Book Club: The 10,000 Year Explosion: pt 5: Gene Flow

Genghis Khan, spreader of genes

Welcome back to the book club. Today we’re discussing Chapter 5 of The 10,000 Year Explosion, Gene Flow. In this chapter, Greg and Henry discuss some of the many ways genes can (and sometimes can’t) get around.

You know, sometimes it is difficult to think of something really interesting to say in reaction to something I’ve read. Sometimes I just think it is very interesting, and hope others find it so, too. This is one of those chapters.

So today I decided to read the papers cited in the chapter, plus a few more related papers on the subject.

High-Resolution SNPs and Microsatellite Haplotypes point to a single, Recent Entry of Native American Y Chromosomes into the Americas

Single-nucleotide polymorphism (SNP) analysis indicated that three major haplogroups, denoted as C, Q, and R, accounted for nearly 96% of Native American Y chromosomes. Haplogroups C and Q were deemed to represent early Native American founding Y chromosome lineages; however, most haplogroup R lineages present in Native Americans most likely came from recent admixture with Europeans. Although different phylogeographic and STR diversity patterns for the two major founding haplogroups previously led to the inference that they were carried from Asia to the Americas separately, the hypothesis of a single migration of a polymorphic founding population better fits our expanded database. Phylogenetic analyses of STR variation within haplogroups C and Q traced both lineages to a probable ancestral homeland in the vicinity of the Altai Mountains in Southwest Siberia. Divergence dates between the Altai plus North Asians versus the Native American population system ranged from 10,100 to 17,200 years for all lineages, precluding a very early entry into the Americas.

However, Asymmetric Male and Female Genetic Histories among Native Americans from Eastern North America

We found that sociocultural factors have played a more important role than language or geography in shaping the patterns of Y chromosome variation in eastern North America. Comparisons with previous mtDNA studies of the same samples demonstrate that male and female demographic histories differ substantially in this region. Postmarital residence patterns have strongly influenced genetic structure, with patrilocal and matrilocal populations showing different patterns of male and female gene flow. European contact also had a significant but sex-specific impact due to a high level of male-mediated European admixture. Finally, this study addresses long-standing questions about the history of Iroquoian populations by suggesting that the ancestral Iroquoian population lived in southeastern North America.

And in Mexico, your different racial mix has something to do with your risk of Type 2 Diabetes, but you know, race is a social construct or something:

Type 2 diabetes (T2D) is at least twice as prevalent in Native American populations as in populations of European ancestry, so admixture mapping is well suited to study the genetic basis of this complex disease. We have characterized the admixture proportions in a sample of 286 unrelated T2D patients and 275 controls from Mexico City and we discuss the implications of the results for admixture mapping studies. … The average proportions of Native American, European and, West African admixture were estimated as 65, 30, and 5%, respectively. The contributions of Native American ancestors to maternal and paternal lineages were estimated as 90 and 40%, respectively. In a logistic model with higher educational status as dependent variable, the odds ratio for higher educational status associated with an increase from 0 to 1 in European admixture proportions was 9.4 (95%, credible interval 3.8-22.6). This association of socioeconomic status with individual admixture proportion shows that genetic stratification in this population is paralleled, and possibly maintained, by socioeconomic stratification. The effective number of generations back to unadmixed ancestors was 6.7 (95% CI 5.7-8.0)…

In other words, Conquistador men had children with a lot of the local ladies. 

Oh hey, while we’re at it: 

The Genomic Landscape of Western South America: 

Studies of Native South American genetic diversity have helped to shed light on the peopling and differentiation of the continent, but available data are sparse for the major ecogeographic domains. These include the Pacific Coast, a potential early migration route; the Andes, home to the most expansive complex societies and to one of the most spoken indigenous language families of the continent (Quechua); and Amazonia, with its understudied population structure and rich cultural diversity. Here we explore the genetic structure of 177 individuals from these three domains, genotyped with the Affymetrix Human Origins array. We infer multiple sources of ancestry within the Native American ancestry component; one with clear predominance on the Coast and in the Andes, and at least two distinct substrates in neighboring Amazonia, with a previously undetected ancestry characteristic of northern Ecuador and Colombia. Amazonian populations are also involved in recent gene-flow with each other and across ecogeographic domains, which does not accord with the traditional view of small, isolated groups. Long distance genetic connections between speakers of the same language family suggest that languages had spread not by cultural contact alone. Finally, Native American populations admixed with post-Columbian European and African sources at different times, with few cases of prolonged isolation. 

In other news: 

Strong Selective Sweep Before 45,000 BP Displaced Archaic Admixture Across the X Chromosome

The X chromosome in non-African populations has less diversity and less Neanderthal introgression than expected. We analyzed X chromosome diversity across the globe and discovered seventeen chromosomal regions, where haplotypes of several hundred kilobases have recently reached high frequencies in non-African populations only. The selective sweeps must have occurred more than 45,000 years ago because the ancient Ust’-Ishim male also carries its expected proportion of these haplotypes. Surprisingly, the swept haplotypes are entirely devoid of Neanderthal introgression, which implies that a population without Neanderthal admixture contributed the swept haplotypes. It also implies that the sweeps must have happened after the main interbreeding event with Neanderthals about 55,000 BP. These swept haplotypes may thus be the only genetic remnants of an earlier out-of-Africa event.

Why not a later out-of-Africa event? Or a simultaneous event that just happened not to mate with Neanderthals? Or sweeps on the X chromosome that happened to remove Neanderthal DNA due to Neanderthal and X being really incompatible? I don’t know. 

The Neolithic Invasion of Europe:

Who are Europeans? Both prehistoric archaeology and, subsequently, classical population genetics have attempted to trace the ancestry of modern Europeans back to the first appearance of agriculture in the continent; however, the question has remained controversial. Classical population geneticists attributed the major pattern in the European gene pool to the demographic impact of Neolithic farmers dispersing from the Near East, but archaeological research has failed to uncover substantial evidence for the population growth that is supposed to have driven this process. … Both mitochondrial DNA and Y-chromosome analyses have indicated a contribution of Neolithic Near Eastern lineages to the gene pool of modern Europeans of around a quarter or less. This suggests that dispersals bringing the Neolithic to Europe may have been demographically minor and that contact and assimilation had an important role.

I wouldn’t call a quarter “minor.” But it is true that the Anatolian farming people who invaded Europe didn’t kill off all of the locals, and then later Europe was invaded by the non-Anatolian, Indo-European people. 

Revealing the prehistoric settling of Australia by Y chromosome and mtDNA analysis

(i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa ≈50–70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event ≈50,000 years ago, … (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged ≈8,000 years ago…

Aboriginal Australian mitochondrial genome variation

Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in the ancient landmass of Sahul (present-day New Guinea and Australia) ~55 thousand years ago. … We have further resolved known Aboriginal Australian mitochondrial haplogroups and discovered novel indigenous lineages by sequencing the mitogenomes of 127 contemporary Aboriginal Australians. In particular, the more common haplogroups observed in our dataset included M42a, M42c, S, P5 and P12, followed by rarer haplogroups M15, M16, N13, O, P3, P6 and P8. We propose some major phylogenetic rearrangements, such as in haplogroup P where we delinked P4a and P4b and redefined them as P4 (New Guinean) and P11 (Australian), respectively. Haplogroup P2b was identified as a novel clade potentially restricted to Torres Strait Islanders. Nearly all Aboriginal Australian mitochondrial haplogroups detected appear to be ancient, with no evidence of later introgression during the Holocene.

Meanwhile, in Indonesia

We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.

I liked the quote from Jared Diamond (say what you will about him, I like Diamond. He at least tries hard to tackle difficult questions):  

“When I was living among Elopi tribespeople in west New Guinea and wanted to cross the territory of the neighboring Fayu tribe in order to reach a nearby mountain, the Elopis explained tome matter-of-factly that the Fayus would kill me if I tried. From a New Guinea perspective, it seemed so perfectly natural and self-explanatory. Of course the Fayus will kill any trespasser…”

This is why people often claim that we moderns are the WEIRDOs. 

Evidence that Alexander the Great got around (the world)–Y-Chromosomal Evidence for a Limited Greek Contribution to the Pathan population of Pakistan

Three Pakistani populations residing in northern Pakistan, the Burusho, Kalash and Pathan claim descent from Greek soldiers associated with Alexander’s invasion of southwest Asia. … In pairwise comparisons between the Greeks and the three Pakistani populations using genetic distance measures sensitive to recent events, the lowest distances were observed between the Greeks and the Pathans. Clade E3b1 lineages, which were frequent in the Greeks but not in Pakistan, were nevertheless observed in two Pathan individuals, one of whom shared a 16 Y-STR haplotype with the Greeks. The worldwide distribution of a shortened (9 Y-STR) version of this haplotype, determined from database information, was concentrated in Macedonia and Greece, suggesting an origin there. Although based on only a few unrelated descendants this provides strong evidence for a European origin for a small proportion of the Pathan Y chromosomes.

Of course, who can discuss genetic spread without mentioning that lord of men, Genghis Khan? 

We have identified a Y-chromosomal lineage with several unusual features. It was found in 16 populations throughout a large region of Asia, stretching from the Pacific to the Caspian Sea, and was present at high frequency: ∼8% of the men in this region carry it, and it thus makes up ∼0.5% of the world total. The pattern of variation within the lineage suggested that it originated in Mongolia ∼1,000 years ago. Such a rapid spread cannot have occurred by chance; it must have been a result of selection. The lineage is carried by likely male-line descendants of Genghis Khan, and we therefore propose that it has spread by a novel form of social selection resulting from their behavior.

“Novel” lol. 

And finally, Blue Eyes

Several studies have shown that the OCA2 locus is the major contributor to the human eye color variation. By linkage analysis of a large Danish family, we finemapped the blue eye color locus to a 166 Kbp region within the HERC2 gene. … The brown eye color allele of rs12913832 is highly conserved throughout a number of species. … One single haplotype, represented by six polymorphic SNPs covering half of the 3′ end of the HERC2 gene, was found in 155 blue-eyed individuals from Denmark, and in 5 and 2 blue-eyed individuals from Turkey and Jordan, respectively. Hence, our data suggest a common founder mutation in an OCA2 inhibiting regulatory element as the cause of blue eye color in humans. In addition, an LOD score of Z = 4.21 between hair color and D14S72 was obtained in the large family, indicating that RABGGTA is a candidate gene for hair color.

What about you? What did you think of this chapter?


I have some hopefully good, deep stuff I am working on, but in the meanwhile, here is a quick, VERY SPECULATIVE thread on my theory for why refined sugars are probably bad for you:

First, refined sugars are evolutionarily novel. Unless you’re a Hazda, your ancient ancestors never had this much sugar.

Pick up a piece of raw sugar cane and gnaw on it. Raw sugar cane has such a high fiber to sugar content that you can use it as a toothbrush after chewing it for a bit.

According to the internet, a stick of raw sugar cane has 10 grams of sugar in it. A can of Coke has 39. Even milk (whole, skim, or fat-free) contains 12 grams of natural milk sugars (lactose) per glass. Your body has no problem handling the normal amounts of unrefined sugars in regular foods, but to get the amount of sugar found in a single soda, you’d have to eat almost four whole stalks of sugarcane, which you certainly aren’t going to do in a few minutes.

It’s when we extract all of the sugar and throw away the rest of the fiber, fat, and protein in the food that we run into trouble.

(The same is probably also true of fat, though I am rather fond of butter.)

In my opinion, all forms of heavily refined sugar are suspect, including fruit juice, which is essentially refined fructose. People think that fruit juice is “healthy” because it comes from fruit, which is a plant and therefore “natural” and “good for you,” unlike, say, sugar, which comes from sugar cane, which is… also a plant. Or HFCS, which is totally unnatural because it comes from… corn. Which is a plant.

“They actually did studies on the sugar plantations back in the early 1900s. All of the workers were healthy and lived longer than the sugar executives who got the refined, processed product.”

I don’t know if I agree with everything he has to say, but refined fructose is no more natural than any other refined sugar. Again, the amount of sugar you get from eating an apple is very different from the amount you get from a cup of apple juice.

Now people are talking about reducing childhood obesity by eliminating the scourge of 100% fruit juice:

Excessive fruit juice consumption is associated with increased risk for obesity… sucrose consumption without the corresponding fiber, as is commonly present in fruit juice, is associated with the metabolic syndrome, liver injury, and obesity.

Regular fruit is probably good for you. Refined is not.

Here’s another study on the problems with fructose:

If calcium levels in the blood are low, our bodies produce more parathyroid hormone, stimulating the absorption of calcium by the kidneys, as well as the production of vitamin D (calcitriol), also in the kidneys. Calcitriol stimulates the absorption of calcium in the intestine, decreases the production of PTH and stimulates the release of calcium from the bone. …

… Ferraris fed rats diets with high levels of glucose, fructose or starch. He and his team studied three groups of lactating rats and three groups of non-pregnant rats (the control group).

“Since the amounts of calcium channels and of binding proteins depend on the levels of the hormone calcitriol, we confirmed that calcitriol levels were much greater in lactating rats,” said Ferraris.  … “However, when the rat mothers were consuming fructose, there were no increases in calcitriol levels,” Ferraris added. “The levels remained the same as those in non-pregnant rats, and as a consequence, there were no increases in intestinal and renal calcium transport.”

You then have two options: food cravings until you eat enough to balance the nutrients, or strip bones of calcium. This is what triggers tooth decay.

Sugar not only feeds the bacteria on your teeth (I think), it also weakens your teeth to pay the piper for sugar digestion. (Also, there may be something about sugar-fed bacteria lowering the pH in your mouth.)

The second thing that happens is your taste buds acclimate to excessive sugar. Soon “Sweet” tastes “normal.”

Now when you try to stop eating sugar, normal food tastes “boring” “sour” “bitter” etc.
This is where you just have to bite the bullet and cut sugar anyway. If you keep eating normal food, eventually it will start tasting good again.

It just takes time for your brain to change its assumptions about what food tastes like.
But if you keep sweetening your food with “artificial” sweeteners, then you never give yourself a chance to recalibrate what food should taste like. You will keep craving sugar.
And it is really hard to stop eating sugar and let your body return to normal when you crave sugar.

If artificial sweeteners help you reduce sugar consumption and eventually stop using it altogether, then they’re probably a good idea, but don’t fall into the trap of thinking you’re going to get just as much cake and ice cream as always, just it won’t have any consequences anymore. No. Nature doesn’t work like that. Nature has consequences.

So I feel like I’ve been picking on fructose a lot in this post. I didn’t mean to. I am suspicious of all refined sugars; these are just the sources I happened across while researching today.

I am not sure about honey. I don’t eat a lot of honey, but maybe it’s okay. The Hadza of Tanzania eat a great deal of honey and they seem fine, but maybe they’re adapted to their diet in ways that we aren’t.

So what happens when you eat too much sugar? Aside from, obviously, food cravings, weight gain, mineral depletion, and tooth decay…

So here’s a theory:

Our bodies naturally cycle between winter and summer states. At least they do if you hail from a place that historically had winter; I can’t speak for people in radically different climates.

In the summer, plant matter (carbohydrates, fiber,) are widely available and any animal that can takes as much advantage of this as possible. As omnivores, we gorge on berries, leaves, fruits, tubers, really whatever we can. When we are satiated–when we have enough fat stores to last for the winter–our bodies start shutting down insulin production. That’s enough. We don’t need it anymore.

In the winter, there’s very little plant food naturally available, unless you’re a farmer (farming is relatively recent in areas with long winters.)

In the winter, you hunt animals for meat and fat.This is what the Inuit and Eskimo did almost all year round.

The digestion of meat and fat does not require insulin, but works on the ketogenic pathways which, long story short, also turn food into energy and keep people alive.

The real beauty of ketosis is that, apparently, it ramps up your energy production–that is, you feel physically warmer when running entirely off of meat and fat than when running off carbs. Given that ketosis is the winter digestive cycle, this is amazingly appropriate.

By spring, chances are you’ve lost a lot of the weight from last summer. Winters are harsh. With the fat gone, the body starts producing insulin again.

At this point, you go from hyperglycemia (too much sugar in your bloodstream if you eat anything sweet, due to no insulin,) to hypoglycemia–your body produces a lot of insulin to transform any plants you eat into energy FAST. (Remember the discussion above about how your body transforms fructose into fat? Back in our ancestral environment, that was a feature, not a bug!)

This lets you put on pounds quickly in the spring and summer, using now-available plants as your primary food source.

The difficulty with our society is we’ve figured out how to take the energy part out of the plants, refine it, and store up huge quantities of it so we can eat it any time we want, which is all the time.

Evolution makes us want to eat, obviously. Ancestors who didn’t have a good “eat now” drive didn’t eat whatever good food was available and didn’t become ancestors.

But now we’ve hacked that, and as a result we never go into the sugar-free periods we were built to occasionally endure.

I don’t think you need to go full keto or anti-bread or something to make up for this. Just cutting down on refined sugars (and most refined oils, btw) is probably enough for most people.

Note: Humans have been eating grains for longer than the domestication of plants–there’s a reason we thought it was a good idea to domesticate grains in the first place, and it wasn’t because they were a random, un-eaten weed. If your ancestors ate bread, then there’s a good chance that you can digest bread just fine.

But if bread causes you issues, then by all means, avoid it. Different people thrive on different foods.

Please remember that this thread is speculative.




Two Denisovan Admixture Events?

Recent genetic analysis suggests that humans mated with the mysterious Denisovans not once, but twice

Asian genomes carry introgressed DNA from Denisovans and Neanderthals

East Asians show evidence of introgression from two distinct Denisovan populations

South Asians and Oceanians carry introgression from one Denisovan population

I can’t read the whole paper, because it’s paywalled, but if correct, this is quite the change. Previously, only small amounts of Denisovan were detected in East Asians, while large amounts (2-6%) were detected in Oceanians (ie, Melanesians, Papuans, and Australian Aborigines.) 

According to Wikipedia:

Statistical analysis of genomic DNA sequences from different Asian populations indicates that at least two distinct populations of Denisovans existed,[50][51] and that a second introgression event from Denisovans into humans occurred. A study of Han ChineseJapanese and Dai genomes revealed that modern East Asian populations include two Denisovan DNA components: one similar to the Denisovan DNA found in Papuan genomes, and a second that is closer to the Denisovan genome from the Altai cave. These components were interpreted as representing separate introgression events involving two divergent Denisovan populations. South Asians were found to have levels of Denisovan admixture similar to that seen in East Asians, but this DNA only came from the same single Denisovan introgression seen in Papuans.[52]  …

The Denisovans, in case you’re new here, are a human species similar to the Neanderthals who lived… well, we’re not sure exactly where they lived, other than the Altai Cave, Siberia. We also don’t know what they looked like, because we have only found a few of their bones–a finger bone and some teeth–but they might have looked a bit like the Red Deer Cave People. Remarkably, though, these were in good enough condition (Siberia preserves things very well,) to allow scientists to extract sufficient DNA to determine that they are indeed a human species, but one that split from the ancestors of Homo sapiens about 600,000-750,000 years ago, and from the Neanderthals about 200,000 years later. 

Just as Homo sapiens mated with Neanderthals, so Denisovans mated with Neanderthals and Homo sapiens–the human family tree is growing increasingly complex. 

We don’t know exactly where these interbreeding events happened, since we know so little about the Denisovans (at least one of the Neanderthal interbreeding events probably happened in the Middle East, given that all non-Africans [and some Africans] have Neanderthal DNA,) but a clue lies in the DNA of the Negrito peoples. 

The Negritoes are a variety of peoples who live in south east Asia and, like the Pygmies of Africa, are rather short. Some of them, like the Aeta of the Philippines, have almost Papuan levels of Denisovan admixture, while others, like the Onge of India, have almost none. Assuming the Negritos are related to each other and not just isolated examples of island dwarfism, this suggests that the interbreeding event really did take places somewhere east of the major Indonesian islands of Sumatra and Borneo (which probably weren’t islands at the time, but connected to the mainland). The Denisovans may have been clever enough to build boats and cross the Wallace Line, surviving in the more isolated islands of Indonesia and the Philippines. 

On a related note, the article I just linked to from John Hawks, “This is where Scientists Might Find the Next Hobbits,” is truly excellent: 

In May, an international team of scientists led by Thomas Ingicco revealed new archaeological findings from Kalinga, in the northernmost part of Luzon, Philippines. Until now, scientists have mostly assumed that the Philippines were first inhabited by modern humans, only after 100,000 years ago. But the artifacts unearthed by Ingicco and coworkers were much older, more than 700,000 years old. …

Luzon was never connected to the Asian mainland, even when sea level was at its lowest during the Ice Ages. To get there, ancient hominins had to float. Who were they, and how did they get there?

Timeline of ancient Indonesian and Filipino hominin findings, from John Hawks’s article

I recommend you read the whole thing.

What’s all of this Denisovan DNA good for, anyway? Quoting Wikipedia again:

The immune system’s HLA alleles have drawn particular attention in the attempt to identify genes that may derive from archaic human populations. Although not present in the sequenced Denisova genome, the distribution pattern and divergence of HLA-B*73 from other HLA alleles has led to the suggestion that it introgressed from Denisovans into humans in west Asia. As of 2011, half of the HLA alleles of modern Eurasians represent archaic HLA haplotypes, and have been inferred to be of Denisovan or Neanderthal origin.[54] The apparent over-representation of these alleles suggests a positive selective pressure for their retention in the human population. A higher-quality Denisovan genome published in 2012 reveals variants of genes in humans that are associated with dark skin, brown hair, and brown eyes – consistent with features found with Melanesians today.[16] A study involving 40 Han Chinese and 40 people of ethnic Tibetan background identified a region of DNA around the EPAS1 gene that assists with adaptation to low oxygen levels at high altitude found in Tibetans is also found in the Denisovan genome.[55][56] In Papuans, introgressed Neanderthal alleles have highest frequency in genes expressed in the brain, whereas Denisovan alleles have highest frequency in genes expressed in bones and other tissues.[57]

It is a great era in genetics. 

Who’s setting Sanders up for a fall?

So the New York Times (which I don’t read, but Steve does so in the end, I do,) ran an article today how Bernie Sanders is a bad guy for inadequately responding to one campaign staffer touching another campaign staffer’s hair back in 2016.

I’ve noticed that SJWs tend to attack low-status people, not high-status (Trump excepted.) For example, a Portland Taco Truck may get driven out of business for “culturally appropriating” Mexican food, but Taco Bell doesn’t. Mere mortals calling Mohammad a pedophile for marrying a 9 yr old might go to prison for insulting Islam, but China can round up millions of Muslims and put them in “re-education camps” and no one makes a peep.

So when SJWs attack someone, it’s safe to say that 1. Their real intent has nothing to do with their claimed intent, and 2. The target is either low-status, losing status, or about to lose status, ie, protection.

The Democratic establishment didn’t like Sanders running the first time and did what they could to prevent him from getting the nomination.

I don’t think it’s any coincidence that Democrats are gearing up for the next election–looking over their candidates and deciding whom to run–as this piece comes out. Looks like a smear job, a hit piece intended to crush the Bernie campaign before it starts.

I wonder who’s behind it.

Book Club: The 10,000 Year Explosion: pt 4 Agriculture

Welcome back to EvX’s Book Club. Today we’re discussing Chapter 4 of The 10,000 Year Explosion: Consequences of Agriculture.

A big one, of course, was plague–on a related note, Evidence for the Plague in Neolithic Farmers’ Teeth:

When they compared the DNA of the strain recovered from this cemetery to all published Y. pestis genomes, they found that it was the oldest (most basal) strain of the bacterium ever recovered. Using the molecular clock, they were able to estimate a timeline for the divergence and radiation of Y. pestis strains and tie these events together to make a new, testable model for the emergence and spread of this deadly human pathogen.

These analyses indicate that plague was not first spread across Europe by the massive migrations by the Yamnaya peoples from the central Eurasian steppe (around 4800 years ago)… Rascovan et al. calculated the date of the divergence of Y. pestis strains at between 6,000 and 5,000 years ago. This date implicates the mega-settlements of the Trypillia Culture as a possible origin point of Y. pestis. These mega-settlements, home to an estimated 10,000-20,000 people, were dense concentrations of people during that time period in Europe, with conditions ideal for the development of a pandemic.

The Cucuteni-Trypilia Culture flourished between the Carpathian Mountains and the Black Sea from 4800-3000 BC. It was a neolithic–that is, stone age–farming society with many large cities. Wikipedia gives a confused account of its demise:

According to some proponents of the Kurgan hypothesis of the origin of Proto-Indo-Europeans … the Cucuteni–Trypillia culture was destroyed by force. Arguing from archaeological and linguistic evidence, Gimbutas concluded that the people of the Kurgan culture (a term grouping the Yamnaya culture and its predecessors) … effectively destroyed the Cucuteni–Trypillia culture in a series of invasions undertaken during their expansion to the west. Based on this archaeological evidence Gimbutas saw distinct cultural differences between the patriarchal, warlike Kurgan culture and the more peaceful egalitarian Cucuteni–Trypillia culture, … which finally met extinction in a process visible in the progressing appearance of fortified settlements, hillforts and the graves of warrior-chieftains, as well as in the religious transformation from the matriarchy to patriarchy, in a correlated east–west movement.[26] In this, “the process of Indo-Europeanization was a cultural, not a physical, transformation and must be understood as a military victory in terms of successfully imposing a new administrative system, language, and religion upon the indigenous groups.[27]

How does it follow that the process was a cultural, not physical transformation? They got conquered.

In his 1989 book In Search of the Indo-Europeans, Irish-American archaeologist J. P. Mallory, summarising the three existing theories concerning the end of the Cucuteni–Trypillia culture, mentions that archaeological findings in the region indicate Kurgan (i.e. Yamnaya culture) settlements in the eastern part of the Cucuteni–Trypillia area, co-existing for some time with those of the Cucuteni–Trypillia.[4]Artifacts from both cultures found within each of their respective archaeological settlement sites attest to an open trade in goods for a period,[4] though he points out that the archaeological evidence clearly points to what he termed “a dark age,” its population seeking refuge in every direction except east. He cites evidence of the refugees having used caves, islands and hilltops (abandoning in the process 600–700 settlements) to argue for the possibility of a gradual transformation rather than an armed onslaught bringing about cultural extinction.[4]

How is “refugees hiding in caves” a “gradual transformation?” That sounds more like “people fleeing an invading army.”

The obvious issue with that theory is the limited common historical life-time between the Cucuteni–Trypillia (4800–3000 BC) and the Yamnaya culture (3300–2600 BC); given that the earliest archaeological findings of the Yamnaya culture are located in the VolgaDonbasin, not in the Dniester and Dnieper area where the cultures came in touch, while the Yamnaya culture came to its full extension in the Pontic steppe at the earliest around 3000 BC, the time the Cucuteni–Trypillia culture ended, thus indicating an extremely short survival after coming in contact with the Yamnaya culture.

How is that an issue? How long does Wikipedia think it takes to slaughter a city? It takes a few days. 300 years of contact is plenty for both trade and conquering.

Another contradicting indication is that the kurgans that replaced the traditional horizontal graves in the area now contain human remains of a fairly diversified skeletal type approximately ten centimetres taller on average than the previous population.[4]

What are we even contradicting? Sounds like they got conquered, slaughtered, and replaced.

Then Wikipedia suggests that maybe it was all just caused by the weather (which isn’t a terrible idea.) Drought weakened the agriculturalists and prompted the pastoralists to look for new grasslands for their herds. They invaded the agriculturalists’ areas because they were lush and good for growing grain, which the pastoralists’ cattle love eating. The already weakened agriculturalists couldn’t fight back.

ANYWAY. Lets get on with Greg and Henry’s account, The 10,000 Year Explosion:

The population expansion associated with farming increased crowding, while farming itself made people sedentary. Mountains of garbage and water supplies contaminated with human waste favored the spread of infectious disease. …

Most infectious diseases have a critical community size, a  number and concentration of people below which they cannot persist. The classic example is measles, which typically infects children and remains infectious for about ten days, after which the patient has lifelong immunity. In order for measles to survive, the virus that causes it, the paramyxovirus, must continually find unexposed victims–more children. Measles can only persist in a large, dense population: Populations that are too small or too spread out (under half a million in close proximity) fail to produce unexposed children fast enough, so the virus dies out.

Measles, bubonic plague, smallpox: all results of agriculture.

Chickenpox: not so much.

I wonder if people in the old Cucuteni–Trypillia area are particularly immune to bubonic plague, or if the successive waves of invading steppe nomads have done too much genetic replacement (slaughtering) for adaptations to stick around?

Harpending and Cochran then discuss malaria, which has had a big impact on human genomes (eg, sickle cell,) in the areas where malaria is common.

In general, the authors play it safe in the book–pointing to obvious cases of wide-scale genetic changes like sickle cell that are both undoubtable and have no obvious effect on personality or intelligence. It’s only in the chapter on Ashkenazi IQ that they touch on more controversial subjects, and then in a positive manner–it’s pleasant to think, “Why was Einstein so smart?” and less pleasant to think, “Why am I so dumb?”


It’s time to address the old chestnut that biological differences among human populations are “superficial,” only skin-deep. It’s not true: We’re seeing genetically caused differences in all kinds of functions, and every such differences was important enough to cause a significant increase in fitness (number of offspring)–otherwise it wouldn’t have reached high frequency in just a few millennia.

As for skin color, Cochran and Harpending lean on the side of high-latitude lightening having been caused by agriculture, rather than mere sunlight levels:

Interestingly, the sets of changes driving light skin color in China are almost entirely different from those performing a similar function in Europe. …

Many of these changes seem to be quite recent. The mutation that appears to have the greatest effect on skin color among Europeans and neighboring peoples, a variant of SLC24A5, has spread with astonishing speed. Linkage disequilibrium… suggests that it came into existence about 5,800 years ago, but it has a frequency of 99 percent throughout Europe and is found at significant levels in North Africa, East Africa, and as far east as India and Ceylon. If it is indeed that recent, it must have had a huge selective advantage, perhaps as high as 20 percent. It would have spread so rapidly that, over a long lifetime a farmer could have noticed the change in appearance in his village.


In humans, OAC2 … is a gene involved in the melanin pathway… Species of fish trapped in caves… lose their eyesight and become albinos over many generations. … Since we see changes in OCA2 in each [fish] case, however, there must have been some advantage in knocking out OCA2, at least in that underground environment. The advantage cannot like in increased UV absorption, since there’s no sunlight in those caves.

There are hints that knocking out OCA2, or at least reducing its activity, may he advantageous… in humans who can get away with it. We see a pattern that suggests that having one inactive copy of OCA2 is somehow favored even in some quite sunny regions. In southern Africa, a knocked-out version of OCA2 is fairly common: The gene frequency is over 1 percent.

And that’s an area with strong selection for dark skin.

A form of OCA2 albinism is common among the Navajo and other neighboring tribes, with gene frequencies as high as 4.5 percent. The same pattern appears in southern Mexico, eastern Panama, and southern Brazil. All of which suggests that heterozygotes…may ave some advantage.

Here is an article on the possibility of sexual selection for albinism among the Hopi.

So why do Europeans have such variety in eye and hair color?


The skeletal record clearly supports the idea that there has been rapid evolutionary change in humans over the past 10,000 years. The human skeleton has become more gracile–more lightly built–though more so in some populations than others. Our jaws have shrunk, our long bones have become lighter, and brow ridges have disappeared in most populations (with the notable exception of Australian Aborigines, who have also changed, but not as much; they still have brow ridges, and their skulls are about twice as thick as those of other peoples.)

This could be related to the high rates of interpersonal violence common in Australia until recently (thicker skulls are harder to break) or a result of interbreeding with Neanderthals and Denisovans. We don’t know what Denisovans looked like, but Neanderthals certainly are noted for their robust skulls.

Skull volume has decreased, apparently in all populations: In Europeans, volume is down about 10 percent from the high point about 20,000 years ago.

This seems like a bad thing. Except for mothers.

Some changes can be seen even over the past 1,000 years. English researchers recently compared skulls from people who died in the Black Death ([approximately] 650 years ago), from the crew of the Mary Rose,a  ship that sank in Tudor times ([approximately] 450 years ago) and from our contemporaries. The shape of the skull changed noticeably over that brief period–which is particularly interesting because we know there has been no massive population replacement in England over the past 700 years.

Hasn’t there been a general replacement of the lower classes by the upper classes? I think there was also a massive out-migration of English to other continents in the past five hundred years.

The height of the cranial vault of our contemporaries was about 15 percent larger than that of the earlier populations, and the part of the skull containing the frontal lobes was thus larger.

This is awkwardly phrased–I think the authors want the present tense–“the cranial vault of our contemporaries is…” Nevertheless, it’s an interesting study. (The frontal lobes control things like planning, language, and math.) 

We then proceed to the rather depressing Malthus section and the similar “elites massively out-breeding commoners due to war or taxation” section. You’re probably familiar with Genghis Khan by now. 

We’ve said that the top dogs usually had higher-than-average fertility, which is true, but there have been important exceptions… The most common mistake must have been living in cities, which have almost always been population sinks, mostly because of infectious disease. 

They’re still population sinks. Just look at Singapore. Or Tokyo. Or London. 

The case of silphium, a natural contraceptive and abortifacient eaten to extinction during the Classical era, bears an interesting parallel to our own society’s falling fertility rates. 

And of course, states domesticate their people: 

Farmers don’t benefit from competition between their domesticated animals or plants… Since the elites were in a very real sense raising peasants, just as peasants raised cows, there must have been a tendency for them to cull individuals who were more aggressive than average, which over time would have changed the frequencies of those alleles that induced such aggressiveness.

On the one hand, this is a very logical argument. On the other hand, it seems like people can turn on or off aggression to a certain degree–uber peaceful Japan was rampaging through China only 75 years ago, after all. 

Have humans been domesticated? 

(Note: the Indians captured by the Puritans during the Pequot War may have refused to endure the yoke, but they did practice agriculture–they raised corn, squash and beans, in typical style. Still, they probably had not endured under organized states for as long as the Puritans.)

There is then a fascinating discussion of the origins of the scientific revolution–an event I am rather fond of. 

Although we do not as yet fully understand the true causes of the scientific and industrial revolution, we must now consider the possibility that continuing human evolution contributed to that process. It could explain some of the odd historical patterns that we see.

Well, that’s enough for today. Let’s continue with Chapter 5 next week.

How about you? What are your thoughts on the book?