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?


Thoughts on Quantrill

Normally I like to do both the Anthropology Friday excerpts and my own thoughts at the same time, but this time I didn’t want to interrupt the narrative’s flow.

The first thing that struck me in all of this was that Quantrill had a considerable number of followers: he lead 450 men to burn and loot Lawrence, Kansas. Pretty good for a guy who wasn’t even in the army. We can explain Quantrill’s motivation in the burning by arguing that he was trying to earn himself a commission in the Confederate Army by proving to them that he was a good commander, but what about his followers? Surely most of them could have joined the (Confederate) army the regular way, without detouring through Kansas.

Even after the burning, when it was quite clear that Quantrill was not going to get a commission and most of his followers had left, he still had some. So did many of the other men we’ll meet in this series, from outlaw bikers to mob bosses. (And pirates as we’ve already seen.)

And while most people are not very fond of criminals, folks like Quantrill and Jesse James found plenty of “safe” places where the locals were willing to shelter them, help them, or at least look the other way and not report them to the authorities.

What was the difference, really, between Quantrill and a regular army commander? Or the guerrilla soldiers known as the Red Legs and Jayhawkers?

Although I was familiar with the phrase “Burning Kansas” from history class, I hadn’t grasped the conflict’s full depth until reading Dago’s account. I’ve never heard anyone from Kansas or Missouri speak ill of each other–whatever bad blood there was in the Civil War’s immediate aftermath seems to have worn off. In Dago’s telling, the Kansas/Missouri border was a burnt-out, lawless zone where blood feuds brought men down for decades.

And what was the difference between an outlaw like Quantrill and a conqueror like Genghis Khan? ISIS? The chief of a Yanomamo tribe? Queen Medb of the Táin Bó Cúailnge?

(The Tain, if you haven’t heard of it before, is an Irish epic that revolves around the attempts by Queen Medb to steal a particular bull from another Irish king, and the efforts of the Irish hero Cu Chulainn to stop her.)

After all, Quantrill, while officially an “outlaw,” had many followers–as did these other men (and woman.)

I propose a simple answer: Quantrill was an “outlaw” because the official powers-that-were declared him one. Had Quantrill been successful enough to attract enough men to his side to not only burn and loot Lawrence, but keep it, he would have been its ruler, plain and simple. Genghis Khan did little more than burn, loot, massacre, and rape, but in so doing he amassed an empire. But Genghis Khan’s enemies were probably much less well-organized and equipped than Quantrill’s–certainly they didn’t have railroads.

War is a universal feature of human society. Even chimps have wars, bashing each other’s brains out with rocks. Early humans had war; pre-agricultural tribes have war. (The horticultural Yanomamo have some of the highest homicide rates in the world.)

We moderns have this odd notion that “war” is an official thing which is officially declared by official governments (and what makes an official government? We could go in circles all day.) We believe that war has rules (or at least that it ought to): that it should be fought only by official soldiers on official battlefields, using officially approved weapons, and only targeting official targets. Anything not by the book, such as targeting women and children, using chemical weapons, hijacking airplanes and flying them into buildings, or fighting on behalf of a group that doesn’t issue uniforms and pay cheques, just confuses us.

But I guarantee you that Genghis Khan did not conquer one of the biggest empires in history by refusing to slaughter women and children.

Similarly, ISIS is nothing but a bunch of outlaws who’ve conquered some territory, but in their case, they have an ideology that justifies their actions and encourages other people to come join them, boosting their numbers.

While tribal, pre-agricultural life was full of war and homicide, it seems that groups rarely got too much of an advantage over each other. Rather, conflict was nearly constant–every so often a battle would break out and a few people would died. When conflicts were particularly bad, small tribes would band together against larger tribes until they balanced out (or slaughtered their enemies.) When conditions approved, tribes split up and people went their own way (until they got into conflicts with each other and the cycle repeated.) But occasionally one tribe developed (or obtained) a distinct advantage over the others: armies mounted on horseback dominated less mobile units. Armies with guns massacred people who had none. Vikings, Spaniards, and later Englishmen built boats which let them conquer large swathes of the world. Etc.

Our present state of relative peace (compared to our ancestors) is due to the fact that all of this conquering eventually led to the amalgamation of large enough states with large enough armies that we now have few enemies willing to take the risk of attacking us. We have nukes; as a result, few formal states with formal armies are willing to attack us. This state of mutual balance is–for now–holding for the developed world.

This state of peace is not guaranteed to last.

I noticed back in The Walls Tear Themselves Down that borders are ironically places of disorder. As Dago notes, criminals take advantage of borders–and stateless zones–to escape from law enforcement.

On a related note, Saul Montes-Bradley has an interesting post about Islamic terrorist groups raising money via drug trade in Latin America:

The tentacles of Jihad extend further than most people realize. …

In particular in South American countries, long the allies of Middle Eastern Fascism, terrorist organizations find support and, most grievously financing. Indeed, the second largest source of financing for Hezballat[1] is drug trafficking and smuggling between Argentina, Paraguay and Chile, often under the protection of local government officials.

This feature of borders will be showing up a lot in the next few Anthropology Fridays.

Mongolia Isn’t Sorry

Genghis Khan killed approximately 40 million people–so many that historians debate whether the massive decrease in agriculture caused by the deaths of so many farmers helped trigger the Little Ice Age. DNA analysis indicates that 1 in 200 people alive today is a direct descendant of Genghis Khan or his immediate male family.

The Genghis Khan Equestrian Statue, erected in 2008 near Ulaanbaatar, Mongolia, stands 130 ft (40 m) tall, its pedestal an entire museum. It is one of the world’s tallest statues–and the tallest equestrian statue–a status it shares primarily with the Buddha and other eastern deities.

Mongolians regard him as the father of their country.

Piracy, Bandits, and Civilization

While reading The Pirates Own Book, I was struck by how much of history has been warfare and banditry:

Piracy has been known from the remotest antiquity; for in the early ages every small maritime state was addicted to piracy, and navigation was perilous. This habit was so general, that it was regarded with indifference, and, whether merchant, traveller, or pirate, the stranger was received with the rights of hospitality. Thus Nestor, having given Mentor and Telemachus a plenteous repast, remarks, that the banquet being finished, it was time to ask his guests to their business. “Are you,” demands the aged prince, “merchants destined to any port, or are you merely adventurers and pirates, who roam the seas without any place of destination, and live by rapine and ruin.”

Where men can make a living through violence and predation, they do. The only thing that stops them is other men strong enough to kill them:

The Danes, Norwegians, and Swedes, from their superior knowledge of navigation, gave into it most; and on whatever coast the winds carried them, they made free with all that came in their way. Canute the Fourth endeavored in vain to repress these lawless disorders among his subjects; but they felt so galled by his restrictions, that they assassinated him. On the king of Sweden being taken by the Danes, permission was given to such of his subjects as chose, to arm themselves against the enemy, pillage his possessions, and sell their prizes at Ribnitz and Golnitz. This proved a fertile nursery of pirates, who became so formidable under the name of “Victalien Broders,” that several princes were obliged to arm against them, and hang some of their chiefs. …

Charles the Bald, not having the power to expel him, engaged the freebooter, for 500 pounds of silver, to dislodge his countrymen, who were harassing the vicinity of Paris. In consequence of this subsidy, Wailand, with a fleet of 260 sail, went up the Seine, and attacked the Normans in the isle of Oiselle: after a long and obstinate resistance, they were obliged to capitulate; and having paid 6000 pounds of gold and silver, by way of ransom, had leave to join their victors. The riches thus acquired rendered a predatory life so popular, that the pirates were continually increasing in number, so that under a “sea-king” called Eric, they made a descent in the Elbe and the Weser, pillaged Hamburg, penetrated far into Germany, and after gaining two battles, retreated with immense booty. The pirates, thus reinforced on all sides, long continued to devastate Germany, France, and England; some penetrated into Andalusia and Hetruria, where they destroyed the flourishing town of Luni; whilst others, descending the Dnieper, penetrated even into Russia.

The text goes on in this manner, and it is just striking how, for so many centuries after the fall of Rome, Europeans lived in constant fear of bandits, with no force strong enough to secure the sea lanes and borders. And even the rulers themselves are, in many cases, ex-bandits themselves: barbarian conquerors .

Genghis Khan

Once a group of bandits becomes strong enough to kill all the other bandits in the area, it settles in and starts taxing instead of stealing.

Even Genghis Khan, once finished conquering, began executing bandits, encouraging trade, and securing the safety of his tax-payers. It is said that a woman carrying a bag of gold could walk, alone, from one end to the other of the Mongol Empire without fear or molestation–an exaggeration, I’m sure, but I know I wouldn’t want to incur the Great Khan’s wrath by robbing one of his subjects.

(In Power and Prosperity, economist Mancur Olson argues that, “under anarchy, a “roving bandit” only has the incentive to steal and destroy, whilst a “stationary bandit”—a tyrant—has an incentive to encourage some degree of economic success as he expects to remain in power long enough to benefit from that success. A stationary bandit thereby begins to take on the governmental function of protecting citizens and their property against roving bandits. In the move from roving to stationary bandits, Olson sees the seeds of civilization, paving the way, eventually for democracy, which by giving power to those who align with the wishes of the population, improves incentives for good government.[5]” )

We can even see this process occurring with ISIS (h/t Will @Evolving_Moloch):

From Brookings: Experts Weigh in: Is ISIS good at Governing?

Humans once hunted goats; today we feed them, give them shelter, and kill their other predators. As a result, there are far more goats than there would be otherwise. We still eat them, of course.

A government of sedentary bandits is still bandits, but at least they’re bandits who want the community to thrive. (Yes, taxation IS theft, but you should see the alternative.)
As a result, we take for granted a level of peace and safety that most of the world has never experienced.

Chimps fight wars. Neanderthals were cannibals. Homicide in primitive tribes was sky-high. You have twice as many female as male ancestors because the majority of men never reproduced.

Western society didn’t become peaceful by singing kumbaya, but by 1. top-down banning cousin marriage, which ended tribalism,

and 2. Becoming powerful enough to catch and execute the bandits.

We forget this at our own peril.

Adoption pt 2: when Genghis Khan kills your parent and makes you his little brother

In Genghis Khan and the Making of the Modern World, Jack Weatherford brings us a fascinating adoption account:

In the long history of steppe warfare, a defeated tribe was looted, some members taken prisoner, and the rest left again to their own devices. … In his defeat of the Jurkin, however, Temujin [Genghis Khan] followed a radical new policy that revealed his ambition to fundamentally alter the cycle of attack and counterattack and of making and breaking alliances.

(In short, he executed all of the Jurkin’s leaders.)

He then took the unprecendented step of occupying the Jurkin lands and redistributing ht remaining members of their group among the households of his own clan. … Temujin took them into his tribe not as slaves, but as members of the tribe in good standing. He symbolized this by adopting an orphan boy from the Jurkin camp and presenting him to Hoelun [his mother] to raise in her ger [yurt] not as a slave but as her son. By having his mother adopt the Jurkin boy, as he had her previously adopt one each from the defeated Merkid, Tayichiud, and Tatars, Temujin was accepting the boys as his younger brothers. …

In a final display of his new power, Temujin ended the Jurkin episode with a feast for both the victorious Mongols and their newly adopted relatives.

In Genghis Khan, Conqueror of the World, Leo de Hartog recounts a similar story:

While they were plundering a Tatar camp the Mongols found a small boy. Genghis Khan took the boy and gave him to his mother, Ho’elun, who adopted him as her son. She called the boy Shigi Qutuqu. There is another version of the story. The child was taken by Genghis Khan in 1182-3, after a raid against the Tatars. He and Borte [Genghis Khan’s wife] at that time had no children. He gave the young tatar to Borte, who brought him up as an adopted son. … Some call him a stepbrother of Genghis Khan, others his adopted son. Shigi Qutuqu, who was very intelligent, later became lord chief justice of the Mongol empire.

Genghis Khan
Genghis Khan, famous softie

Genghis Khan’s sympathy for the orphans of war may have been due to his own childhood experiences; when he was nine years old, his father was murdered by the Tatars and he, his mother, and brothers were driven out of their clan, rendered essentially homeless. Later he was captured and enslaved by the Tayichiud. (Obviously he escaped.)

Approximately 1 in 200 people today appears to be a direct descendant of Genghis Khan, making him the one of the most evolutionarily successful humans in all of history. (If not the most successful.)

If we want to get technical, some of those folk are probably descended from Genghis Khan’s brothers, making Genghis Khan’s dad history’s most successful guy, but Genghis Khan achieved that success by conquering one of history’s biggest empires, and Genghis Khan’s dad achieved his success by siring Genghis Khan.

While I don’t normally advocate “be like Genghis Khan,” simply because I like being alive, if Genghis Khan thought adoption was a good idea, maybe it can be a viable evolutionary strategy.


Tomorrow: A bit of historical and cross-cultural context