Dodecad South Asian ChromoPainter

Dienekes ran ChromoPainter/fineSTRUCTURE analysis of South Asians along with some West Eurasian populations, something I had neglected to do in my own South Asian run.

Using Dienekes' data, I was trying to figure out which South Asian populations had more DNA chunks in common with other groups when I ran into something strange. Looking at the chunkcount spreadsheet, if we focus on a recipient population (i.e., one row), we can see which populations contributed more "chunks". For most populations, the results are expected. It's either the same population or some close population. For example, let's look at top 5 matches for Velamas_M,

Velamas_M Pulliyar_M North_Kannadi Chamar_M Piramalai_Kallars_M
Velamas_M 1265.77 1259.38 1256.06 1255.6 1254.74

However, when we do the same for Pathans, Sindhis, Uttar Pradesh Brahmins, Kshatriyas and Muslims, we get strange results.

Chamar_M Velamas_M UP_Scheduled_Caste_M Piramalai_Kallars_M Muslim_M
Pathan 1229.91 1229.56 1229.53 1229.32 1229.27

Do Pathans match Chamar the best? Pathans don't show up as a donor till #11.

Chamar_M Piramalai_Kallars_M Pulliyar_M Velamas_M North_Kannadi
Sindhi 1234.09 1234.08 1233.85 1233.6 1233.55

Again, Sindhis as donors are #12.

Pulliyar_M Chamar_M North_Kannadi Kol_M Piramalai_Kallars_M
Brahmins_UP_M 1244.6 1244.53 1243.44 1242.88 1241.94

The same Brahmins_UP_M are #13 as donors.

Pulliyar_M Chamar_M North_Kannadi Kol_M Piramalai_Kallars_M
Kshatriya_M 1247.72 1247.36 1246.42 1244.98 1244.56

And #12.

Pulliyar_M Chamar_M North_Kannadi Kol_M Piramalai_Kallars_M
Muslim_M 1255.96 1255.36 1253.96 1251.74 1250.86

Muslim_M are #8 as donors.

There is a pattern here among the top donors for these populations. The same populations show up time and again.

Compare to my results (with a larger South Asian dataset) now. The top 10 matches for Pathans are:

  1. pathan
  2. punjabi-jatt
  3. bhatia
  4. haryana-jatt
  5. rajasthani-brahmin
  6. punjabi
  7. balochi
  8. kashmiri
  9. punjabi-brahmin
  10. sindhi

For Sindhis,

  1. sindhi
  2. bhatia
  3. balochi
  4. makrani
  5. brahui
  6. punjabi-jatt
  7. haryana-jatt
  8. meghawal
  9. pathan
  10. punjabi

For Brahmins from Uttar Pradesh,

  1. bihari-brahmin
  2. haryana-jatt
  3. brahmin-uttar-pradesh
  4. punjabi-jatt
  5. kurmi
  6. sourastrian
  7. bengali-brahmin
  8. bihari-kayastha
  9. bhatia
  10. up-brahmin

For Kshatriyas,

  1. bihari-brahmin
  2. kurmi
  3. meena
  4. kshatriya
  5. rajasthani-brahmin
  6. haryana-jatt
  7. punjabi-jatt
  8. bengali-brahmin
  9. kerala-muslim
  10. sourastrian

For Muslims,

  1. muslim
  2. chamar
  3. kol
  4. oriya
  5. uttar-pradesh-scheduled-caste
  6. bihari-muslim
  7. sourastrian
  8. brahmin-uttaranchal
  9. dusadh
  10. bihari-brahmin

If Dienekes can post a chunkcount file for the clusters computed by fineSTRUCTURE, may be we can try to figure out what happened.


    • When you run ChromoPainter with the -a flag, it assumes all samples (except the one recipient) to be donors. Assuming a population group is somewhat coherent, its members should have high number of chunks being donated from the group to members of the same group. This is not the case for Pathans, Sindhis, etc in the Dodecad analysis. Instead the biggest donors to these populations are unexpected and don't seem right.

  1. This is interesting Zack, one would have thought that Pashtuns would have been more closer to Kashmiris than Punjabi-Jatts. And the Sindhis more closer to Punjabis than Bhatias.

    • Bhatias are Rajputs from Sindh, so no surprise as far as that match is concerned.

    • There are no racially kashmiri muslims from kashmir valley participants in this so-called database. Until then you cannot say anything about relationship between pashtuns and kashmiris. So far there is only one kashmiri hindu pandit from kashmir valley who is participant no. 21, the other participant which is no. 44 and presenting himself as kashmiri in this database is actually pothohari rajput or gujjar from azad Jammu (wrongly called Azad kashmir).

      Kashmiri hindu pandits have no relationship with pashtuns, it is only muslims kashmiris from valley who have a strong proportion of kashmiris that look like afghans/pashtuns. Till date these kashmiri muslims have not been tested genetically except 12 individuals that were included in Qamar et. al. study back in 2000/2001. Indian studies have always included Kashmiri hindu pandits who are lest than 4% of kashmiri population or Gujjars who are actually from Jammu region and not related to kashmiri muslims from valley.

  2. Seeing these admixtures one may say "what is the basis of caste then?, the caste system was a failed system as for stopping mingling"
    I know many who are seeing this site may had thoughts like that.
    My answer to them is that though caste systems is expired now as a rule of prakiti but it never meant by your skin colour or background but by one thing ability. thats why greeks,jews were inducted as brahmins thats why huns,kushans were inducted as kshatriyas. Wherever we see a dominant culture we see the older or facing culture being erased but for the aryas from sapta sindh caste made every to get their position according to their ability but the rigid caste system we consider now is the system from the dark ages(19th-18th century) every culture had their dark ages but thats not their true identity is it?

    • It may well be from a 'dark age' but that dark age was well before the Buddha. The Buddha's discourses describe 'caste' development from the same core set of people - the Rudras. There is also no doubt that by the Buddhist period the Indian society was well stratified. Nevertheless, there has always been some mobility especially to the so called 'kshatriya' ranks which have periodically been dismantled and replaced by ruling clans that have included brahmans, vaisya, kashtriyas, jats, hunas, etc.

  3. Yes indeed thanks for the link.

  4. Hi Zack, any updates from Dienekes about the chunk counts?

  5. Genetic Origins of Pakistan by Razib Khan - Page 6 - pingback on July 30, 2013 at 9:33 am

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