When “Europeans” almost went extinct

200px-Lascaux2A new article in Horizon, Ice-age Europeans roamed in small bands of fewer than 30, on brink of extinction (via Eurogenes), basically gives away the game in the headline. But please keep in mind my earlier post, as low effective population numbers may not accurately convey the actually census size over long periods of time. These results are not particularly surprising, as the ancient genomes we have from hunter-gatherers tend to indicate a very high level of inbreeding in comparison to modern populations. The main difference here is that it seems that they have more and more ancient genomes sampled from diverse locations to add confidence to the original conjecture:

Prof. Pinhasi’s team has found that the genomes sequenced from hunter-gatherers from Hungary and Switzerland between 14 000 to 7 500 years ago are very close to specimens from Denmark or Sweden from the same period.

These findings suggest that genetic diversity between inhabitants of most of western and central Europe after the ice age was very limited, indicating a major demographic bottleneck triggered by human isolation and extinction during the ice age.

The term “very close” is vague. I’m sure he has some quantitative measure in mind (e.g., identity by descent blocks). It is probably not coincidence that you see the same dynamic among Neandertals. Those from Europe are surprisingly similar to those from the Altai. Why the homogeneity? Probably on the huge broad northern expanse of hominin habitation metapopulation dynamics characterized by extinction and resettlement from survivor lineages was very common. There is circumstantial evidence from wolves that the same happened to them. Why? This might simply be a biogeographic tendency among Palearctic species during the Pleistocene.

Of course I’m going to put European in quotes in the title. Europeans, like modern day Puerto Ricans, are trihybrid. They only emerged in their current form in the past ~5,000 years or so. The north-south gradient of increased heterozygosity in Southern Europe may then be a function not of serial founder effects from the expansion of the Pleistocene refugia, but the higher fraction of hunter-gatherer ancestry in Northern Europeans, who exhibited decrease genetic diversity due to the bottlenecks.

Open Thread, 3/29/2015

downloadA few days ago a reader asked for a basic definition of terms which might allow for easier digestion of some of my posts. An easy answer would be to buy Principles of Population Genetics.* But barring that what are the basic terms that readers think are useful? For example, it seems likely that allele, haplotype, and selective sweep, would be the sort of basic vocabulary that would help in understanding the posts. On the other hand the coalescent less so, since it doesn’t come up explicitly very often.

In other news, I recently purchased Wakely’s Coalescent Theory: An Introduction and Roff’s Modeling Evolution: An Introduction to Numerical Methods. I also am receiving a review copy of Nessa Carey’s Junk DNA: A Journey Through the Dark Matter of the Genome. Mildly skeptical of the title, though titles aren’t often under the author’s control. This seems to have been what happened with Pat Shipman’s The Invaders: How Humans and Their Dogs Drove Neanderthals to Extinction, which is far less about our canine companions than you’d think. * One major issue is that many classic texts don’t include extensive treatment of genomics, which is pretty essential to understanding many of the more science oriented posts here.

The rise of patrilineages

The_Journey_of_Man_-_A_Genetic_OdysseyBeing part of a patrilineage is a big deal today. Ask anyone who is a Cohen, or claims to be a Sayyid, or a descendant of Confucious. Old school cultural anthropologists would assume that these patrilineages are “fictive,” that they exist to bind together disparate elite lineages as a social force. To some extent this is likely true. But not entirely. The complex genetic story of the Cohens highlights that kinship may not always be fictive. In the case of the Sayyids I assume that a lot of this is fictive. When it comes to people in South Asia with the surname Khan there isn’t even a pretense that we descend in any way from a Genghiside lineage. Rather, Khan has gone from being a surname to an honorific.

In my post Patriarchy Came with Cain and Abel I connected a social phenomenon with the drastic crash in Y chromosomal effective population in the mid-Holocene, as reported in the new paper in Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Unfortunately some of the press related to paper seems rather misleading. For example, “8,000 Years Ago, Only One Man Had Children for Every 17 Women” (here’s another take). Aside from the fact that the effective population crash only is true for a subset of lineages, like Greg Cochran I’m skeptical of the image of a winner-take-all reproductive mating market. Specifically, I don’t think there was a given generation where only ~5% of men in a given population had offspring, while the others did not. Rather, I assume that cumulative reproductive skew probably had the impact of socially privileging men from particular patrilineages, so that Y chromosomal haplotypes “swept” through the population over the course of many generations.

k10181My basic idea dovetails with Greg Clark’s in The Son Also Rises. Clark’s economic historical data sets suggests that over the long term elite lineages are surprisingly insulated from decay in status. Though there is a great deal of inter-generational churn, over the long haul there is a strong trend line of elite lineages remaining elite, and non-elite ones remaining non-elite. This may be due to cultural or genetic forces; Clark is ultimately agnostic on that. But, it suggests that social status is highly heritable. Was it always so? I suspect that these sorts of dynamics only date to the Holocene, with the rise of complex societies, and social status being connected to accumulation of material objects and power which can be passed from father to son. Additionally, with complex societies there emerged group level competitive games which were winner-take-all, as patrilineages faced off against each other with the ultimate outcome being final victory or defeat.

Ultimate this is very different from the image we have of a literal “harem society” that might emerge in small scale societies with such reproductive skew. Rather, it’s a more subtle and gradual rich-get-richer dynamic, where status and privilege compound over the generations in a genetic sense.

Addendum: Both Greg Cochran and the Genome Research paper point out that effective population does not seem to have crashed concomitantly on the autosome, as you’d expect. One minor point I’d add is that admixture can inflate population size inferences, since it elevates diversity. Most of the Holocene populations seem to have been subject to admixture, so autosomal effective population may have been artificially inflated.

Much ado about inclusive fitness

51Ht9P0jm3L._SY344_BO1,204,203,200_A few years ago there was a huge stir caused by the publication in Nature of a somewhat mathematically abstruse paper, The Evolution of Eusociality. It was huge enough that it got a treatment in The New Yorker, Kin in Kind. Many of the reactions were basically tribal. Most geneticists were rather upset with the publication of this paper for a variety of reasons, both substantive and stylistic. In contrast, I’ve engaged in conversations with ecologists who assume that the authors of this paper basically proved that old-fashioned inclusive fitness theory, as first outlined by W. D. Hamilton in the 1960s, had been shown to be superfluous and irrelevant.

A major point by one of the authors of the original paper, Corina Tarnita, is that their detractors didn’t really engage with the model that they laboriously outlined. Well, until now. A new paper in PLOS BIOLOGY takes the model from the 2010 paper, and argues that it isn’t really all that robust, and therefore does not really speak to whether inclusive fitness is useful at all in comparison. The paper is Relatedness, Conflict, and the Evolution of Eusociality. Nicely it provides a lot of code to go along with the assertions, so I invite readers to dig into it, and the original Nature paper from 2010. And while you’re at it, W. D. Hamilton’s first volume of collected papers which addresses his work in social evolution, Narrow Roads of Gene Land, is highly recommended.

If I had to bet I would say that inclusive fitness is very important across many branches of the tree of life. But, I’d also suggest that among organisms with particular complex and elaborated social structures (e.g., humans) there is probably a lot more going on. Multi-level selection theory does have something useful to add. It’s just that this is evolutionary, not revolutionary, science.

Cuius regio, eius religio, in Anglo-Saxon England

51IQSePVDRL._SY344_BO1,204,203,200_One thousand and five hundred years ago innumerable Germans, Saxons, Angles and Jutes, came to the shores of Britain, and transformed it into England. One thousand and five hundred years ago the trunk of the English language was grafted upon a fundamentally British ethnic root. Post-Roman Britain was subject to a massive migration of Germans in the 6th century, and, the majority of the ancestry of the people of the British Isles derives from the period before the Anglo-Saxon migrations. Both these facts are implied by recent paper, The fine scale genetic structure of the British population (the link should work for those without academic access, though the supplement is probably really what you should read!). This paper is close to  the final answer as to the question of whether Gildas was right, that the British* were driven into the sea by hordes of German barbarians, or, whether post-World War II historians were right, that change occurred through cultural emulation from elites on high. Gildas’ model of ethnic replacement was formulated in the context of his being a British cleric who was admonishing his flock, for they had clearly angered God to lose so much ground to the pagan Germans, who were on the march in the 6th century. In contrast, over the past few decades the thesis that the change in language and ethnic identity in Britain, what became England, must have occurred predominantly through cultural diffusion of Anglo-Saxon norms has been the mainstream position. In Norman Davies’ book The Isles he wrote that the ancestor of English was of “pure Germanic character,” but also observes that “Modern genetic research is showing quite convincingly that the Germanic invasions, like the Celtic invasions before them, were insufficient to transform the existing gene pool to any major degree.” Written in the year 2000 Davies is on strong ground when it comes to the genetics, at least for what he had on hand. But 15 years is a long time in science, and the post-genomic era has blossomed in the intervening period.

nature14230-f1In the figure to the right you see an illustration of the genetic clusters inferred from the new Nature paper extant across modern England. They utilized the fineSTRUCTURE to extract these components. If you want to understand the guts of the method of the paper, I recommend Inference of Population Structure using Dense Haplotype Data by Lawson et al. As repeatedly emphasized within the paper the population genetic structure across the British Isles is very subtle. Another way to say this is that the British Isles is very homogeneous genetically. This is true to some extent of Northern Europe as a whole. When looking at Fst values across very distinct European populations they are quite modest. For example, the value comparing North-Wales and Kent samples is 0.002. That means 0.2% of the genetic variation in a pooled sample of North Welsh and Kentish individuals is partitioned across the populations. In contrast, a European population compared to the Han Chinese will give an Fst value of ~0.10, so that 10% of the genetic variation in a pooled sample is partitioned across the populations. With such small genetic distances it is difficult to tease apart historically informative structure with conventional methods, such as PCA and ADMIXTURE, which rely on genotypes. In contrast, fineSTRUCTURE leverages more information by looking at haplotypes, which encapsulates not just genotypes which vary across populations, but the structure across genotypes in individuals. This gives one a crisper snapshot of more recent patterns of relatedness.

But even with this method you can see that a vast swath of England proper can not be broken apart into local regions with great confidence. That suggests that there’s just little regional genetic structure to be found. The authors argue that this pattern is indicative of the fact that this was the core zone of Roman dominance, and later, of the commonwealth of Anglo-Saxon kingdoms (the Heptarchy). As such it was unified culturally and economically in a manner which likely facilitated gene flow, which prevents the divergence across populations which allow one to infer population history more easily. To make matters worse, the genetic distance between source populations on the Saxon Shore, assorted Germanic groups, and culturally Brythonic groups**, is very low. Around the year 2000 I was curious about the peopling of Iceland, and at that stage the genetics was not very robust when it came to giving definitive answers as to the contribution of Irish and Scandinavian people, because the two groups are genetically very similar unless you use genome-wide methods.

This brings up a very curious angle on the paper: because it took so long to bring into press its background framing is already a touch anachronistic. Last month Nature also published Massive migration from the steppe was a source for Indo-European languages in Europe. And it is this paper which suggests why Northern Europeans are genetically homogeneous: there was massive demographic disruption in the late Neolithic and early Bronze Age. Contrary to Norman Davies asserts above it is quite possible that massive demographic changes ensued with the arrival of the Celtic languages. And, the people who were replaced or marginalized were not the descendants of the Mesolithic hunter-gatherers fleeing Doggerland, but what David Reich’s lab would term “Early European Farmers” (EEF), a compound of populations from West Asia bearing agriculture and a group of Mediterranean hunter-gatherers.

Ioan Gruffudd

Ioan Gruffudd

Within the supplements the authors mention that there is a curious enrichment of Spanish-like ancestry in Northern Wales. They state that “while our data supports some low level of ancestry from southern France/Spain in ancient British populations it is hard to reconcile with major contributions to modern British ancestry from these regions.” While the dominant cluster in England is ~1 percent Spanish-like, in certain Welsh groups it groups it goes above 5 percent. Though the paper is good in other areas to clarify that their clusters are not “real”, but reifications, that is, abstract mappings upon real genetic variation which is distilled and concentrated in a human digestible form, it gets muddled here. There is a good amount of ancient DNA to suggest that the first farmers across much of Northern Europe genetically resembled modern Southern Europeans, due to the demographic migration and expansion of farmers from those regions. Later, a second wave of migrants from the east, possibly Indo-Europeans, replaced and assimilated a great deal of this component, introducing the exotic “Ancestral North Eurasian” (ANE), as well as reintroducing higher fractions of hunter-gatherer ancestry. The elevation of the Spanish-like cluster in western Britain may be a function of the fact that the Indo-European newcomers had less of an impact in those regions.

How does this dovetail with the idea that the original hunter-gatherers of Europe had a modest impact on the modern genetics of this region? One has to go back to the start of the Holocene. A conventional framework dating back decades is that after the last Ice Age Europe was repopulated by a single group of hunter-gatherers who had retreated to “refugia” in the south. This group, expanding rapidly across an empty landscape, had gone through long periods of low effective population, and was genetically homogeneous. Before the arrival of the farmers from the ancient Middle East then the whole of Europe from Spain to the Urals, fading into Siberia, may have been inhabited by a people who exploded out of their Mediterranean fastness. This explains the extremely high representation of Y chromosomal haplogroup I and mtDNA haplogroup U5 in ancient hunter-gatherer remains across the continent. The arrival of intrusive farmers on the southern and eastern edge of the continent from West Asia resulted in a synthetic population, where the farmers amalgamated with a group of European hunter-gatherers, to produce the “Early European Farmers,” EEF. Expanding massively across Europe this group brought both West Asian and hunter-gatherer ancestry across the continent. Later the proto-Indo-European group was formed via amalgamation between disparate elements, and including the far eastern branch of European hunter-gatherers.

With that model in mind, what this paper using the PoBI data set has done is map out the pattern of variation as generated predominantly by the EEF and Indo-Europeans, as well as a later contribution of Germanic people, who themselves are compounds of EEF and Indo-Europeans! But it seems to frame the results in the context of the older model, whereby there is a much larger role for cultural change from hunter-gatherer to agriculturalist, and modern Northern Europeans are the descendants of hunter-gatherers who were long resident in their present locales. Using that lens the people of North Wales are depicted as the most pure descendants of the first hunter-gatherers to arrive in Britain, rather than the group with the greatest affinity to EEF.

This is a minor matter, but, it highlights the fact that this paper took a long time to come to press. It was rather notorious in fact within the human population genetic community for how tardy it was. Joe Pickrell points out to me that the PoBI paper in Nature was submitted in November of 2013, while the Indo-European migration paper was published one month earlier, but submitted in December of 2014. The Lazaridis et al. preprint which has reshaped much of the current thinking on the peopling of Europe during the Holocene was put on biorXiv in December of 2013.

downloadBut the biggest headline finding of this paper, that 10 to 40 percent of the ancestry of the English who are distributed across the expanse of southern and central England, have ancestry derived from German barbarians who arrived in the 6th century, is not much affected by this strange lacunae due to the vicissitudes of publication which I cover above. Reading through the supplements I am moderately confident that this value will stick. The issue that the source populations here are rather close genetically pops up even with the methods and data they have at hand, but it seems likely that they’re converging on the correct value. It would explain why older less powerful methods gave conflicting results.

It also illustrates two facts. First, the English are genetically more like their neighbors of the “Celtic Fringe” than they are like the Germans over the ocean.  Second, the English nevertheless have a substantial dollop of ancestry which indicates a genuine folk wandering occurred of massive proportions (at least by pre-modern standards) across the North Sea after the fall of Rome. The results are in perfect alignment with Peter Heather’s argument in Empires and Barbarians, where he suggests that German tribes who burst into the interior of the Roman world in the last centuries of the Empire, and then took over huge areas after the fall of the Western Empire, were coherent national-tribal entities. This is in contrast to the thesis that they were ad hoc social constructions of motley mercenaries of small numbers, invented de novo in the wake of the emergent post-Roman order. Heather never argues for a predominant replacement of indigenous populations anywhere, rather, he makes the case that many of these migrations were substantial, including women and children, and can be understood in nationalistic terms.

Though the modern English are not predominantly German, ancestry fractions on the order of 10 to 40 percent indicate considerably heft to the migration. And, it serves to explain to us I think why the archaeology and cultural history indicate a rupture of massive proportions, reflecting in fact the apocalyptic tones of Gildas, rather than the more sanguine theses propounded by the doyens of the study of Late Antiquity and the evolution of the Roman world into the medieval one. Gildas was a highborn man, and this holds the clue to why and how east and south Britain became England. The whole of the post-Roman Brythonic elite of these regions was defenestrated in a manner reminiscent of the flight of the earls, except more significant by orders of magnitude. In contrast in what became Francia the German newcomers did not totally marginalize the Roman elite, who retained influence in the Church, and, temporal power across the domains of the lenga d’òc. The Frankish elite in Neustria quickly became Romanized. Why did the German leaders in Britain not accept the norms of the Romanized Brythonic elites?

514QTAjUcSL._SY344_BO1,204,203,200_The ultimate causes can be chalked up to historical contingency. But the large genetic contribution suggests that the German nobility could recreate a Saxony-over-the-Sea in toto. The archaeological evidence seems to be that the agricultural system of post-Roman Britain was radically transformed, indicating wholesale transfer of skills and communities across the North Sea. But for me the key issue is that the Christian Church collapsed in eastern and southern Britain, only to reappear around the year 600 under both Brythonic and Continental missions. Despite the influence of the Celtic Church in the early decades, English Christianity was not an organic outgrowth of a religion which was submerged in the intervening century. Rather, it was a fresh planting of what had died. I have made an analogy before of what happened to Christianity in Britain to what happened to Christianity in the Balkans. While a regression occurred in post-Roman Gaul, what became Francia, it pales in comparison to the cultural devolution and atavism in Britain, what became Francia, and the Latin-speaking world of the Balkans.*** It is fashionable in some quarters to declare that the Christian Church saved European civilization after the collapse of Rome, that the Church was the ghost of Rome. There is some truth in this, but, the example of Britain and the Balkans suggests to me that institutional and formal religion of the sort which we see in Christianity necessarily needs a minimal level of social and economic complexity, and concomitant “buy in” from the elites.

Gildas seems to have been wrong, or, frankly simply lying as to the facts, when it comes to the British folk as a whole across what became England. They were still there, centuries after Gildas flourished. The Law of Ina indicate this clearly. But, they were not the great and powerful, the heirs of Gildas’ hero, Ambrosius Aurelianus. The substantial genetic impact of the Germans probably did not occur simply through a few generations of replacement. Rather, the majority local population may have been marginalized to such an extent that they did not replace themselves, and the German gentry may have experienced downward mobility in Malthusian conditions. The land that they expanded into was not empty, but, without  the complex institutional supports of the Roman system, which was maintained in degraded form by the Brythonic warlords, many fled or diminished. The same could be said about the Balkans, where the Roman system collapsed with the predations of the Huns in the early 5th century. As outlined in the well known paper The Geography of Recent Ancestry Across Europe, the Slavs did have a major impact across Eastern Europe across this period, as their culture replaced what had been there before. But in the Balkans these Slavs seem to have absorbed a considerable number of the local population if genetics is a guide, those which were previously Latin or Illyrian in ethnicity and identity. Just as in Britain the Christian religion disappeared, to appear only in later centuries due to missionary activities.

51YT6NJ34DL._SY344_BO1,204,203,200_

If Gildas was talking only of the Brythonic elites, his language may in fact not have been much of an exaggeration. The collapse of the Christian religion in post-Brythonic Britain-becoming-England also highlights to us the difference between modern mass culture, and that of the ancient and medieval world. The Roman Empire was nominally Christianized by the 5th century. Though there were elite holdouts among the high aristocracy and philosophers, they were a waning force. The Roman identity transitioned to a Christian identity. To be roman was to be a Christian. To be a barbarian was to be a heathen (or, heretic in the case of Arians). The populace as a whole became Christian, because they followed the cultural identity of the elites. But, it can be argued that until the Reformation period the peasantry of Europe to a great extent were de facto pagans. Mass religious identity only took root with the spread of literacy, and confessional competition induced by the emergence of Catholic-Protestant divisions. The principle of cuius regio, eius religio, allowed for the solidification of confessional-national boundaries under the leadership of ruling elites in the 16th century. But a century later the conversion of the House of Hohenzollern to Calvinism from Lutheranism would not result a change in the dominant religion of their subjects. In England the Catholicism of the Duke of York rendered him unfit to rule in the eyes of his subjects, who welcomes the Protestant William and Mary (note, here “subjects” probably really means the nobility and gentry). In the 18th century the previously Protestant Electors of Saxony converted to Catholicism. And yet their domains remained almost wholly Lutheran.

The British peasants who lived under the rule of German elites in 6th century England were likely often descended from nominally Christian ancestors. But Christianity during that period was a religion of the mighty, at least in its full liturgical grandness. That was the legacy of Constantine. Marriage was solemnized in the Church for elites, not the peasants. Though the peasantry no doubt had a vague Christian identity, their understanding of the details of the faith were modest at best (we know this because there were debates by Churchmen whether ignorant conversions were true conversions). There was often a baptize-first and inculcate later policy, as indicated by continued persistence of folk pagan practices across Christian Europe among the peasantry which had to be suppressed by the Church. The removal of an elite which would patronize the Church resulted in its withering, and the reversion of the peasantry which remained to a pagan identity. Consider what happened to the Secret Christians of Japan, who were more obviously zealous than Late Roman peasants likely were, but nevertheless could only maintain a syncretized religious identity.

These results show that a minority, but dominant, population can nevertheless culturally replace a majority in an inferior position. Many of the aspects of a given culture, such as institutional religion and confessional identity, are predicated on particular economic and social preconditions, which once removed result in very rapid change. Additionally, the fact that modern English has little Brythonic Celtic or Latin**** influence from this period (the Latin influence came with the Normans) indicates that upward and horizontal assimilation could exhibit only marginal reciprocity. The majority fraction of non-German ancestry in southern and eastern England could also be a function of later gene flow, equilibrating across the broader English realm.

The caricatures of extreme genetic and culturalist positions in this case misled us, and only resulted in confusion. A true understanding of the dynamics of post-Roman cultural change must take into account the results from genetics, which are the best demographic data we have in light of the collapse of the tax collecting apparatus of the Late Roman state.

* When I say British here I mean the Brythonic speaking Celtic and post-Celtic people who inhabited the British Isles before the arrival of Germans.

** I am being vague here because there is not great clarity whether the people of Roman Britain were Latinized by this time, though they retained some sort of distinctive identity clearly since they reemerged in other parts of Britain as a post-tribal Celtic people.

*** Latin, not Greek, was the dominant language of the hinterlands beyond the coast across the Balkans during the period of the later Roman Empire. The existence of Romanians and Vlachs is a testament to this.

**** A nod to those who argue that the post-Roman British world was one where the peasantry spoke vulgar Latin, as was the case in Gaul.

The once and future genomics of sexual selection

250px-PaonroueEvolutionary biology predates genetics. This is well known. One of the major problems with Charles Darwin’s original theory is that its lack of a plausible mechanism of inheritance meant that it was difficult for him to conceive of how heritable variation could be maintained over the generations. A “blending” model, where the offspring are a synthesis of the trait values of the parent, is intuitively appealing, but also implies that all the variation is going to be “mixed away” very quickly. In contrast, a Mendelian genetic framework, where traits are encoded by discrete and particulate units of inheritance, “genes,” illustrates simply how variation can be maintained despite mixing between lineages in sexual organisms. In short, each generation is simply a reconfiguration of the discrete elements of variation of the previous generation (see: Mendel’s laws).

255217Eventually R. A. Fisher fused what had been rival traditions, the Darwinian/biometrical and Mendelian genetical, into a single framework in his The Correlation between Relatives on the Supposition of Mendelian Inheritance. This was further extended in The Genetical Theory of Natural Selection, and elaborated in more detail by the broader coterie of population geneticists in the early to middle decades of the 20th century.

The fusion of genetics with evolutionary biology allowed for a deeper investigation of the dynamics of evolutionary process. This is because of the fact that genes are concrete and definable units of evolutionary bookkeeping. Though there are models of evolutionary processes which do not rely explicitly on genes, when possible genetic models are optimal. The broader population genetic worldview conceives of evolution as change in allele frequencies over time, and as such made evolution measurable in a very concrete sense via genetic methodologies. The emergence of molecular methodologies in the 1960s, and genomics in the 2000s, has resulted in progressively more power to understand how evolutionary change affects the distribution of genetic variation amongst organisms. With genome-wide analyses now available researchers can ascertain the power of selection (positive, negative, background, and balancing) within natural populations.

But one area of evolutionary biology that has been relatively untouched by the genomics revolution is that of the study of sexual selection. This is a major gap, because sexual selection is an intuitively appealing idea which often serves as a deus ex machina when you have no other explanation on hand. So it was of interesting to me to see this review paper, The locus of sexual selection: moving sexual selection studies into the post-genomics era. There are several major issues with genomics and sexual selection which are highlighted in this review. First, it seems that many sexually dimorphic traits which are being driven by sexual selection vary due to differences in gene expression across the sexes, possibly due to modifications on regulatory elements or alternative splicing. Simple sequence level analyses then may not be good at capturing these sorts of dynamics. Second, sexual selection can leave different signatures because in some cases there are antagonistic pressures between the two sexes. Additionally, sexual selection is often frequency dependent, rather than a simple positive sweep toward fixation (as noted in the paper, a simple sweep would result in exhaustion of variation, meaning sexual selection is a very ephemeral phenomenon). Additionally, there is extensive discussion of the utilization of GWAS to discover loci associated with mating fitness. Much of this work has already been done in Drosophila.

Which brings me to the point that from reading this review I have a hard time believing that sexual selection is a strong force for humans for most of history. The reason being that our reproductive skew is just not that high in comparison to the experimental models cited within the paper. But it seems to me that a better understanding of the relationship between sequence level and regulatory variations in humans could get at this question indirectly. Presumably if sexual selection was copious then there’d be more extant regulatory variation, perhaps maintained by balancing selection.

Citation: Wilkinson, Gerald S., et al. “The locus of sexual selection: moving sexual selection studies into the post‐genomics era.” Journal of Evolutionary Biology (2015).

I, Razib Khan

razibKhanNYTimesOpEdDue to the late unpleasantness certain images of me are floating around the web. To the left is a photo that people can use if they so choose in the future. Just click the link and a much bigger file will pop up. I am not anticipating that this will be needed, but you never known.

Soylent 1.4

2015-03-22 22.55.17So about six months ago or so I ordered Soylent. Specifically, Soylent 1.4. My interest in Soylent is due to the fact that I’m a very busy person plotting the subversion of America’s progressive liberal democratic order, and everyone knows that Peter Thiel and the Illuminati are behind Soylent. More seriously, I’m thinking of replacing lunch with Soylent.

The new version has no oil packets. It took literally 1 minute to make the concoction. Tasting it with a few friends I have to say that it’s not half bad, better than many protein shakes I’ve had. Version 1.4 is very slightly sweet, with some salty aftertaste. It is a bit reminiscent of pancake batter according to one of my friends. I’d recommend it.

The Etruscan origins mystery and genetics

51g09iHP59L._SY344_BO1,204,203,200_Since 2006 genetics has gotten very deeply involved in the origins of the Etruscans, a non-Indo-European group in ancient Italy often termed “mysterious” for a reason. The two dominant models of their origins in antiquity, and the present, involve a Near Eastern influence, or a totally indigenous one. Since genetics originally came down on the side of at least a partial Near Eastern origin in 2006 the argument has gone back and forth. A new paper in PLOS ONE seems to lend some tentative support for an external influence, Mitogenomes from The 1000 Genome Project Reveal New Near Eastern Features in Present-Day Tuscans. Because the mitochondrial genome has been widely sampled geographically the authors managed to compare the lineages of Tuscans to many other populations, and it turns out that a small minority are surprisingly clustered with populations in the South Caucasus. They really couldn’t put a good time peg on the result, but it strikes me that the peculiarity of this association in Tuscany in particular suggests that this region was influenced by a specific Near Eastern group which did not settle the rest of Italy, which was mostly inhabited by various Indo-European groups at that point. In Spain the possible non-Indo-European group, the Iberian languages, are mostly in the south with the exception of that of the Basques. The possibility of ancient Sardinian as non-Indo-European also makes sense in light of that island’s isolation.

From the most recent work on the genetics of likely Indo-European groups it seems possible that arrival of these people to Southern Europe probably occurred on the order of 3 to 4 thousand years ago. The persistence of a non-Indo-European substrate in Tuscany, as opposed to other regions of mainland Italy, seems rather strange if that timing is correctly. I think the ultimate answers are going to be found with IBD autosomal segment analyses with large sample sizes and regional coverage.

Open Thread, 3/22/2015

Well, “busy” week.

First, thanks to all the people who have reached out to me. It’s appreciated. There are many of you.

Second, I have to note that some of my most liberal friends seem the most angry in personal correspondence. I believe it is probably a function of the fact that conservatives simply expect these sorts of things to happen. So they weren’t surprised. Since my friends know what type of person I am of course they took offense at the aspersions made by some.

Third, I’ve written ~4 million words over 13 years (excluding comments). I never thought I would be as prominent as I am now, so even were I to be the type who would dissimulate, it did not seem relevant. Trying to get the best handle of truth is important to me. That mean’s I’ve stepped on some toes, violated taboos, and such. I don’t believe in an afterlife, and neither do I seek the accolades of the masses. If I offend because I think I’m asking questions that need to be asked, then I’m going to offend. Naturally in all the ~4 million words and many years of writing I can’t and won’t stand by the substance or style of everything I’ve written, but the totality is something that I’m mildly proud of (if you read things that you wrote/thought 10 years ago I suspect many of you would wince as well). We all grow old and die. We’ll ask ourselves what the point of it all was in the solitude of the precipice of mortality. The point? Not to seem smart. To become smart. The latter is hard and humbling.

Fourth, I would not trade the joys of my life for those of my detractors. I understand that they believe that they destroy evil in the service of good. But sometimes beliefs are false, and have horrible consequences. Often what goes around comes around.

Finally, I have a whole life that does not involve this blog or my “public intellectual” persona. Some readers forget this and make all sorts of assumptions about my life which are not warranted (since I’ve started to become a bit more open over the past few years this is less common than it used to be). But the reality is that what happened this week hasn’t really impacted that dimension of “real life” at all. I went lifting and bought some khakis today at a shopping mall (I don’t go to malls very often, and it’s interesting what a diverse array of America you can see there mushed together!). I graded exams. I replied to emails. It was a good day.

I don’t listen to “bro country” often, but when I do it’s Brantley Gilbert

k10386After the events of today I’m going to curl up with Xunzi: The Complete Text. That’s just how I roll. Most of my friends are more outraged than I am. I don’t know why. It just is that way. It is heartening that people care about me, and I appreciate it. But there’s not much more to say than has been said, and perhaps even less. Things happen. If today I was a dying man and I would tell you that I was the child with a book in hand, not the proud one demanding that my views be heard because of the stridency of my voice. My views aren’t important, the truth as best as I can understand it is important. My friends know who I am, and that is all that matters to me. I regret the day that I am the story. That’s besides the point, and uninteresting to boot.

Yes, I just juxtaposed Brantley Gilbert with Xunzi. Nowhere else….

Open Thread, 3/15/2015

pkMost of you may guess that I’m not big into human interest stories (though I do follow celebrity gossip cursorily). But over the last week I’ve become moderately interested in the death of Paul Kalanithi. A little over a year ago his piece How Long Have I Got Left? was brought to my attention. The issue that he was confronting was that he was suffering from terminal lung cancer. It was particularly of note because Kalanithi was a neurosurgeon who was just ascending up the peak of his professional powers. Now, he was confronting disease and illness from the perspective of a patient, and it was making him reconsider some of the norms of medical practice. Despite his deteriorating health Kalanithi kept writing and speaking out in the media. His last piece, Before You Go, was written not too much before his death, on March 9th of 2015.

His story attracted my interest again because despite his terminal condition he and his wife decided to proceed with starting a family. On July 4th of 2014 his daughter Cady was born. He concluded his last piece of written work:

…There is perhaps only one thing to say to this infant [his daughter, Cady], who is all future, overlapping briefly with me, whose life, barring the improbable, is all but past.

That message is simple: When you come to one of the many moments in life when you must give an account of yourself, provide a ledger of what you have been, and done, and meant to the world, do not, I pray, discount that you filled a dying man’s days with a sated joy, a joy unknown to me in all my prior years, a joy that does not hunger for more and more, but rests, satisfied. In this time, right now, that is an enormous thing.

A minute after my daughter was born she opened her eyes, and looked straight at me. And at that moment I slipped beyond the event horizon.

Second, does anyone know a good book about the “Age of Discovery”? I can’t think of one off the top of my head.

Selection in Europeans, but it still sweeps!

selectGroup

David Reich’s lab has a new preprint out, Eight thousand years of natural selection in Europe, which serves as a complement to Massive migration from the steppe is a source for Indo-European languages in Europe. Where the previous work has focused on the relationships of ancient and modern populations, this research puts the spotlight on patterns of natural selection which have shaped ancient and modern populations. The method utilizes the explicit model which is supported by the previous work, that Europeans are best approximated as a model of a three population admixture of a group represented by the hunter-gatherers of Western Europe, the first farmers which brought agriculture to Europe, and the peoples of Central Eurasia which likely brought the Indo-European languages to Europe. In the parlance of this group WHG, EFF, and Yamnaya. Basically they have allele frequencies of these ancestral groups, thanks to ancient DNA techniques, and the frequencies in modern populations. By comparing the frequencies one can then infer if the deviations from expectation are large enough to satisfy the conditions you’d expect for a locus subject to a selective sweep of some sort.

lctFirst, it is very obvious that lactase persistence in Europe has been under strong selection over the past 4,000 years. Even in the Bronze Age Central European samples did not exhibit frequencies of the derived variant common across Western and South-Central Eurasia on the LCT locus which is associated with persistence today. A quick survey of the 1000 Genomes data shows that this variant has wide variation in modern European populations which are phylogenetically close. The frequency in the Spanish data set is ~50 percent, but in the Tuscan Italian samples is ~10 percent, for the derived variant. In Denmark and Sweden the derived allele frequency goes up to ~75 percent (the phenotypic expression is dominant, so that means ~95 percent lactase persistence), though in the Finnish sample it is closer to the frequency of the Spanish data set. In South Asia the 1000 Genomes data as well as earlier work shows that frequencies are 25 percent or more in Northwest India, in the Punjab, where dairy culture is most pervasive. It drops as a function of distance from this zone, to 5 percent in the Southern and Eastern South Asia. The haplotype network around this particular mutation implies that it probably originated in Central Eurasia, so the varied frequencies across the Old World is suggestive of both migration and selection.  Intriguingly, the lactase persistence allele is not present in the Yamnaya, but begins to appear in cultures such as the Corded War, though at far lower frequencies than is presently the case in this region.

But the story of lactase persistence is not entirely surprising. It’s late evolutionary trajectory in relation to the rise of cattle culture and complex societies in Eurasia points to the reality that evolutionary change in the biological dimension requires a powerful cultural scaffold. That existed in the form of agro-pastoralism in Eurasia. Similar forces are at play across regions of Africa, where signatures of selection are even more evident in groups dependent upon cattle, likely because of the recency of the emergence of the trait, caught in mid-sweep.

A new face in the world?

A new face in the world?

There are few other signatures evident in these data. Three of them have to do with pigmentation, SLC24A5, SLC45A2, and HERC2. Ewen Callaway reported on the peculiarity last year that Paleolithic European hunter-gatherers may have had dark skin and light eyes. The reasoning here is that a large fraction of the complexion difference between Europeans and Africans is attributable to a derived mutation on SLC24A5, which is nearly fixed in modern Europeans. And yet ancient European hunter-gatherers on the whole were not fixed at this locus, and Western European hunter-gatherers, exhibited the ancestral variants. To get a sense of how peculiar this is the vast majority of the alleles in much of the Middle East are in the derived state, as are about half the alleles in South Asia (I am a homozygote for the derived allele for what it’s worth, and my skin is still notably brown, though obviously not extremely dark). The best available data suggests that the mutant allele emerged recently in the Middle East SLC45A2 is different in that its distribution is far more constrained to within Europe, though it is found at appreciable frequencies in the Middle East, and at lower frequencies in South Asia. The same for HERC2, though I was surprised to see that the “European” variant associated with blue eye color is actually found at a 0.10 proportion in the 1000 Genomes data in Bangladesh (I am a homozygote for the ancestral variant), the same fraction as the Punjabi sample.*

The results here seem to suggest that all these loci are under selection. The two SLC genes are under positive selection, though SLC24A5 probably got its first boost from EFF with the arrival of agriculture, and was subsequently fixed even when that group fused with the hunter-gatherers who lacked it. Curiously HERC2 is under some negative selection. Remember that all the hunter-gatherers seem to carry the derived variant, so the frequency could only but go down. But in Southern Europe it is likely being driven down in frequency, while it Northern Europe it has been maintained, or rebounded.

Of course one of the major issues we have when evaluating pigmentation loci and their relationship to selection is it’s not always clear if the target of selection is the trait of pigmentation, or something else which the locus modulates, and pigmentation happens to be a salient side effect. There are many theories about why populations have become depigmented, but none of them are truly well supported in my opinion. Another question is whether we know the genetic architecture of pigmentation well enough to actually infer that these ancient populations are easily predicted by modern models which map genotype to phenotype. In other words, were Paleolithic Europeans light skinned because of different alleles? The genetic architecture of skin color is relatively well understood in extant populations. Though it is possible, it so happens that modern Northern Europeans, and to a lesser extent Southern Europeans, harbor a substantial portion of European ancestry which is rooted in the Paleolithic. Studies in admixed African American populations, which are about ~20 percent European, indicate that the primary variants which determine complexion are the ones extant in modern populations, though it may be that there isn’t power to detect the ones from WHG, etc. Of course it could be that the lightening alleles of the Paleolithic Europeans were subject to negative selection, excepting the HERC2/OCA2 locus. But that’s not a particularly parsimonious solution.

A secondary issue in relation to pigmentation is that the Yamnaya population does not seem to have been particular fair of hair or azure of eye. The frequency of the derived HERC2 SNP is in the range of North Indian populations, while the SLC45A2 SNP is in the same frequency range as Middle Eastern groups. One might suggest that the Yamnaya are not representative of the population which was intrusive to Europe, but note that the frequency during the Late Neolithic and Bronze Age are intermediate between it and modern groups. These results imply in situ evolution within Europe over the Holocene, and down into historical times, toward the phenotype which we ascribe uniquely to Europeans. This is strange especially in light of the fact that a later eastern branch of Indo-Europeans seem to have been quite light. I don’t think we can make final inferences, but to me it is starting to look like the “Proto-Indo-European” complex of peoples was highly cosmopolitan and heterogeneous. Should we expect anything other? As the Mongols expanded in all directions their divergent tendrils were embedded in different ethnic substrate (e.g., Tatars, Khitai and Jurchen in China, Kipchak Turks in Russia, etc.).

The other major locus that showed up was one related to fatty acid metabolism, FADS1. Many tests for selection in humans and domestic animals show changes in the ability to process nutritive inputs. It seems an eminently plausible candidate phenotype to target for selection. Using polygenic score methods they also find that there was selection for shorter stature in early Neolithic populations in places like Spain. I think in the future one area of investigation is going to be in the domain of biological adaptations on the margin of farming populations which are put into a Malthusian pressure cooker. Humans, on average, were getting smaller until recently in comparison to their average stature during the Last Glacial Maximum. The Yamnaya people, in contrast to the Neolithic Iberians, seem to have been rather tall. Perhaps it had something to do with the nature of agro-pastoralism? (though do note that without lactase persistence they’d miss out on about 1/3 of the calories in the form of lactose sugar, though not the protein and fat)

edarmotalaBut there’s a twist which I haven’t gotten to, and that’s the one in regards to the hunter-gatherers from the Scandinavian region. Unlike the WHG samples you can see that they exhibit mixed frequencies of derived and ancestral alleles at the SLC loci. That’s peculiar, since geographically they are more distant from the core region from which EFF issued. We do know that their ancestry is somewhat exotic, as paper on Indo-European migrations pointed out that they seem to carry the same ancestral component which the Indo-Europeans brought to most of Europe, that of the Ancestral North Eurasians (albeit at far lower fractions than the EHG group which was a partial precursor of the Yamnaya population). The past is complex and doesn’t fit into a solid narrative. And yet the weirdest aspect of the Scandinavian samples is that they carry the East Asian/Native American variant of EDAR at appreciable frequencies! The figure to the right illustrates this. In blue you have the focal SNP (dark is homozygote, light is heterozygote, dark circle means only one allele was retrieved). In the Chinese from Beijing population (CHB) the derived variant is at high frequency. In the sample of Northwest Europeans from Utah (CEU) it is not present. You can confirm these findings in the 1000 Genomes and elsewhere. In European EDAR of the East Asian form seems only to be found in Finland and associated populations. Using ALDER the authors conclude that admixture occurred on the order of 1 to 2 thousand years before the present, from an East Asian-like group (in the Indo-European paper they found this source best matched the Nganasans of North Central Siberia). An interesting fact which also comes out of this finding is that the haplotype that the derived SNP arose against is relatively common in Northern Europe. The arrows in the figure point to individuals who carry the ancestral SNP, but exhibit the same haplotype which is dominant in East Asia (and also among the Scandinavian hunter-gatherers with the derived variant). The authors state that “The statistic f4(Yoruba, Scandinavian hunter-gatherers, Han, Onge Andaman Islanders) is significantly negative (Z=-3.9) implying gene flow between the ancestors of Scandinavian hunter-gatherers and Han so this shared haplotype is likely the result of ancient gene flow between groups ancestral to these two populations.” Though in earlier work on these data sets they left open the possibility of gene flow between Eastern and Western Eurasia during the Paleolithic as a way to explain some results, it was not offered as a result for the Scandinavian hunter-gatherers. I do not know what to think of the fact that the haplotype that the derived East Asian SNP arose in is common in Northern Europe (though without the derived SNP, which is likely only present in a few populations due to recent Siberian admixture). Could it be that ancient gene flow from Western Eurasian Paleolithic people occurred into East Asian populations, and that then this haplotype accrued the mutation which later swept to near fixation? If that is the case I’m curious about haplotype networks, as Northern Europeans should be more diverse when it comes to the haplotype in question.

In the near future we’ll probably have better and more numerous whole genome sequences of ancient samples. Some of the confusions engendered by this work will be cleared up, as better data renders paradox crisply coherent. The preprint is free to anyone, and I invite readers to dig deeply into it. Though the results yielded only a few positive signals of selection, they’re subtle and complex in their implications. I certainly haven’t thought through everything….

* The fraction of blue eyes is MUCH higher among Punjabis than Bengalis in my experience. It goes to the point that blue eyes likely expresses against the genetic background found in Europeans, where there are other depigmenting alleles near fixation.

Patriarchy came with Cain and Abel

figure2

figure1I do like to suggest that the genetic and archaeological record support the conjecture of Conan the Barbarian in terms of what our male ancestors thought was “good in life.” Basically, to conquer your enemies and seize their women, which is a distillation of a disputed quote from Genghis Khan. Conan may be fiction, but Genghis Khan is not. As it happens there is a fair amount of circumstantial evidence that the genetic legacy of Genghis Khan is enormous. Not only did Khan father many sons, but so did their sons, and so forth. Tens of millions of men around the world are direct paternal descendants of Genghis Khan and his family.

This is known. But now more is known, thanks to a new paper out of Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. The upside of this paper is that it uses whole genome sequence of Y chromosomes to generate phylogenetic inferences. This is important because the Y chromosome has very little genetic variation relative to much of the rest of the genome. The downside is that because techniques were utilized to perform whole genome sequencing of the Y, the sample size, at 299, is not as large as we’ve gotten used to for analyses of uniparental lineages. That will change in the future, as there are many thousands of whole genome sequences of the Y in databases around the world, though perhaps not enough computational power allocated by funding agencies to crunch through them in the fashion on display in the paper (they didn’t use the whole sequence for a lot of the analysis, but ~35,000 SNPs).

So what are the major findings of the paper? Using a Bayesian Skyline Plot (BSP) it is rather clear that 4-8 thousand years ago there was a sharp drop in male effective population sizes across many world populations. It is also clear that the female effective population did not experience the same drastic contraction. The supplements have individual figures, and many of the events of history and archaeology can be easily mapped onto these population size changes. For example, the later reduction of African population sizes probably is due to the later adoption of agriculture in that continent, and timed with the Bantu expansion. In the New World the data seem to show late and persistent reduction in effective population size. The Columbian Exchange and massive population contraction subsequent to that is probably being picked up by this result. figure3Intriguingly there is a detection of a two events in the European data, where the sample size is relatively large. The first major drop seems to coincide with the arrival of the “First Farmers” (e.g., LBK culture) in Northern Europe. In the Middle East (orange) you see collapse, and then a rapid ascent very early. This comports well with the early history of agriculture here. But in the European samples there is a rapid ascent, and then a level off ~3,000 years ago or so. This could be the arrival of Indo-European cultures to Europe. If the sample sizes for other regions were as large and representative as Northern Europe such subtle details might also have emerged there with the BSP method (to be clear, I suspect the crash in effective size in Europe is due to haplogroup I, while the delayed expansion is due to R1a and R1b arriving a few thousand years later).

Also of interest are is the deep structure of the different clades. Those of you stepped in Y chromosomal haplogroups can extract more from the figure to the top left, but it shows relationship of the primary groups as well as their recent expansion. The affinity of the Q and R clades to me indicate that those who argue that these are somehow related to the “Ancestral North Eurasians” are correct. Similarly, the position of I and J in the same clade points to their common descent from ancient West Eurasian Pleistocene groups. The I lineage is most exclusively associated with European hunter-gatherers, while J is traditionally associated with groups of farmers expanding out of the Middle East in all directions (note that one branch of J is found in the Middle East, Central Asia, South Asia, and Europe). I agree with Dienekes that the branch of E that corresponds to the lineages which span Sub-Saharan Africa and Western Eurasia are a indicating a back migration to Africa, probably in the Pleistocene. I do wonder as well whether they have some association with the mysterious “Basal Eurasians.”

An important part of the paper that they emphasize is that ~50,000 years before the present there was a profusion of haplogroups associated with the ones which are today common across Eurasia, and Y chromosomal Ne was ~100. This seems to agree with the rapid expansion of non-Africans in the wake of the “Out of Africa” event, though the authors note they don’t have enough power to reject a model of a separate “Southern Route” migration, which might be detected with autosomal data. This is a good caution on the limitations of Y and mtDNA data; archaic admixture was rejected by these two loci because the non-African hominin lineages went extinct (mtDNA and Y have higher turnover rates than the recombining autosomal regions). figure4Additionally there were some major lacunae in the sampling. For example, among the African populations it doesn’t seem like some of the hunter-gatherer groups, the Khoisan or eastern Pygmy, were included in the data set. The map also shows that Northeast Asia (China, Japan and Korea) and Oceania were not extensively sampled. But these are minor issues in the broader picture of the insights from the population coverage that they did have.

The most important implication of these sorts of results have to do with the nature of the change of human social organization and behavior over the course of the existence of modern humans. The authors of the above paper seem to understand this, as there is extensive focus on the topic within the paper:

An increase in male migration rate might reduce the male Ne but is unlikely to cause a brief drastic reduction in Ne as observed in our empirical data…However, in models with competition among demes, an increased level of variance in expected offspring number among demes can drastically decrease the N e (Whitlock and Barton 1997). The effect may be male-specific, for example, if competition is through a male-driven conquest. A historical example might be the Mongol expansions (Zerjal et al. 2003). Innovations in transportation technology (e.g., the invention of the wheel, horse and camel domestication, and open water sailing) might have contributed to this pattern. Likely, the effect we observe is due to a combination of culturally driven increased male variance in offspring number within demes and an increased male-specific variance among demes, perhaps enhanced by increased sex-biased migration patterns (Destro-Bisol et al. 2004; Skoglund et al. 2014) and male-specific cultural inheritance of fitness.

To restate what’s being said here:

1) During the Holocene we saw the rise of powerful patrilineages which engaged in winner-take-all of inter-group competition.

2) Within the “winning” patrilineages there may have been winner-take-all dynamics, or at least high reproductive variance

When it comes to farmers and nomads against each other I do think a model of inter-demic competition is pretty realistic. But when it comes to farmers and nomads against hunter-gatherers I don’t think one can term it competition. The latter in most circumstances would be quickly overwhelmed by the farmers and nomads; eliminated, excluded, or at least assimilated (there are exceptions in areas where the hunter-gatherer density was high and they were sedentary). And as concerns the complex societies of farmers and nomads, even within them the rise of inequality and stratification mean that subordinate or secondary males and their lineages were marginalized, leaving few descendants.

Men are on average 15-20 percent bigger than women. Men are also stronger than women. But the sexual dimorphism is far less than one can find among gorillas. This suggests that intra-sex competition among males was attenuated, or at least it was not in the physical domain. Though I am not of the camp which believes that war as we understand it must necessarily be a feature of Holocene agricultural societies, it seems likely that the pressure cooker of high population densities resulted in a radical increase in the scale of inter-group atrocity. One way to react to this change would have been to grow larger physically, but there are limitations to how fast biological evolution can resculpt the human physique. Not only that, but larger humans presumably require more nutritional inputs, and the agricultural revolution in Malthusian conditions did not enable that on a mass scale. So humans did what they do best: innovate culturally.

The cultural innovations came as package deals. A central role for patriarchal lineages which tended to apply force to maintain social order, as well as take on the position as the sharp end of the stick in inter-group competition, eventually resulted in power accruing to those groups almost exclusively. The importance of patrilineages naturally resulted in an increased importance of paternity certainty, and therefore social mores which emphasized female chastity. These powerful lineages fixed upon a solution which gorillas had long ago arrived at: treat females as chattel and defend them as one would property.

The “men in groups” were evoked by particular social-cultural conditions of agricultural society which they themselves did not necessarily trigger in an any way. But once you had a small benefit to the emergence of a caste of men in groups, groups which developed this caste benefited. Within these groups eventually the caste took over the identity of the group, and made its own interests conterminous with the interests of the group. The Athenian polis was democratic, but only for free males who were born of Athenians. In other words, the most radical experiment in radical democracy in the ancient world was also still relatively exclusionary and delimited in the nature of political power and representation (also, recall that the power of freeborn males of lower economic status in Athens has been connected to their importance in the navy as oarsmen).

Speaking as someone with broadly liberal sympathies, economic and social forces over the past few centuries have resulted in an unwinding of the cultural innovations of the past 10,000 years which have put a straight-jacket on the forces of human liberty. This great unwinding to some extent can be understood as the shattering of the great patriarchal monopolies of old, reflected in the great families and lineages which spanned the world, and democratic representation first for all men and then women. In the West the period between 1800 and 1970 saw massive gains in income to unskilled workers, reversing the tendency toward winner-take-all dynamics which arose with the Neolithic.

That being said, the post-Industrial and post-materialist world, in full flower in places like North Europe, is not exactly like the Paleolithic. Some of the innovations of the post-Neolithic world, such as organized religion, are probably here to stay in a world of social complexity and density. The great devolution to power from the elite male lineages is one specific aspect where I believe the modern age more resembles the Paleolithic. More liberal sexual ethics is also another dimension where the modern world is more like that of hunter-gatherers. But the autonomous individual, an island unto himself, is a fiction. Hunter-gatherers were, and are, social creatures. No doubt they were bound by taboos and rules, just as modern hunter-gatherers are. The vision of egalitarianism promoted by many in the modern West is a reaction against the social controls of the post-Neolithic world, but those social controls themselves are rooted in human cognitive impulses. Competition did not come full formed in the world of grain, and the impulse toward violence and domination was present in man long before the scythe was re-purposed toward bloodier ends.

The elves of the dark forest

The Smithsonian Magazine has a nice report, Humans Relied on Rainforest Riches 12,000 Years Earlier Than Thought. The original paper is in Science, Direct evidence for human reliance on rainforest resources in late Pleistocene Sri Lanka:

Human occupation of tropical rainforest habitats is thought to be a mainly Holocene phenomenon. Although archaeological and paleoenvironmental data have hinted at pre-Holocene rainforest foraging, earlier human reliance on rainforest resources has not been shown directly. We applied stable carbon and oxygen isotope analysis to human and faunal tooth enamel from four late Pleistocene–to–Holocene archaeological sites in Sri Lanka. The results show that human foragers relied primarily on rainforest resources from at least ~20,000 years ago, with a distinct preference for semi-open rainforest and rain forest edges. Homo sapiens’ relationship with the tropical rainforests of South Asia is therefore long-standing, a conclusion that indicates the time-depth of anthropogenic reliance and influence on these habitats.

The idea that humans only inhabited the deep rainforest would seem strange to me form a human historical genetic perspective, there’s evidence that the Pygmy peoples of Africa are deeply diverged. That is, the western groups and the eastern groups separated tens of thousands of years ago. This needn’t imply that this divergence occurred within the rainforest context, but it seems more plausible to me that the low population densities and delimited ranges of this environment would be more conducive to reducing gene flow across populations than if the two populations developed their structure in the savanna.

The Smithsonian piece ends in a strange way to me though:

“If our ancestors were able to gain such crucial knowledge and respect for these ecologies throughout these long periods of time, then it is somewhat arrogant that we think we can now go and change them significantly without there being considerable consequences for animal or human populations living within them, or our species more widely,” says Roberts.

1491-coverThis imputation of post-materialist values upon hunter-gatherers of the forest seems to me to be unwarranted. In 1491 Charles C. Mann reports on evidence that the “primal” rainforest of the Amazon was widely utilized by native peoples before the arrival of Europeans. Its relative emptiness and occupation by less advanced populations may have been a function of collapse induced by the introduction of European disease. In parts of western North America, such as the Willamette valley of Oregon, the same dynamic occurred. The great forests of the bottomlands that the white settlers encountered were relatively recent secondary growth which had developed in the wake of the population declines of native groups in the wake of diseases introduced by the Spanish from the south.

51CvHNNZ6DL._SY344_BO1,204,203,200_The trail of megafaunal extinction from Australia to the New World suggests to me that pre-modern people were just like modern people in how they respected or conceived the environment. That is, their view was one driven by short term concerns of survival, which one would assume from standard evolutionary theory. Over time cultures could iterate and converge upon more sustainable solution, but the initial waves of human refashioning of the ecology through continuous burning and one time pulse extinction of large organisms fit for consumption suggests a mindset which is easy for moderns to imagine I’d think. I doubt the boom and bust cycle driven by irrational manias emerges in a vacuum, the Malthusian conditions which are the consequence of intra-specific competition are a deep part of the nature of most organisms.

The Fourth Law of Behavior Genetics

Citation: The Fourth Law of Behavior Genetics, Chabris et al.

Citation: The Fourth Law of Behavior Genetics, Chabris et al.

The above is a figure from The Fourth Law of Behavior Genetics (ungated), accepted for publication in Current Directions in Psychological Science. It’s an excellent overview of the intersection of behavior genetics and genomics over the past 10 years or so. The full story is outlined in the paper, fleshed out by the copious and informative citations which litter the text. The point of the above figure is to show how robust many inferences from small effect genome-wide associations are. In particular, there is the standard caveat that a variant which is correlated with disease X in population 1 may not be correlated with disease X in population 2. It actually turns out that in most cases they are correlated across populations. Above you see the correlation in effects (odds ratios) between variants and traits between East Asians and Europeans (common variants are also predictive within families).

The Fourth Law of Behavior Genetics makes no sense unless you know the first three laws outlined by Eric Turkheimer:

* First Law. All human behavioral traits are heritable.

* Second Law. The effect of being raised in the same family is smaller than the effect of genes.

* Third Law. A substantial portion of the variation in complex human behavioral traits is not accounted for by the effects of genes or families.

By heritable you simply mean that some of the variation of the trait in the population is explained by variation in genes in the population (you see it in the standard parent-offspring regression). The second law refers to the fact that on many behavior genetic traits the influence of shared family environment in explaining variation can be surprisingly small. The final law points to the reality that a lot of the variation we see in people in outcomes seems pretty much random. It’s labeled non-shared environment, but we should think of it more as a noise factor. These “laws” are robust regularities which you need to take into account when considering the likelihood of any given result. What is the fourth law? It’s pretty straightforward: “A typical human behavioral trait is associated with very many genetic variants, each of which accounts for a very small percentage of the behavioral variability.” To give a concrete example, it looks like the largest effect common variants for behavioral traits explain about 10% the variance as the largest effect variant for complex disease or morphological traits, on the order of 0.01% as opposed to 0.1%.

That’s a mighty small effect. To make sense of the heritabilities estimated using classical methods that means that genetic variation is partitioned across many many genes, on the order of thousands. This is why methods to ascertain loci of effect utilizing small sample sizes (e.g., candidate gene studies) were bound to fail, because they didn’t have the power to detect true results. Rather, many of the hits were simply noise which got published because of low stringency of statistical significance.

One objection then might be that the missing heritability consists of very low frequency (i.e., far less than the 1% threshold used to define common variants in terms of minor allele frequency) mutations which have a larger effect. The authors claim that the research currently does not support that finding. That implies that high coverage whole genome sequencing at reasonable sample sizes won’t make a big difference. Second, there are the results out of the GCTA framework. I won’t go into the details, though check out the paper in AJHG. It’s a powerful way to explore heritabilities using genomic data across unrelated individuals that’s rapidly converging on the heritabilities estimated from classical behavior genetic methods.

Finally, in a similar vein, Dominance Genetic Variation Contributes Little to the Missing Heritability for Human Complex Traits:

For human complex traits, non-additive genetic variation has been invoked to explain “missing heritability,” but its discovery is often neglected in genome-wide association studies. Here we propose a method of using SNP data to partition and estimate the proportion of phenotypic variance attributed to additive and dominance genetic variation at all SNPs (Math Eq and Math Eq) in unrelated individuals based on an orthogonal model where the estimate of Math Eq is independent of that of Math Eq. With this method, we analyzed 79 quantitative traits in 6,715 unrelated European Americans. The estimate of Math Eq averaged across all the 79 quantitative traits was 0.03, approximately a fifth of that for additive variation (average Math Eq = 0.15). There were a few traits that showed substantial estimates of Math Eq, none of which were replicated in a larger sample of 11,965 individuals. We further performed genome-wide association analyses of the 79 quantitative traits and detected SNPs with genome-wide significant dominance effects only at the ABO locus for factor VIII and von Willebrand factor. All these results suggest that dominance variation at common SNPs explains only a small fraction of phenotypic variation for human complex traits and contributes little to the missing narrow-sense heritability problem.

This moral panic shall end too

tnapb4From Tablet, Letting Go of Our Kids Isn’t a Form of Neglect:

…Kidnapping by strangers is wildly uncommon; in New York State, for instance, the Division of Criminal Justice Services announced that 20,309 children were reported missing statewide in 2011; exactly one of those children was confirmed abducted by a stranger. Most—94 percent—were runaways, most of them teenagers.

The article is in response to the state of Maryland’s horrified response in relation to the existence of a family which practices “free range” parenting. Free range being what used to be called normal parenting as far back as the 1980s. Looking at the statistics above this is a clear case of moral panic. It will abate. Too many cultural forces, from overtaxed working mothers to libertarians and Christian parents’ rights sorts, object to the dominant ethos. But, I suspect that technology, the ubiquity of phones with GPS and tracking technology, will play a role in the changing of the Zeitgeist.

Scions of the hairy Ainu, not Amaterasu

Amaterasu_cave_edit2

A few thousand years ago the islands of Japan were settled by a group of rice farmers, ushering in the Yayoi period. Prior to this Japan was home of the Jomon culture, which is notable for being a pre-agricultural society which may have innovated to produce the world’s earliest pottery. Because everything before ~500 A.D. is Japan is prehistory (this date being generous) the relationship of the Jomon and Yayoi, and the ethnogenesis of the Japanese people as a homogeneous group, is somewhat speculative. But, it does seem one group of Jomon descended peopel persisted in northern Honshu, the Emishi. Finally, it is usually understood that the indigenous people of Hokkaido, the Ainu, have some relationship to the Jomon.

220px-Bjs48_02_AinuThe Ainu are of interest because they do not exhibit many of the traditional characteristics of Northeast Asian people in their phenotype. Ergo, they are termed the “hairy Ainu.” Early anthropologists noting the physical uniqueness of the Ainu speculated that they were a lost branch of the white race. But even early ABO blood group analysis suggested that this was not the case. Rather, the closest relatives of the Ainu were the peoples of Northeast Eurasia. Nevertheless, it does seem striking that the Ainu do not exhibit the distinctive features of many other East Asians. I think this makes more sense though when you consider that it is likely that the East Asian physical type is not quite as primal as we might think. The latest work from genetics indicates very rapid population expansion out of the loci of agricultural activity on the North China plain over the past 10,000 years. The relatively uniformity of physical type and genetic relatedness across East Asia today may have more to due with demographic expansion that genetic connectedness through gene flow over long periods of time.

Much of this can be gleaned by inference, implication, and intuition. A new paper in Molecular Biology and Evolution uses explicit model testing to infer whether the modern Japanese the products of population replacement, admixture, or cultural diffusion. In other words, are the Japanese total cultural and biological descendants of the Yayoi. Are the Japanese total cultural and partial biological descendants of the Yayoi. Or, are the Japanese total cultural descendants of the Yayoi, but total biological descendants of the Jomon. The paper, Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data, reports that the middle hypothesis, genetic admixture, is highly supported when compared to the other two.

There are few interesting points. First, reference population matters. I’m rather sure that the Ainu samples they used as proxies for Jomon are imperfect because the Ainu today have recent Japanese admixture, and, as they note the Jomon themselves exhibit population structure (i.e., the Ainu are one lineage of post-Jomon people). This structure goes back to the late Pleistocene, over 10,000 years ago. The divergence between the ancestors of the Jomon and the Ainu goes back ~20,000 years ago, about when East Asian peoples began to diversify in the wake of the Last Glacial Maximum. The estimates for Jomon ancestry are probably inflated by the admixture in the Ainu, but dampened by the fact that the Ainu are not prefect proxies for the Jomon. Additionally, the reference population for the Yayoi, whether Koreans or North Chinese, has an effect.

But these are minor details. The major conclusion in a qualitative sense is that the modern Japanese are predominantly descended on the whole from the Yayoi farmers, but have a substantial minority component of indigenous Jomon ancestry. This almost certainly varies as a function of geography, the modern Japanese people likely can be used to obtain a “ghost phylogeography” of the Jomon whom they absorbed, as presumably admixture occurred locally a fair amount.

The past shall be naked to you

Most readers are aware that ancient DNA has revolutionized historical inference of the past, particularly prehistory. In 15 years we’ve gone from draft genomes of one living human being, to genomes of humans who have lived tens of thousands of years ago! But by and large the ancient DNA revolution has been one of temperate and boreal climates, because of the reduced degradation of DNA in such circumstances. A new paper in PNAS opens up a sliver of a possibility of expanding the purview of this analysis, Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean:

Between 1500 and 1850, more than 12 million enslaved Africans were transported to the New World. The vast majority were shipped from West and West-Central Africa, but their precise origins are largely unknown. We used genome-wide ancient DNA analyses to investigate the genetic origins of three enslaved Africans whose remains were recovered on the Caribbean island of Saint Martin. We trace their origins to distinct subcontinental source populations within Africa, including Bantu-speaking groups from northern Cameroon and non-Bantu speakers living in present-day Nigeria and Ghana. To our knowledge, these findings provide the first direct evidence for the ethnic origins of enslaved Africans, at a time for which historical records are scarce, and demonstrate that genomic data provide another type of record that can shed new light on long-standing historical questions.

Hopefully this is just the beginning. Part of this the economics of innovation. The best ancient DNA labs are training others in their techniques. From what I’m to understand at this point there’s a backlog of remains to be analyzed. As the expertise becomes distributed labor and capital will no longer be the rate limiting step.

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