Timeline
This post is my attempt to simplify what I learned from Who We Are And How We Got Here into a timeline I have a shot of remembering for years, with some padding from Wikipedia where I thought it would help me.
—
As a backdrop to the specifics that follow: humans and human cousins have been sort of ambling out of Africa and back in waves of migration and interbreeding and extinction, for the past two million years.
Around 650K years ago, humans split from the group that will further split 200K years later into Neanderthals and Denisovans. These are the two ‘archaic human’ populations that contributed some genetic material to modern humans, whose DNA we got our hands on. This is also maybe the divergence point of humans and another archaic population in Africa that later mixed back into humans, that we don’t have DNA evidence for.
200K years ago, zoom in on the ambling in and out of Africa, because now some of the ambling groups are what we’d call anatomically modern humans – that is, their phenotypes fit within existing human populations. At this point, the split between the San population (the most different-from-everyone-else population alive today, whose descendants currently live in South Africa) and the rest of living humanity begins.
50K years ago, a period of great interest. We see behavioral modernity starting hereish, at the beginning of a period (lasting ~40K years) we call the Upper Paleolithic. The rate of stone toolmaking innovation speeds up from ‘glacial’ to ‘every few thousand years’. (If that seem like an odd setting change, I agree.) We see the first known jewelry and representational art. Likely we’ll never have a satisfactory explanation of what exactly changed. We almost certainly had language by this point.
Human colonization of Australia and New Guinea happens, while ocean levels are low. This is part of a radiation of a hunter-gatherer lineage spreading out all over Asia. Some of them will eventually go to Siberia and the Americas. Some of them will become the Yangtze River population and some the Yellow River population, who will later mix to produce the majority of mainland East Asians.
40K years ago. After several thousands of years of contact with modern humans, Neanderthals and some other branches more closely related to modern humans go extinct. There’s an Italian supervolcano eruption nowabouts whose climate disruptions in Europe may have intensified competition.
One thing this book has taught me is that it’s misleading to talk about ‘population splits’ outside of the Americas, because lineages diverged and met again many times, but insofar as it’s meaningful to talk about when the European and East Asian lineages diverged, it’s now.
30K years ago. The archaic humans in Africa mix back with humans and contribute 2% of ancestry to some modern African populations.
Around this time, there exists a population called Ancient North Eurasians. Some of them go east, and contribute to the population that will give rise to Native Americans (who are ~1/3 Ancient North Eurasian, ~2/3 ancestors-of-East-Asians). Some of the rest will remain and contribute ancestry to various Eurasian hunter gatherers, as well half the ancestry of the Yamnaya people of the Eurasian steppe, who will later invent horse-and-wagon way of life and become massively successful in Europe.
15K years ago, there are two migrations to America over the Bering land bridge: (1) The First Americans (the Ancient North Eurasian - East Asian group) account for the majority of Native American ancestry. These newcomers quickly zoom through the Americas. They also may have had a startlingly small effective population size – like 250. (2) A mysterious population that contributes some ancestry to a handful of groups in the Amazon, a population whose closest known descendants today are, intriguingly, Australasian. We don’t know much about them.
10K years ago, agriculture arises in the Middle East. Some Anatolian farmers spread out into Europe. Some Iranian farmers spread out to India. A thousand years later, agriculture also begins in China, in the Yangtze River and Yellow River populations.
5K years ago. The horse-and-wagon Yamnaya sweep from the eastern European steppe into northern Europe and largely replace the population there, and account for 25~45% of current European ancestry. The Yamnaya culture is the strongest candidate for the source of the Proto-Indo-European language (which has an elaborate shared vocabulary for wagon-parts). A large part of their success may have been that they were relatively immune to diseases that the rest of Europe was not – they brought plague with them, heretofore unknown to Europe. With the Yamnaya, the Bronze Age; we have evidence of much more social inequality than ever seen before, evident both from archeology and genetics, which tell us that the highest-reproducing individual men starting now are more reproductively successful than ever before.
Around the same time, there’s another wave of migration from Asia to North America – the Paleo-Eskimo lineage – that leaves a ~30% imprint in some parts of North America. The Paleo-Eskimos will be displaced 4K years later by a final wave from Asia, the Neo-Eskimos, who are the ancestors of modern day Inuits.
The Yangtze and Yellow River populations are also spreading out nowish. Their collision produces much of modern East Asians. The Yellow River people are associated with the Han, and the Tibetans. The Yangtze population, where they spread south, provides much of modern Southeast Asian ancestry.
4K years ago, the Indus Valley civilization is hit by a wave of migration for Europeish, by a steppe people who bring Proto-Indo-European culture and language. These steppe people are about half Yamnaya-related, and half ‘the Iranian farmer related populations the steppe people encountered on their way south’. The natives are about three quarters local hunter-gatherers, and one quarter Iranian farmers who mingled in ~2K years earlier. The natives and Yamnaya-ish migrants mix over the next 2K years to form a modern Indian population that’s a mixture of the two, ranging from 80% Yamnaya-ish (especially in the north, and in higher-caste groups) to 20%.
Around now, the first of four great migrations and mixing events of Africa starts – most significant among them is the Bantu migration south, out of Nigeria and into west-central Africa. Most of the present-day population structure of Africa is shaped by these relatively recent expansions, making it hard to tease out ancient splits.
excerpts on indian genetic diversity
The jati system, which few people outside India understand, is much more complicated, and involves a minimum of forty-six hundred and by some accounts around forty thousand endogamous groups. Each is assigned a particular rank in the varna system, but strong and complicated endogamy rules prevent people from most different jatis from mixing with each other, even if they are of the same varna level. …
Around a third of Indian groups experienced population bottlenecks as strong or stronger than the ones that occurred among Finns or Ashkenazi Jews. … Many of the population bottlenecks in India were also exceedingly old. One of the most striking we discovered was in the Vysya of the southern Indian state of Andhra Pradesh, a middle caste group of approximately five million people whose population bottleneck we could date (from the size of segments shared between individuals of the same population) to between three thousand and two thousand years ago. The observation of such a strong population bottleneck among the ancestors of the Vysya was shocking. 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 influx into the Vysya of as little as 1 percent per generation would have erased the genetic signal of a population bottleneck. The ancestors of the Vysya did not live in geographic isolation. Instead, they lived cheek by jowl with other groups in a densely populated part of India.
And the Vysya were not unique. A third of the groups we analyzed gave similar signals, implying thousands of groups in India like this. Indeed, it is even possible that we were underestimating the fraction of groups in India affected by strong long-term endogamy. To show a signal, a group needed to have gone through a population bottleneck. Groups that descended from a larger number of founders but nevertheless maintained strict endogamy ever since would go undetected by our statistics.
People tend to think of India, with its more than 1.3 billion people, as having a tremendously large population, and indeed many Indians as well as foreigners see it this way. But genetically, this is an incorrect way to view the situation. The Han Chinese are truly a large population. They have been mixing freely for thousands of years. In contrast, there are few if any Indian groups that are demographically very large, and the degree of genetic differentiation among Indian jati groups living side by side in the same village is typically two to three times higher than the genetic differentiation between northern and southern Europeans. The truth is that India is composed of a large number of small populations.
Selection against Neanderthal-human hybrids
(I’m going to go with the handy convention that the primary ancestor group of modern humans are called ‘humans’ and other branches aren’t, but I very much think of Neanderthals as a subset of humans.)
One of the most interesting things I got from Who We Are and How We Got Here was more information on Neanderthal-human hybridization. I knew the common factoid that that non-Africans have about 2% Neanderthal ancestry, that this mixture had happened about 40K years ago when humans expanded into Europe, and that Neanderthals went extinct several thousand years afterwards.
Zooming in on that 2% –
The average proportion of Neanderthal ancestry in non-African populations is about 2 percent, but it is not spread evenly. In more than half the genome, no Neanderthal ancestry has been detected in anyone. But in some unusual places in the genome, more than 50 percent of DNA sequences are from Neanderthals.
Where do we see selection against Neanderthal ancestry? In parts of the genome known to be relevant to the fertility of hybrids.
One is the X chromosome, which apparently is a default site of selection-against-minority-ancestry in hybrids:
How is it that hybridization can lead to so much less genetic variation on chromosome X than on the rest of the genome? From studies of a variety of species across the animal kingdom, it is known that when two populations are separated for long enough, hybrid offspring have reduced fertility. In mammals like us, reduced fertility is much more common in males, and the genetic factors contributing to this reduced fertility are concentrated on chromosome X. So when two populations are so separated that their offspring have reduced fertility, but nevertheless mix together to produce hybrids, it is expected that there will be intense natural selection to remove the factors contributing to reduced fertility. This process will be especially evident on chromosome X because of the concentration of genes contributing to infertility on it. As a result, there tends to be natural selection on chromosome X for stretches of DNA from the population that contributed most of the hybrid population’s ancestry. This causes the hybrid population to derive its chromosome X almost entirely from the majority population, leading to an anomalously low genetic divergence on chromosome X between the hybrid population and one of the hybridizing populations, consistent with the pattern seen in humans and chimpanzees.
Another relevant area where Neanderthal ancestry was selected are genes responsible for the male reproductive tissue. Apparently they’re finicky. Genes that are active in the germ cells of testicles have less Neanderthal ancestry on average than genes that are most active in other body tissues.
These aren’t the only parts of the genome where Neanderthal ancestry was selected against, just the sites of strongest selection. Neanderthal genes have been selected against around the majority of genes – there is far more Neanderthal ancestry in noncoding DNA than in coding. The book has this striking visualization of the decline. Neanderthal ancestry in humans was closer to 3~6 percent when hybridization occurred in Europe.
Hybrids were only kind of working out, fertility-wise; Neanderthals and humans must have been on the brink of speciation at the time they met.
Just as interesting as “what was selected against”, if not more: Where do we see selection for Neanderthal ancestry? Skin and hair!
Interbreeding with Neanderthals helped modern humans to adapt to new environments just as interbreeding with Denisovans did. We and others showed that at genes associated with the biology of keratin proteins, present-day Europeans and East Asians have inherited much more Neanderthal ancestry on average than is the case for most other groups of genes. This suggests that versions of keratin biology genes carried by Neanderthals were preserved in non-Africans by the pressures of natural selection, perhaps because keratin is an essential ingredient of skin and hair, which are important for providing protection from the elements in cold environments such as the ones that modern humans were moving into and to which Neanderthals were already adapted.
Other neat Neanderthal facts I’m shoehorning in:
-
They were less genetically diverse than humans (book says ‘the diversity of their genomes was about four times smaller’, but I’m not sure what figure actually represents) – this may have been a problem for them that contributed to their extinction, because low-genetic-diversity populations tend to stack up more detrimental mutations.
-
Neanderthal-human mixing happened in Europe, but the current day group with the most Neanderthal ancestry is East Asians. This is probably because humans mixed with Neanderthals, spread out over Eurasia, and then Europe had another influx of non-Neanderthal human expansion that contributed to the current-day European gene pool and diluted Neanderthal ancestry.
-
Topical: this month, the author’s DNA mentor published a paper showing that a (the?) major genetic risk factor for severe COVID cases is inherited from Neanderthals. https://www.biorxiv.org/content/10.1101/2020.07.03.186296v1
Pigmentation
If I had better priorities I would be less interested in the genetics of skin or hair color, but I’m a superficial monkey and love knowing why some people look the way they do. Behold! One of the most aesthetic things I learned from David Reich’s Who We Are and How We Got Here!
The fusion of these highly different populations into today’s West Eurasians is vividly evident in what might be considered the classic northern European look: blue eyes, light skin, and blond hair. Analysis of ancient DNA data shows that western European hunter-gatherers around eight thousand years ago had blue eyes but dark skin and dark hair, a combination that is rare today. [33] The first farmers of Europe mostly had light skin but dark hair and brown eyes—thus light skin in Europe largely owes its origins to migrating farmers. [34] The earliest known example of the classic European blond hair mutation is in an Ancient North Eurasian from the Lake Baikal region of eastern Siberia from seventeen thousand years ago.
33: I. Olalde et al - “Derived Immune and Ancestral Pigmentation Alleles in a 7,000-Year-Old Mesolithic European,” Nature 507 (2014):225-28.
34: I.Mathieson et al., “Genome-Wide Patterns of Selection in 230 Ancient Eurasians,” Nature 528 (2015): 449-503
Behavioral modernity
The sad truth is that it is possible to count on the fingers of two hands the examples like FOXP2 of mutations that increased in frequency in human ancestors under the pressure of natural selection and whose functions we partly understand. In each of these cases, the insights only came from years of hand-to-hand combat with life’s secrets by graduate students or postdoctoral scientists making engineered mice or fish, suggesting that it will take an evolutionary Manhattan Project to understand the function of each mutation that we have and that Neanderthals do not. This Manhattan Project of human evolutionary biology is one to which we as a species should commit ourselves. But even when it is carried out, I expect that the findings will be so complicated—with so many individual genetic changes contributing to what makes humans distinctive—that few people will find the answer comprehensible. While the scientific question is profoundly important, I expect that no intellectually elegant and emotionally satisfying molecular explanation for behavioral modernity will ever be found.
Information theoretical limit
Here’s the most exciting thing I’ve learned this month: the concrete information theoretic limit to how far back you can learn about ancestral human populations using the DNA of modern humans!
I’m confused by the explanation of ‘splices’ and cannot appreciate this fully, but what I’m getting is still very cool!
Females create an average of about forty-five new splices when producing eggs, while males create about twenty-six splices when producing sperm, for a total of about seventy-one new splices per generation. …
Any person’s genome is derived from 47 stretches of DNA corresponding to the chromosomes transmitted by mother and father plus mitochondrial DNA. One generation back, a person’s genome is derived from about 118 (47 plus 71) stretches of DNA transmitted by his or her parents. Two generations back, the number of ancestral stretches of DNA grows to around 189 (47 plus 71 plus another 71) transmitted by four grandparents. Look even further back in time, and the additional increase in ancestral stretches of DNA every generation is rapidly overtaken by the doubling of ancestors. Ten generations back, for example, the number of ancestral stretches of DNA is around 757 but the number of ancestors is 1,024, guaranteeing that each person has several hundred ancestors from whom he or she has received no DNA whatsoever. Twenty generations in the past, the number of ancestors is almost a thousand times greater than the number of ancestral stretches of DNA in a person’s genome, so it is a certainty that each person has not inherited any DNA from the great majority of his or her actual ancestors.
These calculations mean that a person’s genealogy, as reconstructed from historical records, is not the same as his or her genetic inheritance. The Bible and the chronicles of royal families record who begat whom over dozens of generations. Yet even if the genealogies are accurate, Queen Elizabeth II of England almost certainly inherited no DNA from William of Normandy, who conquered England in 1066 and who is believed to be her ancestor twenty-four generations back in time. This does not mean that Queen Elizabeth II did not inherit DNA from ancestors that far back, just that it is expected that only about 1,751 of her 16,777,216 twenty-fourth-degree genealogical ancestors contributed any DNA to her.
Figure 4. The number of ancestors you have doubles every generation back in time. However, the number of stretches of DNA that contributed to you increases by only around seventy-one per generation. This means that if you go back eight or more generations, it is almost certain that you will have some ancestors whose DNA did not get passed down to you. Go back fifteen generations and the probability that any one ancestor contributed directly to your DNA becomes exceedingly small.
Going back deeper in time, a person’s genome gets scattered into more and more ancestral stretches of DNA spread over ever-larger numbers of ancestors. Tracing back fifty thousand years in the past, our genome is scattered into more than one hundred thousand ancestral stretches of DNA, greater than the number of people who lived in any population at that time, so we inherit DNA from nearly everyone in our ancestral population who had a substantial number of offspring at times that remote in the past.
There is a limit, though, to the information that comparison of genome sequences provides about deep time. At each place in the genome, if we trace back our lineages far enough into the past, we reach a point where everyone descends from the same ancestor, beyond which it becomes impossible to obtain any information about deeper time from comparison of the DNA sequences of people living today. From this perspective, the common ancestor at each point in the genome is like a black hole in astrophysics, from which no information about deeper time can escape. For mitochondrial DNA this black hole occurs around 160,000 years ago, the date of “Mitochondrial Eve.” For the great majority of the rest of the genome the black hole occurs between five million and one million years ago, and thus the rest of the genome can provide information about far deeper time than is accessible through analysis of mitochondrial DNA. Beyond this, everything goes dark.
Europeans and Native Americans
Peeved because I crave knowing ‘when modern populations 1 and 2 diverged’, but it turns out that usually the answer looks kind of like this
Humans / Chimps / Bonobos
When they applied the method to study the separation time of common chimpanzees and their distant cousins, bonobos, they found evidence that the separation was very sudden, consistent with the hypothesis that the species were separated by a huge river (the Congo) that formed rather suddenly one to two million years ago. In contrast, when they applied the method to study humans and chimpanzees, they found evidence for an extended period of genetic interchange after population differentiation began, as expected for hybridization.
sometimes a river cuts a species population in two and one of them grows up extra horny