.000 0.300 0.000 2.700 0.300 0.300
Irula 9 0.194 0.111 0.194 0.111 0.194 1.778 1.000 0.111 0.111 0.111 0.750 0.000 0.194 2.000 0.361 0.194 0.464
Nadar-TNV 13 0.244 0.333 0.397 0.077 0.000 1.077 0.397 0.000 0.141 0.244 1.077 0.000 0.526 0.897 2.603 0.359 0.523
Vadama 10 0.678 0.267 0.456 1.167 0.000 2.100 0.678 0.178 0.400 0.489 0.622 0.100 0.489 2.400 5.122 0.322 0.967
Thiyya 6 0.567 0.667 0.700 1.500 0.000 3.600 0.667 0.000 0.800 0.300 0.400 0.167 0.700 3.767 1.467 0.300 0.975
Haplogroup O
Bondo 13 0.141 0.000 1.077 0.077 0.256 0.000 0.231 0.000 0.000 0.000 0.141 0.000 0.769 1.256 0.308 0.231 0.280
Gadaba 22 0.468 0.537 0.355 0.528 0.355 0.182 0.539 0.045 0.000 0.823 0.314 4.017 0.242 0.970 0.684 0.374 0.652
Koya 3 0.000 1.333 0.333 0.333 0.333 0.000 3.000 0.000 0.000 0.000 0.333 0.000 2.333 1.000 2.333 0.000 0.708
Haplogroup R2
Kota 10 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.178 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.011
Nadar-TNV 4 0.250 0.333 2.250 0.250 0.250 0.250 0.250 0.000 0.667 0.250 2.250 0.250 0.250 0.917 2.917 0.250 0.724
Mullukurumba 3 3.000 0.000 1.333 9.333 0.000 0.333 0.333 0.333 0.333 0.333 1.333 1.333 0.333 0.000 0.333 3.000 1.354
Haplogroup R1a1
Thiyya 11 0.273 0.091 0.418 0.564 0.273 0.491 0.164 0.000 0.000 0.000 0.000 0.091 0.473 0.964 0.091 0.273 0.260
Kota 12 0.083 0.273 0.273 1.333 0.242 0.000 0.152 0.152 0.083 0.083 0.750 0.083 0.265 1.295 0.333 0.333 0.358
Vadama 21 0.433 0.233 0.590 0.690 0.248 0.562 0.048 0.100 0.190 0.190 0.333 0.390 0.390 1.029 0.090 0.490 0.376
Iyengar 4 0.333 0.250 0.667 0.250 0.333 0.000 0.250 0.333 0.000 0.250 0.250 0.667 0.250 1.667 0.250 0.917 0.417
Brahacharanam 5 0.267 0.267 0.667 0.700 0.267 0.667 0.167 0.300 0.167 0.167 1.500 0.400 1.467 1.367 0.000 0.167 0.533
Pallar 5 0.200 0.200 2.200 0.800 0.300 0.200 0.200 0.800 0.800 0.300 0.800 0.000 0.200 4.300 0.300 0.300 0.744
Nadar-TNV 4 2.917 0.250 1.333 2.250 0.333 4.917 0.250 0.000 2.250 0.000 2.250 0.333 0.667 4.917 2.917 2.000 1.724

Highest values in bold

Lowest values italised
Table 18a. Y-STR Allele Frequencies among various haplogroups studied.

Locus / Repeat
HG C HG F* HG H HG J HG L HG O HG R2 HG R1a1
unit

DYS19
13 0.041 0.059 0.016
14 0.177 0.090 0.441 0.735 0.132 0.882 0.032
15 0.588 0.177 0.697 0.441 0.184 0.763 0.508
16 0.059 0.435 0.169 0.059 0.041 0.079 0.429
17 0.294 0.194 0.030 0.059 0.026 0.059 0.016
18 0.059 0.016 0.015
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS389a
11 0.005 0.026
12 0.706 0.097 0.189 0.294 0.612 0.079
13 0.294 0.500 0.557 0.265 0.327 0.684 0.882 0.667
14 0.403 0.229 0.441 0.061 0.211 0.118 0.333
15 0.020
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS389b
14 0.010 0.029
15 0.035 0.059 0.041 0.053 0.706 0.032
16 0.235 0.323 0.517 0.618 0.714 0.474 0.095
17 0.765 0.613 0.358 0.294 0.184 0.289 0.176 0.460
18 0.032 0.070 0.061 0.184 0.059 0.397
19 0.032 0.010 0.059 0.016
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS390
18 0.059
20 0.032 0.015 0.029 0.059
21 0.758 0.224 0.020 0.016
22 0.471 0.145 0.502 0.029 0.857 0.026 0.016
23 0.294 0.032 0.159 0.412 0.061 0.647 0.079
24 0.059 0.070 0.382 0.020 0.184 0.235 0.143
25 0.176 0.032 0.025 0.147 0.041 0.763 0.651
26 0.005 0.026 0.095
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS391
8 0.005
9 0.015 0.020
10 0.765 0.839 0.846 0.941 0.939 0.474 0.941 0.476
11 0.235 0.161 0.124 0.059 0.041 0.500 0.059 0.524
12 0.010 0.026
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Contd…..Table 18a
DYS392
7 0.005
9 0.029 0.016
10 0.015 0.059 0.020 0.882 0.048
11 1.000 0.984 0.836 0.853 0.102 0.026 0.118 0.841
12 0.016 0.119 0.029 0.048
13 0.020 0.029 0.974 0.016
14 0.005 0.776 0.016
15 0.082 0.016
17 0.020
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS393
11 0.015 0.755 0.026
12 0.118 0.065 0.368 0.588 0.143 0.026 0.016
13 0.235 0.387 0.512 0.382 0.082 0.553 0.176 0.857
14 0.647 0.419 0.095 0.029 0.020 0.395 0.824 0.127
15 0.129 0.005
16 0.005
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS426
10 0.005 0.088 0.026 0.016
11 0.941 0.984 0.876 0.853 0.918 0.974 0.176 0.095
12 0.059 0.016 0.080 0.059 0.061 0.824 0.841
13 0.040 0.020 0.048
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS437
14 0.941 0.500 0.716 0.206 0.143 1.000 0.059 0.921
15 0.059 0.484 0.259 0.794 0.776 0.176 0.032
16 0.025 0.082 0.765 0.032
17 0.016 0.016
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS438
9 0.059 0.016 0.463 0.824 0.041 0.026
10 0.941 0.952 0.463 0.147 0.735 0.921 0.118 0.016
11 0.032 0.060 0.029 0.224 0.026 0.882 0.841
12 0.015 0.143
13 0.026
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS439
10 0.032 0.050 0.029 0.041 0.882 0.825
11 0.412 0.145 0.517 0.235 0.122 0.053 0.095
12 0.471 0.516 0.224 0.441 0.469 0.737 0.059 0.032
Contd…..Table 18a
13 0.118 0.226 0.174 0.265 0.245 0.211 0.059 0.048
14 0.065 0.035 0.029 0.122
15 0.067
1.000 1.051 1.000 1.000 1.000 1.000 1.000 1.000
DYS448
10 0.026
14 0.026
15 0.005
16 0.005
17 0.048 0.059
18 0.516 0.129 0.147 0.789
19 1.000 0.194 0.627 0.324 0.959 0.158 0.294 0.175
20 0.226 0.219 0.088 0.041 0.647 0.730
21 0.016 0.010 0.412 0.095
22 0.005 0.029
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS456
12 0.020
13 0.097 0.164 0.294
14 0.235 0.081 0.035 0.206 0.063
15 0.529 0.661 0.418 0.412 0.571 0.632 0.235 0.603
16 0.235 0.129 0.289 0.088 0.347 0.263 0.765 0.270
17 0.070 0.082 0.079 0.063
18 0.032 0.005 0.026
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS458
13 0.020
14 0.016 0.045 0.029 0.163 0.026 0.127
15 0.065 0.045 0.235 0.429 0.079 0.270
16 0.588 0.210 0.194 0.118 0.224 0.447 0.118 0.413
17 0.118 0.226 0.274 0.529 0.061 0.211 0.235 0.095
18 0.235 0.403 0.313 0.029 0.061 0.237 0.647 0.048
19 0.065 0.090 0.029 0.020 0.016
20 0.040 0.029 0.020 0.032
21 0.059 0.016
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
DYS635
11 0.059 0.005
18 0.025 0.020
19 0.005 0.029 0.026
20 0.443 0.206 0.020 0.053
21 0.176 0.468 0.219 0.235 0.102 0.658 0.059 0.016
Contd…..Table 18a
22 0.471 0.274 0.134 0.118 0.061 0.184 0.016
23 0.235 0.177 0.020 0.118 0.224 0.079 0.118 0.825
24 0.048 0.045 0.118 0.265 0.765 0.127
25 0.059 0.016 0.055 0.176 0.224 0.059
26 0.016 0.050 0.082 0.016
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
Y GATA H4
8 0.016
9 0.016 0.059
10 0.059 0.025 0.020 0.421 0.032
11 0.647 0.677 0.463 0.588 0.347 0.526 0.588 0.476
12 0.294 0.226 0.488 0.412 0.612 0.053 0.294 0.413
13 0.065 0.025 0.020 0.059 0.079
1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
N 17 62 201 34 49 38 17 63

Marker with highest frequency in Bold

Marker with lowest frequency Italised
Diagnostic marker Higlighted
Table 18b. DYS19 allele frequency in different populations
HG H-M69 HG R1a1-M17

Population

DYS19=13
DYS19=14
DYS19=15
DYS19=16
DYS19=17
DYS19=18
DYS19=13
DYS19=14
DYS19=15
DYS19=16
DYS19=17

WE EE
Paniya 5 (24) 1 (5) 11 (52) 4 (19)
Kattunaickar 1 (38) 22 (85) 2 (8) 1 (38)
Kurumba 17 (89) 2 (11)
Irula 31 (79) 8 (20)
Bettakurumba 1 (25) 3 (75)
Mullukurumba 8 (100)
Paravar 2 (40) 2 (40) 1 (20)
Thoda 1 (33) 2 (67)
Pallar 1 (25) 4 (75)
Nadar-TNV 4 (25) 8 (50) 3 (19) 1 (6) 1 (25) 1 (25) 1 (25) 1 (25)
Vadama 1 (14) 6 (86) 2 (10) 10 (48) 9 (43)
Brahacharanam 2 (33) 4 (67)
Iyengar 1 (33) 2 (67) 2 (50) 2 (50)
Kota 1 (5) 17 (85) 2 (10) 11 (91) 1 (9)
Thiyya 2 (29) 4 (57) 1 (14) 5 (45) 6 (54)
Koya 16 (100)
Bondo 1 (33) 2 (67)

Percentage frequency given in bracket

WE = Western Europe
EE = Eastern Europe
Table 19. Demographic Parameters from Y-STR data
Most
Average Mean W Ne
Frequ No of Mean
Gene number of (sudden Expansion (Effective
Population ent haplotyp TK r** Expansion
Diversity mismatche expansio age in YBP Populatio
(MF) es (k) Age of HG
(h) s (p) n model) n Size)
HG
Haplogroup C
Bondo 2 2.000 *
Irula 3 0.167 2.667 *
Kurumba 1 *
Paniya MF 10 0.274 4.378 *
Paravar 1 *
Parayar 1 *
Thiyya 1 *
Vadama 3 0.542 8.667 7.376 1.291 0.444 59,484 521 59,484
Total 22
Total / N
Haplogroup F*
Bettakurumba MF 5 0.175 2.800 *
Koya 11 0.209 3.345 *
Bondo 9 0.212 3.389 2.495 0.894 0.121 20,121 360
Irula 6 0.300 4.800 1.580 3.220 0.400 12,742 1,298
Paniya MF 12 0.372 5.955 4.406 1.548 0.070 35,532 624
Kota 3 0.396 6.333 3.505 2.828 0.444 28,266 1,140
Kattunaickar 7 0.488 7.810 4.225 3.585 0.116 34,073 1,446
Nadar-TNV 6 0.496 7.933 7.094 0.840 0.053 57,210 339
Mullukurumba MF 3 0.500 8.000 3.641 4.359 1.111 29,363 1,758
Total 57 26.946
Total / N 3.849 31,044 31,044
 Haplogroup H
Mullukurumba MF 8 0.170 2.714 1.844 0.870 0.204 14,871 351
Thoda 3 0.208 3.333 1.097 2.236 1.000 8,847 902
Koya 16 0.237 3.792 0.688 3.104 0.198 5,548 1,252
Kota MF 20 0.279 4.468 2.062 2.407 0.069 16,629 971
Kurumba MF 19 0.288 4.608 1.839 2.769 0.014 14,831 1,117
Kattunaickar MF 26 0.385 6.154 3.121 3.033 0.026 25,169 1,223
Paniya MF 21 0.395 6.314 4.428 1.886 0.021 35,710 760
Bettakurumba MF 4 0.479 7.667 4.174 3.493 0.444 33,661 1,408
Thiyya 7 0.485 7.762 6.110 1.652 0.077 49,274 666
Irula MF 40 0.501 8.019 6.185 1.835 0.026 49,879 740
Paravar 5 0.550 8.800 8.101 0.699 0.160 65,331 282
Bondo 3 0.563 9.000 4.641 4.359 0.667 37,427 1,758
Brahacharanam 3 0.604 9.667 *
Nadar-TNV 16 0.615 9.833 *
Vadama 7 0.640 10.238 *
Iyengar MF 3 0.646 10.333 *
Total 201 44.290
Total / N 3.691 29,765 29,765

Haplogroup J
Kattunaickar 3 0.104 1.667 *
Thoda MF 9 0.224 3.583 2.303 1.280 0.100 18,573 516
Paravar MF 9 0.375 6.000 4.414 1.586 0.135 35,597 640
Nadar-TNV 3 0.458 7.333 *
Kota 3 0.479 7.667 6.034 1.633 0.444 48,661 658
Thiyya 4 0.531 8.500 *
Vadama 3 0.750 12.000 *
Total 34 12.751
Total / N 4.250 34,277 34,277
 Haplogroup L
Mullukurumba MF 6 0.136 2.200 1.862 0.338 0.293 15,016 136
Paravar 5 0.225 3.600 *
Irula MF 9 0.342 5.472 2.596 2.876 0.390 20,935 1,160
Nadar-TNV MF 13 0.420 6.718 5.622 1.096 0.038 $ 45,339 442
Vadama 10 0.514 8.222 5.467 2.755 0.057 44,089 1,111
Thiyya 6 0.567 9.067 *
Total 49 15.547
Total / N 3.887 31,345
Haplogroup O
Bondo 13 0.259 4.141 2.366 1.775 0.126 19,081 716
Koya 3 0.436 7.000 *
Gadaba MF 22 0.443 7.087 6.073 1.014 0.030 48,976 409
Total 38 8.439
Total / N 4.220 34,028 34,028
Haplogroup R2
Kota MF 10 0.022 0.356 *
Irula 2 0.125 2.000 *
Paravar 2 0.250 4.000 *
Thoda 2 0.250 4.000 *
Thiyya 2 0.438 7.000 *
Mullukurumba MF 3 0.563 9.000 3.708 5.292 0.444 29,903 2,134
Nadar-TNV MF 59 0.573 9.167 5.346 3.821 0.278 43,113 1,541
Kurumba 2 0.813 13.000 *
Kattunaickanr 1 *
Bettakurumba 1 *
Pallar 1 *
Total 85 9.054
Total / N 4.527 36,508
 Haplogroup R1a1
Kota MF 12 0.292 4.667 1.754 2.912 0.111 14,145 1,174
Thiyya MF 11 0.327 5.236 *
Brahacharanam MF 5 0.563 5.400 *
Vadama MF 21 0.432 6.905 *
Pallar 5 0.500 8.000 *
Iyengar MF 4 0.562 9.000 *
Nadar -TNV 4 0.646 10.333 *
Total / N 62 14,145

* = Imposible to estimate the parameters of the sudden expansion model of Rogers 1995
using the current observed mismatch distribution
** = rageddeness index , significant below 0.05 indicates demographic expansion
P values for Chi square between observed and expected mismatches are significant
$ = significant raggedness index
Table 20a. Synopsis of population histories through various statistics applied for Y SNP
Statistics based on HG frequency
HG Frequency$ Radial Dendrogram SNP HG diversity Tajima's D Fs (table Age in ybp
Group Popluation N Fst (tables 12,13)
(table 8) (fig. 15a) (table 8) (table 14) 14) (table 14)
SNP
Significantly Higher distance with
Group I Paniya 82 C, F* , H Distant in H branch Low Negative 2,354**
Plains populations
Significantly Higher distance with
Kattunaickan 52 F*, H Distant in H branch Low Negative 40,766
Plains populations
Kurumba 38 H Distant in H branch Highest Fst Lowest Negative 48,387
Significantly Higher distacet with
Group II Irula 105 C, F*, H, L Most Distant in H branch Low Negative 29,935
Plains populations
Distant in F* branch with H
Bettakurumba 24 F*, H, L Less distant with hill tribes Low Negative 25,233**
and L
Mullukurumba 34 F*, H, L, R2 H branch Less distant with hill tribes Low Positive 35,516**
Group III Kanikaran 18 F, G, H, J, L, Q, R2 H branch Less distant with hill tribes High 26,065
Paravar 57 H, J, Q, L J branch Less distant with hill tribes High Negative$ 25,056
Distant form Hills and Plains
Thoda 33 C, J, L, R2 J branch High 29,121
Populations
Less distant form Plains
Group IV Parayar 37 G, H, J, L, R2 Most proximal in H branch High Negative 28,355
Populations
Less distant form Plains
Pallar 105 G, H, J, L, R2, R1a1 Proximal in L branch High Positive 31346**
Populations
Less distant form Plains
Nadar TNV 73 F*, G, H, L, Q, R2 L branch High 30,419
Populations
Proxiaml in F* branch without Less distant form Plains
Maravar 92 F*, G, J, Q, R2 High Negative 30572**
with H and L Populations
Less distant form Plains
Nadar MDU 19 L, Q, R2 Most distal in L branch High Negative 31,492
Populations
Less distant form Plains
Vanniyar 32 C, F*, L, R2, R1a1 Distal in L branch High 32,629
Populations
Most proxiaml in F* branch Less distant form Plains
Nadar Cape 25 C, F*,G, J, L, O, R1a1 Highest Negative 27,484
without with H and L Populations
Less distant form Plains
Mukuvar 21 H, J, R2, R1a1 R2 branch near H High Positive 40,121
Populations
Less distant form Plains
Agamudaiyar 22 G, H, R2 H branch High 37,177
Populations
Less distant form Plains
Sakkiliyar 11 H, L, R H branch High 35,073
Populations
Less distant form Plains
Group V Telugu Brahmin 11 G, L, R2 L branch High 36,234
Populations
 Less distant form Plains
Vadama 78 C, L, R1a1 Distal R branch High 39,790
Populations
Less distant form Plains
Groups VI Brahacharanam 25 H, J, R1a1 Distal R branch High 40,952
Populations
Less distant form Plains
Iyengar 14 H, J, R1a2 R branch High Positive 41,806
Populations
Less distant form Plains
Moopanar 14 C, G, H, Q, R1a1 R branch Highest 33,153**
Populations
Less distant form Plains
Naidu 14 C, H, J, R2, R1a1 R2 branch near H High 34,427
Populations
Less distant form Plains
Kota 69 H, Q, R2, R1a1 R2 branch near H High Positive 42,129
Populations
Less distant form Plains
Vellala 14 H, R2, R1a1 R2 branch near H High Positive Negative 40,242
Populations
Less distant form Plains
Kerala Pulaya 23 C, H, J, R2 J branch High Negative 38,790
Populations
Less distant form Plains
Saliya 11 F*, H, L, O, R2 Near O branch High 27,573
Populations
Less distant form Plains
Thiyya 127 C, J, L, R2, R1a1 R branch High 35,016
Populations
Less distant form Plains
Nair 62 L, Q, R2, R1a1 R branch High Negative 32,847
Populations
Distant in F* branch with H Less distant form Plains
Vannan 15 F, L, R1a1 High 29,048
and L Populations
Less distant form Plains
Kerala Brahmin 9 H, J, L, R2, R1a1 R branch High 37,113
Populations
Less distant form Plains
Mapilla 60 J, L, R2, R1a1 Most proximal in L branch High Negative 32,395
Populations
Distant in F* branch with H Less distant form Plains
Kammalar 19 F, H, L, R2, R1a1 High 31,831
and L Populations
Less distant form Plains
Maniyani 18 L, Q, R2, R1a1 L branch High 33,331
Populations
Orissa Koya 100 F, H, O O branch Distant form most populations Low 17,669**
Bondo 92 F, O O branch Distant form most populations Low 12,661**
Gadaba 91 O O branch Highest distance Lowest Negative 17,645

* = Highest in bold $ = population expansion

** = Significant raggedness
*** = Sample size too low, excluded from analysis
Table 20b Synopsis of Population Histories through various statistics applied for Y STR
Gene Diverstiy
Founder Gene Diverstiy
(Age of
Group Popluation Haplotypes for Y N Variance (table 18) Network N Variance (Age of Network Dendrogram N
Expansion) table
STR (Table 15) Expansion)
20
C F*
Torso, separate Betakurumba, Paniya,
Group I Paniya 10 0.257 0.274 Close cluster 12 0.356 0.372 (35,532**) 21
branch Kattunaickan 2nd branch

Betakurumba, Paniya,
Kattunaickan 1 for HG H Very little HG C 7 0.949 0.488 (34,072) Torso 26
Kattunaickan 2nd branch
Kurumba Very little HG C Very little F* 19

Group II Irula 4 for HG H 3 2.750 0.167 Periphery 6 0.287 0.300 (12,741) Torso 3rd branch 40

Betakurumba, Paniya,
Torso, Out group
Bettakurumba No HG C 5 0.144 0.175 Kattunaickan 2nd branch, 4
Joins
Most distant
Mullukurumba 1 for HG H No HG C 3 1.146 0.500 (29,363) Separate branch 3rd branch 8

Group III Paravar Very little HG C Very little F* 5

Thoda *** Very little F* 3

Group IV Pallar Very little HG C Very little F*
Nadar TNV No HG C 6 0.727 0.496 (57,210**) Periphery 3rd branch 14

Group V Vadama 3 0.542 (59,484) Periphery Very little F* 7

0.458
Groups VI Brahacharanam No HG C Very little F* 3
Iyengar No HG C No F* 3
1each for HG H,
Kota No HG C 3 0.604 0.396 (28,266) Periphery 3rd branch 20
R2, R1a1
Kerala Thiyya Very little F* 7

Orissa Koya 1 for HG H No HG C 11 0.137 0.209 Torso Cluster with Bondo 16

Bondo Very little HG C 9 0.238 0.212 (20,120) Lineage from Koya Cluster with Koya 3
Gadaba Very little HG C Very little F*
 Gene Diverstiy Gene Diverstiy
Gene Diverstiy
Variance Network Dendrogram N Variance (N) (Age of Network N Variance (N) (Age of Network N
(Age of Expansion)
Expansion) Expansion)
H J L

0.526 0.395 (35,709**) 3 lineages observed 3rd branch No J Very little L

Torso, IInd cluster Out group joins, Ist

0.705 0.385 (25,169**) 1st branch 3 0.417 0.104 Very little L
in Torso cluster
0.432 0.288 (14,830**) Torso 1st branch No J Very little L
IInd cluster in
Torso, Outgroup
1.030 0.501 (49,879**) 3rd branch Very Little J 9 0.464 20,935 Torso I
Joins, Most
dispersed

0.396 0.479 (33,661) Periphery 3rd branch No J ***

Torso I, Outgroup
0.232 0.170 (14,871) Central cluster 1st branch No J 6 0.160 0.136 (15,016)
Joins
Central cluster
0.712 0.550 (65,330) 2nd branch 9 0.356 0.375 (35,596) Ist cluster ***
periphery
Central cluster
0.094 0.208 (8,846) 2rd branch 9 0.391 0.224 (18,572) IInd cluster ***
periphery
*** Very Little J ***
Joins Clusters I and
1.091 0.615 Dispered 3rd branch 3 0.667 0.458 13 0.523 0.420 (45,338***) Torso II
II
1.158 0.640 Dispersed 3rd branch 3 0.979 0.750 Periphery 10 0.967 0.514 (44,088) Distal branch

0.542 0.604 Dispersed 3rd branch *** ***

0.896 0.646 Dispersed 3rd branch *** ***
0.271 0.297 (16,629) Torso 1st branch 3 0.646 0.479 (48,661) IInd cluster ***
Central cluster
0.589 0.487 (49,274) 1st branch 4 1.010 0.531 Periphery 6 0.975 0.567 Distal branch
periphery
Torso, joins through Clusters with
0.269 0.273 (5,548) No J No L 3
Kota Nilgiris
1.521 0.563 (37,427) Periphery 3rd branch No J No L 13
Very little H No J No L 22
 Gene Diverstiy Gene Diverstiy
Gene Diverstiy
Variance (N) (Age of Network N Variance (N) (Age of Network N Variance (N) Network Conclusion
(Age of Expansion)
Expansion) Expansion)
O R2 R1a1

No O Very little R2 Very little R1a1 Possible Founder for F* lineages

No O Very little R2 No R1a1 Possible Founder for F* lineages

No O Very little R2 Very little R1a1 Origin of H

HG C from other sources, HG H origin and

No O Very little R2 No R1a1
expansion in Irula

No O Very little R2 Very little R1a1 Possible Founder for F* lineages

No O 3 1.354 0.563 (29,903) Outgroup Joins No R1a1 Bottle neck

Very little O *** Very little R1a1 Distinct J lineage

Very little O *** No R1a1 Distinct J lineage

No O *** 5 0.744 0.500 Distal R1a1 from other sources
No O 4 0.724 0.573 (43,112) Periphery 4 1.724 0.646 Dispersed Earliest L expansion in plains populayion
Torso, Most R1a1 from ancient source, expanding population,
Very little O No R2 21 0.376 0.432
dispersed L back flow
No O Very little R2 5 0.533 0.563 Torso R1a1 from ancient source, expanding population
No O No R2 4 0.417 0.562 Periphery R1a1 from different sources
Torso, Outgroup
No O 10 0.011 0.022 Centre 12 0.358 0.292 (14,145) R1a1, R2 from ancient source
Joins
L, derived form others. R1a1 from ancient source
Very little O *** 11 0.260 0.327 Torso
L back flow
HG H from Dravidian tribes, HG O form Gadaba,
0.708 0.436 Periphery No R2 No R1a1
F* different form Nilgiris
2 lineages from Derived HG O from Gadaba, F* differnet form
0.280 0.259 (19,080) No R2 No R1a1
Gadaba Nilgiris
0.652 0.443 (48,975**) Torso, Dispersed No R2 No R1a1 HG O Orgin and expansion in Gadaba