Who We are and How We Got Here—Ancient DNA and the New Science of the Human Past

Author: David Reich

Publisher: Pantbeon Books 2018

A human genome is written out in two chains of abut 3 billion chemical blocks (6 billion in all) that can be thought of as letters of an alphabet;  A(Adenine), C(Cytosine), G(Guanine), and T(Thymine).  Any person’s genome is derived from 47 stretches of DNA corresponding to 46 chromosomes and the mitochondrial DNA.  (A human cell has 23 pairs of chromosomes: 23 are paternal and 23 are maternal.) Two of these chromosomes are identified as X and Y.  A father passes down both X and Y chromosomes, but the mother passes down no Y chromosomes.  Therefore, the paternal lineage is often traced using the Y chromosome.  Mitochondrial DNA is—one 200,000th portion of a genome—passed down along the maternal line only.

A gene consists of tiny fragments of the genome typically around 1000 letters long.  Genes are used as templates to assemble the proteins that do most of the work in cells.  In between genes is noncoding DNA, sometimes referred to as junk DNA.

There are occasional differences between DNA sequences.  These differences are due to random errors in copying of genomes known as mutations that occurred sometime in the past.  Mutations accumulate at a more or less constant rate of time.  It is these differences, occurring about one every thousand letters or so in both genes and in junk that geneticists study to learn about the past.  

When you compare two genome sequences, and if you find a higher density of differences separating two genomes, then the longer it had been since the segments shared a common ancestor.  

Before 2006, most genetic studies were done comparing mitochondrial DNA and Y chromosomes.  Since 2006, geneticists can compare sequences from the whole genome.  As a result, geneticists can reconstruct each persons tens of thousands of ancestral lines of decent.  Scientists can gather orders of magnitudes more data and test whether the history of our species suggested by the whole genome was the same as that told by mitochondrial DNA and Y chromosome.

It is in the area of human migrations that the genome revolution has been a runaway success.

From now on I will restrict this note mostly to chapters 5 and 6 of the book.

“Yamnaya” is a pastoral group of people that spread from Asian steppes to both Europe and India around 5000 years ago.  Yamnaya who arrived in northwestern Europe replaced or overwhelmed the existing population almost completely.  Yamnaya invented the most sophisticated weapons of those times, the domestication of horses, and the horse driven carts.  They used these new inventions first to spreadout in steppes, and then to migrate west to Europe, East and South to India.  The single most important source of ancestry across northern Europe today is the Yamnaya or groups closely related to them.  It is likely, that at least some Indo-European languages, if not all, were spread by the Yamnaya.

How did Yamnaya replaced the the existing populations in Europe?  Large part of the northern Europe were transformed from partial forests to grasslands, suggesting that Yamnaya may have cut down forests, and transformed the landscape to be more like Steppes.  Another explanation is that they spread deceases that the original inhabitants had no antibodies for.

Almost everyone in India is a mixture of highly divergent ancestral populations, one of which derived about half if its ancestry from Yamnaya.

North Sentinel Andaman Island is populated by one of the largely isolated stone age people in the world.  They speak languages that are not derived from any other in Eurasia.  Reich joined two Indian geneticists who have collected DNA from all groups of people in India and Andaman Islanders.  After jumping through several political hoops they managed to study 25 groups at Reich’s lab at Harvard.  Once they analyzed the data, they have found that Indians today descended from a mixture of highly divergent ancestral populations, one being the “West Eurasians” or Yamnaya.   Reich faced another serious political roadblock at this juncture.  Indian geneticists objected to the use of words Eurasians (or Yamnaya).  They did not want to be part of a study that suggested a major West Eurasian incursion into India.  They suggested that this could be politically explosive.  They sat together and came up with new names for ancient Indian groups; “Ancestral North Indians (ANI) and “Ancestral South Indians” (ASI).  

The fact is, everyone in India today is a mix, albeit in different proportions.  No group in India can claim genetic purity.

Sentinel Andamanese are related distantly to ASI but do not have the West Eurasian ancestry that is present in all mainland Indians.  They have found that West Eurasian-related mixture in India ranges from 20% to as high as 80%.  Groups who speak Indo-European languages typically have more ANI ancestry and those who speak Dravidian languages have more ASI ancestry.  Groups of traditionally higher social status in the cast system typically have higher proportion of ANI ancestry than those of lower social status.  Even within the same state of India where everyone speaks the same language, Brahmins tend to have more ANI ancestry.  

Reich and his group found that ANI-ASI mixture dates between 4000 and 2000 years ago, with Indo-European language speakers having a more recent mixture dates on average than that of Dravidian language speakers.  This suggests that there were several waves of mixing and the people who were the products of the first mixtures in Northern India could plausibly, over thousands of years, have mixed with or migrated to Southern India.  

This means that the population structure of India before around 4000 years ago was profoundly different from what it is today.  

Around 20 to 40 percent of Indian men and around 30 to 50 percent of east European men have a Y-chromosome type that descends in the last 6800 - 4800 years from the same male ancestor.  In contrast, the mitochondrial DNA, passed down along the female line, is almost entirely came from ASI even in the north.  

Male immigrants were extraordinarily successful at leaving offsprings while female immigrants, if any, made far less of a genetic contribution.

The genetic data also reveal another story.  Around a third of Indian groups analyzed experienced population bottlenecks.  These occur when relatively small number of individuals have many offsprings and their descendants too have many offsprings and remain genetically isolated from the people who surround them due to social or geographical barriers.  (In India’s case, it is mostly social barriers.) Many of the bottlenecks in India were exceedingly old.  The bottleneck of Vysya of Andhra Pradesh, approximately 5 million people, dates to between 3000 to 2000 years ago.  It meant that after the population bottleneck, the ancestors of the Vysya had maintained strict endogamy, allowing essentially no genetic mixing into their group for thousands of years.  (Even an average rate of 1% influx into Vysya per generation could have erased the genetic signal of population bottleneck.)

And Vysya were not unique.  A third of the groups analyzed gave similar signals implying that for thousands of groups of India, despite proximity to other groups, the endogamy rules and group identity have been so strong that they maintained strict social isolation from their neighbors, and transmitted the culture of social isolation to each and every subsequent generation.

In China, having mixed freely today has a large “Chinese” population.  However in India, despite having a similar large population is not an “Indian” population.  The truth is, India is composed of a large number of small populations.

Rare mutations that are innocuous when a person inherits a copy from only one parent, can be lethal if the person inherits copies from both parents.  When these mutations increase in frequency due to a population bottleneck, the chances of a person inheriting such a mutation from both parents are high.  For example, Vysya are known to have high rate of prolonged muscle paralysis.

Today, finding genes for rare recessive diseases is cheap with modern genetic technology.  Since arrange marriages are common in India, perhaps they should test and compare genes of the couples than comparing their horoscopes.  Matchmakers should not introduce young people to each other if they carry the same mutation.

This is a must read for everyone.  Reich has given many talks lately.  I also suggest that you listen to some of these talks.

In the first link below, you will find a talk given by Reich about the chapters 5 and 6 of this book to an Indian audience.  The person who was handling the technology did a very poor job and you see more Reich in this video than his slides.

https://www.youtube.com/watch?v=PUsPCsAjsbs

In the second link, Reich talks about the entire book.

https://www.youtube.com/watch?v=3-vHByC14bc