Are pants really more comfortable than skirts?

Recently I stumbled upon this paper from a few years back, The invention of trousers and its likely affiliation with horseback riding and mobility: A case study of late 2nd millennium BC finds from Turfan in eastern Central Asia. Basically, it seems that trousers emerge with mounted cavalry. The dominance of mounted cavalry in the years after the fall of Rome resulted in the emergence of a trousered elite, and the shift away from the tunics of antiquity.

Today we don’t ride horses, so the utility of trousers in that context is gone. It seems that if you work in blue-collar professions and it cold climates trousers are still useful. But is there a reason for men in warm climates in white-collar professions to continue going with trousers as opposed to a simple tunic? Are we just stuck with tradition?

W. D. Hamilton, Darwin’s 20th century heir

Today on Twitter there was a discussion about why there wasn’t a biography of John Manyard Smith. One reason might be that John Maynard Smith was a pretty nice and congenial fellow. There wasn’t much excitement from what I know.

In contrast, if you read R.A. Fisher: The Life of a Scientist, you get the sense that he was a bit of a dick (the book was written by his daughter). Of course, Fisher was a great scientist, an eminence is both statistics and evolutionary biology. Nevertheless, his irascible personality lends itself to biographical treatment, though rarely hagiographical (a friend is writing a book on Fisher’s life; he too confirms, the guy was a dick).

The evolutionary biologist who yearned to be Fisher’s heir, W. D. Hamilton, was not a dick, but something of a dope. Hamilton has had a full-length biography devoted to him, Nature’s Oracle. But he makes appearances in Defenders of the Truth: The Sociobiology Debate, The Price of Altruism: George Price and the Search for the Origins of Kindness, and A Reason for Everything: Natural Selection and the British Imagination.

I say Hamilton was a dope because he was socially awkward, and obviously got himself in trouble through his guilelessness. If he were alive today Hamilton would be in a whole lot of trouble I suspect, except for the fact that he’d be emeritus. Unfortunately, Bill Hamilton died in 2000 due to malaria contracted from field work (or malaria medication).

Yet Hamilton has left us two books where provides autobiographical sketches interleaved between his scientific papers, Narrow Roads of Gene Land: Evolution of Social Behavior, and Narrow Roads of Gene Land: Evolution of Sex (the third volume has biographical sketches from collaborators). In case you are not aware, Hamilton was the originator of the idea of “inclusive fitness.” At the same time, John Maynard Smith was developing “kin selection.” Hamilton distrusted Maynard Smith because of this coincidence, suspecting some sort of scientific fraud (both of them were in communication with George Price at the time).

Narrow Roads of Gene Land: Evolution of Sex was published without revisions to a very long draft of autobiographical sketches because Hamilton had died. It is quite a rambling and sometimes incoherent piece of work because editors couldn’t give any feedback. But it’s fascinating because it’s an unvarnished window into Hamilton’s strange brain.

Of course, the primary reasons to read the three volumes on the scientific papers. I’ve read the famously notationally-inscrutable paper on inclusive fitness published in 1964 many a time. Bill Hamilton had an interesting life and a quirky mind. I’m quite sad that he’s not here anymore.

The Insight, Episode 23: Patrick Wyman, Barbarian Genetics


This week on The Insight we talk to Patrick Wyman of Tides of History. Patrick is now a professional podcaster for Wondery, but I got to know him originally through comments on this weblog. Patrick is a historian of Late Antiquity. We originally encountered each other in 2010 after I had just finished a period where I was originally interested in the topic of his professional study, and he was interested in paleogenetics.

As Patrick said before we began recording, this podcast was a long time in coming. More precisely, the time is right, and it will get more right. More and more preprints like Amorin et al.’s Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics will be coming out in the next few years. Ancient DNA extraction is cheap enough now that it will be used to explore historical lacunae, for example, what happened in sub-Roman Britain?

To get a sense of the period that we talk about in this podcast, I would highly recommend first The Fall of Rome: And the End of Civilization. This is a materialist treatment whch makes clear how thoroughgoing the collapse of economic production was across much of the Roman world. Then, Peter Heather’s Empires and Barbarians: The Fall of Rome and the Birth of Europe, anticipates some of the work coming out of genetics. Heather at the time was making the case that many of the barbarian groups that entered the Roman Empire were in fact coherent ethno-cultural entities. That the period of the “folk wandering” were literally folk wanderings.

Finally, you can finish up with Chris Wickham’s The Inheritance of Rome: Illuminating the Dark Ages 400-1000.

As a complement, one might check out Hugh Kennedy’s two books on the early history of Islam, The Great Arab Conquests: How the Spread of Islam Changed the World We Live In and When Baghdad Ruled the Muslim World: The Rise and Fall of Islam’s Greatest Dynasty. Kennedy doesn’t present a revisionist view, but that’s OK. Sometimes you need the null model. Like neutral theory.

Open Thread, 06/05/2018

The Cultural Brain Hypothesis: How culture drives brain expansion, underlies sociality, and alters life history. I keep suggesting to everyone that they need to read more cultural evolution! But to be honest it’s hard for me to keep up. So much easier reading evolutionary genomics, since I know the literature and the models far better.

Book recommendations, The Secret of Our Success: How Culture Is Driving Human Evolution, Domesticating Our Species, and Making Us Smarter. Yeah, it’s good. But for the more technically inclined, Mathematical Models of Social Evolution: A Guide for the Perplexed. At some point might get the author of the second book on the podcast.

Two issues of guilt: I haven’t been keeping up with the comments, and also the South Asian Genotype Project. I’ll try to do better on that in the near future. Though a major cost there is I will then post less.

Probably keep an eye out for more stuff from me in NRO and India Today in the near future. Though if you follow my total content feed the NRO stuff already gets pushed into that automatically.

She Has Her Mother’s Laugh was reviewed in The New York Times. I plan on trying to get a review into NRO. Here is an important point: it’s a pretty diverse and long book, so any review is going to run with only a small sliver of the narrative. Honestly the stuff about marine cancer and chimerism is probably the most novel material, but that’s probably not going to take center stage in most reviews because it would take a lot of explanation.

In contrast, people “get” race, eugenics and epigenetics (or so they think).

I found the second half of The Rise and Fall of American Growth: The U.S. Standard of Living since the Civil War more of a slog than the first half. Why? I think it’s because I didn’t viscerally understand as well the difference between 1870 and 1940. In contrast, I get what’s changed between 1940 and 2010 (I think?).

I still think it’s worth a read. Lots of facts and footnotes.

So many in my “stack” before I could ever get to The Rise and Fall of the Dinosaurs: A New History of a Lost World. But this looks like a really good book.

Lots of debate on the Twitter on whether the Enlightenment “invented” racism. The problem that I see is that this is correct if you define racism in a very specific way. To be frank, an entirely Eurocentric way.

In God’s War: A New History of the Crusades, there is a section which covers tensions in the Egyptian court during the period of the Crusader kingdoms (I believe in the middle 1200s). Basically, black slaves who traditionally guarded the harem had taken a more prominent leadership role. The Circassian military slaves found this offensive on grounds of race and caste. The cultural context was clearly not anything that a 17th century Englishmen would recognize, but it’s pretty obvious that the tensions at court organized themselves around race.

You might say it wasn’t racism because there wasn’t an explicit Linnean taxonomy. But the implication is clear that the Circassians were not going to tolerate domination by black slaves who were customarily, if not by statute, subordinate. Kind of sounds racist.

Though I’ve read books like The History of White People, in general, I find them too Eurocentric, with a particular focus on Anglo-America. Not that that matters as such, it’s just not to my taste to understand the general human condition.

But when we get into arguments about racism being invented in a clear and distinct fashion during the Enlightenment, it helps to have read books like God’s War, and have really good recall. Or a bit of Ibn Khaldun and his rather crass ethnography. Or you might read a history of Ming dynasty China, and recall that sometimes Portuguese sailors who were washed ashore were executed by officials, because they had blonde hair and blue eyes, and so were assumed to be Dutch (who were a priori pirates). The Ming were not racist as such, but they generalized racially in a manner which was unfortunate for fair Portuguese (and probably good for dark Dutch, those these instances are not recorded, for obvious reasons).

Of course we know most people don’t know any of this, or Aristotle’s taxonomies, or the literature on folk biology.

Additionally, one thing I’ve noticed over the years is that in public debates historians often lie. They don’t lie in a bald-faced manner, they lie like Protagoras might lie. They play fast and loose with terminologies and shade the conclusions in a way that benefits their chosen tribe. Unlike physics, history is really hard and requires a lot of honesty. Unlike physics, historians seem to lack that quite often.

I know enough to be able to see them in action because I know enough to know when they’re engaging in misdirection.

I have no solution. As with journalists, you need to know as much as they do to know when they lie when they tell the truth. Unfortuately, historians are usually more clever than journalists.

Speaking of history, John Julius Norwich has died. His Byzantium books are decent. Though you should always graduate to Warren Treadgold’s A History of Byzantine State and Society.

Uncertainty about social interactions leads to the evolution of social heuristics.

The genetic basis of mutation rate variation in yeast.

Andy Ngo Patreon. Honestly, I agree with him too much to read him a lot!

Outstanding questions in the study of archaic hominin admixture. Follow the citations.

The Discourse of Race in Modern China. I read this book 13 years ago. It was written 25 years ago. Seems like it is more relevant today than it was then.

Mystery ghost ape species found hidden in bonobo’s genome. Sometimes I wonder if the term “species” and “population” are just getting totally overwhelmed with the complexity of the models that genomics is now throwing at us.

I don’t think genomics has transformed evolutionary biology in the broad sketches. But, it has really specified a lot of details and filled in gaps, and terms which had previously been pretty clear and distinct are getting really muddled.

Don’t usually say it straight out, but I might not be posting as frequently for a while. Need to catch up on family, keep up on work, etc. I feel like I’ll probably crank it up again when the next batch of ancient DNA papers come out.

Also, Patrick Wyman is on this week’s episode of The Insight (should be up by Wednesday night EDT). We take on ancient DNA and Late Antiquity. I think you’ll like it. Only 14 reviews on iTunes to go before I stop pestering you guys on that!

Any other population genetics blogs you read? Any books of note?

The great bottleneck after the post-Eemian separation


I’ve been thinking about effective population size. Basically it’s the inferred breeding population you estimate in the present, or in many cases the past, based on the genetic variation you see within the population. Another way to say it is that it’s the population size that can explain the genetic drift that you see in the data.

To give a concrete example, the population of the New England states of America was ~1,000,000 during the 1790 Census. The vast majority of this was due to natural increase from a settler population of about ~50,000 in 1650 (total fertility rate of women in New England was seven children in the years between 1650 and 1700). Of these, ~23,000 were Puritans or the offspring of Puritans who migrated around between 1630 and 1643 (due to religious differences with the English government of the period). One might think that a population of ~1,000,000 would be genetically diverse, but the ~50,000 in 1650 matter a lot more than the ~1,000,000 in 1790. The rate of mutation accumulation is pretty slow, so a population bottleneck or subsample has a huge long-term effect.

In fact, as you probably know one of the biggest determinants of genetic variation in New England whites of 1790 is the bottleneck that they share with all other non-Africans that dates to 50,000 years or more before 1790!

And these are just the coarse demographic considerations on the broader population/historical scale. In any normal random-mating human population, there’s some reproductive variance by chance (usually it is modeled as a poisson distribution; mean and variance being the same, though from I have read the variance in mammals is usually greater than the mean).

Some people have more children, and some people have fewer children. That means that there is a census population, and a breeding population, and the breeding population is invariably smaller than the census population. Some individuals don’t reproduce to the next generation, obviously. But there are also cases where some individuals have large numbers of surviving offspring, while others have only a few.

To make it concrete I plotted the distribution of the number of children of women older than 50 years of age from the year 2000 and later in the General Social Survey (GSS). You can see that the most common number is two, but there are a fair number with three. Only about 10% of women 50 years and older have no children in the GSS.

But the curious thing is that if you weight the number by the proportion, you notice that women who have three children may not be as common as women who have two children, but they are contributing more children to the next generation than women who have the more typical two children. And, though the number of women who have five or more children is only 11% of the sample, as opposed to 14% who have one child, they contribute nearly five times as many children as those with one child to the next generation (women with six children alone contribute more than women with one child).

Basically, not all the genetic variation in a given generation is created equally. Some people will contribute more to the next generation, and that has a homogenizing effect (there are models of mutation/selection/drift which establish equilibria values of variation in a stationary state).

I’m revisiting all of this for two reasons. First, in Who We Are And How We Got Here David Reich talks about a long period of a shared population bottleneck for “Out of Africa” (all non-Africans) groups before the primary expansion ~60,000 years ago. Second, in my conversation with Matt Hahn, he was very skeptical of drawing any correspondence between effective population and some inferred census size. In hindsight I think part of it is that in most organisms census quotes are more an art than science. Not so with humans.

This made me look more into the literature for humans again. Recently Browning et al. published Ancestry-specific recent effective population size in the Americas. It’s a great paper. Basically, it uses identity by descent tracts of different ancestry to tease apart the distinctive pre-admixture effective population sizes. If you take an admixed population and assume that it was a single population random-mating indefinitely, and then work backward in time, you’re probably going to produce rather strange effective population sizes (if the two groups are about the same genetic diversity beforehand, they’ll probably show an inflated effective population, because you are assuming the two groups were a big random-mating population long before they were randomly mating!).

There are many ways to infer effective population, and the identity by descent method seems reasonable for recent time periods. And one thing about recent population size estimates for humans is that you have reasonable census estimates (you don’t just check with simulations):

Our simulations showed that biased sampling of a structured population results in underestimation of most recent effective population size. When we compare the estimated current effective sizes of HCHS/SOL country-of-origin populations to World Bank population sizes (accessed via Google Public Data Explorer) from 1995 (when the average age of the sampled individuals was around 25), we find that the ratio of current estimated effective size to 1995 population size ranges from approximately 1/60 (Ecuador) to approximately 1/4 (Cuba), with typical values around 1/10. Although estimates of effective size in the most recent generations are affected by these issues, our simulations also showed that less recent generations are not affected. Thus our estimates are useful for learning about the effective population sizes at and before admixture.

The structured part is important. For example, the paper On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference? explores how structured models of gene-flow might be confused when genomic inferences assume a panmictic population. Last year a paper in PNAS, Early history of Neanderthals and Denisovans, suggested that Neanderthals were characterized by a high structured meta-population, and that low effective populations from sampled genomes in this group of humans reflects this, rather than a genuinely low census size.

Browning et al. focused on recent population size inferences. I was curious about these inferences because we can compare them to real census sizes. From this I think I can tune my intuition at least to the possibily that census size of a random mating population is not likely to be two orders of magnitude above the inferred effective population size. Conversely, the rough mammalian value of an effective population size of ~1/3 the census size seems to be a ceiling. Population structure and bottleneck aside, humans seem to have enough basal reproductive skew that effective population size is less than half of the census size.

To focus on ancient population growth (or lack thereof), I reread Inferring human population size and separation history from multiple genome sequences (Schiffels et al. 2014), Exploring Population Size Changes Using SNP Frequency Spectra (Liu et al. 2015) and Neutral genomic regions refine models of recent rapid human population growth (Gazavea et al. 2014). The first two papers seem to suggest an “Out of Africa” population bottleneck that’s pretty long, with an effective population that’s somewhat lower than 5,000 individuals. In contrast, the last paper seems to have a sharp bottleneck of 200 individuals.

Remember, different models can produce the same empirical patterns in the genome. You can reduce genetic diversity by a modest, but long, bottleneck. Or, through a very sharp short bottleneck.

In Who We Are and How We Got Here David Reich definitely leans toward a long, but more modest, bottleneck. For anthropological and archaeological reasons this seems more plausible now than it did ten years ago.

But perhaps it makes more sense now that we have more ancient DNA and a more elaborated model of human history seen through the lens of population genetics. In Schlebusch and Jakkbonson’s Tales of Human Migration, Admixture, and Selection in Africa the authors come out say “For our species’ deep history in Africa, both paleoanthropological and genetic evidence increasingly point to a multiregional origin of AMHs [anatomically modern humans] in Africa.”

They’re only saying what I hear other people talking about.

Instead of the “Out of Africa bottleneck” being defining for our species, it’s only a phenomenon which is important for peoples outside of Sub-Saharan Africa. Arguably for the majority of the existence of our species something closer to multi-regionalism was operative within modern humans.

If fact, isn’t that what the new ancient DNA shows? Pulses of admixture and gene-flow between distinct groups? Arguably multiregionalism might be the answer to our origins, but also characterize many of the dynamics after the “Out of Africa” event.

In any case, the best evidence now points to the likelihood that modern human lineages began to diversify and diverge before 200,000 years ago. Conversely, most of the ancestry of modern humans outside of Africa dates to an expansion around ~60,000 years before the present (ancient DNA and archaeology seem to agree here).

This is probably right before the Neanderthal admixture event with non-African humans, at least the modern lineages we have around today. But, it turns out it does not define the point when non-African humans diverged from the ancestral African population. Another group, “Basal Eurasians” (who may not have been Eurasian at all), diverged before the expansion of all eastern non-Africans, Oceanians, as well as the ancestors of Pleistocene Europeans and Siberians. It does not seem that Basal Eurasians had any Neanderthal admixture. Basal Eurasian ancestry is substantial in the Middle East today (although lower than 50%), and non-trivial across broad swaths of Europe and South Asia, due to the expansion of farming. They seem to have been well mixed in places like North Africa with other Eurasian groups ~15,000 years ago. Presumably that was a “back to Africa” migration, since these people had Neanderthal ancestry.

All of this leads to the conclusion that the ancestors of Basal Eurasians/non-Africans must have gone through their shared bottleneck well before ~60,000 years before the present. And, it may have happened on the African continent. So with that, I’ll quote Schiffels et al.:

This comparison reveals that no clean split can explain the inferred progressive decline of relative cross coalescence rate. In particular, the early beginning of the drop would be consistent with an initial formation of distinct populations prior to 150kya, while the late end of the decline would be consistent with a final split around 50kya. This suggests a long period of partial divergence with ongoing genetic exchange between Yoruban and Non-African ancestors that began beyond 150kya, with population structure within Africa, and lasted for over 100,000 years, with a median point around 60-80kya at which time there was still substantial genetic exchange, with half the coalescences between populations and half within (see Discussion). We also observe that the rate of genetic divergence is not uniform but can be roughly divided into two phases. First, up until about 100kya, the two populations separated more slowly, while after 100kya genetic exchange dropped faster.

David Reich’s group, and others, now posit the existence of “Basal Human” population that mixed into West Africans, who can be modeled as primarily proto-East African (without Eurasian admixture), as well as this ancient outgroup. This means that estimates of divergences with non-Africans from something like MSMC may generate a composite if proto-East Africans are closer to the ancestors of non-Africans, which seems likely. One likely model is that the “Out of Africa” population emerged out of the northern edge of this proto-East African distribution of modern humans over 100,000 years ago (but after groups like the Khoisan and Basal Humans had already diverged).

Looking at Schiffel et al., they seem to posit lower in divergence times than seems likely to me. Is that perhaps due to unaccounted for admixture in lineages which fuse together groups which were earlier distinct?

In any case, with details about the divergence dates set aside, the MSMC results are actually in line with a new congealing consensus. Deep structure within Africa, but gene-flow between distinct populations, for at least ~100,000 years (possibly more). This is the period when population structure was quite fluid and indistinct along the East Africa continuum out of with non-Africans emerged.

Also, the archaeological evidence is now strongly suggestive of modern humans in places like Southeast Asia over 10,000 years before the wave which led to the ancestry of most extant populations. In fact, we know that this sort of early migration with no descendants isn’t abnormal. The first modern humans in Europe left no descendants (at least in any appreciable quantity). And the Altai Neanderthal seems to have modern-like admixture that dates to ~100,000 years before the present.

With all the evidence that modern humans were present in Africa, and expansively so, for hundreds of thousands of years, it seems unlikely that they never mixed with “archaic” Eurasian  lineages (and vice versa). In fact, as we obtain more and more Neanderthal and Denisovan genomes perhaps we’ll find that a rapid expansion like the one that occurred ~60,000 years ago across Eurasia and Oceania happened before, out of and/or into Africa.

Looping back to the effective population issue, the effective population of modern non-Africans seems to have been below ~5,000 for a while. There was minimal gene-flow with other populations for many generations. Reich has a schematic of 40,000 years between 90,000 and 50,000 BP in Who We Are and How We Got Here. But that’s obviously just a ballpark figure. I have a hard time believing that the census size was around 500,000. The world population 10,000 years ago is usually estimated to be 1 to 10 million. Human populations were probably much larger at the end of the Pleistocene than 100,000 years ago. But a figure of 10% effective would give 50,000, which seems a reasonable number, especially with the likelihood that we’re talking about many tribes over a wide ecological zone. Meta-population dynamics of extinction and resettlement in inclement periods probably drove down the effective population.

The separation seems to be distinct from the older multiregional phase. What could explain it? The existence of the Sahara, and periods of extreme desertification seems the most likely candidate. I can’t say much with any credibility because I don’t know the archaeology and paleoclimate literature, but before domesticated animals, it was probably difficult for hunter-gatherers to make a go of it in the deep Sahara during the driest phases.

If I had to bet, the Eemian interglacial, 130 to 115 thousand years ago, is when I would assume there was:

  1. Lots of gene flow across the Sahara, perhaps in both directions
  2. A major population expansion of humans, of all sorts

This gives plenty of time for a wave of modern humans to push east, probably going through milder climates, rather than expanding north into Neanderthal or Denisovan territory. Eventually, some group must have mixed with the ancestors of the Altai Neanderthals. It seems likely that a cold and dry spell after the Eemian would have been optimized more to the well adapted Eurasian groups, and modern populations would have withdrawn into refugia. The brutally expanding Sahara would have divided the majority of modern humans, who existed in the meta-populations to the south that dated back hundreds of the thousands of years, from the groups on the northern fringe.

One can imagine that large numbers of modern humans were either absorbed or went extinct with the expansion of Neanderthals and other archaics. Though Neanderthals and Denisovans were interfertile with moderns, the lineages were still distinct enough that it looks like there was some hybrid breakdown. Just as modern humans seem to have purged many Neanderthal alleles from our genome, the opposite dynamic was probably at work.

There was clearly some structure in the relict modern human group that was separated from the African populations. Basal Eurasians did not mix with Neanderthals, but the ancestors of all other non-African humans did. Though one has to be careful about such geographical inferences, that suggests to me that the range of modern humans in the period between 60,000 to 80,000 years ago extended further back into pockets of northeast Africa, where no contact with Neanderthals would have occurred. Perhaps, in the end, we’ll end up thinking that the Basal Eurasians in some ways were a lot more like Africans south of the Sahara, as they didn’t undergo the massive range expansion of other populations during the Upper Paleolithic.

I’ll end with some predictions.

  • Ancient DNA of proto-moderns and archaics in eastern Eurasia dated to between 50,000 to 100,000 years BP will be analyzed at some point and will exhibit a fair amount of admixture. That is, the Altai Neanderthal was not exceptional, and probably relatively attenuated. I’m moderately confident of this.
  • The pre-60,000 year eastern Eurasians will be found to have left some of their genes in modern eastern Eurasians. Especially in Southeast Asia and Oceanian. Probably in the 1-10% range. I’m moderately confident of this.
  • The Denisovan ancestry in Oceanians is mediated by a “first wave” group “Out of Africa.” I have low confidence in this, but I really wouldn’t be surprised either way. My confidence in my confidence is low!
  • At some point we’ll obtain sequence from a 1 million year old hominin somewhere in the colder/drier climes of Eurasia (we have a 900,000 year old horse genome). This will predate Neanderthal/Denisovans. We will see from this that some of these super-archaic populations left their heritage in later archaics, and therefore our own lineage. I’m rather confident of this.
  • By hook or crook we’ll get more ancient genomes out of African samples, and confirm a lot of ancient population structure, as well as some gene-flow from archaic non-modern lineages. Probably around the same range you see in non-Africans (though some of the gene-flow may also apply to non-Africans, since they didn’t separate from eastern Africans until 100,000 to 150,000 years ago). I’m rather confident of this.
  • H. naledi will return sequence at some point. I’m very confident of this. I don’t have inside knowledge, but I know they’re going to keep trying. They are getting more samples.
  • H. naledi will be found to have contributed ancestry to modern southern African populations. I’m moderately confident of this.
  • At some point ancient genomes from the Americas will confirm the existence of an earlier group which was only distantly related to modern New World populations descended mostly from Siberians. There is indirect evidence of this group from South American populations, but we’ll get individuals who are much more distinct at some point in the future. I’m moderately confident of this.
  • Basal Eurasians will be found to have inhabited Southern Arabia/Persian Gulf region. But “pure” population will have been found to have disappeared around the Last Glacial Maximum ~20,000 years ago, as the human populations to the north moved south, and the Near East’s southern fringe became drier. I’m moderately confident of this.

The 4,000 year explosion


The figure above shows a most interesting result from a new preprint, FADS1 and the timing of human adaptation to agriculture. It shows the allele frequency change using ancient Eurasian genomes for the derived allele at FADS1.

In case you don’t know why FADS1 is important, it’s been implicated in variation long-chain polyunsaturated fatty acids (LC-PUFA) metabolism. The derived allele, embedded in haplotype D in the above preprint, seems more optimized for plant-based diets, because of the higher activity of synthesis of LCPUFAs (which one might otherwise obtain from marine resources, as is likely among Inuit).

So the standard model is that the Neolithic changed things, as humans began to adapt to cereal-based diet diets. This preprint suggests maybe not:

Our analysis shows that selection at the FADS locus was not tightly linked to the development of agriculture. Further, it suggests that the strongest signals of recent human adaptation may not have been driven by the agricultural transition but by more recent changes in environment or by increased efficiency of selection due to increases in effective population size.

The authors are explicit that the derived allele at FADS1, which is at ~60% in modern Europeans, was under strong selection during the Bronze Age. In fact, this allele, which is common in Africans, may have been absent in most Paleolithic Eurasians. Using various methods they infer in fact that the ancestors of non-Africans may have been subject to selection for the ancestral variant. Their timing estimates indicate that this predates the standard expansion period starting ~60,000 BP (there was also an older selection event for the derived variant within Africa). Additionally, the authors posit that the derived variant was introduced into Europeans due to the Basal Eurasian ancestry in farmers.

They posit two dynamics that might drive the Bronze Age selection events. First, they suggest that the change in environment was actually more dramatic than that during the Paleolithic-Neolithic transition. Second, they suggest that effective populations were much smaller before the Bronze Age, so selection was not as efficacious (or, more precisely, drift effects were dominant in shaping variation).

This idea that the Neolithic isn’t quite as important, or singular, is somewhat of a surprise. But we may need to consider it. Another line of research, using high-quality modern day sequences rather than ancient genotypes, implies that there has been a lot of recent selection, and that’s likely going on today.

Second, one of the major takeaways from The Fate of Rome is that pandemics probably weren’t a feature of Neolithic small-scale societies. Rather, pandemics relied on long-distance trade and movement, as well as concentrations such as urban centers. Though certain endemic diseases probably arose in the Neolithic, the periodic sweep of pandemics required greater social and cultural complexity and overall human density.

The analogy then is rather straightforward. Just as microbes can move faster and more efficiently in an interconnected world, so such a world is much closer to a panmictic one. Earlier work suggested that effective population size of Neolithic farmers was not particularly small, but perhaps there are dynamics being missed by that simple summary value when it comes to the interconnectedness of the Eurasian landscape triggered by the emergence of pastoralism, and the necessary reaction of larger-scale polities.

A simple test of this would be to compare selection signals in a place like Papua New Guinea, which did not seem to undergo the same sort of pressures as Bronze Age Eurasian societies in relation to reduced diversity. I presume that New World societies as well would be an interesting test.

The cultural conditions of star-shaped phylogenies

In the generality, I think intergroup selection of paternal lineages is the answer to why star-shaped phylogenies are so evident in the phylogenetic record ~4,000 years ago. More precisely, most of the major clades of R1a, R1b, and I1 undergo massive expansion after a sharp reduction in effective population size around this period. The R lineages diversified during the Pleistocene, probably in Central Eurasia (it is a brother clade to Q). The I lineage derives from Western European hunter-gatherers, probably the late Pleistocene expansion which eventually gave rise to the Mesolithic groups that encountered the early farmers.

But what happened here specifically? Let me quote a section of Peter Turchin’s excellet Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth:

Lanchester’s Square Law yields an enormous return to social scale. If the opposing forces use a mix of ranged and shock weapons, numerical superiority will still be amplified, although not as much as with purely projectile weapons. So there is an intense selection pressure for cultural groups living in flat terrain to scale up, and a very high price to pay by those that fail to do s….

Though human interaction with horses as domesticates is probably older, light chariots emerged on the Pontic steppe ~4,000 years ago. Within a few centuries, this technology was ubiquitous in the Near East. The Indo-Aryan Mitanni arrive with chariots in modern Syria/Northern Iraq by ~3,750 years ago.

In the Near East chariots and bows were closely associated. The evidence from the Eurasian steppe during the Bronze Age seems less definitive (simply, bows may not preserve very well), though by the Iron Age the mounted archer became a ubiquitous feature of the military landscape.

The combination of chariots, likely bows, and the Sintashta/Srubna/Andronovo culture’s known focus on metallurgy, make it hard for me to deny the likelihood that the expansion of R1a1a-Z93 has something to do with intergroup conflict. The reality is that Lanchester’s Square Law means that even small initial advantageousness for a given paternal lineage will probably snowball. One victory will lead to an increase in territory and resources, which will produce later advantage. A sort of Y chromosomal Matthew Effect.

But this doesn’t explain what occurred in Europe, where R1b and I1 also underwent a massive expansion (and R1a as well). Europe’s relatively forested territory beyond the Hungarian plain always blunted the power and reach of mounted archers later in history. We do know that chariots arrived in the Mediterranean around the same time as in the Near East. But the rise to dominance of the Corded Ware and Bell Beaker peoples predates light chariots. Perhaps it is something as simple as the fact that metaethnic institutions and identities that could dampen intergroup conflict hadn’t emerged, but it’s still curious to me that one could have a ~90% population replacement in Britain in a few centuries.

Perhaps we will find out that it has to do with a disease as our understanding of ancient epidemics gets better.

 

Soft & hard selection vs. soft & hard sweeps


When I was talking to Matt Hahn I made a pretty stupid semantic flub, confusing “soft selection” with “soft sweeps.” Matt pointed out that soft/hard selection were terms more appropriate to quantitative genetics rather than population genomics. His viewpoint is defensible, though going back into the literature on soft/selection, e.g., Soft and hard selection revisited, the main thinkers pushing the idea were population geneticists who were also considering ecological questions.*

The strange thing is that I had already known the definitions of hard and soft selection on some level because I had read about them as I was getting confused with hard and soft sweeps! But this was more than ten years ago now, and since then I haven’t given the matter enough thought obviously, as I defaulted back to confusing the two classes of terms, just as I used to.

Matt pointed out that truncation selection is a form of hard selection. All individuals below (or above) a certain phenotype value have a fitness of zero, as they don’t reproduce. In a single locus context, hard selection would involve deleterious lethal alleles, whose impact on the genotype was the same irrespective of ecological context. So in a hard selection, it operates by reducing the fitness of individuals/genotypes to zero.

For soft selection, context matters much more, and you would focus more on relative fitness differences across individuals/genotypes. Some definitions of soft vs. hard selection emphasize that in the former case fitness is defined relative to the local ecological patch, while the latter is a universal estimate. Soft selection does not necessarily operate through the zero fitness value for a genotype, but rather differential fitness. Hard selection can crash your population size. Soft selection does not necessarily do that.

Though I won’t outline the details, one of the originators of the soft/hard selection concept analogized them to density-dependent/independent dynamics in ecology. If you know the ecological models, the correspondence probably is obvious to you.

As for hard and soft sweeps, these are particular terms of relevance to genomics, because genome-wide data has allowed for their detection through the impact they have on the variation in the genome. A “sweep” is a strong selective event that tends to sweep away variation around the focus of selection. A hard sweep begins with a single mutant, and positive selection tends to drive it toward fixation.

A classical example is lactase persistence in Northern Europeans and Northwest South Asians (e.g., Punjabis). The mutation in the LCT gene is the same across a huge swath of Eurasia. And, the region around the genome is also the same, because regions of the genome adjacent to that single mutation increased in frequency as well (they “hitchhiked”). This produces a genetic block of highly reduced diversity since the hard selective sweep increases the frequency of so many variants which are associated with the advantageous one, and may drive to extinction most other competitive variants.

Someone is free to correct me in the comments, but it strikes me that many hard selective sweeps are driven by soft selection. Fitness differentials between those with the advantageous alleles and those without it are not so extreme, and obviously context dependent, even in cases of hard sweeps on a single locus.

The key to understanding soft sweeps is that there isn’t a focus on a singular mutation. Rather, selection can target multiple mutations, which may have the same genetic position, but be embedded within different original gene copies. In fact, soft selection often operates on standing variation, preexistent alleles which were segregating in the population at low frequencies or were totally neutral. Genetic signatures of these events are less striking than those for hard sweeps because there is far less diminishment of diversity, since it’s not the increase in the frequency of a singular mutation and the hitchhiking of its associated flanking genomic region.

Soft sweeps can clearly occur with soft selection. But truncation selection can occur on polygenic traits, so depending on the architecture of the trait (i.e., effect size distribution across the loci) one can imagine them associated with hard selection as well.

Going back to the conversation I had with Matt the reason semantics is important is that terms in population genetics are informationally rich, and lead you down a rabbit-hole of inferences. If population genetics is a toolkit for decomposing reality, then you need to have your tools well categorized and organized. On occasion it is important to rectify the names.

* There are two somewhat related definitions of soft/hard selection. I’ll follow Wallace’s original line here, though I’m not sure they differ that much.

Open Thread, 05/28/2018

She Has Her Mother’s Laugh is now available. The interview with Carl Zimmer will be live on The Insight Wednesday night (EDT).

If you haven’t, please consider leaving a 5-star review on iTunes or Stitcher.

I’ve told that you can already read The University We Need on Google Books. I can’t vouch for this, but on Amazon the publication date is July 10th.

I suspect the field of cultural evolution is going to become big in the next ten years, breaking out its relatively rarified ghetto. If you haven’t, I’d recommend The Secret of Our Success by Joe Henrich.

The older, more technical books, are Cultural Transmission and Evolution, Culture and the Evolutionary Process.

I noticed the other day that the spam filter was a little overactive recently. Just in case you notice comments not going through….

Y chromosomal star-phylogenies as inter-group competition between paternal lineages

The figure to the left should be familiar to readers of this weblog. It is taken from A recent bottleneck of Y chromosome diversity coincides with a global change in culture (Kamin et al.). Over the past few years a peculiar fact long suspected or inferred has come into sharp focus: some of the Y chromosome haplogroups very common today were not so common in the past, and their frequency changed very rapidly over a short time period.

What Kamin et al. did was look at sequence data across the Y chromosome to make deeper inferences. The issue is that the Y chromosome is not genetically very diverse. Earlier generations of researchers focused on highly mutable microsatellite regions for identification. While microsatellites are good for identification and classification because of their genetic diversity, they are not as good when it comes to making evolutionary inferences about parameters such as time since last common ancestor. They have very high and variable mutation rates.

Single nucleotide polymorphisms (SNPs) are probably better for a lot of evolutionary inference, but the Y chromosome doesn’t have too many of these. SNP-chip era technology which focuses on a select subset of polymorphisms at specific locations didn’t have much to choose from and likely missed rare variants.

This is where whole-genome sequence of the Y comes in. It retrieves maximal information, and with that, the authors of Kamin et al. could definitely confirm that some Y chromosomal lineages under explosive expansion ~4,000 years ago after a bottleneck.

By and large ancient DNA take a different angle, focusing on genome-wide autosomal ancestry, and lacking in high-coverage whole-genome sequences. But they have confirmed the inferences from whole-genomes that some of these lineages exhibit explosive growth in the last ~4,000 years. One moment they were rare, and the next moment ubiquitous.

But geneticists are geneticists. They’re interested in genetical questions, methods, and dynamics. To be frank cultural models for how those genetic patterns might have come about are either exceedingly simple and probably true (e.g., gene-culture coevolution with lactase persistence), or vague and handwavy. With the surfeit of genomic data to analyze it isn’t surprising that this happens.

This is why researchers in the field of cultural evolution need to get involved. They’re model-builders and should see which models predict the copious empirical results we have now when it comes to genetic change over time.

For several years now I have been asserting that inter-group competition of paternal lineages best explains the pattern of Y chromosome expansions ~4,000 years ago. A new paper brings forth a formal model which explores this hypothesis, Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck:

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

Their model is interesting because inter-group competition between paternal lineages can result in a loss of haplogroup diversity without huge reproductive skew. That is, instead of a highly polygynous society, one can simply posit that group dynamics of expansion and extinction produce expansions of Y chromosomal lineages.

A formal model synthesized with genomic results is a major step forward, though I haven’t dug into the methods (computational or analytic). Presumably, this is a first step.

But the discussion does review a lot of anthropological literature about the nature of human conflict and social interaction. Basically, it seems that between nomadic hunter-gatherers and before chiefdoms, biologically defined paternal clans were often the organizing principle of society. To some extent this makes total sense since the meta-ethnic religious and social identities explicitly appeal to fictive relationships of blood even after blood was no longer paramount. Ancient Near Eastern kings addressed each other in familial terms (e.g., “brother” and “son”), while universal religions deploy the construct of brotherhood.

In Empires of the Silk Road the author makes the case that these bands of brothers were more influential in shaping history than we realize today. Not surprisingly, the authors of the above paper suggest that the Inner Asian nomad zone is where star-phylogenies have been most pervasive and persist down to historical time. As in Steven Pinker’s The Better Angels of Our Nature it seems that the rise of the state suppressed the viciousness of the paternal kin group. How do we know this? Because the period of the maximal explosion of star-phylogenies seem to be a transient between the early Neolithic and the historical age.

The Y chromosomal literature is just the low hanging fruit. I suspect in the next decade cultural evolutionary models will be brought to bear on the huge mountain of genomic data….

Citation: Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck Tian Chen Zeng, Alan J. Aw & Marcus W. Feldman.