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 actual 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. The Ice Age was tough, and the glaciers were capricious, and the warming could be ephemeral (see the Younger Dryas).

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 GeneticsBut 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 on social evolution, Narrow Roads of Gene Land, is highly recommended (if you want some full-throated anti-Hamiltonian viewpoints, Unto Others: The Evolution and Psychology of Unselfish Behavior, might interest you, though only the first half is much focused on evolutionary genetic aspects). 51aEM-jiATL._SY344_BO1,204,203,200_

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. Also there is more than can be explained by reciprocal altruism. So I’ll go on the record that for humans something similar to multi-level selection theory does have something useful to add, especially when it comes to cultural evolution, where standard objections to low between group variance do not hold. It’s just that this is evolutionary, not revolutionary, science. I wish the enemies of inclusive fitness would calm down with the bromides, and just get on with good science. The truth will tell.

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 a recent paper published in Nature, 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 observed 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.” Writing 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 fineSTRUCTURE to extract these components. If you want to understand the guts of the methods, 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.

51LfBq2WMlLBut 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 authors are good in other areas to clarify that their clusters are not “real”, but reifications, that is, abstract mappings upon 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. So 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 in a rapid explosive sweep 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 sea.  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 in analogous manner?

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. There was no need to abandon the old gods and old ways, because their reshaped their new land in the imagine of their old one. 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 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. Without the support of the powerful these sorts of institutional religions decay rapidly back toward primal animism and folk paganism. The old gods of the Celts and Romans were memories, but the new gods of the Germans were living and vital. It was a natural fit for the small scale economies which arose in the post-Roman landscape of proto-England.

download2Gildas 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 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. And just as in Britain the Christian religion disappeared, only to reappear only in later centuries due to missionary activities.


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, Romanitas sanctified by Christ. 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, culminating in the Neo-Darwinian Synthesis.

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 (the reason that economics is the most prominent of the social sciences also is grounded in the existence of transparent currencies which mediate exchanges). 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 analysis. 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 great interest to me to see this review paper, The locus of sexual selection: moving sexual selection studies into the post-genomics era, in the Journal of Evolutionary Biology. 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). Finally, 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 notable 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, since there are still live debates as to the long term nature of human mating patterns. 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

betterDue 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 know.

P.S. Example, Ebony didn’t ask for permission to use this photo, which is my own (can be found at a lab website).

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.

Update: Over the past few days several of my friends have tried Soylent 1.4. First, there’s a consensus that without flavoring it’s basically like drinking pancake batter. Second, there don’t seem to be major issues with gas, as has been the case with previous iterations of Soylent.

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 is correct. Probably the ultimate answers are going to be found with IBD autosomal segment analyses, as in the Peter and Coop paper from a few years back, but with large world-wide 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 if I were the type to dissimulate, it never seemed relevant. Trying to get the best handle on truth is important to me. That means 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, 15 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.

Update: I have to say something that has been on my mind. The PoBI paper came out. In it the implication seems to be that a significant, but minority, contribution in southeast England (the “Saxon Shore”) was from Germans. The Angles, Saxons, and Jutes. To me this is interesting because from what I have read in regards to archaeology the Germans culturally ablated the Romano-British. In particular, the standard model is that institutional Christianity died, replaced by German paganism until the subsequent re-conversion of the early 7th century. What does this mean then? Assuming that the two facts are true (I am moderately confident in the genetic findings, though need to dig deeper), then I think it points to the importance of the elite social stratum in determining the complex features of human culture. There is a thesis that for all practical purposes the European peasantry were quasi-pagans until the modern era, because Christianity was fully elaborated only among the elites, who for all practical purposes ran the Church, and for whom the Church was relevant in their lives (e.g., their marriages were solemnized, the peasants often had common law marriages). There is even circumstantial evidence that some British warriors assimilated to the German culture (the legendary founder of the House of Wessex, had a typically non-German name). The succession of the “higher” Christian culture by the “lower” pagan German one may seem strange to us today, but cyclical dynamics were far more common, so perhaps it is not surprising.