Derived PLK4 variant not common in Bushmen

I get sad when I read things like this in Slate, Twitter at the Crossroads: The company knows it’s in trouble. And its options are bleak. That’s because in areas such as genomics so much of the cutting-edge discussion has moved to Twitter that you can be privy to information which was previously the purview of the “scientific 1%.” Today for example I see the above from Pontus Skoglund.

I’ve discussed this issue before, Miscarriage as a behavioral strategy and Human uniqueness is not unique. Basically a derived mutational variant is found in PLK4 which is correlated with higher miscarriage rates, and seems to be maintained at appreciable frequencies by balancing selection. Derived because Neandertals carry the ancestral variant. Balancing selection because 1000 Genomes results make it pretty clear that it’s not fixed or absent all across Africa, Eurasia, and the New World. If it increases miscarriage rates, why isn’t it extinct yet? If it is beneficial, why isn’t it fixed somewhere? Ergo, balancing selection presents itself as an option.

But above Skoglund reports that it does seem nearly absent among the Bushmen. Or at least among the Ju’/hoansi. What about that 1 copy among the 38? Well, the Bushmen are admixed somewhat with newcomers to the region, so it could be a recent introduction. I asked Skoglund about the Pygmies, and he reported that it is at low frequencies in the Mbuti. It may be that this variant differentiates African hunter-gatherers from the rest of humanity. Remember that the latest genomic data implies that Bushmen diverged from the main lineage leading to other human groups about ~1/3 of the time back to the divergence the ancestors of Neandertals from those of modern humans. Depending on the measure and genetic data the agriculturist Sub-Saharan Africans may actually be closer to the rest of non-African humanity than they are to extant hunter-gatherers, at least the non-admixed ones.*

Addendum: Years ago Greg Cochran told me that Pygmies are reported to have very low miscarriage rates.

* Main qualifier is that human genetic history seems to be highly reticulate, as opposed to tree-like.

How human culture makes war inevitable

warLike slavery war has a long history in our species, but it does have a history, a beginning, and perhaps an end. That is the sort of message you can take away from a paper such as Zefferman and Mathew’s An Evolutionary Theory of Large-Scale Human Warfare: Group-Structured Cultural Selection. War is a culturally mediated human phenotype, and one which requires particular contingent conditions to flourish, and others to diminish. Perhaps the best survey I’ve read on this topic is Azar Gat’s War in Human Civilization (which is $9.99 on the Kindle, so I just got a copy even though I already read this book!). But Gat doesn’t seem to come to any definitive conclusion as to the nature of war from what I could tell (the book is long and meandering). And that makes sense, because war is complicated, and the behavioral phenotype isn’t clear and distinct. What exactly qualifies as war? World War II clearly does. But how about the feud between the Hatfields and McCoys? Obviously there is a continuum, and we have to draw lines. The phenomenon which Zefferman and Mathew focus on is the paradox of mass intergroup conflicts which are defined by clashes between coalitions of unrelated males. More concretely, in wars between nation-states you have old men sending young men to their deaths in large numbers. Why do these young men put themselves in harm’s way?

The authors focus on two species as a contrast with humans, common chimpanzees and social insects, Argentine ants, which have been known to engage in war. War here can be thought of as coalitional intergroup conflict. Chimpanzees are informative toward any discussion of human evolution because they are phylogenetically close to our own lineage, while social insects are not, but like humans are highly complex in their organization (they even farm!). But, there are important contrasts between the wars of chimpanzees and social insects, and those of humans. Chimpanzee wars are of small scale, on the level of the band, and always opportunistic. That is, they occur in a manner which could be modeled as competing firms acting in their own rational interests. When two bands interact, and one of them is much larger, then the larger band proceeds to attack the smaller. Chimpanzees do not engage in conflict by and large when there is parity between two bands. The attackers take on little risk, to the point where there hasn’t been a documented instance of casualty on the part of attacking bands in field observation. Social insects are very different. The scale of their warfare is on the same order of that of humans, millions of ants for example may be party to conflict. But, unlike humans the coefficient of relatedness of the opposing coalitions are such that it can be explained via traditional inclusive fitness theory.

warbeforeThe figure above, from the paper, illustrates how humans are different. Humans engage in high intensity conflict despite most of the genetic variation being partitioned within the groups. In other words, unrelated individuals (almost always, but not exclusively, men) are fighting and dying for each other. In the examples above over ~20% of the genetic variation across Argentine ants is partitioned across the groups. You may know that across geographical populations a similar order of magnitude of human variation is partitioned across groups; for example, ~10% of the variation between Chinese and English populations is between the two groups. But for the ants we’re talking about adjacent groups, not those geographically distinct. As the figure above makes clear in the vast majority of cases where conflict might arise because of competition over resources or simple opportunity the genetic distance between the groups is very small. That is because a small amount of gene flow can quickly equilibrate differences between populations (1 migrant per generation across groups is sufficient to prevent genetic divergence if they separate). ~7,000 years ago the amount of variation partitioned in Europe between Mesolithic hunter-gatherers and the first farmers in parts of Central Europe which were co-resident was ~10%. Today, the average difference between national groups (e.g., Czech vs. Portuguese) is on the order of ~1%. Gene flow quickly removes variation, which is important, because without variation natural selection can not operate. Heritable variation is its raw material. morrisEvolutionary pressures can maintain intergroup conflict on a massive scale among social insects because of the high degree of relatedness within colonies and supercolonies. In other words, they’re superorganisms. Similarly, moderately social behavior among chimpanzees manifests in a manner such that elegant individual level evolutionary dynamics such as inclusive fitness and reciprocal altruism are sufficient to explain interactions, in addition to the close relatedness of the males because of patrilocality. Larger groups of chimpanzees attack smaller groups of chimpanzees because it is the rational behavior in the context of minimal risk to self. Higher level group explanations are not really necessary.

Cultural_Evolution__How_Darwin_2_28_2013_10_16_35_PMThe answer to the question for why humans often, but not always, engage in warfare from Zefferman and Mathew is “group-structured cultural selection.” Often this phenomenon goes by labels such as “cultural group selection” or “multi-level selection,” but the authors assert that these terms are somewhat fraught, so they seem to be presenting their own so that there is a precise and distinctive understanding of what they are getting at without old baggage. As you can see above the Fst between cultural groupings is far higher than that for genetics. Why? Intuition can lead us to the answer easy enough: genetics is a straightjacket in terms of the nature of inheritance, while cultural is more flexible. If, for example, one group defeats another in war and kills all the males and older females, but takes the younger females as slaves, then the genes of the defeated may persist. But often the culture will go totally extinct.  Conversely, a group victorious in war may increase demographically through amalgamation, while preserving to a great extent its cultural distinctiveness and identity. As an example, the Zulu were two centuries ago simply one clan among the Nguni. Today, they are one of the major tribes of South Africa thanks to the victories of Shaka and his successors. The recent genetic results coming out of Britain, which suggest that Anglo-Saxons had an impact, but a secondary one genetically, illustrates how a demographic minority can drive a cultural rupture among a conquered populace. The language of the people of Devon, which was once Dumnonia, is a sibling to that of the Germans across the North Sea, with no relationship to the Brythonic Celtic of their ancestors (I choose Devon because this is a region of the British Isles with very little Anglo-Saxon genetic footprint; Dumonia was even conquered after the Anglo-Saxons had become Christian, and so postdates the sub-Roman era).

0226712842If war as a behavioral pattern is selected on the level of a culture, a group, what does that imply for its innateness? Probably that there is not a “war instinct,” and, that war may not be primal as an ancestral character for our lineage. Rather, war is a social phenomenon which emerges out of the constellation of other cognitive traits which we have as part of our ancestral heritage. In that way, it may be like organized religion or representational sculpture, aspects of evoked culture. Given particular conditions war may bubble up out of the possibilities for human behavior “naturally,” and then be selected upon as Zefferman and Mathews imply (its benefits are made explicit in works such as Ian Morris’ War! What is It Good For?). The reason that there are hundreds of millions of people who are the cultural descendants of Romans and their Latin allies, rather than Etruscans, is that the latter were defeated in war and absorbed by the Romans. Clearly there was a benefit to the Romans as a culture for developing social institutions which made them incredibly effective as a nation at arms. Some of the glory of victory was likely demographic, insofar s Roman colonies spread far and wide, but most of it was in terms of posterity and memory. Though the French may conceptualize themselves today as the descendants of Gauls (genetically this is probably correct), their language and religion come down to them because of the Romans.*

If memes, rather than genes, are the targets of selection, and groups are the units, how is it then that the genes for males who engage in highly risky behaviors persist? Shouldn’t cheaters have a higher fitness? Some of this is likely explained by the benefits to the group. Even though risk is entailed in war, the fitness benefits can be quite great for successful males. But there’s something else going on too. Zefferman and Mathew refer to the tendency toward conformity. This is an innate psychological bias which humans exhibit, and it allows for rapid change in cultural norms and expectations. Twenty years ago Bill Clinton did not hesitate to sign the Defense of Marriage Act in the interests of his political ambition, while today he wouldn’t hesitate to term someone opposed to gay marriage/marriage equality a “bigot.” In Daniel Schacter’s The Seven Sins of Memory he recounts how white American Southerners who came of age from the 1960s to 1980s often remember themselves as being ahead of the times when it came to segregation and race relations, a recollection belied by longitudinal studies. Psychological conformity as an individual level trait allows for rapid homogenization of cultural norms very fast and across wide swaths of the population. in relation to warfare it can explain why the Japanese can shift their national consciousness from that of being very militaristic on the whole to being opposed to the existence of a standing army which engages in force projection. Culture is protean because of a fixed aspect of human nature, social intelligence which fosters group conformity. Those who lack the tendency toward conformity exist, but they are often ostracized, and are considered disagreeable. Though cheating may be beneficial, it may be that the same psychological trait which allows for conformity and agreeableness means that few will wish to betray their “little platoon” for self-interest. War’s raw material exists because it is highly beneficial at a lower level of organization in terms of human social interaction. Humans sacrifice as a consequence of being human as we understand it, embedded in a network of trust, friendship, and affinity.

End_of_War_lores20130205-2-1ovxa4rHuman psychology also means that John Horgan’s hope in The End of War that this phenomenon may have a “sell by” date is not futile. Perhaps the best analogy here is to slavery, an institution which arose during the Neolithic in a mass form which many thinkers across time took as a given, whether it was for the good or bad (Aristotle believed there were natural slaves, while other thinkers accepted it as an inevitable evil). And yet a cultural shift, enabled likely by economic and social forces, occurred over the past few centuries, and de jureslavery is now all but abolished, and de facto chattel slavery exists only furtively in the hidden places beyond the reach of modern human norms. Like war the institution of slavery was universal among complex societies, though its magnitude and manifestation varied in detail. With the emergence of radical stratification, with some individuals deified, it stands to reason that the lowest form of abasement within a society would be to utterly dehumanize. Mind you, the anthropological evidence seems clear that dehumanization is common among humans, even in the primal condition, but this was of the Other, those outside of the tribe. Though slavery often had a tribal connotation (e.g., blacks or non-Muslims could be enslaved), the key difference between it and dehumanization in the generality is that slaves became human tools integrated into the body of society, part and parcel of the fabric of human cultures. The abolition of slavery was the revenge of the dignity of the individual, as the circle of human empathy was expanded outward and totality. Hierarchy and inequality persist, but they are dampened by novel cultural institutions and ancient intuitions.**

The_Better_Angels_of_Our_NatureI do not know how war will end exactly, or, if it will end. History is not filled with many inevitable end points. But, the evidence in Steven Pinker’s The Better Angels of Our Nature is moderately compelling to me. Humans do have a nature, and it explains why war emerges so often in our history. But that nature also holds the keys for why it may diminish into irrelevance. If psychological conformity can be aligned with non-zero sum interactions then we may see an opportunity to avoid the conflicts that arise because of disputes over finite resources and opportunities.

* The French self-conception has gone through several iterations, some of which are much more philo-Roman than others.

** Do unto others as you would have done unto to you is simply a formalization of an iterated game.

Citation: Zefferman, Matthew R., and Sarah Mathew. “An evolutionary theory of large‐scale human warfare: Group‐structured cultural selection.” Evolutionary Anthropology: Issues, News, and Reviews 24.2 (2015): 50-61.

Who thinks only genetically modified tomatoes have genes?

41rxx-UtsWL._SY344_BO1,204,203,200_Genetically modified organisms (GMO) are a topic I have some interest in, even though I don’t talk about it much. That’s partly because I’m a genetically modified organism; on the order of 8% of my genome was inserted by viruses. More importantly a moral panic about GMO is currently an obstacle to their utilization in full. Yes, GMO are in corn and soybean, but their application is constrained by explicit and implicit bars. Of course these constraints are quite popular. This is why Chipotle is removing GMO from their food. It’s a matter of capitalism, not science or health.

Often when you drill down to it fear of GMO come down to two issues. First, there is the “wisdom of repugnance.” People who are not aware of how common horizontal gene transfer in the natural world is are frightened by the idea of “fish genes in tomatoes.” How about snake genomes in cow? That is not something man hath wrought. Then there is the issue of corporations and monoculture. But this is not a necessary function of GMOs. Organics are very popular with corporations because they can charge a premium through price discrimination (the poor can’t afford organics, while the upper middle class will pay more for them). And monocultures in food production has been an issue which goes back at the latest to the Irish potato famine. Well before transgenics of the scientific sort.

I was curious about opinions about GMO in the General Social Survey. I found the variable TOMATOES. It states: “Ordinary tomatoes do not contain genes, while genetically modified tomatoes do. (Is that true or false?)”

The correct answer is obviously false. But I was curious what proportion of the population would answer “true.” Here are some demographics….

  True %
Sex Male 28.3
  Female 31.9
Highest level of education Less than HS 48.6
  High School 33.4
  Junior College 36.3
  Bachelor 18.1
  Graduate 17.6
Political ideology Liberal 26.8
  Moderate 33.3
  Conservative 28.3
Belief about nature of God Atheist 25.2
  Agnostic 23.2
  Believe in higher power 20.5
  Believe in God sometimes 30.1
  Believe with some doubts 34.6
  Know God exists 31.8
Belief about nature of Bible Word of God 38
  Inspired word of God 31.3
  Book of fables 18.2
Age 35 and under 34.5
  35 to 64 24.7
  65 and over 40.8
Correct number on vocab test 0 to 4 59.1
  5 41.5
  6 40.7
  7 28.6
  8 13.6
  9 to 10 7.1

I decided to check these variables against a logit regression. The results are as so:

Logit Coefficients Test That Each Coefficient = 0
  B SE(B) Exp(B) T-statistic Probability
WORDSUM 0.413 0.099 1.511 4.173 0
DEGREE 0.226 0.15 1.254 1.504 0.134
SEX -0.841 0.367 0.431 -2.291 0.023
POLVIEWS 0.063 0.127 1.065 0.491 0.624
BIBLE -0.068 0.242 0.934 -0.28 0.779
GOD -0.076 0.145 0.926 -0.525 0.6
AGE -0.003 0.01 0.997 -0.258 0.796
Constant -0.433 1.406 0.649 -0.308 0.759

The big variable here that remains very significant is WORDSUM. The score on a vocabulary test from 0 to 10 which has a correlation with general intelligence of 0.71. Perhaps only the intelligent can really comprehend or understand this question? Looking at the descriptive results above it shouldn’t be surprising. The educational gap turns out to mostly be explained by WORDSUM. If your remove WORDSUM then DEGREE becomes a very big deal.

Note: the question was asked in 2010, and the sample size was on the order of 1,000 (depends on the crossing variable). Also, I understand some people will claim that the question is priming respondents and confusing people with minimal science understanding. I would suggest you’d get confused if you aren’t very smart or thoughtful. Or, you think “genes” are unnatural and the reason we can’t have nice things.

Robert Trivers, friends and enemies

51fjBuOLFnL._SY344_BO1,204,203,200_Robert Trivers is one of the giants of modern evolutionary biology, with a diverse portfolio of interests. Apparently he has an autobiography coming out in the near future, and his editors did not think it was prudent to include a chapter where he launched salvos against enemies, while praising his friends. Ron Unz has published it in unexpurgated form, Vignettes of Famous Evolutionary Biologists, Large and Small. It’s fascinating, though probably on the whole not surprising to those who have followed Trivers’ career.

I can’t help but note that much of the reflection here seems to be an elaboration of observations you can find in Natural Selection and Social Theory: Selected Papers of Robert Trivers. If you haven’t read this, do so. It’s important, and Trivers is always an interesting writer. W. D. Hamilton and George C. Williams are gone (not to mention John Maynard Smith and George R. Price). Trivers is one of the witnesses to a major revolution in our understanding of the evolution of behavior, so I’m definitely curious as to his reflections on the life he’s led.

The extinction of Middle Eastern religious minorities

51Odj8gZIeL._SY344_BO1,204,203,200_Gerard Russell’s Heirs to Forgotten Kingdoms is a somewhat uneven work with a surprisingly broad thematic coverage. The subhead is “Journeys Into the Disappearing Religions of the Middle East.” But one of the groups covered, the pagan Kalash, are not Middle Eastern. A group like the Mandaeans, who have disappeared from the region due to the 2003 invasion of Iraq, are not in any way comparable to the Coptic Christians of Egypt, who number in the millions.

Rather, the bigger issue that is being put into focus is how religious minorities are faring in the Islamic world. The short answer is not very well. The recent events on Mount Sinjar, where the Yezidi were targeted for what seems a classical case of genocide by the Islamic State, illustrates that. The issue though is less that the Islamic State is eliminationist in its intent, but that the Muslim majorities are quite apathetic or uninterested in how religious minorities fair. Russell relates how non-Muslim Kalash children were converted to Islam by teachers who made them recite the shahada, after which they were barred from identifying as non-Muslim due to the punishments enforced upon apostates. In this way a whole generation of Kalash were extracted from their broader family networks and cultural heritage individual by individual. This is in complement to the mass expulsion of peoples in the aftermath of the late lamented Iraq invasion, which sent ripples throughout the region. It is ironic that George W. Bush, an evangelical Christian, was instrumental in the eventual disappearance of Christian traditions which are nearly 2,000 years old from their ancestral homelands.

downloadA more interesting, and less depressing, aspect of Heirs to Forgotten Kingdoms, is the historical speculation by the author that many heterodox groups such as the Druze, Yezidi, Alawites, and Mandeans, preserve elements of Middle Eastern religious thought derived from antiquity. In particular, the influence of the Sabians of Harran looms large. This was a clearly pagan group which persisted down through the early Muslim centuries by asserting that they were the Sabians mentioned in the Koran, ergo, deserving of protection as People of the Book. The true religious identity of the Sabian seems to have been a synthesis of the ancient traditions of the Fertile Crescent, as well as Hellenistic Neo-Platonism. Sabians such as Thābit ibn Qurra were instrumental in the dissemination of Greek philosophy in the Baghdad created by Harun al-Rashid. Russell documents how threads of these beliefs have persisted among groups as disparate as the Yezidi, Alawites, Druze, and Mandaeans.

But these may be the last generations of these religious sects, who are grappling with the consequences and implications of modernity. The collective/corporate identities which insulated them in the past are fading, and dislocation and migration to the individualistic societies of the West are rendering them vulnerable to deracination. Heirs to Forgotten Kingdoms is then perhaps useful as it records a world which will fade into memory before this generation shall expires.

Addendum: One of the more fascinating aspects in the narrative are references to a book with the title The Nabataean Agriculture. The aim of the work is mostly utilitarian. But, in an offhand manner the author, who lived in the first few centuries of Islam, recounts ethnographic detail which is strongly suggestive of the likelihood that in many rural areas of unmodified rural paganism dating to antiquity persisted in the Fertile Crescent. This, in contrast to the organized and “high culture” paganism of Harran. This is not entirely surprising, and is perhaps analogous to the survival of the Kalash into modern times. The “high religions” were dominant in urban areas among elites, but often took a laissez faire attitude toward the peasantry.

Open Thread, 04/26/2015

51Odj8gZIeL._SY344_BO1,204,203,200_On a plane trip I finally finished Heirs to Forgotten Kingdoms: Journeys Into the Disappearing Religions of the Middle East. It’s about equal parts travelogue, ethnography, and historical speculation. Though not a scholarly work there’s a lot of peculiar and fascinating data. I’d recommend the book, and will probably have a longer review up at some point. NPR had an interview with the author a while back, in part because he has a chapter about the Yezidis, who were in the news at the time because of the attack of ISIS on Sinjar.

So I have determined that I’m going to go to ASHG 2015 and PAG as far as conferences go in the near future, though I’m a little confused why ASHG decided to pick Baltimore rather than D.C.. I assume there’ll be a Bay Area Population Genomics meeting before that of course.

It’s strange, but I’ve noticed something about Twitter for me. I’ve been on since April of 2009. I finally topped 6,000 followers. That’s fine, but it’s literally ~1,000 followers per year. Below you can see the Twitter analytics, which dates to August of 2012. It’s basically a linear progression, except for a kink here and there.

Screenshot from 2015-04-25 22:51:21

Also, I’ll be on the third episode of Through the Wormhole. Premiers mid-May.

Agriculture came with men to the Indian subcontinent


51IZQjMbVlL._SY344_BO1,204,203,200_I am often asked by people online to give an “elevator pitch” as to the genetic history of the Indian subcontinent. At this point we’ve got ~90 percent of the story I think. Modern humans arrived in the Indian subcontinent ~50,000 years ago, and pushed onward to East Asia, but over the past ~10,000 years massive changes have occurred genetically due to the intrusion of populations form the northwest and northeast, with likely total cultural turnover. What do I mean by this? First, it’s highly probable that all of the extant language families of the Indian subcontinent are rooted in lineages which were present outside of the Indian subcontinent before the Holocene. In other words, during the Ice Age the ancestral linguistic entities which gave rise to Indo-European, Dravidian, and Austro-Asiatic, were present outside of confines of India, Pakistan, Bangladesh, Sri Lanka, Nepal, and Bhutan. The only exception here are the languages of the indigenous peoples of the Andaman Islanders.*

516ma6FzHPL._SY344_BO1,204,203,200_Older historical works on South Asia often have a preface which suggests that the Austro-Asiatic Munda languages, and those of the Dravidians, were deeply indigenous to the region, to be marginalized in the north and west of the subcontinent by Indo-Aryan dialects which arrived relatively recently. This strikes me as likely wrong in terms of broad brush impressions. I now believe that Peter Bellwood was probably correct to argue in First Farmers that the arrival of Dravidian languages to the subcontinent was mediated through the arrival of agriculturalists, and perhaps may not have predated the Indo-Aryans by very much time at all in most of the subcontinent. I am even more confident that the Munda people are descended from a group with relatively recent origins on Southeast Asia, approximately contemporaneous with, though likely marginally preceding, the arrival of Indo-Aryans. What you see in South Asia today when it comes to linguistic-cultural agglomerations is the jostling of groups whose origins are all exogenous and date to the post-Neolithic period. Though the Pleistocene genetic heritage of South Asia persists to a great extent, as culturally coherent units I doubt there is much of the Pleistocene left in the region (with the exception again of the Andaman Islands).

51MGYd330tL._SY344_BO1,204,203,200_Let’s talk about the Munda people first. Most of South Asian social-demographic analysis focuses on a divide between two disparate elements. Culturally, Indo-Aryan vs. Dravidian. Religiously, Hindu vs. Muslim. Genetically, Ancestral North Indian (ANI) vs. Ancestral South Indian (ASI). These dyads are useful analytically, but they elide the more richly textured diversity of the subcontinent (in the case of Muslim vs. Hindu, neither groups, especially the “Hindu” category, are very homogeneous). According to a new paper, A late Neolithic expansion of Y chromosomal haplogroup O2a1-M95 from east to west, as much as ~15% of the Y chromosomal lineages of South Asia may be attributed to these populations. This group uses quite old-fashioned methods. That is, they’re about 10-15 years old, an eon in modern genetics! Basically the focus is on fast evolving microsatellite lineages, and the patterns of variation thereof. But, the power of the paper is the massive data set, which has strong representation of many populations. By looking at thousands of individuals from some regions they were able to observe patterns with a very high degree of confidence as to their representativeness of a given group.

The following table illustrates what I’m talking about:

Adapted from A late Neolithic expansion of Y chromosomal haplogroup O2a1-M95 from east to west
Adapted from A late Neolithic expansion of Y chromosomal haplogroup O2a1-M95 from east to west


The cultural-historical debate is whether the Austro-Asiatic languages are indigenous to South Asia or not. The balance of the evidence now seems to be that they are not. What likely occurred is that the Austro-Asiatic languages waxed with the rise of an agricultural Diaspora, whose locus of origin was in what is today the southern regions of China proper. More precisely, the Austro-Asiatic languages may have spread with rice farming across Southeast Asia and eastern South Asia. Likely they were the first on the scene in Southeast Asia, as Bellwood reports in First Farmers  and First Migrants that archaeology and anthropometrics can detect admixture between the farmers arriving from the north and native hunter-gatherers in places like the Red river valley in northern Vietnam ~4,000 years ago. The frequency of O2a1-M95 for regions and populations is subdivided very precisely in the above paper, and it is clear that in island Southeast Asia its proportions match those in an earlier paper on autosomal inferences of Austro-Asiatic ancestry. Populations in eastern Indonesia and in the Philippines have minimal numbers of males carrying lineages of O2a1-M95, while the densely populated island land of Java has frequencies of ~50%.

The clincher for why O2a1-M95, and therefore Austro-Asiatic populations, are likely exogenous to India genetically would be the genetic diversity of the lineages. In short, there is tentative information from the variation on the microsatellites that the coalescence of the diverse lineages in Laos are the deepest by a few thousand years. But there was another paper from a few years back which makes my confidence in these results higher, Population Genetic Structure in Indian Austroasiatic speakers: The Role of Landscape Barriers and Sex-specific Admixture, which presented autosomal data which was very persuasive to me. In particular, the derived variation of EDAR which is present in very high frequencies among Northeast Asians and Amerindian populations, is present at about ~5% frequency among Munda groups. Among Dravidian populations in South India according to the 1000 Genomes Browser the frequency is less than 1%, while it is absent among populations in Northwest India, aside from those with clear East Asian admixture.

Next we address the issue of the Dravidian languages. A new paper in Human Genetics, West Eurasian mtDNA lineages in India: an insight into the spread of the Dravidian language and the origins of the caste system, points to an association between particular mtDNA lineages in South India and southern Iran, in particular the region which was once inhabited by the Elamites, who have been posited to have an association with the Dravidian languages. I don’t put particular stock in the philological association between Dravidian langauges today and Elamite; I can’t judge it with any degree of certainty or competency. But the genetic data is certainly suggestive. Here’s the portion which is relevant:

The autochthonous subhaplogroups—HV14a1 and U1a1a4 uniquely found in contemporary Dravidian speakers share their ancestry primarily with the Near East-Iran populations (Derenko et al. 2013). The coalescence times of HV14a1 and U1a1a4 were estimated to be ~10.5–17.9 kya. The shared ancestry of the Dravidian of South India and Iranian of Near East populations has been shown in the HV14 and U1a1 phylogeny (Fig. 1a) and their time estimates are consistent with the proto-Elamo-Dravidian language diffusion. hypothesis which emphasized that the proto-Dravidian language evolved over 15 kya, specifically in western Asia before the beginning of agricultural development ~11 kya. This language was introduced by Neolithic pastoralists, and was thought to be associated with the spread of these west Eurasian-specific mtDNAs to peninsular India (Pagel et al. 2013). The Y-chromosome haplogroup L1a has added a further dimension to this hypothesis. The subclades of haplogroup L such as L1a, L1b, and L1c were found predominantly in Iranian populations of western Asia (Grugni et al. 2012). In India, only the L1a lineage was observed and was largely restricted to the Dravidian-speaking populations of south India (Sahoo et al. 2006; Sengupta et al. 2006). The coalescence time (~9.1 kya) (Sengupta et al. 2006) and the virtual absence in Indo-Aryan speakers in north indicate that the L1a lineage arrived from western Asia during the Neolithic period and perhaps was associated with the spread of the Dravidian language to India

There has long been a presumption to assume that the Dravidian languages are primal to South Asia. But that was before modern genomics revolutionized our understanding of Indian genetic history. More or less all South Asian populations are a fusion between a deeply indigenous strain which distant affinities to the peoples of eastern Eurasia (ASI), and a group very close to the ones typically found in Western Eurasia (ANI). There are no pure indigenes. South Indian tribal populations, who are presumed to be the closest to indigenous groups are at least ~25% ANI, if not more. To presume that the Dravidian languages are indigenous to South Asia one would have to assume that this exogenous element was absorbed by the cultural substrate, something I find implausible on cross-cultural grounds (more dominant South Asian social elites, even ones of pure Dravidian extraction, such as the Reddy group, have higher fractions of ANI). Additionally, Dravidian languages themselves are not particularly variegated, as one might expect if there was deep local structure, as is the case in inland Papua and pre-Columbian America.

Of course the title of this post has to do with males, so with that, let’s look back to a paper which was first posted on the web last year (though finally “published” this March), The phylogenetic and geographic structure of Y-chromosome haplogroup R1a. Here’s the important part:

…Using the 8 R1a lineages, with an average length of 48 SNPs accumulated since the common ancestor, we estimate the splintering of R1a-M417 to have occurred rather recently, ~5800 years ago (95% CI: 4800–6800). The slowest mutation rate estimate would inflate these time estimates by one-third, and the fastest would deflate them by 17%.

With reference to Figure 1, all fully sequenced R1a individuals share SNPs from M420 to M417. Below branch 23 in Figure 5, we see a split between Europeans, defined by Z282 (branch 22), and Asians, defined by Z93 and M746 (branch 19; Z95, which was used in the population survey, would also map to branch 19, but it falls just outside an inclusion boundary for the sequencing data4). Star-like branching near the root of the Asian subtree suggests rapid growth and dispersal. The four subhaplogroups of Z93 (branches 9-M582, 10-M560, 12-Z2125, and 17-M780, L657) constitute a multifurcation unresolved by 10 Mb of sequencing; it is likely that no further resolution of this part of the tree will be possible with current technology. Similarly, the shared European branch has just three SNPs.

The authors emphasize that the TMRCA has a wide confidence interval. I don’t think so. There’s now a fair amount of work on sequencing R1b and R1a lineages which are very common across Eurasia, and one thing is clear: they’re star-shaped phylogenies which are likely reflecting massive population expansions relatively recently (see A recent bottleneck of Y chromosome diversity coincides with a global change in culture). Additionally, they note that the “Asian” (which includes South, Central, Southwest Asia) and the European branches of R1a1a are relatively well separated, and, the greatest diversity of R1a1a can be found in Iran.

I doubt that R1a1a was associated with one ethno-linguistic group at the end of the last Ice Age. It is present at relatively high frequencies in low caste and tribal populations in South India, so I am skeptical of an exclusive association with Indo-Europeans, though in Europe it may actually be that it arrived only with Indo-Europeans. But, the fact that R1a1a is so common all across Eurasia points to a genetic-cultural revolution. Just as Haplogroup O2a1 is almost certainly rooted in populations outside of South Asia before the Holocene, so is the case with R1a1a. They came with groups of men who brought a new dominant lifestyle. From the west came wheat and cattle. From the east, rice.

The latest research suggests about half the ancestry of modern South Asians dates to the Pleistocene. That is, it predates 10,000 BC. The majority of the mtDNA lineages are from this ancestral element. But culturally this group likely had minimal influence. One question which comes to mind is whether the ASI ancestry is from many groups, or, from only a few which were assimilated into an expanding group of agriculturalists. If the former, then one expects that the ASI ancestral segments which exhibit a tendency toward regional structure. I suspect thought that this is not the case, that the genetic landscape of modern India is characterized by overlapping populations which are all hybrids of different regional groups which only recently expanded. The pattern of Munda groups in South Asia, surrounded by Dravidian and Indo-European speaking groups, points one to the possibility that these groups were pioneers of some sort, but eventually lost.

* Language isolates like Kusunda and Nihali may date to the era before the Holocene, but without relatives we can’t really make a good guess. Possible relationships of Kusunda to Andaman or Papuan languages strike me as implausible due to the time depth of separation.

Drakas! (?) Probably not

Drakas_coverEveryone and their mother has heard of the story about the CRISPRed embryos by now. If you haven’t, the original paper is open access. Second, Carl Zimmer’s primer is excellent, Editing Human Embryos: So This Happened. For those who are overly alarmed by the non-ethical aspects, I think this is key:

Just because this experiment came out poorly doesn’t mean that future experiments will. There’s nothing in this study that’s a conceptual deal-breaker for CRISPR. It’s worth recalling the early days of cloning research. Cloned embryos often failed to develop, and animals that were born successfully often ended up with serious health problems. Cloning is much better now, and it’s even getting to be a business in the world of livestock and pets. We still don’t clone people, though–not because we can’t, but because we choose not to. We may need to make the same choice about editing embryos before too long.

Livestock and pets. And plants. I think CRISPR is going to be a big deal. It already is a big deal. But some people are worried now about a profusion of designer babies. We need to get calm here. For something to become a consumer product it needs to get much better in terms of probability of outcomes, and we’re a long long way from that. As Ramez Naam pointed out people are very risk averse with their children.

Rather, the real danger is more one of ethics. Something out of S. M. Stirling’s Draka series where a government or society isn’t bound by normal human ethical standards, and begins to basically treat their population like livestock. As is usually the case the major issues looming are not scientific, but have to do with human volition.

Open Thread, 4/19/2015

41ncnodwApL._SY344_BO1,204,203,200_Beauty can lie all too easily, while oftentimes truth is ugly on first inspection. I’ve been reading Inventing the Individual: The Origins of Western Liberalism, and it is a beautiful book, full of style and erudition, and paragraph after paragraph of mellifluous argumentation. It is far more gossamer than Victor Lieberman’s Strange Parallels, which is weighted down by turgid prose. But where Lieberman’s narrative is dense in unique and distinctive data, Larry Siedentop’s Inventing the Individual circles around the same big facts. Siedentop promotes a bold, if not original, thesis, that the Hebrew-Hellenic synthesis which became Christianity was the seed for the invention of liberal individualism, which reigns ascendant today, at least in name if not reality. Lieberman makes an observation about the parallel development of societies across Eurasia, even in its isolated and far-flung regions in the protected peninsulas and archipelagos of Southeast Asia, and gropes confusedly at overarching explanations. And yet it is the “ugly duckling” of Strange Parallels that is more satisfying than the crisp and elegant theses of Inventing the Individual. The latter is a joy to read, but if you know a fair amount of 61LXo6U7a4L._SY344_BO1,204,203,200_history, and cross-cultural history at that (I do), a lot of it comes off as hot air and naked assertion. It’s a great read, but will only persuade the persuaded, and unfortunately is a little thinner on “dense description” than I would have liked for a work which I knew I was going to look at skeptically (that is, even if you find a work uncongenial on the whole, there are often great gains to be made in extracting nuggets of information).

The ultimate problem that confronts me when entertaining the core contention of Inventing the Individual is sentences such as the following on page 77: “But texts are facts. And the facts remain.” The question is whether they are non-trivial facts, and that is debatable. There is a school of thought that ideas are the drivers of history, and Inventing the Individual takes that position as a premise. If one is wobbly on that premise, the force of the argument falls flat.

Second, do readers have any particular papers/books on domestication that they think are particularly good? My professional research focus is in this area and I need to do a thorough survey of the literature.

Third, I am not an “adaptationist” as Larry Moran has asserted. I’m “dynamic agnostic,” and am wary of null hypotheses of what drives variation in organisms as a whole (i.e., I think neutrality may be more justified for some branches of the tree of life than others).

Fourth, I should mention again that if you are following an RSS feed for my content, is preferred. The reason is that it bundles all my content, and I don’t like to cross-post notifications across blogs. E.g., if I write for The Guardian again or something it will show up in that feed, and I’m liable not to mention it on this blog (though it will show up in Twitter since that pushes the above feed).

An amnesia of historical memory

22522805Amazon believes that e-books are price-elastic. That is, the lower the price, the more units sell. The print list price for Kazuo Ishiguro’s The Buried Giant is $26.95. I noticed it was $5.99 in the Kindle version, so I purchased it on a whim. It’s basically cheaper than lunch. I can say with some confidence that if it was priced at “normal” e-book rates, which are still discounted, I probably wouldn’t have purchased it. I don’t read much fiction, and when I do I tend to shy away from material with too many mainstream plaudits because the mainstream often strikes me as banal in their preoccupations.

I stated last week I probably wouldn’t get to finishing The Buried Giant very soon. I was wrong. It’s a quick read, and I was just on an airplane, so the book is done. Overall I’d say it was worth the money. Ishiguro writes well and evocatively threads through his broader themes, while still allowing the narrative itself to have some drive to it.

The Buried Giant operates in the area between the literary allusive opacity of Gene Wolfe’s The Book of the New Son and the sort of sincere and transparent high fantasy you see in Brandon Sanderson’s The Way of Kings. Because it is notionally set in post-Roman but pre-Anglo-Saxon Britain you might think The Buried Giant exhibits some of the historical fantasy flavor you see in works such as Guy Gavriel Kay’s Sarantine Mosaic (or quasi-scholarship about this period, such as Nikolai Tolstoy’s The Coming of the King). But it does not.

Though the Saxons and the Britons are real people who coexisted in a real time, the world is anachronistic and laced through with fantastical elements. There are dragons and ogres, but also Norsemen and knights. The latter are features of periods centuries after the late 5th century. One aspect that is difficult to not acknowledge in a book about this time period is the foreshadowing of the Saxon conquest of lowland Britain, what became England. But, I do think as a point of historical fact one should note that as late as the early 7th century Celtic British kings such as Cadwallon ap Cadfan were conquering eastern areas of England, with armies reaching the North Sea. Though the Germanization of Britain seems inevitable now, it is possible to imagine a scenario where the late 6th century marked the low point from which Britons reconquered the islands, in a manner that the Christians in Spain reconquered their peninsula. But The Buried Giant operates under the assumption of Saxon inevitability, with the Britons being portrayed faintly as if they are a feckless and complacent people, with more civilized refinement than genuine honor.

68520Finally, one aspect of this book that many readers of traditional fantasy will find disappointing is that its description of the world and the people within it is very understated. Ishiguro exhibits an admirable economy of prose, but at the sacrifice of a rich and deep color of character and landscape. For example, I can not tell you what the main characters looked like aside from the thinnest of generalities (e.g., two characters were aged, one was a strong warrior, etc.). Obviously this makes it difficult to conceptualize them in one’s mind’s eye, but perhaps the point was to identify with the character and their life rather than their embodiment. The fact that concrete aspects of character and landscape were put into the background probably allowed the broader themes to be more clearly obvious.

I can see why mainstream audiences might find The Buried Giant appealing, as it doesn’t push them too far. The fantastical elements are unobtrusive background furniture. But if you want real a real “Dark Age” Arthur, I highly recommend Bernard Cornwell’s Warlord Chronicles.