Castes are not just of mind

Before Nicholas Dirks was a controversial chancellor of UC Berkeley, he was a well regarded historian of South Asia. He wrote Castes of Mind: Colonialism and the Making of Modern India. I read it, along with other books on the topic in the middle 2000s.

Here is Amazon summary from Library Journal:

Is India’s caste system the remnant of ancient India’s social practices or the result of the historical relationship between India and British colonial rule? Dirks (history and anthropology, Columbia Univ.) elects to support the latter view. Adhering to the school of Orientalist thought promulgated by Edward Said and Bernard Cohn, Dirks argues that British colonial control of India for 200 years pivoted on its manipulation of the caste system. He hypothesizes that caste was used to organize India’s diverse social groups for the benefit of British control. His thesis embraces substantial and powerfully argued evidence. It suffers, however, from its restricted focus to mainly southern India and its near polemic and obsessive assertions. Authors with differing views on India’s ethnology suffer near-peremptory dismissal. Nevertheless, this groundbreaking work of interpretation demands a careful scholarly reading and response.

The condensation is too reductive. Dirks does not assert that caste structures (and jati) date to the British period, but the thrust of the book clearly leaves the impression that this particular identity’s formative shape on the modern landscape derives from the colonial experience. The British did not invent caste, but the modern relevance seems to date to the British period.

This is in keeping with a mode of thought flourishing today under the rubric of postcolonialism, with roots back to Edward Said’s Orientalism. As a scholar of literature Said’s historical analysis suffered from the lack of deep knowledge. A cursory reading of Orientalism picks up all sorts of errors of fact. But compared to his heirs Said was actually a paragon of analytical rigor. I say this after reading some contemporary postcolonial works, and going back and re-reading Orientalism.

To not put too fine a point on it postcolonialism is more about a rhetorical posture which aims to destroy what it perceives as Western hegemonic culture. In the process it transforms the modern West into the causal root of almost all social and cultural phenomenon, especially those that are not egalitarian. Anyone with a casual grasp of world history can see this, which basically means very few can, since so few actually care about details of fact.

Castes of Mind is an interesting book, and a denser piece of scholarship than Orientalism. Its perspective is clear, and though it is not without qualification, many people read it to mean that caste was socially constructed by the British.

This seems false. It has become quite evident that even the classical varna categories seem to correlate with genome-wide patterns of relatedness. And the Indian jatis have been endogamous for on the order of two thousand years. From The New York Times, In South Asian Social Castes, a Living Lab for Genetic Disease:

The Vysya may have other medical predispositions that have yet to be characterized — as may hundreds of other subpopulations across South Asia, according to a study published in Nature Genetics on Monday. The researchers suspect that many such medical conditions are related to how these groups have stayed genetically separate while living side by side for thousands of years.

This is not really a new finding. It was clear in 2009’s Reconstructing Indian Population History. It’s more clear now in The promise of disease gene discovery in South Asia.

Unfortunately though science is not well known in any depth among the general public. The ascendency of social constructionism is such that a garbled and debased view that “caste was invented by the British” will continue to be the “smart” and fashionable view among many intellectual elites.

SLC24A5 is very important, but we don’t know why

The golden of pigmentation genetics started in 2005 with SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Prior to that pigmentation genetics was really to a great extent coat color genetics, done in mice and other organisms which have a lot of pelage variation.

Of course there was work on humans, mostly related to melanocortin 1. But more interesting were classical pedigree studies which indicated that the number of loci controlling variation in pigmentation was not that high. This, it was a mildly polygenic trait insofar as some large effect quantitative trait loci could be discerned in the inheritance patterns.

From The Genetics of Human Populations, written in the 1960s, but still useful today because of its comprehensive survey of the classical period:

Depending on what study samples you use variance on a locus of SLC24A5 explains less than 10% or more than 30% of the total variance. But it is probably the biggest effect locus on the whole in human populations when you pool them altogether (obviously it explains little variance in Africans or eastern non-Africans since it is homozygous ancestral by and large in both groups).

One aspect of the derived SNP in this locus is that it seems to be under strong selection. In a European 1000 Genomes sample there are 1003 SNPs of the derived variant, and 3 of the ancestral. Curiously this allele was absent in Western European Mesolithic European hunter-gatherers, though it was present in hunter-gatherers on the northern and eastern fringes of the continent. It was also present in Caucasian hunter-gatherers and farmers from the Middle East who migrated to Europe. It seems very likely that these sorts of high frequencies are due to selection in Europe.

The variant is also present in appreciably frequencies in many South Asian populations, and there seems to have been in situ selection there too, as well as the Near East. In Ethiopia it also seems to be under selection.

It could be something due to radiation…but the Near East and South Asia are quite high intensity in that regard. As are the highlands of Ethiopia. About seven years ago I suggested that rather that UV radiation as such the depigmentation that has occurred across the Holocene might be due to agriculture and changes in diet.

But a new result from southern Africa presented at the SMBE meeting this year suggests that this can not be a comprehensive answer. Meng Lin in Brenna Henn’s lab uses a broad panel of KhoeSan populations to find that the derived allele on SLC24A5 reaches ~40% frequency. Probably a high fraction of West Eurasian admixture in these groups is around ~10% being generous. Where did this allele come from? The results from Joe Pickrell a few years back are sufficient to explain: there was a movement of pastoralists with distant West Eurasian ancestry who brought cattle to southern Africa, and so resulted in the ethnogenesis of groups such as the Nama people (there is also Y chromosomal work by Henn on this).

Sad human with two derived alleles of SNP of interest

Lin reports that the haplotype around SLC24A5 is the same one as in Western Eurasia. Iain Mathieson (who is now at Penn if anyone is looking for something to do in grad school or a post-doc) has told me that the haplotype in the Motala Mesolithic hunter-gatherers and in the hunter-gatherers from the Caucasus are the same. It seems that this haplotype was widespread early in the Holocene. Curiously, the Motala hunter-gatherers also carry the East Asian haplotype around their derived EDAR variant.

I don’t know what to make of this. My intuition is that if a haplotype like this is so widespread nearly ~10,000 years ago recombination would have broken it apart into smaller pieces so that haplotype structure would be easier to discern. As it is that doesn’t seem to be the case.

And we also don’t know what’s going on withSLC24A5. Obviously it impacts skin color. It has been shown to do so in admixed populations. But it is hard to believe that that is the sole target of natural selection here.

The fad for dietary adaptations is not going away

Food is a big deal for humans. Without it we die. Unlike some animals (here’s looking at you pandas) we’re omnivorous. We eat fruit, nuts, greens, meat, fish, and even fungus. Some of us even eat things which give off signals of being dangerous or unpalatable, whether it be hot sauce or lutefisk.

This ability to eat a wide variety of items is a human talent. Those who have put their cats on vegetarian diets know this. After a million or so years of being hunters and gatherers with a presumably varied diet for thousands and thousands of years most humans at any given time ate some form of grain based gruel. Though I am sympathetic to the argument that in terms of quality of life this was a detriment to median human well being, agriculture allowed our species to extract orders of magnitude more calories from a unit of land, though there were exceptions, such as in marine environments (more on this later).

Ergo, some scholars, most prominently Peter Bellwood, have argued that farming did not spread through cultural diffusion. Rather, farmers simply reproduced at much higher rates because of the efficiency of their lifestyle in comparison to that of hunter-gatherers. The latest research, using ancient DNA, broadly confirms this hypothesis. More precisely, it seems that cultural revolutions in the Holocene have shaped most of the genetic variation we see around us.

But genetic variation is not just a matter of genealogy. That is, the pattern of relationships, ancestor to descendent, and the extent of admixtures across lineages. Selection is also another parameter in evolutionary genetics. This can even have genome-wide impacts. It seems quite possible that current levels of Neanderthal ancestry are lower than might otherwise have been the case due to selection against functional variants derived from Neanderthals, which are less fitness against a modern human genetic background.

The importance of selection has long been known and explored. Sickle-cell anemia only exists because of balancing selection. Ancient DNA has revealed that many of the salient traits we associate with a given population, e.g., lactose tolerance or blue eyes, have undergone massive changes in population wide frequency over the last 10,000 years. Some of this is due to population replacement or admixture. But some of it is due to selection after the demographic events. To give a concrete example, the frequency of variants associated with blue eyes in modern Europeans dropped rapidly with the expansion of farmers from the Near East ~10,000 years ago, but has gradually increased over time until it is the modal allele in much of Northern Europe. Lactase persistence in contrast is not an ancient characteristic which has had its ups and downs, but something new that evolved due to the cultural shock of the adoption of dairy consumption by humans as adults. The region around lactase is one of the strongest signals of natural selection in the European genome, and ancient DNA confirms that the ubiquity of the lactase persistent allele is a very recent phenomenon.

But obviously lactase is not going to be the only target of selection in the human genome. Not only can humans eat many different things, but we change our portfolio of proportions rather quickly. In a Farewell to Alms the economic historian Gregory Clark observed that English peasants ate very differently before and after the Black Death. As any ecologist knows populations are resource constrained when they are near the carrying capacity, and England during the High Medieval period there was massive population growth due to gains in productivity (e.g., the moldboard plough) as well as intensification of farming and utilization of all the marginal land.

After the Black Death (which came in waves repeatedly) there was a massive population decline across much of Europe. Because institutions and practices were optimized toward maintaining a much higher population, European peasants lived a much better lifestyle after the population crash because the pie was being cut into far fewer pieces. In other words, centuries of life on the margins just scraping by did not mean that English peasants couldn’t live large when the times allowed for it. We were somewhat pre-adapted.

Our ability to eat a variety of items, and the constant varying of the proportions and kind of elements which go into our diet, mean that sciences like nutrition are very difficult. And, it also means that attempts to construct simple stories of adaptation and functional patterns from regions of the genome implicated in diet often fail. But with better analytic technologies (whole genome sequencing, large sample sizes) and some elbow grease some scientists are starting to get a better understanding.

A group of researchers at Cornell has been taking a closer look at the FADS genes over the past few years (as well as others at CTEG). These are three nearby genes, FADS1FADS2, and FADS3 (they probably underwent duplication). These genes are involved in the metabolization of fatty acids, and dietary regime turns out to have a major impact on variation around these loci.

The most recent paper out of the Cornell group, Dietary adaptation of FADS genes in Europe varied across time and geography:

Fatty acid desaturase (FADS) genes encode rate-limiting enzymes for the biosynthesis of omega-6 and omega-3 long-chain polyunsaturated fatty acids (LCPUFAs). This biosynthesis is essential for individuals subsisting on LCPUFA-poor diets (for example, plant-based). Positive selection on FADS genes has been reported in multiple populations, but its cause and pattern in Europeans remain unknown. Here we demonstrate, using ancient and modern DNA, that positive selection acted on the same FADS variants both before and after the advent of farming in Europe, but on opposite (that is, alternative) alleles. Recent selection in farmers also varied geographically, with the strongest signal in southern Europe. These varying selection patterns concur with anthropological evidence of varying diets, and with the association of farming-adaptive alleles with higher FADS1 expression and thus enhanced LCPUFA biosynthesis. Genome-wide association studies reveal that farming-adaptive alleles not only increase LCPUFAs, but also affect other lipid levels and protect against several inflammatory diseases.

The paper itself can be difficult to follow because they’re juggling many things in the air. First, they’re not just looking at variants (e.g., SNPs, indels, etc.), but also the haplotypes that the variants are embedded in. That is, the sequence of markers which define an association of variants which indicate descent from common genealogical ancestors. Because recombination can break apart associations one has to engage with care in historical reconstruction of the arc of selection due to a causal variant embedded in different haplotypes.

But the great thing about this paper is that in the case of Europe they can access ancient DNA. So they perform inferences utilizing whole genomes from many extant human populations, but also inspect change in allele frequency trajectories over time because of the density of the temporal transect. The figure to the left shows variants in both an empirical and modeling framework, and how they change in frequency over time.

In short, variants associated with higher LCPUFA synthesis actually decreased over time in Pleistocene Europe. This is similar to the dynamic you see in the Greenland Inuit. With the arrival of farmers the dynamic changes. Some of this is due to admixture/replacement, but some of it can not be accounted for admixture and replacement. In other words, there was selection for the variants which synthesize more LCPUFA.

This is not just limited to Europe. The authors refer to other publications which show that the frequency of alleles associated with LCPUFA production are high in places like South Asia, notable for a culture of preference for plant-based diets, as well as enforced by the reality that animal protein was in very short supply. In Europe they can look at ancient DNA because we have it, but the lesson here is probably general: alternative allelic variants are being whipsawed in frequency by protean shifts in human cultural modes of production.

In War Before Civilization Lawrence Keeley observed that after the arrival of agriculture in Northern Europe in a broad zone to the northwest of the continent, facing the Atlantic and North Sea, farming halted rather abruptly for centuries. Keeley then recounts evidence of organized conflict in between two populations across a “no man’s land.”

But why didn’t the farmers just roll over the old populations as they had elsewhere? Probably because they couldn’t. It is well known that marine regions can often support very high densities of humans engaged in a gathering lifestyle. Though not farmers, these peoples are often also not nomadic, and occupy areas as high density. The tribes of the Pacific Northwest, dependent upon salmon fisheries, are classic examples. Even today much of the Northern European maritime fringe relies on the sea. High density means they had enough numbers to resist the human wave of advance of farmers. At least for a time.

Just as cultural forms wane and wax, so do some of the underlying genetic variants. If you dig into the guts of this paper you see much of the variation dates to the out of Africa period. There were no great sweeps which expunged all variation (at least in general). Rather, just as our omnivorous tastes are protean and changeable, so the genetic variation changes over time and space in a difficult to reduce manner. The flux of lifestyle change is probably usually faster than biological evolution can respond, so variation reducing optimization can never complete its work.

The modern age of the study of natural selection in the human genome began around when A Map of Recent Positive Selection In the Human Genome was published. And it continues with methods like SDS, which indicate that selection operates to this day. Not a great surprise, but solidifying our intuitions. In the supplements to the above paper the authors indicate that the focal alleles that they are interrogating exhibit coefficients of selection around ~0.5% or so. This is rather appreciable. The fact that fixation has not occurred indicates in part that selection has reversed or halted, as they noted. But another aspect is that there are correlated responses; the FADS genes are implicated in many things, as the authors note in relation to inflammatory diseases. But I’m not sure that the selection effects of these are really large in any case. I bet there are more important things going on that we haven’t discovered or understood.

Obviously genome-wide analyses are going to continue for the foreseeable future. Ten years ago my late friend Mike McKweon predicted that at some point genomics was going to have be complemented by detailed follow up through bench-work. I’m not sure if we’re there yet, but there are only so many populations you can sequence, and only to a particular coverage to obtain any more information. Some selection sweeps will be simple stories with simple insights. But I suspect many more like FADS will be more complex, with the threads of the broader explanatory tapestry assembled publications by publication over time.

Citation: Ye, K., Gao, F., Wang, D., Bar-Yosef, O. & Keinan, A. Dietary adaptation of FADS genes in Europe varied across time and geography. Nat. Ecol. Evol. 1, 0167 (2017).

The Bronze age demographic transformation of Britain

In Norman Davies’ the excellent The Isles: A History, he mentions offhand that unlike the Irish the British to a great extent have forgotten their own mythology. This is one reason that J. R. R. Tolkien created Middle Earth, they gave the Anglo-Saxons the same sort of mythos that the Irish and Norse had.

But to some extent I think we can update our assessments. Science is bringing myth to life. The legendary “Bell Beaker paper” is now available in preprint form, The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe. The methods are not too abstruse if you have read earlier works on this vein (i.e., no Nick Patterson authored methodological supplement that I saw). And the results are straightforward.

And what are those results?

First, the Bell Beaker phenomenon was both cultural and demographic. Cultural in that it began in the Iberian peninsula, and was transmitted to Central Europe, without much gene flow from what they can see. Demographic in that its push west into what is today the Low Countries and France and the British Isles was accompanied by massive gene flow.

In their British samples they conclude that 90% of the ancestry of early Bronze Age populations derive from migrants from Central Europe with some steppe-like ancestry. In over words, in a few hundred years there was a 90% turnover of ancestry. The preponderance of the male European R1b lineage also dates to this period. It went from ~0% to ~75-90% in Britain over a few hundred years.

If most of the genetic-demographic character of modern Britain was established during the Bronze Age*, then there has been significant selection since the Bronze Age. The figure to the left shows ancient (Neolithic/Bronze age) frequencies of selected SNPs, with modern frequencies in the British in dashed read. The top-left SNP is for HERC2-OCA2, the region related to brown vs. blue eye color, and also associated with some more general depigmentation. The top-right SNP is in SLC45A2, the second largest effect skin color locus in Europeans. The bottom SNP is for a mutation on LCT, which allows for the digestion of milk sugar as adults.

The vast majority of the allele frequency change in Britons for digestion of milk sugar post-dates the demographic turnover. In other words, the modern allele frequency is a function of post-Bronze Age selection. This is not surprising, as it supports the result in Eight thousand years of natural selection.

1000 Genomes derived SLC45A2 SNP frequency

At least as interesting are the pigmentation loci. The fact that the derived frequency in HERC2-OCA2 is lower in both British and Central European Beaker people samples indicates that the lower proportion is not an artifact of sampling. Britons have gotten more blue-eyed over the last 4,000 years. Second, SLC45A2 is at shocking low proportions for modern European populations.

HGDP derived SLC45A2 SNP frequency

In the 1000 Genomes the 4% ancestral allele frequency is almost certainly a function of the Siberian (non-European) ancestry. In modern Iberians the ancestral frequency is 18% (and it is even higher in Sardinians last I checked), but in Tuscans it is ~2%. Though not diagnostic of Europeans in the way the derived SNP at SLC24A2 is, SLC452 derived variants are much more constrained to Europe. Individuals who are homozygote ancestral for SNPs atSLC45A2 rare in modern Northern Europeans (pretty much nonexistent actually). But even as late as the Bronze Age they would have been present at low but appreciable frequencies.

This particular result convinces me that the method in Field et al. which detected lots of recent (last 2,000 years) selection on pigmentation in British populations is not just a statistical artifact. Though these papers are solving much of European prehistory, they are also going to be essential windows into the trajectory of natural selection in human populations over the last 5,000 years.

* In the context of this paper the Anglo-Saxon migrations tackled by the PoBI paper are minor affairs because the two populations were already genetically rather close. Additionally, the PoBI paper found that the German migrations were significant demographic events, but most of the ancestry across Britain does date to the previous period.

So what’s point of demographic models which leave you scratching your head

There’s a new paper on Tibetan adaptation to high altitudes, Evolutionary history of Tibetans inferred from whole-genome sequencing. The focus of the paper is on the fact that more genes than have previously been analyzed seem to be the targets of natural selection. And I buy most of their analyses (not sure about the estimate of Denisovan ancestry being 0.4%…these sorts of things can be tricky).

But they fancy it up with a ∂a∂i model of population history, as well as using MSMC to account for gene flow. I don’t understand why they didn’t use something simpler like TreeMix, which can also handle more complex models. I guess because they wanted to focus on only a few populations?

Years ago I asked the developer of MSMC, Stephan Schiffels, if assuming an admixed population is not admixed might cause weird inferences. Why yes, it would. For example, admixed populations might show higher effective population since they’re pooling the histories of two separate populations. As for ∂a∂i, the model above leaves me literally scratching my head.

…predicted that the initial divergence between Han and Tibetan was much earlier, at 54kya (bootstrap 95% C.I 44 kya to 58 kya). However, for the first 45ky, the two populations maintained substantial gene flow (6.8×10-4 and 9.0×10-4 per generation per chromosome). After 9.4 kya (bootstrap 95% C.I 8.6 kya to 11.2 kya), the gene flow rate dramatically dropped (1.3×10-11 and 4×10-7 per generation per chromosome), which is consistent with the estimate from MSMC.

Mystifying. The separation between Chinese and Tibetans is pretty much immediately after modern humans arrive in East Asia. Then there’s a lot of reciprocal gene flow…which ends during the Holocene.

We’re being told here that there are two populations which persisted in some form for ~45,000 years. Is this believable? That these two populations maintained some sort of continuity, and, remained in close proximity to engage in gene flow. And then ~10,000 years ago the ancestors of the Tibetans separated from the ancestors of the modern Han Chinese.

The latter scenario I can imagine. It’s this ~45,000 year dance I’m confused by. If there is substantial gene flow between the two groups why did they keep enough distinctive drift to be separate populations?

With what we know about ancient DNA from Europe if we posited such a model for that continent we’d be way off. There’s been too many population turnovers. Is East Asia different? I’m moderately skeptical of that. I think perhaps researchers should be very aware of the limitations of ∂a∂i when it comes to fine-grained population genomic analyses.

Note: This is a cool paper, and this small section is not entirely relevant. Which is why I’m confused about it since it seems the weakest part of the analysis in terms of originality, and the least believable.

Beyond “Out of Africa” and multiregionalism: a new synthesis?

For several decades before the present era there have been debates between proponents of the recent African origin of modern humans, and the multiregionalist model. Though molecular methods in a genetic framework have come of the fore of late these were originally paleontological theories, with Chris Stringer and Milford Wolpoff being the two most prominent public exponents of the respective paradigms.

Oftentimes the debate got quite heated. If you read books from the 1990s, when multiregionalism in particular was on the defensive, there were arguments that the recent out of Africa model was more inspirational in regards to our common humanity. As a riposte the multiregionalists asserted that those suggesting recent African origins with total replacement was saying that our species came into being through genocide.

Though some had long warned against this, the dominant perception outside of population genetics was that results such the “mitochondrial Eve” had given strong support to the recent African origin of modern humans, to the exclusion of other ancestry. 2002’s Dawn of Human Culture took it for granted that the recent African origin of modern humans to the total exclusion of other hominin lineages was established fact.

In 2008 I went to a talk where Svante Paabo presented some recent Neanderthal ancient mtDNA work. It was rather ho-hum, as Paabo showed that the Neanderthal lineages were highly diverged from modern ones, and did not leave any descendants. Though of course most modern human lineages did not leave any descendants from that period, Paabo took this evidence supporting the proposition that Neanderthals did not contribute to the modern human gene pool.

When his lab reported autosomal Neanderthal admixture in 2010, it was after initial skepticism and shock internally. I know Milford Wolpoff felt vindicated, while Chris Stringer began to emphasize that the recent African origin of modern humanity also was defined by regional assimilation of other lineages. The data have ultimately converged to a position somewhere between the extreme models of total replacement or balanced and symmetrical gene flow.

This is not surprising. Extreme positions are often rhetorically useful and popular when there’s no data. But reality does not usually conform to our prejudices, so ultimately one has to come down at some point.

The data for non-Africans is rather unequivocal. The vast majority of (>90%) of the ancestry of non-Africans seems to go back to a small number of common ancestors ~60,000 years ago. Perhaps in the range of ~1,000 individuals. These individuals seem to be a node within a phylogenetic tree where all the other branches are occupied by African populations. Between this period and ~15,000 years ago these non-Africans underwent a massive range expansion, until modern humans were present on all continents except Antarctica. Additionally, after the Holocene some of these non-African groups also experienced huge population growth due to intensive agricultural practice.

To give a sense of what I’m getting at, the bottleneck and common ancestry of non-Africans goes back ~60,000 years, but the shared ancestry of Khoisan peoples and non-Khoisan peoples goes back ~150,000-200,000 years. A major lacunae of the current discussion is that often the dynamics which characterize non-Africans are assumed to be applicable to Africans. But they are not.

A 2014 paper illustrates one major difference by inferring effective population from whole genomes: African populations have not gone through the major bottleneck which is imprinted on the genomes of all non-African populations. The Khoisan peoples, the most famous of which are the Bushmen of the Kalahari, have the largest long term effective populations of any human group. The Yoruba people of Nigeria have a history where they were subject to some population decline, but not to the same extent as non-Africans.

What do we take away from this?

One thing is that we have to consider that the assimilationist model which seems to be necessary for non-Africans, also applies to Africans. For years some geneticists have been arguing that some proportion of African ancestry as well is derived from lineages outside of the main line leading up to anatomically modern humans. Without the smoking gun of ancient genomes this will probably remain a speculative hypothesis. I hope that Lee Berger’s recent assertion that they’ve now dated Homo naledi to ~250,000 years before the present may offer up the possibility that ancient DNA will help resolve the question of African archaic admixture (i.e., if naledi is related to the “ghost population”?).

The second dynamic is that the bottleneck-then-range-expansion which is so important in defining the recent prehistory of non-Africans is not as relevant to Africans during the Pleistocene. The very deep split dates being inferred from whole genome analysis of African populations makes me wonder if multiregional evolution is actually much more important within Africa in the development of modern humans in the last few hundred thousand years. Basically, the deep split dates may highlight that there was recurrent gene flow over hundreds of thousands of years between different closely related hominin populations in Africa.

Ultimately, it doesn’t seem entirely surprising that the “Out of Africa” model does not quite apply within Africa.

Addendum: Over the past ~5,000 years we have seen the massive expansion of agricultural populations within the continent. The “deep structure” therefore may have been erased to a great extent, with Pygmies, Khoisan, and Hadza, being the tip of the iceberg in terms of the genetic variation which had characterized the Africa during the Pleistocene.

The logic of human destiny was inevitable 1 million years ago

Robert Wright’s best book, Nonzero: The Logic of Human Destiny, was published nearly 20 years ago. At the time I was moderately skeptical of his thesis. It was too teleological for my tastes. And, it does pander to a bias in human psychology whereby we look to find meaning in the universe.

But this is 2017, and I have somewhat different views.

In the year 2000 I broadly accepted the thesis outlined a few years later in The Dawn of Human Culture. That our species, our humanity, evolved and emerged in rapid sequence, likely due to biological changes of a radical kind, ~50,000 years ago. This is the thesis of the “great leap forward” of behavioral modernity.

Today I have come closer to models proposed by Michael Tomasello in The Cultural Origins of Human Cognition and Terrence Deacon in The Symbolic Species: The Co-evolution of Language and the Brain. Rather than a punctuated event, an instance in geological time, humanity as we understand it was a gradual process, driven by general dynamics and evolutionary feedback loops.

The conceit at the heart of Robert J. Sawyer’s often overly preachy Neanderthal Parallax series, that if our own lineage went extinct but theirs did not they would have created a technological civilization, is I think in the main correct. It may not be entirely coincidental that the hyper-drive cultural flexibility of African modern humans evolved in African modern humans first. There may have been sufficient biological differences to enable this to be likely. But I believe that if African modern humans were removed from the picture Neanderthals would have “caught up” and been positioned to begin the trajectory we find ourselves in during the current Holocene inter-glacial.

Luke Jostins’ figure showing across board encephalization

The data indicate that all human lineages were subject to increased encephalization. That process trailed off ~200,000 years ago, but it illustrates the general evolutionary pressures, ratchets, or evolutionary “logic”, that applied to all of them. Overall there were some general trends in the hominin lineage that began to characterized us about a million years ago. We pushed into new territory. Our rate of cultural change seems to gradually increased across our whole range.

One of the major holy grails I see now and then in human evolutionary genetics is to find “the gene that made us human.” The scramble is definitely on now that more and more whole genome sequences from ancient hominins are coming online. But I don’t think there will be such gene ever found. There isn’t “a gene,” but a broad set of genes which were gradually selected upon in the process of making us human.

In the lingo, it wasn’t just a hard sweep from a de novo mutation. It was as much, or even more, soft sweeps from standing variation.

Mouse fidelity comes down to the genes

While birds tend to be at least nominally monogamous, this is not the case with mammals. This strikes some people as strange because humans seem to be monogamous, at least socially, and often we take ourselves to be typically mammalian. But of course we’re not. Like many primates we’re visual creatures, rather than relying in smell and hearing. Obviously we’re also bipedal, which is not typical for mammals. And, our sociality scales up to massive agglomerations of individuals.

How monogamous we are is up for debate. Desmond Morris, who is well known to many from his roles in television documentaries, has been a major promoter of the idea that humans are monogamous, with a focus on pair-bonds. In contrast, other researchers have highlighted our polygamous tendencies. In The Mating Mind Geoffrey Miller argues for polygamy, and suggests that pair-bonds in a pre-modern environment were often temporary, rather than lifetime (Miller is now writing a book on polyamory).

The fact that in many societies high status males seem to engage in polygamy, despite monogamy being more common, is one phenomenon which confounds attempts to quickly generalize about the disposition of our species. What is preferred may not always be what is practiced, and the external social adherence to norms may be quite violated in private.

Adducing behavior is simpler in many other organisms, because their range of behavior is more delimited. When it comes to studying mating patterns in mammals voles have long been of interest as a model. There are vole species which are monogamous, and others which are not. Comparing the diverged lineages could presumably give insight as to the evolutionary genetic pathways relevant to the differences.

But North American deer mice, Peromyscus, may turn to be an even better bet: there are two lineages which exhibit different mating patterns which are phylogenetically close enough to the point where they can interbreed. That is crucial, because it allows one to generate crosses and see how the characteristics distribute themselves across subsequent generations. Basically, it allows for genetic analysis.

And that’s what a new paper in Nature does, The genetic basis of parental care evolution in monogamous mice. In figure 3 you can see the distribution of behaviors in parental generations, F1 hybrids, and the F2, which is a cross of F1 individuals. The widespread distribution of F2 individuals is likely indicative of a polygenic architecture of the traits. Additionally, they found that some traits are correlated with each other in the F2 generation (probably due to pleiotropy, the same gene having multiple effects), while others were independent.

With the F2 generation they ran a genetic analysis which looked for associations between traits and regions of the genome. They found 12 quantitative trait loci (QTLs), basically zones of the genome associated with variation on one or more of the six traits. From this analysis they immediately realized there was sexual dimorphism in terms of the genetic architecture; the same locus might have a different effect in the opposite sex. This is evolutionarily interesting.

Because the QTLs are rather large in terms of physical genomic units the authors looked to see which were plausible candidates in terms of function. One of their hits was vasopressin, which should be familiar to many from vole work, as well as some human studies. Though the QTL work as well as their pup-switching experiment (which I did not describe) is persuasive, the fact that a gene you’d expect shows up as a candidate really makes it an open and shut case.

The extent of the variation explained by any given QTL seems modest. In the extended figures you can see it’s mostly in the 1 to 5 percent range. In Carl Zimmer’s excellent write up he ends:

But Dr. Bendesky cautioned that the vasopressin gene would probably turn out to be just one of many that influence oldfield mice. Though it is strongly linked to parental behavior, the vasopressin gene accounts for 6.7 percent of the variation in nest building among males, and only 2.9 percent among females.

The genetic landscape of human parenting will turn out to be even more rugged, Dr. Bendesky predicted.

“You cannot do a 23andMe test and find out if your partner is going to be a good father,” he said.

Sort of. The genetic architecture above is polygenic…but not incredibly diffuse. The proportion of variation explained by the largest effect allele is more than for height, and far more than for education. If human research follows up on this, I wouldn’t be surprised if you could develop a polygenic risk score.

But I don’t have a good intuition on how much variation in humans there really is for these sorts of traits that are heritable. I assume some. But I don’t know how much. And how much of the variance in behavior might be explained by human QTLs? Humans don’t lick or build nests, or retrieve pups. Also, as one knows from Genetics and Analysis of Quantitative Traits sexually dimorphic traits take a long time to evolve. These are two deer mice species. Within humans there may not have been enough time for this sort of heritable complexity of behavior to evolve.

There are a lot of philosophical issues here about translating to a human context.

Nevertheless, this research shows that ingenious animal models can powerfully elucidate the biological basis of behavior.

Citation: The genetic basis of parental care evolution in monogamous mice. Nature (2017) doi:10.1038/nature22074

Women hate going to India

For some reason women do not seem to migrate much into South Asia. In the late 2000s I, along with others, noticed a strange discrepancy in the Y and mtDNA lineages which trace one’s direct male and female lines: in South Asia the male lineages were likely to cluster with populations to the north an west, while the females lines did not. South Asia’s females lines in fact had a closer relationship to the mtDNA lineages of Southeast and East Asia, albeit distantly.

One solution which presented itself was to contend there was no paradox at all. That the Y chromosomal lineages found in South Asia were basal to those to the west and north. In particular, there were some papers suggesting that perhaps R1a1a originated in South Asia at the end of the last Pleistocene. Whole genome sequencing of Y chromosomes does not bear this out though. R1a1a went through rapid expansion recently, and ancient DNA has found it in Russia first. But in 2009 David Reich came out with Reconstructing Indian population history, which offered up somewhat of a possible solution.

What Reich and his coworkers found that South Asia seems to be characterized by the mixture of two very different types of populations. One set, ANI (Ancestral North Indian), are basically another western or northwestern Eurasian group. ASI (Ancestral South Indian), are indigenous, and exhibit distant affinities to the Andaman Islanders. The India-specific mtDNA then were from ASI, while the Y chromosomes with affinities to people to the north and west were from ANI. In other words, the ANI mixture into South Asia was probably through a mass migration of males.

But it’s not just Y and mtDNA in this case only. A minority of South Asians speak Austro-Asiatic languages. The most interesting of these populations are the Munda, who tend to occupy uplands in east-central India. Older books on India history often suggest that the Munda are the earliest aboriginals of the subcontinent, but that has to confront the fact that most Austro-Asiatic language are spoken in Southeast Asia. There was no true consensus where they were present first.

Genetics seems to have solved this question. The evidence is building up that Austro-Asiatic languages arrived with rice farmers from Southeast Asia. Though most of the ancestry of the Munda is of ANI-ASI mix, a small fraction is clearly East Asian. And interestingly, though they carry no East Asian mtDNA, they do carry East Asian Y. Again, gene flow mediated by males.

The same is true of India’s Bene Israel Jewish community.

A new preprint on biorxiv confirms that the Parsis are another instance of the same dynamic: The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection:

Zoroastrianism is one of the oldest extant religions in the world, originating in Persia (present-day Iran) during the second millennium BCE. Historical records indicate that migrants from Persia brought Zoroastrianism to India, but there is debate over the timing of these migrations. Here we present novel genome-wide autosomal, Y-chromosome and mitochondrial data from Iranian and Indian Zoroastrians and neighbouring modern-day Indian and Iranian populations to conduct the first genome-wide genetic analysis in these groups. Using powerful haplotype-based techniques, we show that Zoroastrians in Iran and India show increased genetic homogeneity relative to other sampled groups in their respective countries, consistent with their current practices of endogamy. Despite this, we show that Indian Zoroastrians (Parsis) intermixed with local groups sometime after their arrival in India, dating this mixture to 690-1390 CE and providing strong evidence that the migrating group was largely comprised of Zoroastrian males. By exploiting the rich information in DNA from ancient human remains, we also highlight admixture in the ancestors of Iranian Zoroastrians dated to 570 BCE-746 CE, older than admixture seen in any other sampled Iranian group, consistent with a long-standing isolation of Zoroastrians from outside groups. Finally, we report genomic regions showing signatures of positive selection in present-day Zoroastrians that might correlate to the prevalence of particular diseases amongst these communities.

The paper uses lots of fancy ChromoPainter methodologies which look at the distributions of haplotypes across populations. But some of the primary results are obvious using much simpler methods.

1) About 2/3 of the ancestry of Indian Parsis derives from an Iranian population
2) About 1/3 of the ancestry of Indian Parsis derives from an Indian popuation
3) Almost all the Y chromosomes of Indian Parsis can be accounted for by Iranian ancestry
4) Almost all the mtDNA haplogroups of Indian Parsis can be accounted for by Indian ancestry
5) Iranian Zoroastrians are mostly endogamous
6) Genetic isolation has resulted in drift and selection on Zoroastrians

The fact that the ancestry proportion is clearly more than 50% Iranian for Parsis indicates that there was more than one generation of males who migrated. They did not contribute mtDNA, but they did contribute genome-wide to Iranian ancestry. There are wide intervals on the dating of this admixture event, but they are consonant oral history that was later written down by the Parsis.

So there you have it. Another example of a population formed from admixture because women hate going to India.

Citation: The genetic legacy of Zoroastrianism in Iran and India: Insights into population structure, gene flow and selection.
Saioa Lopez, Mark G Thomas, Lucy van Dorp, Naser Ansari-Pour, Sarah Stewart, Abigail L Jones, Erik Jelinek, Lounes Chikhi, Tudor Parfitt, Neil Bradman, Michael E Weale, Garrett Hellenthal
bioRxiv 128272; doi:

Genetic variation in human populations and individuals

I’m old enough to remember when we didn’t have a good sense of how many genes humans had. I vaguely recall numbers around 100,000 at first, which in hindsight seems rather like a round and large number. A guess. Then it went to 40,000 in the early 2000s and then further until it converged to some number just below 20,000.

But perhaps more fascinating is that we have a much better catalog of the variation across the whole human genome now. Often friends ask me questions of the form: “so DTC genomic company X has about 800,000 SNPs, is that enough to do much?” To answer such a question you need some basic numbers in your head, as well as what you want to “do.”

First, the human genome has about 3 billion base pairs (3 Gb). That’s a lot. But most of the genome famously doesn’t code for proteins. The exome, the proportion of the genome where bases directly translate into a protein accounts for 1% of the whole genome. That’s 30 million bases (30 Mb). But this small region of the genome is very important, as the vast majority of major disease mutations are found in the exome.

When it comes to a standard 800K SNP chip, which samples 800,000 positions across the 3 Gb genome, it is likely that the designers enriched the marker set for functional positions relevant to diseases. Not all marker positions are created equal. Though even outside of those functional positions there are often nearby SNPs that can “tag” them, so you can infer one from the state of the other.

But are 800,000 positions enough to make good ancestry inference? (to give one example) Yes. 800,000 is actually a substantial proportion of the polymorphism in any given genome. There have been some papers which improved on the numbers in 2015’s A global reference for human genetic variation, but it’s still a good comprehensive review to get an order-of-magnitude sense. The table below gives you a sense of individual variation:

Median autosomal variant sites per genome

When it comes to single nucleotide polymorphisms (SNPs), what SNP chips are getting at, an 800K array should get a substantial proportion of your genome-wide variation. More than enough for ancestry inference or forensics. The singleton column shows mutations specific to the individual.  When focusing on new mutations specific to an individual that might cause disease, singleton large deletions and nonsynonymous SNPs is really where I’d look.

But what about whole populations? The plot to the left shows the count of variants as a function of alternative allele frequency. When we say “SNP”, you really mean variants which exhibit polymorphism at a particular cut-off frequency for the minor allele (often 1%). It is clear that as the minor allele frequency increases in relation to the human reference genome the number of variants decreases.

From the paper:

The majority of variants in the data set are rare: ~64 million autosomal variants have a frequency <0.5%, ~12 million have a frequency between 0.5% and 5%, and only ~8 million have a frequency >5% (Extended Data Fig. 3a). Nevertheless, the majority of variants observed in a single genome are common: just 40,000 to 200,000 of the variants in a typical genome (1–4%) have a frequency <0.5% (Fig. 1c and Extended Data Fig. 3b). As such, we estimate that improved rare variant discovery by deep sequencing our entire sample would at least double the total number of variants in our sample but increase the number of variants in a typical genome by only ~20,000 to 60,000.

An 800K SNP chip will be biased toward the 8 million or so variants with a frequency of 5%. This number gives you a sense of the limited scope of variation in the human genome. 0.27% of the genome captures a lot of the polymorphism.

Citation: 1000 Genomes Project Consortium. “A global reference for human genetic variation.” Nature 526.7571 (2015): 68-74.