The Genetic Architecture of the Indian Subcontinent: A Deep Dive Into 50,000 Years of Human History

By Veteran Brigadier Azad Sameer

Up until modern times we theorised and formulated ancient history through archeology and historical linguistics. Archeologists dug up ancient sites and by the study of artifacts and other evidence from these sites formulated their inferences. In historical linguistics, scholars use related languages as archeological sites, and they dig through layers of vocabulary and grammar to uncover the past. This multi-disciplinary field has now entered the science of Population Genetics and Paleo- Genomics which help solve the jigsaw puzzle with a lot more clarity.

Back in school a half century ago we learnt about the Aryan and Dravidian ancient history of India. How has science changed this old narrative if at all? The Aryan-Dravidian narrative has shifted from a story of conquest and pure races to a much more complex story of deep-time mixing. The modern Indian population is often described as a subcontinent-sized mystery. However, through the lens of paleo-genomics—the study of ancient DNA—we can now reconstruct the history of India not just through ruins and texts, but through the very cells of its people. Modern population genetics has replaced the old labels with three primary ancestral building blocks or three pillars that exist in almost every Indian today, regardless of whether they speak a Dravidian or Indo-Aryan language and regardless of from where they hail in the subcontinent or their religion or caste. So, let’s delve into each of these three building blocks as almost every Indian has inherited genes from all three blocks to a lesser or greater extent.

The Foundation: The Out of Africa Pioneer Group

The story begins with the First Indians, also probably the first Homo sapiens around 50,000 to 65,000 years ago, a small band of Homo sapiens migrated out of Africa, likely crossing the Bab-el-Mandeb strait and via the Arabian Peninsula, following the Southern Coastal Route into India. The migration Size was relatively small and perhaps covered a thousand plus years. Genetic modeling by Narasimhan et al. (2019)[i] suggests a significant bottleneck. While thousands may have left Africa, only a few hundred to a few thousand successfully founded the lineage that would populate the whole of South Asia. These pioneers are referred to as Ancient Ancestral South Indians (AASI) and should be considered as the indigenous people of India as they are known to be the first Homo sapiens who arrived in the subcontinent more than 50000 years ago. It is not conclusively known if humans lived in the subcontinent before the AASI, but if they did, they have left no genetic signature in the population of today.  Currently, no pure AASI population exists on the mainland; they are a ghost population whose DNA is found mixed into nearly every person in India. The closest living relatives to this ancient lineage are the Andamanese hunter-gatherers (Onge and Jarawa).

It is also very likely that archaic Humans (other than Sapiens) lived in the subcontinent prior to the arrival of this group out of Africa and possibly coexisted with them for many centuries. Indians today have about 2% DNA of these archaic humans (Neanderthal and Denisovan), the highest for any population outside Africa

The Neolithic Revolution and the Indus Valley Civilisation (IVC)

Between 10,000 and 7,000 years ago, a new genetic stream entered from the west—people related to the early farmers of the Zagros Mountains (Iran). These Iranian-related migrants did not replace the AASI; they merged with them. This Indus Periphery mixture created the genetic basis for the Indus Valley Civilisation (IVC). A pivotal study by Shinde et al. (2019)[ii] sequenced the DNA of a 4500-year-old female skeleton from Rakhi Garhi. The results were revolutionary: she had zero Steppe ancestry. This proved that the great cities of Harappa and Mohenjo-Daro were built by a population that was a mix of AASI and Iranian-related ancestry, before the arrival of Central Asian groups. Most scholars now believe that the Indus Valley people spoke a proto-Dravidian language (their script is sadly still not deciphered)

The Steppe Migration and the ANI/ASI Split

Around 2000 BCE to 1500 BCE, as the IVC began to decline (likely due to climate change and drying rivers), a third major group arrived: Steppe Pastoralists from the Eurasian grasslands (modern-day Russia/Kazakhstan or the Yamnaya culture). These migrants brought Indo-European languages and early Vedic culture. Their arrival triggered a massive demographic shift:

The North:  Steppe migrants mixed with the IVC people in the North, creating the Ancestral North Indians (ANI). This is the foundation on which the Vedic civilization was built.  The early Vedas written in Sanskrit, have quite a few Dravidian loan words. This possibly shows the affinity/ descend of the Vedic people to the IVC people, who scholars believe spoke some kind of proto-Dravidian language.

The South: IVC people who moved South, further mixing with local AASI hunter-gatherers, formed the Ancestral South Indians (ASI). They formed the base for the Dravidian culture and civilization.

The Melting Pot

These two were not watertight, separate and pure Aryan/Dravidian entities. For the next two millennia or so (from 2000 BCE to 0 CE), they mixed freely with gene flows taking place throughout the subcontinent. It was clearly a no caste bar situation throughout the length and breadth of the subcontinent. Reich et al. (2009)[iii] demonstrated that most modern Indians are a cline (a sliding scale) between these two groups. A person in Kashmir might have 50-60% ANI ancestry, while a person in Tamil Nadu might have 20-30% ANI ancestry, but almost everyone has both North and South Indian ancestry. Population Genetics has thus conclusively proved that the whole of India has a by and large a common genetic heritage. Pure Aryan/ Dravidian heritage in India is something of a myth. There is a certain oneness in the common ancient heritage of every Indian.

The Endogamy Freeze (2,000 Years Ago)

Perhaps the most Indian aspect of this genetic story is not the mixing, but when the mixing stopped.  Moorjani et al. (2013)[iv] discovered that around 1,900 years ago, genetic data shows a sudden freezing of the gene pool. This aligns with the late Gupta period when the Manusmriti was composed, and the social structures of the Caste System became rigid. From this point on, people began marrying only within their specific sub-castes (Jatis). This created thousands of distinct genetic groups. India is therefore not one large population; it is a collection of thousands of small, endogamous populations living side-by-side and interestingly all having a common heritage. This rigid monogamy froze the genetic proportions in place, which is why genetically and otherwise we still see distinct regional and caste differences today despite the shared ancient roots. This gene flow freeze that prevails till today gave rise to several deleterious effects socially, economically and biologically. That calls for a separate discussion altogether.

Religion, Gene Flow, and Regional Nuance

Modern socio-political identities often suggest deep divides, but the DNA tells a story of shared heritage. Study after study on religious groups, including Reich (2018), has shown that Indian Muslims and Christians are genetically indistinguishable from the Hindu castes of their specific region. For example, a Kerala Syrian Christian shares the same ancestral proportions as a Kerala Namboothiri or Nair. The closest genetic kin of a Kashmiri Muslim is the Kashmiri Pandit. Almost identical heritage. For most of us it would be somewhat disconcerting that a Punjabi Hindu or Sikh is genetically closer to a Punjabi Pakistani Muslim, than a Hindu from say Tamilnadu. Gene flows don’t recognize borders and genetically the concept of Akhand Bharat is very much a valid concept

There is an ethnic group called Brahui who now predominantly live in the mountains of Balochistan with much smaller populations in Iran, Afghanistan, and Gujarat and Rajasthan. Genetically they are predominantly ANI stock but the Brahui language that they speak today is essentially a Dravidian language strongly suggesting a IVC lineage.

Gene Flow from the East

In Northeast India and among Munda-speaking tribes in Central India, there is a significant fourth stream of DNA besides the three discussed above. This comes from Austroasiatic (AAA) and Tibeto-Burman migrations from Southeast Asia and East Asia roughly 3,000 to 4,000 years ago.

Summary Table: The Layers of Indian Ancestry

LAYERGROUPARRIVALFORMATION/IMPACT
1AASI(FIRST INDIANS)50000 + years agoFoundational DNA of all Indians
2Iranian related farmers10000-70000 years agoMixed with AASI to build the Indus Valley civilisation
3Steppe Pastoralists2000-1500 BCEIntroduced Indo European languages; formed the ANI
4East Asian/ Austroasiatic2000-1000 BCE 

Out of India Theory (OIT)

Also known as Indigenous Aryanism, the Out of India Theory is the hypothesis that Indo European language family and speakers originated within the Indian subcontinent and migrated outward to Europe and Central Asia, rather than entering India from outside. This hypothesis stands in direct opposition to the mainstream Aryan migration Theory. In the academic world of genetics, archeology and linguistics the OIT is largely considered discredited. However, it remains a popular and culturally significant idea. In some sense the theory is valid in that the Indian Civilisation has immense indigenous continuity even before the arrival of the Steppe Pastoralists.

Old School Narrative and Modern Genetic Reality

The old schoolbooks often portrayed the Aryans/Dravidians as two separate, non-overlapping groups. Genetics shows they are more like a spectrum. According to the old school narrative Dravidians were Indigenous people pushed South by invaders. According to modern genetics this group (often called Ancestral South Indians or ASI) formed when the Indus Valley people migrated South and mixed further with local hunter-gatherers (AASI the original out of Africa indigenous people). The old school narrative describes Aryans as a foreign race that conquered the North. According to modern genetics this group is a mixture of Steppe Pastoralists and the existing Indus Valley population. This group (called Ancestral North Indians or ANI) is genetically closer to West Eurasians but still contains significant indigenous Indian DNA.

Key Changes in Knowledge

The Invasion is now a Migration: The violent Aryan Invasion Theory has been largely debunked. Genetic evidence suggests a slow, multi-century migration of Steppe people who intermarried with local populations.

Everyone is mixed. There is no pure Aryan or Dravidian. Nearly every Indian—from a Kashmiri Pandit to a Tamil Brahmin to a tribal member in Kerala—carries a combination of these three ancestral lines. The difference is only in the proportions (e.g., higher Steppe ancestry in the North/Upper Castes; higher AASI ancestry in the South/Tribal groups).

So, in a nutshell we can summarize that the current Indian population is not a monolith but a mosaic of varying shades, a picture largely accepted by the Centre for Cell and Molecular Biology (CCMB), Hyderabad, a premier research institution that has carried out groundbreaking research in this field.


[i] Narasimhan, V. M., et al. (2019). The formation of human populations in South and Central Asia. Science. (Detailed the three-way mix of AASI, Iranian-farmers, and Steppe).

[ii] Shinde, V., et al. (2019). An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers. Cell. (The definitive study on the Indus Valley genome).

[iii] Reich, David (2018). Who We Are and How We Got Here. (A comprehensive overview of ancient DNA findings in India and globally).

[iv] Moorjani, P., et al. (2013). Genetic Evidence for Recent Population Mixture in India. American Journal of Human Genetics. (Identified the shift to endogamy 1,900 years ago).

Book Review : Mojo in a Mango Tree by Vikram Cotah

Kudos to Vikram, the author, for bringing out a wonderful book based on life lessons. The book is replete with life experiences and ‘interesting’ anecdotes- many where someone has gone an extra mile.  The aspects covered deals with the hospitality industry, but is applicable to all professions and also in everyday life.  The hotel industry, like any other profession, renders many an opportunity to go that extra mile and a good leader/ employee must seek it out.  The leaders and employers have to grant that ‘extra’ to an employee who goes that extra mile to encourage others to follow.  Empowering the employees will go a long way. In most organisations, red tape is the biggest hindrance to achieving the extra mile.   It is all about maturing relationships and enjoying the trust of the customers and subordinates.

The history of hotel industry enunciated in the book is educative and informative.  Consumers evolve and the industry got to be in sync, but the need for a good service culture will remain forever.  Emotions and gastronomy will add value to the guests’ experience.  There is never a second-chance in hospitality as there are no runners-up in a war.

It is all about kindness, compassion and empathy.   Get out of your comfort zone, explore the world and recoup your energy.  A guest is never a room number;  so are your employees and subordinates.  You need a thick skin dealing with complaints and worries and learn to say ‘No’ with a ‘Yes.’  One who manages  crisis  better will always succeed as you are sure to face many.  Feedbacks are more important than compliments.

The author  brings out many life lessons.  Happiness is being positive.  Plan your day well.  Have a dream, set your aims and achieve your goals.  Create a bucket list the earliest and keep ticking them off – Do these consistently – in small measures. Smile is the best weapon in your life.

Success and failures  are integral to life.  Failures provide you opportunities to become  smarter.  Branding is very important today and I have tested and tasted all the elements charted in the book. Life cycle of a hotel from inception applies well to all businesses. Why?  Even true for a soldier.

The reader will appreciate and also identify easily with some well brought out instance like giving out perfumes to the hotel staff – a  novel and a much required need in the Indian context.  Changing the lobby mat with ‘Good Morning’ and ‘Good Evening’ – I never thought of.  Wall panels to make selfies look great – need of the day.

Learning is a lifelong process.  I ran away from studies to join the Army – neither did I stop running nor studying thereafter.

‘Leaders of the future will need to balance technology quotient and emotional quotient.  This will be the Extra Quotient of the future.

After Action Report -Thai Cave Rescue


In their first public appearance since emerging from their ten-day ordeal in the cave, the boys recounted their side of an extraordinary story that captured the imagination of the world.


(Photo courtesy (Vincent Thian/The Associated Press)

A packed crowd greeted the youngsters after they were discharged from hospital in Chiang Rai, and watched as they played with footballs on a small makeshift pitch before taking their seats.

Sitting beside the boys were the Thai Navy SEALs who stayed inside the cave with them after they were found, as well as members of the medical team who looked after them after the rescue.

Thai authorities organised a  press conference, for which questions were pre-screened,  More than 100 questions were sent in by the media, though only a handful were selected.   The media was urged to give the boys uninterrupted time with their families so as not to harm their recovery

Dressed in matching team shirts, the boys and their coach Ake appeared happy and relaxed as they faced the world’s media.  The boys introduced themselves  with their nicknames and the position they played on the team.

The largely joyous mood of the press conference was tempered, however, when the boys and Ake discussed the loss of Saman Kunan, the former Thai Navy SEAL who had died during the rescue effort. Ake said the team were shocked to learn of Saman Kunan’s death, called him a hero.   In memory of the navy diver, Ake and the boys decided to spend time as novice Buddhist monks — a practice considered a high honour in Thailand.

The boys thanked their rescuers and medical staff, and paid tribute to Kunan. They also bowed before a portrait of the Thai king.

The boys explained as to when they realised that they were trapped, how they adapted to their surroundings and their eventual joy at being found, ten days later.  They described their rescue as a miracle, thanked the experts who saved them and discussed how the experience would affect the rest of their lives.

Contrary to the belief that the team entered the cave complex to celebrate the birthday of Night on the day the team went missing, Ake said that the boys were merely curious to look inside as some of them had never been there before.  He said it was not unusual for the group to participate in group activities after soccer practice on Saturday afternoons.

They explored the caves for about an hour, before deciding to return.   By this time the cave had become partially flooded and their exit was blocked.   All the boys can swim, country to earlier reports, and they to swam to safety when the water started rising.

At his point, they realised that they were trapped. With no obvious way out, the group retreated about 200 meter further into the cave to find somewhere to rest for the night.

There they found a bit of slope with a small water source,  Ake instructed the team to drink water dripping from the roof of the cave as it would be purer than the dirty floodwater on the floor.   Having eaten after soccer practice, the boys had no food during their ordeal.  Instead, they drank water from the cave.

Before they slept, Ake told them to say a prayer and they prayed that night. The team were not scared and Ake hoped the water level would drop the next day, and that help would arrive.

The waters did not subside, however.  Instead the levels rose fast.  Ake ordered the group to find higher ground. Concerned that they might soon be submerged, he instructed the boys to start digging and look for a potential exit.  They managed to burrow a hole into the cave in shifts after the water rose by three meter.

Adun, the only member who spoke English, responded with a “Hello”  in disbelief  to the first British diver who reached the group.  Adun, like other members of the group, was busy digging — looking for a possible way out — when some of the boys thought they heard the sound of people talking.  Ake instructed the group to stay quiet. He asked one of the boys to move closer to the ledge and shine a flashlight on the water, but the boy was too scared, and Adun volunteered instead.

The boys described how they formed a bond with the Thai Navy SEALs who remained with them in the cave while rescuers worked out a plan to free them. They played checkers — and one of the Navy SEALs sitting alongside them at the press conference always won.   This SEAL was titled ‘King of the Cave.  One SEAL had spent most of the time in just his underwear and a small piece of foil, having stripped off his clothes to give to the boys to keep warm.

None of the boys wanted to leave the cave first when rescuers asked for volunteers when the decision was made to extract the boys through the floodwaters.  Ake joked he and the boys made the decision on who should go first based on who lived the furthest away. Ake thought the rescued kids would go straight home and those who got out first could spread the word.

When asked about the lessons they’ve learned from the incident, Ake said he was going to live life more carefully.   Ardun said though people can’t predict the future, the experience had taught him about the consequences of acting carelessly.   Other boys said though they still dreamed of becoming soccer players, some said they now wanted to become Navy SEALs.

The boys and Ake apologised to their parents for not telling them they went to the cave.

Thai authorities are concerned about their long-term psychological health.  They urged the media to respect the boys’ privacy in the future, out of concern for their mental health.  They are also in the process of granting four team members who are stateless Thai citizenship.

The day after the press conference the boys were allowed to go home.   Doctors have advised their families that they should avoid contact with journalists for at least a month.

 

Wild Boar Boys Football Team Rescue Operations


Rescue operations of Thai Wild Boar Boys Football Team and coach, a group of ‘Unlucky Thirteen’ captured the world’s attention, as divers successfully brought them out of the flooded Tham Luang cave complex.  “The number 13 may be lucky or unlucky, but one cannot blame the number for it and will always follow number 12 and precede number 14” – from my blogpost ‘Arithmetic of Licence Plates.’

‘God Himself never did any miracle, but it was always through humans’, I had written in my earlier blogpost ‘Randomness of Life.’  We must thank the God Almighty for the efforts of the rescue team, but should never forget to thank all those members of the rescue team, who untiringly executed the dangerous rescue operation.


First, let us bow our heads and say a few prayers for Kunont, also known as Gunan or Kunan, who laid down his life, without caring for his personal safety.  He was part of the North Face Adventure Team, one of Thailand’s top trail runners and a former Navy Seal diver.

Kunont made his way through a submerged cave to bring oxygen.  He  then ran out of oxygen on his way back to the entrance, highlighting how hard it would be to rescue the boys untrained in diving.  On his way back he lost consciousness and  his friend tried to help bring him out.  Kunont, in a soldierly way, did the supreme sacrifice in trying to save others.


(Image Courtesy Australian Associated Press)

Dr Richard Harris, 53, an anesthesiologist from Adelaide, works for the South Australian Ambulance Services.  He is an expert in cave-diving.  He joined the rescue team on the request of British officials.

Risking his own life, Harris made the treacherous trip into the subterranean chamber to check on the boys after they had been trapped for more than two weeks.  After examining them, Harris recommended that the weakest of the boys be rescued before their stronger teammates — against the earlier opinion of saving the strongest first.


Ekapol Chantawong, affectionately known as “Ake,” is the assistant coach of the football team.  Ekapol had already cheated death; when he was just 10 years old.  His parents and brother were killed by a disease that ravaged his village, only sparing him.  He lived with extended family members for a short time after his family’s deaths, but felt sad and lonely.  This lead him to be a Buddhist Monk.

Ake would be there at the field waiting for kids to show up after school. According to him, it is a great way to keep the children healthy, away from modern gizmos and other diversions and also to interact with friends.  The members of the Wild Boars are a team on and off the soccer field, traveling to competitions, cycling mountain roads and swimming in waterfalls together.

The team entered the cave complex to celebrate the birthday of Peerapat Sompiangjai, nicknamed Night, turned 17 on 23 June, the day the team went missing.  Before they were found, the group had to survive for nine days in the darkness unaware of the desperate search efforts.

How did this team survive through the ordeal?

Air.    Most caves naturally ‘breathe’ through various pores and cracks.  However, as the days went on, oxygen levels dipped to about 15% where the team were huddled. The usual level is about 21%.  Ake, being a Buddhist Monk, had trained the team in breathing techniques to make sure they used as little air as possible,

Food.    The team had bought snacks to celebrate Night’s birthday, and it was these snacks that helped sustain them after getting trapped in the caves. Ake reportedly refused to eat any food so the boys would have more for themselves, leaving him the weakest when divers eventually found the team on 2 July.  What a great leader!

Water.    Humans  can survive for many months without food, but water is an absolute necessity.  As it was monsoon season, the cave had adequate water  and they chose clean water to drink,  Water dripping from the cave ceiling would have really helped.

Hypothermia.    It is a medical emergency that occurs when your body loses heat faster than it can produce.  It can often be a risk underground, especially in flooded caves.  The team used rocks to dig five metres deeper into the cave to create a tunnel so that they could keep warm.

Disorientation.   The team had to handle the total darkness of the cave, without any awareness of time or of the massive search efforts to find them.  Meditation training by Ake helped the team withstand disorientation.

Stress.   The efforts of Ake must have been instrumental in keeping them calm.  Meditation would have helped them handle the stress.

When the rescuers managed to get through to the team, they delivered letters from their families and took notes back to allow them communication with the outside world.  In his letter, Ake apologised to the parents for taking the boys into the cave network, but several replied to say they did not blame him.

“I promise I will take care of the kids as best as I can,” he wrote.

Lesson to be learnt from the rescue operations are:-

Planning and Coordination of Rescue Efforts.    Coordination between various Thai agencies and also international agencies ensured speedy rescue. A mission which was expected to take a few weeks was executed in few days.

Leadership of the Coach Ake.    Exemplary leadership demonstrated by the coach of Wild Boars football team in ensuring survival of the entire team.   Surely, he must be well trained in First-Aid, CPR, survival skills, child psychology, etc. Our son works as a Swimming Instructor and Life Guard in Canada and he is well trained in these aspects.

Team-Work.     The entire team of teens must have listened to their coach – else they would not have survived through this ordeal.

Trust in the Leader.    The coach must be enjoying a lot of trust and confidence of the team of teens for sure.

Dedication of the Rescue Team.     Despite losing a rescue diver, Saman Kunan, the rescue team endured to complete the dangerous mission.

Composition of Rescue Team.    A doctor with cave-diving experience first went into the chamber and approved the boys for the operation.

No VIPs.    The VIPs kept away from the scene, thus all resources like helicopters, road-space, etc were available to the rescue team.

No Media Presence.    Media and their camera crew were kept away from the scene and there were no reporters milling around to give the ‘latest situation reports.’

Crowd Management.    Local population appear to have cooperated with the authorities and there was no crowding – especially those with their cellphones – all ready to post images on the social media.


Quarantining of the Team
..    Thai health officials said that some of the first boys freed had elevated white-blood cell levels, indicating infections, and two showed signs of pneumonia but were responding well to treatment. They are expected to be quarantined in hospital for at least seven days.

Post Trauma Support.    A psychiatrist is evaluating the rescued team and would provide needed counseling and psychological support.

Kudos to all those involved in this rescue mission and Rest In Peace Saman Kunan,  – you have achieved Great Glory – true to the spirit of a soldier.