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March 18, 2019

The evolution of languages

Filed under: Culture,Evolution,Linguistics — Razib Khan @ 2:59 pm
Map of language families of the world today

The story in the Bible about the “Tower of Babel” was the explanation that the ancient Hebrews gave for why there was so much linguistic diversity in the world around them. Ancient people were curious and observant enough to notice that their neighbors did not speak like them. The word “barbarian” comes from the ancient Greek perception of what non-Greeks sounded like to Greeks.

Sometimes linguistic differences can be more subtle, but still critical to life and death. The meaning of the term shibboleth comes out of the context where different ancient Israelite groups pronounced s differently and used that to identify members of an enemy tribe. The limits of your language are often the limits of your tribe.

But evolutionary genetics tells us humans share a common ancestor. That we are one tribe in our genealogy. In fact, the most recent common ancestors of all human populations lived within the last 200,000 years. Outside of Africa, they lived within the last 50,000 years. And, in North and South America it is within the last 15,000 years. We are a young species.

And yet you have a situation such as in the highlands of New Guinea where people who live in different valleys positioned next to each other speak two totally different languages. In North America, Europeans encountered thousands of languages and many language families. And yet we know that most of the ancestors of the natives of North America arrived within the last 15,000 years!

The situation in the Americas may have been the norm in the recent past. Today 40% of the world’s population speak Indo-European languages, but 6,000 years ago it is likely that very few Europeans or Indians spoke Indo-European languages. The spread of English, Arabic, and Chinese occurred in historical time. Their rise to dominance is due to social and political realities of the last 2,000 years.

The ancient world points to incredible linguistic diversity which faded with rising of the “empires of the word.” Over four thousand years ago in Mesopotamia, what is now modern Iraq, many of the people spoke Semitic dialects. Related Arabic and Hebrew. But Sumerian flourished at the time in the south, a language unrelated to any we know of today. In the far north, the people spoke Hurrian, again, a language unrelated to any which flourish today. In the mountains to the east there lived the Guti and Kassites, who seem to have spoken languages unrelated to any spoken today as well.

Etruscans spoke a non-Indo-European language, but influenced the Romans

The Romans record the presence of Etruscans, who influenced their culture, and spoke a language which was not Indo-European. To the further north, there were Ligurians, hugging the coast around modern Genoa, while in the hills there lived tribal Samnites and Oscans. To the south, there were Greek cities and obscure native peoples such as the Sicils. The island of Sardinia was inhabited by speakers of what we now term “Paleo-Sardinian,” perhaps related to Basque. The ancient world was one great Babel.

What this highlights is that while genetic evolution proceeds slowly, gradually, and continuously, linguistic evolution can be riotous, rapid, and proliferate at light speed toward unintelligibility.

Just by physical inspection, one can tell that Finns and Swedes share common ancestors. That they are genetically related. But linguistically they are as different as can be. Finnish is no closer to Swedish phylogenetically than it is to Bantu or Chinese! Swedish as a language is most definitely closer to Bengali, Spanish, or ancient Hittite, than it is to Finnish.

Evolution simply describes a change in characteristics which be defined on a phylogenetic tree. This can be biological, as with genetic evolution, or, it can be cultural. But clearly, the mechanisms matter here. Mendel’s laws impose constraints and regularity to biological evolution which culture lacks. Half of your genetic material comes from each parent. There is no such constraint with culture. In fact, your cultural inheritance may come from someone who is not your biological parent.

Whereas genetic evolution can be traced through modern scientific methods to billions of years in the past, elements of cultural evolution shift so fast that most researchers are skeptical of the possibility of going more than ten thousand years in the past. We have a Neanderthal genome, but it is unlikely we will ever be able to reconstruct the Neanderthal languages (there were certainly many!).

The diversity of languages of North and South America illustrates how a small number of people, perhaps a few thousand genetically, can give rise to thousands of languages hundreds of generations later. The diversity we see around us today in the modern era is but a shadow of what was likely the human norm for most of our species’ history. It is as if a massive process of selection has winnowed down the languages spoken down to a few huge families.

And yet we can still discern similarities across many languages separated by history and large geographical distances. This is most famously illustrated by the “Indo-European” languages.

The affinities between Indian languages and those of Europe were discerned by Sir William Jones in the 18th century. After the fact, the similarities are clear to native speakers. A focus on core words that were more likely to be preserved gave rise to “Swadesh lists.”

Here is the number “nine” in various languages:

Finnish: yhdeksän, Hungarian: szám, Basque: zenbakia, Swedish: nio, Czech: neun, French: neuf, Armenian: inn, Bengali: naẏa, Arabic: tis3a, Turkish: dokuz

Even if you are not a linguist or philologist peculiar similarities may jump out at you (as well as discordances). This is because a large number of languages in that list are Indo-European, and share a common origin within the last ~5,000 years. Paired with them are nearby languages which are non-Indo-European.

It is almost certainly the case that most of those languages above are spoken by people who share ancestors within the last ~50,000 years…but evolution on vocabulary is fast enough that the signal of shared ancestry is lost much faster than in genetic evolution.

This is why many historical linguists focus on grammar, rather than vocabulary. Just going by a list of the number of words within the lexicon you might conclude that English is a Latinate language, like French, Spanish or Italian. But if you look at grammar, it is clear that English is a Germanic language. Vocabulary is something that is easily shared, and quite protean. Consider how quickly different generations develop their own slang and preferred terms.

Grammar is much more conservative, and non-standard speech is often indicative that someone learned English as an adult, and retained the grammar of the language in which they were raised.

Vocabulary evolves fast and responds to selection. People who live in a forested environment may have many ways to describe types of trees. Those who live on a grassland may not. But grammar is part of the deep structure of any language and is evolutionarily conserved. If Noam Chomsky is correct, all grammar is a local expression of “universal grammar,” which is hardwired into our species on the deepest levels.

And yet all of this fascinating research and knowledge is constrained by the fact that most of the world’s languages are disappearing. This mass extinction is happening due to globalization, trade, and the advantages of speaking an ‘international’ language. Of the world’s 7,000 living languages, nearly half are in danger of going extinct.

With the extinction of a language, a peoples’ whole memory fades into oblivion, as well as the record of human diversity from which we can make inferences about the power and range of evolutionary processes in culture.


The evolution of languages was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The evolution of languages

Filed under: Diversity,Evolution,Language,Linguistics — Razib Khan @ 2:56 pm
Map of language families of the world today

The story in the Bible about the “Tower of Babel” was the explanation that the ancient Hebrews gave for why there was so much linguistic diversity in the world around them. Ancient people were curious and observant enough to notice that their neighbors did not speak like them. The word “barbarian” comes from the ancient Greek perception of what non-Greeks sounded like to Greeks.

Sometimes linguistic differences can be more subtle, but still critical to life and death. The meaning of the term shibboleth comes out of the context where different ancient Israelite groups pronounced s differently and used that to identify members of an enemy tribe. The limits of your language are often the limits of your tribe.

But evolutionary genetics tells us humans share a common ancestor. That we are one tribe in our genealogy. In fact, the most recent common ancestors of all human populations lived within the last 200,000 years. Outside of Africa, they lived within the last 50,000 years. And, in North and South America it is within the last 15,000 years. We are a young species.

And yet you have a situation such as in the highlands of New Guinea where people who live in different valleys positioned next to each other speak two totally different languages. In North America, Europeans encountered thousands of languages and many language families. And yet we know that most of the ancestors of the natives of North America arrived within the last 15,000 years!

The situation in the Americas may have been the norm in the recent past. Today 40% of the world’s population speak Indo-European languages, but 6,000 years ago it is likely that very few Europeans or Indians spoke Indo-European languages. The spread of English, Arabic, and Chinese occurred in historical time. Their rise to dominance is due to social and political realities of the last 2,000 years.

The ancient world points to incredible linguistic diversity which faded with rising of the “empires of the word.” Over four thousand years ago in Mesopotamia, what is now modern Iraq, many of the people spoke Semitic dialects. Related Arabic and Hebrew. But Sumerian flourished at the time in the south, a language unrelated to any we know of today. In the far north, the people spoke Hurrian, again, a language unrelated to any which flourish today. In the mountains to the east there lived the Guti and Kassites, who seem to have spoken languages unrelated to any spoken today as well.

Etruscans spoke a non-Indo-European language, but influenced the Romans

The Romans record the presence of Etruscans, who influenced their culture, and spoke a language which was not Indo-European. To the further north, there were Ligurians, hugging the coast around modern Genoa, while in the hills there lived tribal Samnites and Oscans. To the south, there were Greek cities and obscure native peoples such as the Sicils. The island of Sardinia was inhabited by speakers of what we now term “Paleo-Sardinian,” perhaps related to Basque. The ancient world was one great Babel.

What this highlights is that while genetic evolution proceeds slowly, gradually, and continuously, linguistic evolution can be riotous, rapid, and proliferate at light speed toward unintelligibility.

Just by physical inspection, one can tell that Finns and Swedes share common ancestors. That they are genetically related. But linguistically they are as different as can be. Finnish is no closer to Swedish phylogenetically than it is to Bantu or Chinese! Swedish as a language is most definitely closer to Bengali, Spanish, or ancient Hittite, than it is to Finnish.

Evolution simply describes a change in characteristics which be defined on a phylogenetic tree. This can be biological, as with genetic evolution, or, it can be cultural. But clearly, the mechanisms matter here. Mendel’s laws impose constraints and regularity to biological evolution which culture lacks. Half of your genetic material comes from each parent. There is no such constraint with culture. In fact, your cultural inheritance may come from someone who is not your biological parent.

Whereas genetic evolution can be traced through modern scientific methods to billions of years in the past, elements of cultural evolution shift so fast that most researchers are skeptical of the possibility of going more than ten thousand years in the past. We have a Neanderthal genome, but it is unlikely we will ever be able to reconstruct the Neanderthal languages (there were certainly many!).

The diversity of languages of North and South America illustrates how a small number of people, perhaps a few thousand genetically, can give rise to thousands of languages hundreds of generations later. The diversity we see around us today in the modern era is but a shadow of what was likely the human norm for most of our species’ history. It is as if a massive process of selection has winnowed down the languages spoken down to a few huge families.

And yet we can still discern similarities across many languages separated by history and large geographical distances. This is most famously illustrated by the “Indo-European” languages.

The affinities between Indian languages and those of Europe were discerned by Sir William Jones in the 18th century. After the fact, the similarities are clear to native speakers. A focus on core words that were more likely to be preserved gave rise to “Swadesh lists.”

Here is the number “nine” in various languages:

Finnish: yhdeksän, Hungarian: szám, Basque: zenbakia, Swedish: nio, Czech: neun, French: neuf, Armenian: inn, Bengali: naẏa, Arabic: tis3a, Turkish: dokuz

Even if you are not a linguist or philologist peculiar similarities may jump out at you (as well as discordances). This is because a large number of languages in that list are Indo-European, and share a common origin within the last ~5,000 years. Paired with them are nearby languages which are non-Indo-European.

It is almost certainly the case that most of those languages above are spoken by people who share ancestors within the last ~50,000 years…but evolution on vocabulary is fast enough that the signal of shared ancestry is lost much faster than in genetic evolution.

This is why many historical linguists focus on grammar, rather than vocabulary. Just going by a list of the number of words within the lexicon you might conclude that English is a Latinate language, like French, Spanish or Italian. But if you look at grammar, it is clear that English is a Germanic language. Vocabulary is something that is easily shared, and quite protean. Consider how quickly different generations develop their own slang and preferred terms.

Grammar is much more conservative, and non-standard speech is often indicative that someone learned English as an adult, and retained the grammar of the language in which they were raised.

Vocabulary evolves fast and responds to selection. People who live in a forested environment may have many ways to describe types of trees. Those who live on a grassland may not. But grammar is part of the deep structure of any language and is evolutionarily conserved. If Noam Chomsky is correct, all grammar is a local expression of “universal grammar,” which is hardwired into our species on the deepest levels.

And yet all of this fascinating research and knowledge is constrained by the fact that most of the world’s languages are disappearing. This mass extinction is happening due to globalization, trade, and the advantages of speaking an ‘international’ language. Of the world’s 7,000 living languages, nearly half are in danger of going extinct.

With the extinction of a language, a peoples’ whole memory fades into oblivion, as well as the record of human diversity from which we can make inferences about the power and range of evolutionary processes in culture.

February 19, 2019

Arabia between Africa & Eurasia

Filed under: Evolution,Genetics,Human Evolution,science — Razib Khan @ 1:57 am

Arabia between Africa and Eurasia

Shanidar cave in Iraq, once occupied by Neanderthals

For hundreds of thousands of years Neanderthals and the ancestors of modern humans interacted in the broad zone of territory we now call the “Middle East.” Neanderthals occupied sites across the Fertile Crescent, while Arabia and parts further north were settled on and off by people related to and possibly ancestral to modern humans. Before the expansion of our ancestors across Eurasia, and into Oceania, 50,000 years ago, a situation of dynamic equilibrium persisted as the Near East existed as an ecozone in flux between that of northern Eurasia and northern Africa. Between Neanderthal and modern human.

Though there is no doubt that Africa is the great reservoir for the vast majority of human ancestry today, by dint of their locations Arabia and the Fertile Crescent are essential pieces of the broader jigsaw puzzle of the human story. Modern humans either migrated north through the Sinai from Africa. Or, they crossed the straits that divide modern Yemen from Africa on the southern edge of the Red Sea. Of course, they could have done both!

But as modern humans were pushing north and east, this region was long occupied by Neanderthals. Today we know that all non-Africans carry Neanderthal ancestry. One of the simplest explanations for this is that the admixture occurred in the Middle East, as modern humans came into contact with their cousins. As they migrated onward, north and east, they did not mix so much with the Eurasian hominins that lived in those regions.

The problem with this theory is that different methods of analysis have shown that Neanderthal ancestry varies across many populations, even when you remove African ancestry from the equation. In short, many assessments conclude that East Asians have more Neanderthal ancestry than Europeans, who have more Neanderthal ancestry than people in the Middle East.

Why could this be? One of the most popular explanations is that East Asians have had more mixture with Neanderthal-like populations. That is, there was a later mixture event. Meanwhile, people in the Fertile Crescent and Arabia mixed with people who were not African but split from other “Out of Africa” populations before the admixture with Neanderthals. These people are awkwardly called “Basal Eurasians,” meaning they split off before the other groups diversified into all the lineages from Europe to Australia.

But new research suggests another possibility: all Africans may have ancestry from “West Eurasian” populations which moved back into Africa after the “Out of Africa” event ~50,000 years ago. For statistical reasons beyond the purview of this post, this affinity between West Eurasians and Africans may lead to incorrect estimates of Neanderthal ancestry varying across Eurasian groups, when in fact it is simply affinity to Africans which varies across groups. West Eurasians and Africans are simply genetically more similar than East Eurasians and Africans.

More work needs to be done about who these West Eurasians were. But, keep in mind that Arabians and Levantines do show less Neanderthal ancestry in the older framework than even Europeans, implying that the “West Eurasians” were likely from the Near East, which is the most reasonable scenario geographically in any case for a “back migration” to Africa.

Though it is certainly true that “we are all Africans” under the skin, least within the last 50,000 years, in some sense all Africans may be a bit Arabian….

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Arabia between Africa & Eurasia was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

February 14, 2019

Love, oxytocin and evolution

Filed under: Evolution,love,oxytocin,science,valentines-day — Razib Khan @ 1:52 am
Gibbons form pair-bonds

On some level, most scientists would say that everything is reducible to material and mechanism. But to say that “everything is due to the swerve of atoms” doesn’t get us much further than the ancient Greeks, who were the first to elaborate on such materialist ideas philosophically.

At the other extreme from scientists are those humanists who assert that concepts such as “love” or “hate” are not reducible to scientific analysis and decomposition. In this framework, love and hate are both emotions which exist in a particular social and cultural context, and general systematic analysis may miss the forest from the trees.

But if physics does not offer answers beyond the trivial, a better understanding of behavior or mental characteristics can be obtained by looking at sciences such as cognitive neuroscience and evolutionary biology, which exist at a higher level of phenomenological complexity. Behavior comes from the mind, and the mind is an expression of the brain, which itself is shaped by evolutionary pressures.

Romantic love as an emotion then exists in the context of our evolutionary history, and that history likely has something to do with mating and pair-bonding. Our “reproductive fitness” is conditional on the very act of mating, and often survival is dependent on aid and help from others. For birds, monogamy is so common because both parents are often required to warm and tend to eggs. In mammals, in contrast, males tend to be less involved in provisioning for offspring. But there are exceptions.

An “alpha couple” among wolves

Wolves, and some primates such as gibbons and humans, tend to be monogamous. This is evident in the minimal difference in the size between the two sexes, as well as genetic data which shows that the “effective population size” of males and females over time has been in the same order of magnitude. That is, a reasonable proportion of both males and females contribute genes to the next generation.

Humans have extended childhoods

One reason that humans have elaborate emotions related to bonding seems to be that our childhoods are extremely long. This means that parents, and in particular the mother, develops a strong bond to their offspring, which is reciprocated. In the complex social systems of our species feelings of connectedness extend to kinship, and the bond between mates is solidified with romantic love and companionship. Love comes in many forms in our lineage, but it is clearly a feature and not a bug.

This is ultimately a consequence of genetics. The tendency toward prosociality and empathy seem to be heritable. That is, some of the variation of the characteristics within a population is due to variation in genes. This is clearest in prairie voles, where different species exhibit radically different behaviors in relation to bonding and mating, and also different genetic profiles.

Individuals with more “G” allele have more empathy

In humans, the neuropeptide oxytocin has been implicated in variation in characteristics such as empathy and bonding. This research began with relatively small samples, but a recent study with 1,830 individuals reports a single mutation with the OXTR locus is associated with variation in empathy. This is not entirely unreasonable in light of the fact that in the modern human population there are differences in personality, and dispositions, including empathy. The persistence of various personality types indicates that there’s no singular way in which one maximizes long-term fitness, but many alternative strategies (within limits).

Romantic love in terms of its biological basis may have a fundamentally material and evolutionary origin: a tight bond between parents results in a greater likelihood that offspring grow up to adulthood. It emerges from a complex set of neurobiological pathways, which themselves vary due to genetic factors from person to person.

But just as sugar is a molecule we understand but find still delicious, so the sweetness of love remains even after unmasking the underlying science.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Love, oxytocin and evolution was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

February 13, 2019

The Insight Show Notes — Season 2, Episode 14: Love & biology

Filed under: Evolution,love,valentines-day — Razib Khan @ 6:51 pm

The Insight Show Notes — Season 2, Episode 14: Love & biology

This week on The Insight (Apple Podcasts, Stitcher and Google Podcasts)we discuss “love” from the perspective of an evolutionary biologist. More specifically, we had a wide-ranging discussion with Steve Phelps, a professor at the University of Texas in Austin. He studies the intersection of behavior, evolution, and neuroscience, with genetic tools.

First, we addressed whether love is a cultural invention of the last few thousand years. Particularly, of the West.

The reality is that love, and in particular romantic love, is a primal urge that likely existed in the environment of our “evolutionary adaptedness.” But its particularities are cultural. There is a lot of diversity “on top” of the basic source code. But there is a human universal we recognize.

We talked about inclusive fitness and the origins of love as an emotion in socialization. In particular, the common neurological and evolutionary origins of love in the context of parent-child, family, and partners.

A debate emerged about whether humans are ancestrally “monogamous” or “polygamous.” The terms differ in definition across discipline (genetics, behavior, anthropology), but the consensus seemed to be that we’re more monogamous than gorillas or chimpanzees.

There was much discussion of the literature on the association between empathy at the OXTR locus. Mostly commonly studied in voles, there are also suggestive results in humans. But much work needs to be done!

We talked Helen Fisher’s work in the neurobiology of love and attachment, and her excellent books such as Anatomy of Love.

Steve finished with a discussion on frequency-dependent selection, and how a diversity of behavior and disposition might be maintained.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The Insight Show Notes — Season 2, Episode 14: Love & biology was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

February 12, 2019

Why Charles Darwin matters

Filed under: darwin,Evolution,science — Razib Khan @ 2:11 am

Charles Robert Darwin was born on February 12th, 1809. He was the son of a prosperous and prominent lineage. His grandfather, Erasmus Darwin, was a physician and public intellectual. Like his more famous grandson, the elder Darwin was a natural philosopher who propounded theories of evolution. On his mother’s side, Charles Darwin was the grandson of the manufacturer Josiah Wedgewood. If Erasmus Darwin reflected the intellectual currents of England during the late 18th century, Wedgewood illustrated the rise of the merchant class with the industrialization of Britain.

Growing up in comfortable circumstances, Charles Darwin had many opportunities to succeed, or fail. His university career was checkered at best. At one point it seemed likely that he would become a clergyman in the Church of England, satisfying his interest in the natural world as an avocation.

Life had different plans for him. He famously went on a voyage around the world, and his observations of the geology, flora, and fauna, fed into his later theories. But the truth is that the immediate consequence of Darwin’s travels was a book, The Voyage of the Beagle, which made him something of a minor celebrity in Victorian England. Even without The Voyage of the Beagle his name would likely have been noted in the pedigree of the prominent Darwin-Wedgewood family.

If Charles Darwin had never published The Origin of Species, history would have remembered him, albeit as a minor figure of the 19th century.

But Darwin did publish The Origin of Species. And after this, he published other books, most famously The Descent of Man. But Charles Darwin’s fame rests primarily on a single book published in 1859, whose full title was On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

Charles Darwin the man led a fascinating and full life. His lineage was colorful, his times were exciting, while his marriage was loving and passionate. Charles Darwin had enough texture and tension within his life that feature films can easily revolve around him as a character. He was a man in full.

But we are talking about Charles Darwin today because of the science which he assembled and presented within The Origin of Species. Though evolutionary ideas had been around since the time of the ancient Greeks, it was Charles Darwin who brought the idea to life through a plausible, compelling, and ubiquitous dynamic and underlying mechanism in the form of adaptation through natural selection. There were earlier evolutionary thinkers in the 19th century, but the reason that we use the term “Darwinism” interchangeably with evolutionary biology is that the model presented in The Origin of Species laid the foundation for the whole scientific discipline.

Science is not a single idea. It is not a hunch. It is the assembling of observations, the construction of theory, and the generation of predictions. With Alfred Wallace, Charles Darwin presented to his contemporaries the hypothesis that natural selection was the motor which drove the riotous diversification of form and function around us in the living world.

The development of genetics as field after 1900 revived Darwinian evolutionary biology as the study of the process of natural selection became a core element of the field of evolutionary genetics. Though others had proposed the tree of life and common descent, it was Darwins’ ideas of how that tree diversified which transformed what had been a stale description into a dynamic representation of what we now call evolutionary process.

It is true that despite the fertility of his mind many scientists today within biology do not read Darwin’s original works. But that is because his conjectures and certainties are laced through fields, part, and parcel of the axioms which are taken for granted by working researchers.

Today all biologists implicit stand on Darwin’s shoulders to see further and more clearly.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Why Charles Darwin matters was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

January 23, 2019

The Insight Show Notes — Season 2, Episode 11: Cultural Evolution

Filed under: anthropology,Cultural Evolution,Culture,Evolution — Razib Khan @ 4:45 pm

The Insight Show Notes — Season 2, Episode 11: Cultural Evolution

This week on The Insight (Apple Podcasts, Stitcher and Google Podcasts)we discussed the field of cultural evolution with Richard McElreath of Max Planck Institute for Evolutionary Anthropology. The past, present, and future possibilities within this discipline.

Genealogically the modern study of culture in an evolutionary context goes back to L. L. Cavalli-Sforza and M. W. Feldman’s Cultural Transmission and Evolution: A Quantitative Approach. This approach was extended by Peter Richerson and Robert, such as in their book Not By Genes Alone. McElreath himself has written Mathematical Models of Social Evolution, illustrating the formal bent of this field.

We discussed the difference between the methods within cultural evolution, which borrow heavily from population and quantitative genetics, and cultural anthropology. While cultural anthropology is descriptive and avoids generalities, cultural evolution leans heavily on mathematical modeling. McElreath points out that today there is a society for his field, the Cultural Evolution Society.

Differences between cultural evolution and evolutionary psychology were discussed. While the former is mathematical as well as depending on fieldwork, the latter is a branch of social psychology informed by evolution that is more verbal and experimental.

The relevance of group selection to cultural evolution and its irrelevance to evolutionary genetics was also explored.

Two papers that McElreath was involved with, Greater wealth inequality, less polygyny: rethinking the polygyny threshold model and Sustainability of minority culture when inter-ethnic interaction is profitable, were discussed.

Finally, we also alluded to a non-obvious finding from cultural evolution: that social cognition explains cultural complexity we see around us, rather than individual intelligence. This is a central theme of Joe Henrich’s book The Secret of Our Success.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


The Insight Show Notes — Season 2, Episode 11: Cultural Evolution was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

January 16, 2019

To understand Neanderthals we need to understand ourselves

Filed under: Evolution,Genetics,Genomics,Neanderthals — Razib Khan @ 1:56 pm

In 2010 researchers sequenced the whole genome of a single Neanderthal. From comparing this genome to that of humans alive today they concluded, to their surprise, that many modern human populations had Neanderthal ancestry! More specifically, all populations outside of Africa seem to have some Neanderthal ancestry.

Over the last decade, researchers have come to agree that this finding is a true one. That is, modern humans do have Neanderthal ancestry. In fact, most scientists now believe that there is also ancestry from a third human population, Denisovans, across eastern Eurasia and Oceania.

But there is more to the story than we understood in 2010. Then, researchers argued there was a single admixture as humans left Africa. Today, some researchers contend there were multiple Neanderthal admixtures, with East Asians having more Neanderthal ancestry than Europeans. Others argue that European Neanderthal ancestry is diminished by later mixing with a human population without Neanderthal ancestry! Finally, some researchers have suggested these differences can be explained by natural selection, whereby Neanderthal genes are removed from the population due to their selective effects, which had different power across different populations (the larger the population, the stronger natural selection is)

Despite the widespread agreement about Neanderthal ancestry in modern humans, the discovery has triggered many more questions.

A new paper in PNAS, The Limits of long-term selection against Neandertal introgression, aims to resolve this muddle by two primary means:

  1. Use multiple Neanderthal samples of different relatedness to modern humans to obtain a better estimate of proportions.
  2. Add complexity to our understanding of the interactions between various ancestral human populations, and see how that affects estimates of Neanderthal ancestry.

The authors conclude that the decline in Neanderthal admixture discovered in Europeans may, in fact, be an artifact. First, it neglects gene-flow between African populations, as well as from Eurasian populations back into Africa (in particular, from European and Near Eastern groups). Second, using two Neanderthal samples, one much more closely related to the group which contributed to modern humans, allows for more precise direct estimates.

Though the authors found some evidence for natural selection, these results suggest that this force is not necessary to explain the differences between modern human populations.

This is unlikely to be the final world. The moral of the story is that moving beyond simple models and a few samples add complexity and nuance to our understanding of how our Neanderthal ancestry fits into the broader narrative of our ancestors’ tales.

Discover your Neanderthal story today!


To understand Neanderthals we need to understand ourselves was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

January 9, 2019

On the edge of Africa and Eurasia

Filed under: Evolution — Razib Khan @ 5:43 pm
Rub’ al Khali

The sands of Arabia harbor romantic allure for many, despite their desolation. At the nexus between Eurasia and Africa, the Arabian peninsula serves as both a conduit and barrier for trade and migration. On its northern fringe arose the first civilizations, while far to the south the bleak deserts give way to the mountains and fields of what the Romans termed “lucky Arabia,” the verdant highlands of Yemen. From the sands of the north the armies marched, while the coasts of the south are where trade routes across the Indian ocean began.

From the Queen of Sheba to the rise of Islam and the centrality of oil in the modern economy, Arabia plays a pivotal role in the history of the world.

But the importance of this peninsula on the southwest edge of Eurasia is much deeper in an evolutionary sense. To the north in the mountains of modern Iraq were the southern edges of Neanderthal occupation in Eurasia, in the caves of Shanidar. To the northwest, just outside of Arabia proper, were the Skhul and Qafzeh hominins, a group of modern humans who flourished ~100,000 years ago, and whose roots seem to have been Africa.

Hominins have been present outside of Africa for nearly two million years. And yet their origins are ultimately in Africa. Both Neanderthals and modern humans derive from migrations from Africa within the last one million years. Logically Arabia must have been a stopping-off point for humans for millions of years.

Citation: Petraglia, M. D., Breeze, P. S., & Groucutt, H. S. (2019). Blue Arabia, green Arabia: examining human colonisation and dispersal models. In Geological Setting, Palaeoenvironment and Archaeology of the Red Sea (pp. 675–683). Springer, Cham.

Just as the complex geography of Arabia made it the nexus of history, so the scaffolding of water, mountains, and deserts have made it a central element of the human evolutionary odyssey. Humans have two plausible avenues of migration out of Africa. In the north, through the Sinai, or in the south across the Bab-el-Mandeb strait between Yemen and the African mainland.

The reality is that both routes may have been important, as the region seems to have been witness to many migrations of humans over the past two million years, as well as movements back toward Africa, whether it be the Neanderthal shift south during cold periods or the movements of agriculturalists from the Fertile Crescent over the past 10,000 years. Because of variations in climate over this time, multiple routes may have opened up, whether due to reduced sea levels, or the existence of perennial rivers on the Arabian peninsula during times of greater precipitation.

The mountains of Yemen in southwest Arabia

And Arabia may not simply have been a transit point. The latest ancient genetic work suggests that the humans who left Africa were separated into two primary ones. One population did not mix with the Neanderthals to the north and east. While another group did. This second group became the ancestors of all the humans today found in Europe, Asia, Oceania, and the New World. The first group seems to have remained close to Africa and mixed eventually with the first group, giving rise to the various peoples of West Asia and North Africa.

The historical romances set in Arabia are well known today, but in the future, this peninsula may hold the keys to the origin of humans outside of Africa!

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


On the edge of Africa and Eurasia was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

December 29, 2018

Variation in general intelligence and our evolutionary history

Filed under: Evolution,Intelligence,IQ — Razib Khan @ 9:16 pm

In a bit of “TMI”, I’m far more intellectually promiscuous than I am in my personal life. My primary focus on this blog, if I have one, is probably historical population genetics of the sort highlighted in David Reich’s Who We Are and How We Got Here. But I have plenty of other interests, from economic history to cognitive psychology. Like religion, I have precise and clear opinions about a topic like “intelligence.” Unlike many people with an interest in evolutionary genetics I have read psychometric work, am familiar with some of the empirical results, as well as being personally acquainted with people in the field of psychometrics.

A few days ago Nassim Nicholas Taleb opined on intelligence, and I was silent. Today some individuals who I know from within the field of cultural evolution, another one of my interests, discussed intelligence, and I was silent. I’ve said all I really have to say over 15 years, and it isn’t as if I reanalyze psychometric data sets. But, a question that Taleb acolytes (and presumably Taleb) have brought up is if intelligence is such an important heritable trait, why isn’t everyone much smarter?

Think of this as the second Von Neumann paradox. What I’m alluding to is the fact that we know for a fact that human biology is capable of producing a god-made-flesh. With all due respect to another Jew who lived 2,000 years earlier than him, I speak here of John Von Neumann. We know that he is possible because he was. So why are the likes of Von Neumann bright comets amongst the dust of the stars of the common man, rather than the norm?

First, consider the case of Von Neumann himself. He had one daughter and two grandchildren. That is, within two generations genetically there was less “Von Neumann” than there had been. Though his abilities were clearly mentat-like, from the perspective of evolution Von Neumann was not a many sigma individual. He was within the normal range. Close to the median, a bit below in fecundity and fitness.

Taking a step back and focusing on aggregate populations, the fact that intelligence seems to be a quantitative trait that is at least moderately heritable and normally distributed due to polygenic variation tells us some things evolutionarily already. In Principles of Population Genetics is noted that heritable quantitative traits are often those where directional selection is not occurring due to huge consistent fitness differentials within the population.

Breaking it down, if being very smart was much, much, better than being of average smarts, then everyone would become very smart up to the physiological limit and heritable genetic variation would be removed from the population. Characteristics with huge implications for fitness tend not to be heritable because natural selection quickly expunges the deleterious alleles. The reason that fingerprints are highly heritable is that the variation genetically is not much impacted by natural selection.

The fact that being very intelligent is not evolutionarily clearly “good” seems ridiculousness to many people who think about these things. That’s because if you think about these things, you are probably very good at thinking, and no one wants to think that what they are good at is not evolutionarily very important. The thinking man cannot comprehend that thinking is not the apotheosis of what it is to be a man (similarly, the thinking religious man sometimes confuses theological rumination with the heights of spirituality; reality is that man does not know god through analysis, man experiences god).

So let’s talk about another quantitative trait which is even more heritable than intelligence, and easier to measure: height. In most societies males, in particular, seem to be more attractive to females if they are taller. As a male who is a bit shorter than the American average, it is obvious that there is some penalty to this in social and potentially reproductive contexts. And yet there is normal variation in height, and some populations seem to be genetically smaller than others, such as the Pygmy peoples of the Congo rainforest. Why?

Though being a tall male seems in most circumstances to be better in terms of physical attractiveness than being a short male, circumstances vary, and being too tall increases one’s mortality and morbidity. Being larger is calorically expensive. Large people need to eat more because they have larger muscles. Selection for smaller size in many marginalized rainforest populations is indicative of the fact that in such calorically challenging environments (humans in rainforests have to work hard to obtain enough calories in a hunter-gatherer context), the fitness gain due to intrasexual competition is balanced by reduced fitness during times of ecological stress as well as individual correlated responses (very large males die more often than smaller males).

Additionally, for height I mentioned the sexual component: there does not seem to be a necessary association with higher reproductive fitness with being a tall woman. Though this is subject to taste and fashion, there is likely some antagonistic selection across the two sexes at work, where tall men are the fathers of taller daughters, whose reproductive fitness may actually be lower than smaller women. And vice versa, as short men may produce more fit short daughters (though again, this depends on ecological context and cultural preconditions).

Being very large impacts fitness through the genetic correlation of size with other characteristics. Very large males are subject to higher risk for sudden tears in their lungs, or suboptimal cardiac function. Humans select chickens to be very large in the breast for food, but these chickens can barely walk, and may not be able to reproduce without assistance. Evolution in a quantitative genetic sense may then be all about trade-offs.

So let’s go back to intelligence. What could be the trade-offs? First, there are now results presented at conferences that very high general intelligence may exhibit a correlation with some mental pathologies. Though unpublished, this aligns with some prior intuitions. Additionally, there is the issue where on some characteristics being “species-typical” increases reproductive fitness (an average size nose), while in other characteristics being at an extreme is more attractive (very curvy women with large eyes and small chins; secondary sexual characteristics). Within intelligence, one could argue that being too deviated from the norm might make socialization and pair-bonding difficult. Here is an anecdote about the genius Von Neumann:

Neumann married twice. He married Mariette Kövesi in 1930. When he proposed to her, he was incapable of expressing anything beyond “You and I might be able to have some fun together, seeing as how we both like to drink.”

Apparently having a very fast analytic mind which can engage in abstraction and conceptual manipulation does not mean that one can come up with anything better than that when it came to procuring a mate. And procuring a mate is one of the only “good” things from an evolutionary perspective.

The human mind is neither universally plastic, nor it is a prefabricated set of specialized modules. It is a mix of both. We clearly have some “pre-loaded” code, such as the ability to recognize faces intuitively and rapidly (which a small proportion of the population lacks). But other competencies develop over time, co-opting neurological architecture that grew organically for other purposes. In Reading in the Brain Stanislas Dehaene recounts how the region which specializes in the ability to recognize letter shapes is a preexistent visual-spatial module, probably developed for ecological adaptation to environments where recognition of various organic and inorganic objects was of fitness relevance (obviously now tied in to regions of the brain geared toward verbal comprehension). Dehaene even seems to suggest there may be a trade-off between various cognitive capacities when comparing individuals from urban developed societies and individuals from non-literate small-scale societies.

As human societies have specialized over the last 10,000 years a small number of people who naturally were on the end of a particular distribution in abstraction-and-analysis ability began to preferentially fill exotic niches that had previously not existed. From all we can tell the ancient polymath Archimedes was a Von Neumann for his age. Archimedes seems likely to have been of aristocratic background, and part of the class of leisured intellectuals. The fact that he had such innate talent and disposition, combined with his life circumstances, was simple happenstance.

Today we live in a different age. Specialization, and the post-industrial economy, put a premium on competencies associated only with individuals on the “right tail” of the IQ distribution. Similarly, our genetic background predisposes many of us to obesity because the modern environment is “obesogenic.” The reality is that obesity was not an issue for almost all of human history, so genetic variation (often behavioral/cognitive) that is associated with obesity today was not so associated with it in the past. There could be no selection against obesity when it wasn’t a trait within the population.

Just as the modern environment is potentially “obesogenic,” it is also potentially “intelligenic.” Here’s what I’m talking about, The Science Behind Making Your Child Smarter:

The research also lends insight into why many apps and training programs aimed at raising IQ fail to produce lasting effects, says Elliot Tucker-Drob, an associate professor of psychology at the University of Texas at Austin, and co-author of the study.

Raising IQ may require the kind of sustained involvement that comes with attending school, with all the practice and challenges it entails. “It’s not like you just go in for an hour of treatment a week. It’s a real lifestyle change,” he says

.

To be a “nerd” is a lifestyle only possible in the modern information-rich environment. The Flynn effect is evidence that changing environments can shift the whole distribution. But just as with obesity or adult-onset diabetes risk, there is also heritable variation latent across the genome that seems to affect one’s response to the intelligenic environment.

Humans have large brains for our size. We are smarter than other primates. But evolutionary genetics today seems to be coming to the conclusion that it wasn’t a quantum jump, but gradual selection and change. Having a very low intellectual capacity was probably correlated with low fitness in the past (though small brains are calorically less greedy). But, having a very high general intelligence does not seem to have resulted in that great of a gain in social or cultural status in comparison to being of normal intelligence. In fact, if the genetic correlation is such that it’s associated with some higher risk for mental instability, it could simply be that a form of stabilization selection over time kept humans within the “normal range” because that was evolutionarily optimal. Be smart enough. But not too smart that you are weird.

And, as theorists from cultural evolution have observed, we are a “hive-mind” which leverages collective wisdom. Most of us don’t have to derive mathematical equations, we can use the formula provided to us. Though it’s useful to have a few people around who can invent statistics that the rest of us use…

November 24, 2018

On the anniversary of the publication of the On The Origin of Species

Filed under: Evolution — Razib Khan @ 3:25 pm

Today on this date Charles Darwin’s On The Origin of Species was published. If you haven’t, you should read it. I’m not sure if it’s the most influential book of the last few centuries, but it’s definitely up there.

That being said, sometimes people want to read something different that’s more recent. I would highly recommend Evolution: The First Four Billion Years. It’s an anthology of different thinkers from evolutionary biology, from paleontology, to genetics, and even to philosophy.

October 11, 2018

Why PCA and genetics are a match made in heaven

Filed under: Evolution,Genetics,science — Razib Khan @ 8:13 pm
Insitome customers and selected populations

The image above is not the work of a small child trying to sketch out a B-2 Stealth Bomber. Rather, it is a PCA plot, which shows the distribution of a subset of Insitome’s customers who have purchased the Regional Ancestry Insight — in terms of how they relate to each other genetically.

In green, I have added some British individuals, in red some Africans from Nigeria, and in blue individuals who are ethnically Chinese. The majority of our customers are of Northern European heritage, but a substantial minority are African-American or Asian-American and various mixes therein.

So why do we use Principal Components Analyses, PCA, in the first place? And how does it work to matches our intuitions about relatedness through abstruse mathematical formulae?

Why we use PCA in genetics

Real genetic varition…a little bit

Consider this slice of diversity to the left. Six individuals, top to bottom, genotyped on a small number of genetic positions, left to right. You should recognize the letters, as they are DNA base pairs, A, C, G, and T. You can see above that there are variations between the positions across individuals. Now imagine attempting to gain insight from looking at thousands of individuals (rows) across hundreds of thousands of markers (columns).

Raw genetic data is basically just a huge text file. When you are concerned with the variation on a single position, you can view from the results for individuals or populations in a table and expect most people to immediately understand the implications. Europeans who are lactose tolerant have a variant on a particular marker. If you are TT or CT you can digest milk sugar, lactose, as an adult. If you are CC, you can’t. There are only one a few things to keep track of: the person, and their genotype.

Representing variation on a single marker, a single variable, isn’t necessary because the human mind can process all that information. In contrast, lots of simultaneous variables are impossible to understand just by visually looking at a table. PCA is just one of many excellent ways to extracting signal out of the noise.

The plot to the left was generated from ~30,000 markers on a few hundred individuals from eight populations. This is not a large dataset today. The time it took to run the function which generated the raw PCA result output was the period between me pressing “enter” on the keyboard and me looking at the computer screen.

And yet despite the modesty of this dataset can you imagine me looking at 30,000 variables across 200 samples, and obtaining any understanding? Perhaps if I devoted my life to the project!

What about the math?

The way it works mathematically is that it takes the voluminous raw data, which is totally incomprehensible to the human mind and summarizes it into a set of independent equations — making it completely essential to the analytical toolkit. The data is actually a “matrix.” PCA transforms it with a series of distinct equations which can define the total variation of the underlying data.

A matrix of genotypes

These equations, or more properly dimensions, are arrayed in order of proportion of variation in the data explained. On a conventional PCA plot, you see the first two dimensions, which explain the largest and second largest proportion of the variation, as the x and y-axes. But there are many more dimensions you can break the data apart by, though quite often for genetic analysis the largest ones are sufficient to smoke out the population structure that you are interested in. The values of individuals in each dimension that drops out of the data can then be placed onto a coordinate system, which is much easier to digest than a table of raw variation.

The branching of human populations

But how can a mathematical framework make biological variation comprehensible through maps so well — especially with regards to genetic differences between populations? The answer to this is straightforward: human evolutionary history has a pattern, and that pattern leaves its stamp on the genome. PCA is just a pattern extraction method.

The raw material of variation are mutations, and the pattern of mutations in any human genome is defined by a pedigree back to common ancestors. People who tend to share common ancestors share mutations — and mutations are the raw material for the genetic variation that PCA summarizes.

When used in evolutionary genetics, PCA should ideally recapitulate the phylogenetic tree. Assuming that sample sizes are balanced, humans in worldwide datasets have the first principal component of variation, which invariably a dimension that separates Africans from non-Africans.

Why? Because this is the earliest separation between large lineages, and so this ‘separation’ has had the most time to accumulate distinct and unique mutations in their two respective lineages. The second dimension is usually one that defines the difference between people from the Eastern portion of Eurasia and those from the western portion of Eurasia. Again, this is an important phylogenetic distinction because these two groups seem to have diverged soon after their ancestors left Africa.

And so on. PCA is not the only way to visualize the data. If you run a computer program that counted up raw similarities and differences between individuals at each genetic position, you would notice that some individuals are more similar to others, some groups more similar to other groups, and this too would reflect the phylogenetic history. If you had more time and wanted to dig deeper, you could construct various models of population history, and see how well the data fit those models.

PCA is not the only way to understand genetic variation. PCA itself is not the genetic variation, but a way to represent that variation, but it is a fast method that starts with few assumptions and lends itself to easy graphical representation. It’s not coincidence that it remains popular to this day.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Why PCA and genetics are a match made in heaven was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

September 12, 2018

Season 2, Episode 1: The Legacy of L. L. Cavalli-Sforza

Filed under: anthropology,Evolution,Genetics,History — Razib Khan @ 1:15 pm
L. L. Cavalli-Sforza, 1922–2018

This week on The Insight (Apple Podcasts, Stitcher and Google Play) we discussed the life and legacy of L. L. Cavalli-Sforza, who died on August 31st, 2018. See the Stanford obit. From John Hawks, The man who tried to catalog humanity on Medium is probably the most thorough review of his life and works.

Cavalli-Sforza’s magnum opus

We discussed the popularization of PCA and phylogenetic trees by Cavalli-Sforza and his colleagues, outlined in his magnum opus The History and Geography of Humans. The methods of analysis developed in the 20th century prepared us for the avalanche of data we confront into the 21st century.

Also, Cavalli-Sforza’s collaboration with Marcus Feldman that laid the seed for the field of cultural evolution. See the book Cultural Transmission and Evolution. Today the field of cultural evolution is being pushed by researchers such as Joe Henrich.

Cavalli-Sforza was also instrumental in synthesizing the application of formal demographic models to archaeology. See The Neolithic Transition and the Genetics of Populations in Europe.

L. L. Cavalli-Sforza remained active into the 21st century. See this interview from 2012.

After his retirement, several labs have carried on the project of exploring population genetic history. David Reich’s lab’s publications. Also, see Eske Willerslev’s work.

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. A 2008 study that uses the HGDP sample on a SNP-array, bringing The History and Geography of Humans into the 21st century!

Finally, the cultural anthropologist wrote a full-length biography of L. L. Cavalli-Sforza’s life, with a focus on his scientific contributions, A Genetic and Cultural Odyssey.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!


Season 2, Episode 1: The Legacy of L. L. Cavalli-Sforza was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

May 25, 2018

Arise the coalescent!

Filed under: Biology,Evolution,Genetics,science — Razib Khan @ 12:14 pm
Citation: Modeling Human Population Separation History Using Physically Phased Genomes

Evolution is sometimes difficult to comprehend in terms of how it plays out in your mind’s eye. This is different from believing that evolution occurred. Evolutionary ideas were in the air when Charles Darwin and Alfred Russell Wallace both developed a theory of morphological change and speciation driven by adaptation in the middle of the 19th century. Their genius was introducing natural selection as the motive force underlying the change. But both of these thinkers lacked a true mechanism of heredity, so the formal extension of the field was hobbled.

With the emergence of genetics in the years after 1900, evolutionary science developed into a new and powerful form, what we now call the “Neo-Darwinian Synthesis.” This project combined the descriptive richness of natural history, the explanatory power of classical conceptual Darwinism, and the formal precision of population genetics.

The Neo-Darwinian Synthesis rests to a great extent on population genetic models. The most elementary of those models is that of the Hardy-Weinberg Equilibrium (HWE) — a large random mating population not subject to selection or drift. Deviations from the conditions of these models allow us understand the processes that are occurring in specific populations.

In the lab, researchers use matings between organisms such as Drosophila that deviate from the assumptions underneath the models, and see what the outcomes are. Scientists mate together flies with similar or dissimilar traits, violating random mating. They select individuals based on their characteristics, or collapse reproductive pedigrees down to a family lineage to explore inbreeding, introducing selection and random genetic drift.

But laboratory research can be both time intensive and tedious. With the rise of powerful computing tools in the last half of the 20th century scientists realized that they could simulate outcomes of their models. Just like in an experiment, researchers could change the conditions, the parameters, and see the results to the final outcome!

State of the art simulator, 1985

In the beginning, the power of simulations and computing seemed almost magical to researchers. No more time intensive sampling in the field, or expensive construction of laboratory facilities.

But over time, they began to realize that simulations also have their limitations. Computer memory and disk space costs money too, and scientists quickly found that the law of scarcity was not abolished. They couldn’t explore infinite possibilities because infinite took forever, even in a computer.

Imagine that you start with a few hundred individuals and simulate them randomly “mating.” You stipulate that their population grows 2% every generation. After a 100 generations, your population size is 10 times larger. The possible number of “mates” in your program is now 10 times greater, and there are so many more possible interactions. Anyone who has tried to work with large files knows that computing resources are finite, and simulations running forward in time run into the limits of that finitude soon enough.

But what if you moved back in time? Imagine you began with 10,000 individuals, and traced the ancestors of these 10,000 back across the generations. Genealogies can be complicated. But consider a single gene copy in your body, and compare it to another copy in another person. At some point in the distant past, the two copies share a common ancestor — they coalesce.

The coalescent sounds science fictional, but really it’s just a way to work backward from the genetic data you have now, to the past. You can create a tree of relationships back into the distant past, reversing direction with a genetic time machine. And the beauty of the coalescent from the perspective of 2018 is that computationally it is much more feasible to work back in time. With each step, you have fewer and fewer branches in the genealogy to model — back to a single common ancestor.

Instead of being overwhelmed by computational tasks, the coalescent converges upon the elegant simplicity of the last common ancestor, bring together late 20th century mathematics, 21st century computing, and the original conceptual insight of Darwin and Wallace of common descent.

Explore your Regional Ancestry story today.


Arise the coalescent! was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

August 10, 2017

But evolution converges!

Filed under: Evolution,Genetics — Razib Khan @ 10:43 pm

Stephen Jay Gould became famous in part for his book Wonderful Life: The Burgess Shale and the Nature of History. By examining the strange creatures in the Burgess Shale formation Gould makes the case that evolution is a highly contingent process, and that if you reran the experiment of life what we’d see might be very different from what we have now.

But the scientist whose study of the formation that inspired Gould’s interpretation, Simon Conway Morris, had very different views. Though it can sometimes be churlish, his rebuttal can be found in The Crucible of Creation: The Burgess Shale and the Rise of Animals. Simony Conway Morris does not believe that contingency is nearly as powerful a force as Gould would have you believe. And his viewpoints are influential. Richard Dawkins leaned on him to make the case for convergence in evolution in The Ancestor’s Tale.

This crossed my mind when reading Carl Zimmer’s new column, When Dinosaurs Ruled the Earth,
Mammals Took to the Skies
:

Today, placental mammals like flying squirrels and marsupials like sugar gliders travel through the air from tree to tree. But Volaticotherium belonged to a different lineage and independently evolved the ability to glide.

They were not the only mammals to do so, it turns out. Dr. Luo and his colleagues have now discovered at least two other species of gliding mammals from China, which they described in the journal Nature.

Dr. Meng said that the growing number of fossil gliders showed that many different kinds of mammals followed the same evolutionary path. “They did their own experiments,” he said.

This ultimately comes down to physics. There are only so many ways you can make an organize that flies or glides. Mammals come to the table with a general body plan, and that can be modified only so many different ways.

This is not a foolproof point of datum in favor of convergence as opposed to contingency. Frankly these are often vague verbal arguments which are hard to refute or confirm. And even molecular evolutionary analyses come to different conclusions. It may be that we are asking the wrong question. But, it does suggest that evolution may work in a much narrower range of parameters as time progresses because of the winnowing power of selection.

June 2, 2017

What determines the rate of evolution

Filed under: Evolution — Razib Khan @ 7:32 pm


The tweet above from Wiley relates to a paper, Polygamy slows down population divergence in shorebirds. It’s a cool paper. I tweeted it. But does it relate to the “rate of evolution”?

There’s no definitive answer to this question. Different people will have different answers, as it was evident on Twitter. For me my surprise was due to my definition for what evolution is: change is allele frequencies over time. This is far more fundamental than speciation. But then I don’t think much about speciation.

Some people brought up divergence. But divergence for me is not necessary, a population could remain unitary but exhibit large allele frequency changes. Then again, if you study phylogenetics on a macroevolutionary scale, as most people who study phylogenetics do, then you would focus on divergence.

May 10, 2017

The Bronze age demographic transformation of Britiain

Filed under: Bell Beaker,Britain,Evolution,History,Human Genetics,Human Genomics — Razib Khan @ 8:52 am

In Norman Davies’ the excellent The Isles: A History, he mentions offhand that unlike the Irish the British to a great extent have forgotten their own mythology. This is one reason that J. R. R. Tolkien created Middle Earth, they gave the Anglo-Saxons the same sort of mythos that the Irish and Norse had.

But to some extent I think we can update our assessments. Science is bringing myth to life. The legendary “Bell Beaker paper” is now available in preprint form, The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe. The methods are not too abstruse if you have read earlier works on this vein (i.e., no Nick Patterson authored methodological supplement that I saw). And the results are straightforward.

And what are those results?

First, the Bell Beaker phenomenon was both cultural and demographic. Cultural in that it began in the Iberian peninsula, and was transmitted to Central Europe, without much gene flow from what they can see. Demographic in that its push west into what is today the Low Countries and France and the British Isles was accompanied by massive gene flow.

In their British samples they conclude that 90% of the ancestry of early Bronze Age populations derive from migrants from Central Europe with some steppe-like ancestry. In over words, in a few hundred years there was a 90% turnover of ancestry. The preponderance of the male European R1b lineage also dates to this period. It went from ~0% to ~75-90% in Britain over a few hundred years.

If most of the genetic-demographic character of modern Britain was established during the Bronze Age*, then there has been significant selection since the Bronze Age. The figure to the left shows ancient (Neolithic/Bronze age) frequencies of selected SNPs, with modern frequencies in the British in dashed read. The top-left SNP is for HERC2-OCA2, the region related to brown vs. blue eye color, and also associated with some more general depigmentation. The top-right SNP is in SLC45A2, the second largest effect skin color locus in Europeans. The bottom SNP is for a mutation on LCT, which allows for the digestion of milk sugar as adults.

The vast majority of the allele frequency change in Britons for digestion of milk sugar post-dates the demographic turnover. In other words, the modern allele frequency is a function of post-Bronze Age selection. This is not surprising, as it supports the result in Eight thousand years of natural selection.

1000 Genomes derived SLC45A2 SNP frequency

At least as interesting are the pigmentation loci. The fact that the derived frequency in HERC2-OCA2 is lower in both British and Central European Beaker people samples indicates that the lower proportion is not an artifact of sampling. Britons have gotten more blue-eyed over the last 4,000 years. Second, SLC45A2 is at shocking low proportions for modern European populations.

HGDP derived SLC45A2 SNP frequency

In the 1000 Genomes the 4% ancestral allele frequency is almost certainly a function of the Siberian (non-European) ancestry. In modern Iberians the ancestral frequency is 18% (and it is even higher in Sardinians last I checked), but in Tuscans it is ~2%. Though not diagnostic of Europeans in the way the derived SNP at SLC24A2 is, SLC452 derived variants are much more constrained to Europe. Individuals who are homozygote ancestral for SNPs atSLC45A2 rare in modern Northern Europeans (pretty much nonexistent actually). But even as late as the Bronze Age they would have been present at low but appreciable frequencies.

This particular result convinces me that the method in Field et al. which detected lots of recent (last 2,000 years) selection on pigmentation in British populations is not just a statistical artifact. Though these papers are solving much of European prehistory, they are also going to be essential windows into the trajectory of natural selection in human populations over the last 5,000 years.

* In the context of this paper the Anglo-Saxon migrations tackled by the PoBI paper are minor affairs because the two populations were already genetically rather close. Additionally, the PoBI paper found that the German migrations were significant demographic events, but most of the ancestry across Britain does date to the previous period.

May 6, 2017

Synergistic epistasis as a solution for human existence

Filed under: epistasis,Evolution,Evolutionary Genetics,Genetics,Genomics — Razib Khan @ 12:16 am

Epistasis is one of those terms in biology which has multiple meanings, to the point that even biologists can get turned around (see this 2008 review, Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems, for a little background). Most generically epistasis is the interaction of genes in terms of producing an outcome. But historically its meaning is derived from the fact that early geneticists noticed that crosses between individuals segregating for a Mendelian characteristic (e.g., smooth vs. curly peas) produced results conditional on the genotype of a secondary locus.

Molecular biologists tend to focus on a classical, and often mechanistic view, whereby epistasis can be conceptualized as biophysical interactions across loci. But population geneticists utilize a statistical or evolutionary definition, where epistasis describes the extend of deviation from additivity and linearity, with the “phenotype” often being fitness. This goes back to early debates between R. A. Fisher and Sewall Wright. Fisher believed that in the long run epistasis was not particularly important. Wright eventually put epistasis at the heart of his enigmatic shifting balance theory, though according to Will Provine in Sewall Wright and Evolutionary Biology even he had a difficult time understanding the model he was proposing (e.g., Wright couldn’t remember what the different axes on his charts actually meant all the time).

These different definitions can cause problems for students. A few years ago I was a teaching assistant for a genetics course, and the professor, a molecular biologist asked a question about epistasis. The only answer on the key was predicated on a classical/mechanistic understanding. But some of the students were obviously giving the definition from an evolutionary perspective! (e.g., they were bringing up non-additivity and fitness) Luckily I noticed this early on and the professor approved the alternative answer, so that graders would not mark those using a non-molecular answer down.

My interested in epistasis was fed to a great extent in the middle 2000s by my reading of Epistasis and the Evolutionary Process. Unfortunately not too many people read this book. I believe this is so because when I just went to look at the Amazon page it told me that “Customers who viewed this item also viewed” Robert Drews’ The End of the Bronze Age. As it happened I read this book at about the same time as Epistasis and the Evolutionary Process…and to my knowledge I’m the only person who has a very deep interest in statistical epistasis and Mycenaean Greece (if there is someone else out there, do tell).

In any case, when I was first focused on this topic genomics was in its infancy. Papers with 50,000 SNPs in humans were all the rage, and the HapMap paper had literally just been published. A lot has changed.

So I was interested to see this come out in Science, Negative selection in humans and fruit flies involves synergistic epistasis (preprint version). Since the authors are looking at humans and Drosophila and because it’s 2017 I assumed that genomic methods would loom large, and they do.

And as always on the first read through some of the terminology got confusing (various types of statistical epistasis keep getting renamed every few years it seems to me, and it’s hard to keep track of everything). So I went to Google. And because it’s 2017 a citation of the paper and further elucidation popped up in Google Books in Crumbling Genome: The Impact of Deleterious Mutations on Humans. Weirdly, or not, the book has not been published yet. Since the author is the second to last author on the above paper it makes sense that it would be cited in any case.

So what’s happening in this paper? Basically they are looking to reduced variance of really bad mutations because a particular type of epistasis amplifies their deleterious impact (fitness is almost always really hard to measure, so you want to look at proxy variables).

Because de novo mutations are rare, they estimate about 7 are in functional regions of the genome (I think this may be high actually), and that the distribution should be Poisson. This distribution just tells you that the mean number of mutations and the variance of the the number of mutations should be the same (e.g., mean should be 5 and variance should 5).

Epistasis refers (usually) to interactions across loci. That is, different genes at different locations in the genome. Synergistic epistasis means that the total cumulative fitness after each successive mutation drops faster than the sum of the negative impact of each mutation. In other words, the negative impact is greater than the sum of its parts. In contrast, antagonistic epistasis produces a situation where new mutations on the tail of the distributions cause a lower decrement in fitness than you’d expect through the sum of its parts (diminishing returns on mutational load when it comes to fitness decrements).

These two dynamics have an effect the linkage disequilibrium (LD) statistic. This measures the association of two different alleles at two different loci. When populations are recently admixed (e.g., Brazilians) you have a lot of LD because racial ancestry results in lots of distinctive alleles being associated with each other across genomic segments in haplotypes. It takes many generations for recombination to break apart these associations so that allelic state at one locus can’t be used to predict the odds of the state at what was an associated locus. What synergistic epistasis does is disassociate deleterious mutations. In contrast, antagonistic epistasis results in increased association of deleterious mutations.

Why? Because of selection. If a greater number of mutations means huge fitness hits, then there will strong selection against individuals who randomly segregate out with higher mutational loads. This means that the variance of the mutational load is going to lower than the value of the mean.

How do they figure out mutational load? They focus on the distribution of LoF mutations. These are extremely deleterious mutations which are the most likely to be a major problem for function and therefore a huge fitness hit. What they found was that the distribution of LoF mutations exhibited a variance which was 90-95% of a null Poisson distribution. In other words, there was stronger selection against high mutation counts, as one would predict due to synergistic epistasis.

They conclude:

Thus, the average human should carry at least seven de novo deleterious mutations. If natural selection acts on each mutation independently, the resulting mutation load and loss in average fitness are inconsistent with the existence of the human population (1 − e−7 > 0.99). To resolve this paradox, it is sufficient to assume that the fitness landscape is flat only outside the zone where all the genotypes actually present are contained, so that selection within the population proceeds as if epistasis were absent (20, 25). However, our findings suggest that synergistic epistasis affects even the part of the fitness landscape that corresponds to genotypes that are actually present in the population.

Overall this is fascinating, because evolutionary genetic questions which were still theoretical a little over ten years ago are now being explored with genomic methods. This is part of why I say genomics did not fundamentally revolutionize how we understand evolution. There were plenty of models and theories. Now we are testing them extremely robustly and thoroughly.

Addendum: Reading this paper reinforces to me how difficult it is to keep up with the literature, and how important it is to know the literature in a very narrow area to get the most out of a paper. Really the citations are essential reading for someone like me who just “drops” into a topic after a long time away….

Citation: ScienceNegative selection in humans and fruit flies involves synergistic epistasis.

April 28, 2017

Beyond “Out of Africa” and multiregionalism: a new synthesis?

Filed under: Africa,Evolution,Genetics,Genomics,Human Evolution,Human Genetics — Razib Khan @ 4:14 pm

For several decades before the present era there have been debates between proponents of the recent African origin of modern humans, and the multiregionalist model. Though molecular methods in a genetic framework have come of the fore of late these were originally paleontological theories, with Chris Stringer and Milford Wolpoff being the two most prominent public exponents of the respective paradigms.

Oftentimes the debate got quite heated. If you read books from the 1990s, when multiregionalism in particular was on the defensive, there were arguments that the recent out of Africa model was more inspirational in regards to our common humanity. As a riposte the multiregionalists asserted that those suggesting recent African origins with total replacement was saying that our species came into being through genocide.

Though some had long warned against this, the dominant perception outside of population genetics was that results such the “mitochondrial Eve” had given strong support to the recent African origin of modern humans, to the exclusion of other ancestry. 2002’s Dawn of Human Culture took it for granted that the recent African origin of modern humans to the total exclusion of other hominin lineages was established fact.

In 2008 I went to a talk where Svante Paabo presented some recent Neanderthal ancient mtDNA work. It was rather ho-hum, as Paabo showed that the Neanderthal lineages were highly diverged from modern ones, and did not leave any descendants. Though of course most modern human lineages did not leave any descendants from that period, Paabo took this evidence supporting the proposition that Neanderthals did not contribute to the modern human gene pool.

When his lab reported autosomal Neanderthal admixture in 2010, it was after initial skepticism and shock internally. I know Milford Wolpoff felt vindicated, while Chris Stringer began to emphasize that the recent African origin of modern humanity also was defined by regional assimilation of other lineages. The data have ultimately converged to a position somewhere between the extreme models of total replacement or balanced and symmetrical gene flow.

This is not surprising. Extreme positions are often rhetorically useful and popular when there’s no data. But reality does not usually conform to our prejudices, so ultimately one has to come down at some point.

The data for non-Africans is rather unequivocal. The vast majority of (>90%) of the ancestry of non-Africans seems to go back to a small number of common ancestors ~60,000 years ago. Perhaps in the range of ~1,000 individuals. These individuals seem to be a node within a phylogenetic tree where all the other branches are occupied by African populations. Between this period and ~15,000 years ago these non-Africans underwent a massive range expansion, until modern humans were present on all continents except Antarctica. Additionally, after the Holocene some of these non-African groups also experienced huge population growth due to intensive agricultural practice.

To give a sense of what I’m getting at, the bottleneck and common ancestry of non-Africans goes back ~60,000 years, but the shared ancestry of Khoisan peoples and non-Khoisan peoples goes back ~150,000-200,000 years. A major lacunae of the current discussion is that often the dynamics which characterize non-Africans are assumed to be applicable to Africans. But they are not.

A 2014 paper illustrates one major difference by inferring effective population from whole genomes: African populations have not gone through the major bottleneck which is imprinted on the genomes of all non-African populations. The Khoisan peoples, the most famous of which are the Bushmen of the Kalahari, have the largest long term effective populations of any human group. The Yoruba people of Nigeria have a history where they were subject to some population decline, but not to the same extent as non-Africans.

What do we take away from this?

One thing is that we have to consider that the assimilationist model which seems to be necessary for non-Africans, also applies to Africans. For years some geneticists have been arguing that some proportion of African ancestry as well is derived from lineages outside of the main line leading up to anatomically modern humans. Without the smoking gun of ancient genomes this will probably remain a speculative hypothesis. I hope that Lee Berger’s recent assertion that they’ve now dated Homo naledi to ~250,000 years before the present may offer up the possibility that ancient DNA will help resolver the question of African archaic admixture (i.e., if naledi is related to the “ghost population”?).

The second dynamic is that the bottleneck-then-range-expansion which is so important in defining the recent prehistory of non-Africans is not as relevant to Africans during the Pleistocene. The very deep split dates being inferred from whole genome analysis of African populations makes me wonder if multiregional evolution is actually much more important within Africa in the development of modern humans in the last few hundred thousand years. Basically, the deep split dates may highlight that there was recurrent gene flow over hundreds of thousands of years between different closely related hominin populations in Africa.

Ultimately, it doesn’t seem entirely surprising that the “Out of Africa” model does not quite apply within Africa.

Addendum: Over the past ~5,000 years we have seen the massive expansion of agricultural populations within the continent. The “deep structure” therefore may have been erased to a great extent, with Pygmies, Khoisan, and Hadza, being the tip of the iceberg in terms of the genetic variation which had characterized the Africa during the Pleistocene.

April 23, 2017

The logic of human destiny was inevitable 1 million years ago

Filed under: Evolution,Genetics,Genomics,Human Evolution,Human Genetics — Razib Khan @ 1:11 pm

Robert Wright’s best book, Nonzero: The Logic of Human Destiny, was published near 20 years ago. At the time I was moderately skeptical of his thesis. It was too teleological for my tastes. And, it does pander to a bias in human psychology whereby we look to find meaning in the universe.

But this is 2017, and I have somewhat different views.

In the year 2000 I broadly accepted the thesis outlined a few years later in The Dawn of Human Culture. That our species, our humanity, evolved and emerged in rapid sequence, likely due to biological changes of a radical kind, ~50,000 years ago. This is the thesis of the “great leap forward” of behavioral modernity.

Today I have come closer to models proposed by Michael Tomasello in The Cultural Origins of Human Cognition and Terrence Deacon in The Symbolic Species: The Co-evolution of Language and the Brain. Rather than a punctuated event, an instance in geological time, humanity as we understand it was a gradual process, driven by general dynamics and evolutionary feedback loops.

The conceit at the heart of Robert J. Sawyer’s often overly preachy Neanderthal Parallax series, that if our own lineage went extinct but theirs did not they would have created a technological civilization, is I think in the main correct. It may not be entirely coincidental that the hyper-drive cultural flexibility of African modern humans evolved in African modern humans first. There may have been sufficient biological differences to enable this to be likely. But I believe that if African modern humans were removed from the picture Neanderthals would have “caught up” and been positioned to begin the trajectory we find ourselves in during the current Holocene inter-glacial.

Luke Jostins’ figure showing across board encephalization

The data indicate that all human lineages were subject to increased encephalization. That process trailed off ~200,000 years ago, but it illustrates the general evolutionary pressures, ratchets, or evolutionary “logic”, that applied to all of them. Overall there were some general trends in the hominin lineage that began to characterized us about a million years ago. We pushed into new territory. Our rate of cultural change seems to gradually increased across our whole range.

One of the major holy grails I see now and then in human evolutionary genetics is to find “the gene that made us human.” The scramble is definitely on now that more and more whole genome sequences from ancient hominins are coming online. But I don’t think there will be such gene ever found. There isn’t “a gene,” but a broad set of genes which were gradually selected upon in the process of making us human.

In the lingo, it wasn’t just a hard sweep from a de novo mutation. It was as much, or even more, soft sweeps from standing variation.

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