A new paper posted on bioArxiv surveys Y chromosomal and mtDNA diversity using over 600 males from the HGDP data set. Their goal is to compare differences in variation and long term demography between the two sexes. This is not an unimportant topic, sex specific demographics are relevant to mating patterns, and effective population size is of broader evolutionary interest in the way they can frame different dynamics. For instance, species with high male reproductive skew and genetic polygyny tend to be subject to more powerful sexual selection, as males have a much larger potential upper reproductive bound (a phenomenon which drives greater sexual dimorphism). This sort of evaluation with the Y and mtDNA has been attempted before, but the power of this data set is greater because they have a much larger fraction of the Y chromosome (500 kilobases) and whole mtDNA genomes (often in the past they used STRs for the Y and only the HVR in the mtDNA). These data from 600 males allowed them to construct the figure you see above, which shows the branching pattern of human migration out of Africa at given time periods, male and female effective population sizes, and later expansions (female red, male blue).
Even accounting for the possible smaller effective population sizes of uniparental lineages due to greater drift (haploid inheritance cuts down the pool of parents) I am struck again by the shockingly small number of inferred individuals who left Africa. It does not seem unreasonable to give a number closer to 100 as opposed to 1,000 for the ur-population which settled the world outside of Africa, at least when it comes to the neo-African ancestry (i.e., excludes the residual archaic admixture). But is the answer so simple? What I’m primarily concerned with is the treelike representation of human migration above. It is highly likely that less than half of the ancestry of modern Europeans dates to the original settlement date given above. So those inferred male and female effective population sizes need to be taken with a grain of salt. Much the same can be said for elsewhere. Additionally, there may have been two Out-of-Africa events in close succession (here I’m alluding to ‘basal Eurasian’ vs. the ancestors of western and eastern Eurasians proper).
Overall I can accept the broad picture painted of greater female effective population sizes, and the rise in reproductive skew in the more recent past is intriguing, and dovetails with particular conjectures of some anthropologists and economists (i.e., a rise of “winner-take-all” stratification). And the small effective population sizes at particular bottleneck events is broadly creditable looking at genome-wide patterns (e.g., high sequence level diversity in Africa vs. non-Africa). But these surveys need more textured detail in this data and age. I hope later revisions will flesh that out, as well as acknowledge the findings of Sayres et al.
Nine women in Sweden have successfully received transplanted wombs donated from relatives and will soon try to become pregnant, the doctor in charge of the pioneering project has revealed.
The women were born without a uterus or had it removed because of cervical cancer. Most are in their 30s and are part of the first major experiment to test whether it is possible to transplant wombs into women so they can give birth to their own children.
Life-saving transplants of organs such as hearts, livers and kidneys have been done for decades and doctors are increasingly transplanting hands, faces and other body parts to improve patients’ quality of life.
For various reasons the Y chromosome is something of a big deal. As you probably recall from high school biology if you are a male you have a Y chromosome, which lacks most functional gene copies, along with an X, which has the full complement of genes.* If you are female you carry two X chromosomes. The redundancy of having two X chromosomes results in the phenomenon of sex-linkage, where recessive traits which are generally masked in one sex are expressed in the other (this is often well known from pathologies, from the mild such as color blindness to the severe such as haemophilia).
But aside from the proximate functional importance, there are bigger evolutionary questions of interest when it comes to the sex chromosomes. About a decade ago the biologist Bryan Sykes floated the possibility of the extinction of human males due to the long term degeneration of the Y chromosome. The reasoning is straightforward. Because most of the Y chromosome is non-recombining it can not easily purge deleterious mutations which have been fixed within a population, since these will be linked with all the other loci. In contrast in the recombining genome favored and disfavored alleles will be mixed in match. Over time the Y chromosome tends to degenerate as most of the functionality becomes biased towards sexual phenotypes, such as the SRY region. A major problem with this sort of model (which Sykes himself mentions) is that it seems that sex chromosomes have emerged multiple times across multiple lineages, and also disappeared as well. The chromosomal organization of a species is not a static and fixed aspect of their construction, but a function of evolutionary processes through duplications and fusions. A “Y chromosome” does not magically make a male a male, especially seeing as how there are males in lineages without the Y chromosomes (in birds the females are the heterogametic sex).
But the lack of recombination is not always a problem. It is because the Y chromosome, like mitochondrial DNA, does not recombine that it is extremely amenable to phylogenetic inference using a coalescent framework. Most of the genome subject to recombination is constantly sliced, diced, and amalgamated, in a fashion which makes inference of genetic lineages difficult. In contrast the mtDNA and Y are inherited as long blocks of genes with numerous variants which generate long haplotypes that can be useful information in reconstructing trees of ancestry and descent. Though limited to the male line of descent the utility of the Y for this reason made it extremely useful for phylogeographic studies in the late 1990s and early 2000s, culminating in works such as Spencer Wells’ The Journey of Man. Though there are still Y chromosomal studies being published, with whole-genome sequences and large sample sizes, the golden years of this program are likely past us.
One of the primary assumptions behind these genealogical trees was that variation was being generated in a neutral fashion. By this, I mean that genetic variation was being distributed through random forces, and so that variation was a reasonable proxy for the demographic history of the populations. A new paper in PLoS GENETICS adds some nuance into this bigger picture, Natural Selection Reduced Diversity on Human Y Chromosomes. Various versions of this paper have been floating around for several years, and the earliest I knew about the general thesis was at ASHG 2012. The basic observation is that the diversity of the Y chromosome is far lower than it should be. Much of the early work on Y chromosomal phyogenetics was done with microsatellites, highly repetitive and mutable regions of the genome. While the mutation rate of SNPs might be 10-8, microsatellites turn over on the order of 10-4. This makes them highly informative for forensic purposes, and also allows one to differentiate very similar populations. Initial attempts to use SNPs on the Y chromosome failed because the variation was too low. Today with more powerful genomic techniques those obstacles are gone, and a reasonable number of whole-genome analyses of Y chromosomes have been performed.
The research in the paper above focuses on 16 individuals sequenced on the Y from Africa and Europe. One conventional explanation for why the Y is so much less diverse is that there is a reproductive skew among males, so that the male effective population is lower. This means that there is less variation being sampled from for males than females every generation, so in terms of diversity your rank order should be Y < autosomal < X chromsome < mtDNA. But using forward simulations and modulating the sex ratio it was clear that reproductive skew could not explain the extremely low diversity of the human Y chromosome.
An alternative explanation would be selection. In particular they found evidence of selection of the purifying form, where deleterious alleles are removed, but along with them linked regions of the genome. In the case of the Y that linked region would be the whole chromosome, perhaps explaining the low diversity as variation is constantly removed by functional constraint. Intriguingly the authors also found that mutations around nonsynonymous regions of the genome which code for protein could not account for the effect they were seeing. Rather, they suggested that ampliconic regions (repetitive sequences) are being constrained strongly. There’s a lot of molecular genetic detail at this point (e.g., intra-chromosomal interactions), and I won’t go into it, but it seems that it is correct that researchers should now focus on these genomic regions to understand what’s going on in terms of mechanistic detail. There is more to be imagined in the Y than in the wildest dreams of our philosophy!
Finally, let me reiterate these results do not invalidate the nearly two decades of Y chromosomal phylogenetics. Background selection has the same effect across the topology, so the shape would be maintained, though the branch lengths would shorten. In other words the coalescence of Y chromosomal lineages might be deeper than has currently be implied. But all these results are inferred from 16 genomes. There are many more whole-genomes out there, and a more thorough survey seems necessary. It seems that the authors could not reject the possibility that composite positive selection across different lineages were responsible for some of the decrease in diversity. If this was the case then our Y chromosomal phylogenies would in fact be totally misleading in terms of true demographic history.
In Peter Heather’s The Fall of the Roman Empire the author relates how the aristocratic elite of ancient Rome could recognize each other by the manners of speech and the literary allusions made in casual conversation. Despite the militarization of the late Empire, elite Roman society remained a fundamentally civilian and lettered subculture. The first Roman Emperor who was reputedly illiterate did not ascend to the purple until the 6th century, and this may itself have been a scurrilous accusation by his enemies. A similar ethos of cultured learning permeated much of the Chinese ruling class for most of the history of that civilization. This stands in contrast to the orientation of the aristocracy of Europe after the fall of Rome, which was fundamentally that of a barbarian warrior caste which overthrew the old Roman order, even if it genuflected in a superficial sense to their predecessors. Charlemagne was responsible for the preservation of much of ancient learning through his patronage of the Carolingian Renaissance, but the first Holy Roman Emperor never learned to write. Despite their real cultivation of the arts and sciences, the European nobility did not transition away from a martial ethos until the rise of firearms, which led to the transformation of war into a process which involved mobilization of nations, as opposed to a personalized clash between ruling classes.
The point is that societies organize themselves around a particular ethos. In traditional societies since the Neolithic Revolution the numerous sons of the ruling class have found various ways to form bonds, whether on the fields of battle, or in the halls of the academy. The milieu is less important than the fact that those bonds must be made in some fashion. Individuals must have common currency of experience, whether concrete or intellectual. Two strangers who may not know each other may still feel some comfort if they fought in the same battle, or absorbed the same book. Therefore the Classical and Chinese elites looked to specific literary touchstones which would have been read by all. This model isn’t unfamiliar to us, as post-Renaissance European culture resurrected classical education as a form of preparing males of the ruling elite for their role in society.
This is the perspective and framework I bring to the table when attempting to understand what is going on with the latest flair up over the humanities in the academy within the broader culture. It began with a column by my friend Heather Mac Donald, The Humanities Have Forgotten Their Humanity. In Slate Rebecca Schuman responded with the perspective of what I take to be the average academic humanist, pointing to an even stronger response from a faculty member at Yale. You can read the opinions of the protagonists yourself. Rather than deconstructing particular arguments, I will admit right now that most fundamentally humanistic production is a matter of politics, insofar as it reflects and projects what we think is of value in the social order. And it is always important to remember who the particular “we” is. In the American contexts conservatives tend to defend Great Books in the fashion which Mortimer Adler would understand. In contrast the literary academic avant-garde is naturally rather unenthusiastic about reflection upon a static canon. I am not a Platonist about literature or human creative production, and have some understanding and sympathy for those who would favor a more flexible understanding of the canon. But ultimately I tend to side with conservative critiques for two different specific reasons. The first is one of depth, and the second one of breadth. In short, too much of both.
In regards to the first I believe that close reading often devolves into a process of such irrelevancy that it is like extracting blood from a rock. Of course close reading in a modern sense has an ancient pedigree in terms of the exegetic glosses which were common forms of intellectual production in the domains of philosophy and religion for several thousand years. I believe that these earlier endeavors were frankly a waste of time, in that they did not contribute much to the broader society and had little substantive content in and of themselves aside from advancing narrow professional careers. I believe that contemporary attempts at close reading are nothing more than intellectual masturbation sessions, analogous to the later incarnations of medieval scholasticism. What would be far more fruitful than reading works closely would be to produce one’s own works, even if they might not measure up. Creativity in that sense is at least future-directed, and in keeping with the whiggish sensibility at the heart of modern society.
The second problem I see with modern humanistic “discourse” is that it is highly fragmented, unfocused, and selective. With the academy scattering out across domains of “race, class, gender, sexuality, and disability” as perspectives and paradigms it has lost both broad universal relevance and also began to give rise to politically preferred silos. As I argued above a coherent society requires an ethos, and an emphasis on the lack of a unified ethos (“diversity”) is both incoherent and futile. The modern secular academy does not focus too much on the whole area of evangelical Christian fiction to my knowledge. Why? Because for some reason this domain of religious diversity is not of particular interest to many scholars. That is totally acceptable, but, it does point out that the range of diversity explored in the modern academy is delimited by their own presuppositions (notice that the quote above from the Yale academic leaves out religion, which is arguably one of the most important fissures in modern society).
With the rise of diverse perspectives individuals are now becoming fragmented even more than their “race, class, gender, sexuality, and disability” would imply, because they lack access to the same common vocabulary of ideas. This is a tragedy because the reality is that most literary themes do reflect human universal impulses and conditions. One might state them in spare aphoristic forms, but we are a storytelling species, and embedded within a narrative they are much more likely to spread, persist, and impact. The fracturing of the narrative shatters even the barest pretense of elite coherency, and likely will add to confusions which might not otherwise emerge.
Finally, on a less relativistic and instrumental note, I suspect one reason many revolt against literary narratives of dissent from particular subcultures is that we haven’t had enough time to discern the great from the not-so-great in many areas. The canons of the traditional civilizations have accumulated organically over time over thousands of years. A list of great works in queer literature is going to be the opinion of a small number of professors who matured in the same recent intellectual milieu. It is unlikely that it will be as stellar a series of narrative works simply because top-down judgment by critics with the same intellectual orientations is unlikely to be a very good sifter.
Ultimately the reason that the conservative vision of Shakespeare etc. is appealing is because they have a coherent vision. In contrast the modern humanistic academy seems to think they are the revolutionary vanguard of cultural change. Perhaps they are, but in that case they should not be surprised when the non-revolutionary majority rejects their project and deems it abhorrent.
A phenotypic takeaway from the ancient European DNA preprint has been that the hunter-gatherer from Luxembourg was light eyed and darker skinned (and dark haired), while the early farmer from Germany was lighter skinned and darker eyed (and dark haired). In yesterday’s post a reader pointed out that I misinterpreted the genotypes of these two individuals at a very important pigmentation locus: I thought that it was homozygous for the lighter skin conferring allele which is at very high frequency in modern Europeans. I was wrong. A SNP at this locus, SLC45A2, correlated with darker complexion and eyes, is present at ~3% in Europeans (as opposed to ~100% in East Asia and Sub-Saharan Africa). In a European American sample the genotypes are as follows:
Both the hunter-gather and the farmer are CC. Combined with the hunter-gatherer being GG (which is nearly absent in modern Europeans) at SLC24A5 it does seem that as the authors of the preprint were right, the hunter-gatherer had darker skin. The twist is that the region of the genome, OCA2/HERC2, that seems to explain most of the blue vs. non-blue eye color difference in Europe, is homozygous for the blue variant in the hunter-gatherer. I would say that if I had just the pigmentation loci I would think that the hunter-gatherer in this study was from a population mixed between Europeans and non-Europeans. For example, inhabitants of Cape Verde.
The hunter-gatherer individual sequenced from Loschbour rock shelter may be an anomaly. But you wouldn’t find this sort of individual among modern Europeans without recent non-European ancestry, even as an anomaly. So there’s something to explain.
One of the most interesting results in the preprint on ancient European genetics (or more accurately, the ethnogenesis of Europeans in a genetic sense) is the fact that the ~8,000 year old hunter-gatherer sample from Luxembourg had a GG genotype on the SLC24A5 locus. Actually, interesting isn’t the right word, shock, and frankly a little skepticism is more precise. The reason for my reflexive incredulity is that the GG genotype is very much the minor variant in Western Eurasia, and extremely rare among unadmixed Europeans. Europeans have such a high fraction of the A allele that some population genetic statistics to test for selection at a locus are not viable, because there’s not enough variation segregating in that region. This allele also is present outside of Europe, with the A allele being the major variant in South Asians, albeit at a lower fraction, verging on ~50% or less in some South Indian groups. Yet it is not entirely implausible that this allele only swept to fixation over the past 8,000 years in Europe looking at the genomic features* of the region in which it is embedded.
I want to make more concrete why this result is a pretty big deal. If you look at the 1000 Genomes data you have results for British, Finnish, Tuscan, and Spanish individuals, as well as a well characterized sample of white Utahans of Northwest European heritage. There is also a less well characterized pooled data set of “European Americans.” Here are the genotype counts by population:
Yesterday on Twitter I suggested that I’d want at least 10,000 individuals of unadmixed Northern European ancestry before I might take a bet that I’d find someone with a GG genotype. I don’t think I was exaggerating. The sample size might be one, but the fact that the individual was homozygous for GG implies to me that the G allele was present at a far higher fraction in Northern Europe 8,000 years ago than today. In contrast the LBK farmer individual was AA on SLC24A5. Why this matters functionally is that no matter how you look at it, when comparing Europeans and dark skinned populations (e.g., Africans, South Indians, and Australasians) this locus is the one that explains the highest proportion of the variation on pigmentation of any gene. Comparing simply people of African ancestry and Europeans the variation at this gene accounts for on the order of ~1/3 of the difference.** I myself have the “European” AA genotype, with most of my other large effect loci being of the “dark” correlated alleles. The pigmentation difference between a Sub-Saharan African and myself is probably accounted for just by this locus alone. But a twist on this story is that the hunter-gatherer also exhibited the genotype associated with blue eyes in Europeans. In contrast, the farmer genotype was the one not correlated with blue eyes. On another locus which is not quite fixed for a derived light encoding variant, but very close in Europeans (and found in much lower proportions in other West Eurasians), SLC45A2, it looks as if both the hunter-gatherer and the farmer carry the modal European form.
Rather that squeezing too much more out of a few samples, I want to posit that these results increase the plausibility that the suite of genetic variants across many loci which are often diagnostic of the complexion of Northern Europeans are a function of a combination of admixture and then selection within the resultant Northwest European lineages. It seems plausible that independent selection events were occurring across these groups, and with admixture more novel variants were present in the combined population which allowed for a skew even further along the phenotypic continuum, toward the physiological limit (at least for non-albinos). Though it looks like the majority of the ancestry of Northern Europeans, especially populations around the coastal East Baltic region, derive from hunter-gatherer groups indigenous to the continent (i.e., pre-Holocene), if they were not fixed for the derived variant on SLC24A5 it seems implausible that these ur-Europeans were defined by the rosy complexions which are archetypical for Northern Europeans. This is part of the broader picture whereby the phenotypically salient population clusters we see around us today, as if they are Platonic ideals of underlying racial forms, may themselves be phenomena distinctive to the Holocene.
* A large correlated block of markers which seem to have risen in frequency recently and rapidly within the population.
** Northeast Asians have their own distinct mutations which confer light skin.
Update: This is a piece from last June, so not actually timely. Rather, it was being passed around on Twitter recently. So I’m wrong in some details of when the piece as published, but I think my point about the “take home” of Wilcox’s profile as a public intellectual still holds water.
Totally on cue after my last postThe Atlantic has a piece out from the omnipresent W. Bradford Wilcox, The Distinct, Positive Impact of a Good Dad. The portions of the article outlining the descriptions of how fathers interact differently with their offspring are totally unpersuasive to me for the reasons I’ve outlined earlier: I believe on average many long term life outcomes which are due to cultural influences are from one’s milieu, one’s “village” so to speak, not one’s parents. The more interesting and superficially persuasive element of Wilcox’s argument has to do with correlations. In particular:
The story told by this data, then, suggests that there is a case to make against the fathers who fail to have good-enough relationships with their children. At least on these outcomes, single mothers do about as well for their children, compared to dads who have poor-quality relationships with their children. By contrast, great, and even good-enough dads, appear to make a real difference in their children’s lives.
I accept the correlations. But I think Wilcox’s case is totally gene-blind.* To illustrate the problem, imagine that you saw a correlation between fathers and sons in terms of empathy. One hypothesis might be that children learn how to engage with others from seeing how their parents engage with others. But another model would take into account genetic dispositions in personality.** When Wilcox reports that individuals who had a bad relationship with their parents have worse life outcomes he neglects to consider that these parent-offspring pairs may share a heritable disposition toward disagreeability.
When I say fathers don’t matter that much, I mean that some of the correlation that you see in these sorts of comparisons are almost certainly due to heritable dispositions which lead to a wide range of life outcomes. For example, having a quick temper and being unable to suppress your emotional responses are going to cause problems within your family and probably diminish chances for success in the workplace. If this tendency is heritable in any way you’re naturally going to see a correlation between families with violence and strife, and offspring who have lower career success and familial stability than their intelligence or education might predict. Of course it is likely that fathers matter in substantive ways. The problem is simply to attribute all of the effect seen in these studies to the environmental shaping of paternal behavior. Sperm matters.
* More precisely, he’s heritability-blind, but you get the picture.
** For readers who are not clear on this, I believe cultural norms are probably the biggest variable which explains many personality traits. Though variation within cultures is still going to be substantially heritable.
As a parent it is important to me that my daughter grow up in the context of a two-parent monogamous household. Not only do I find this arrangement congenial for a variety of personal reasons, it is also what society is most optimally set up for. But there is a strong class element today in the United States as to the realization of this ideal. While 94 percent of college educated women giving birth are married, 57 percent of women with a high school education or less are unmarried when they have their first child. These striking correlations emphasize to many social conservatives the importance of marriage in shaping individual outcomes.* The lesson being that if you get get married and complete your education you will not be poor. What immediately comes to mind though is that those who do not get married and finish their education are not an arbitrary subset of the population. For example, they are less likely to have a range of personality traits which allow for trading off utility in the short term for gains in the long term. Giving someone a marriage license and keeping them locked in school may not change these underlying habits of mine and behavior. But this attitude toward the causes and dynamics at work in social ills is not limited to ideological conservatives. It is a widespread view informed by common sense observations. Though many individuals from broken homes do very well, on the whole it is clear from anecdotes and social science that this life history adds stress and diminishes life prospects.
Or does it? Over ten years ago Judith Rich Harris published The Nurture Assumption: Why Children Turn Out the Way They Do. Though the basic argument of the book, which draws from peer-reviewed behavior genetic literature, was outlined extensively in The Blank Slate, it has gotten very little broad cultural traction (though it occasionally pops into the public discussion thanks to economists such as Bryan Caplan and Steven Levitt, who see similar patterns as the behavior geneticists). The primary lesson is that main distinctive contribution parents seem to make to the outcomes of their children in a behavioral and social sense is their genetic contribution. This does not mean that behavioral traits are primarily genetic in terms of explaining the variation in outcomes. Rather, it means that the environmental contribution is not something that parents have much direct control over. In The Nurture Assumption the author proposes that the primary environmental causal factor are peer groups. Though this has not been extensively validated to my knowledge, it seems a plausible enough candidate. For example, children tend to speak with the accents and lexicon of their friends, not that of their parents. If upper-class parents from a particular region share linguistic characteristics with their offspring, it has little to do with the direct parental modeling, as opposed to being embedded in a common social milieu.
As the year progresses you will read a great deal in the press about sociological dynamics and how they effect individuals, often for the worse. In response conservatives will point to the importance of individual responsibility and collective norms in enforcing ideal behavior and life outcomes. Liberals will allude to various structural factors which set up people to make wrong choices, and various governmental solutions which might mitigate and even counter-act these forces. What both viewpoints will neglect is that much of the variation in outcomes in individuals, and across social sets, is likely due to heritable differences in personality. In plainer language individual differences matter, much of which is due to genetic differences. To illustrate what I am talking about, consider the robust correlation between children who are abused who abuse then their own offspring when they become parents. A commonsense explanation here is that inappropriate behavior was modeled, and the parents are now recapitulating what they learned. But one immediate issue that comes to mind is that parents who beat their children with no compunction may have a particular personality profile tending toward low empathy and lack of self-control. This personality profile is likely heritable, and passed to their offspring, who naturally exhibit the same characteristics.
The complexity of life outcomes is such that we must be cautious about how we appropriate the weight of a given causal factor on a social, let alone individual, level. When it comes to complex traits with a genetic component how that variation manifests on a social level is strongly conditioned by cultural context. In a society where physical punishment of children is highly normative abuse may not be due to any personality profile at all, because most people are conformist enough that they follow the broader script. Perhaps it is in societies where the norm is changing and not standardized where personal dispositions come most strongly into play as a factor. Similarly, when it comes to a social ideal like marriage obviously cultural headwinds were such that two generations ago no matter your personality profile the expectation of being wedded was so strong that most individuals fell into line. My point is that as you read story after story this year about the impact of various purely social forces in the media, do not neglect the power of genetic variation in many phenomena. It will give you a better and more complete understanding of what’s really going on, which is the point of it all in the end….
Addendum: Long-standing readers may wonder why I’m posting this, since it’s not particularly original. Because every now and then the unoriginal needs to be restated, because it’s actually original to many.
* It is critical to note that lower SES individuals actually value the idea of marriage as much, or more, than higher SES individuals. Rather, they fail to realize their ideal. Often the idealization of marriage manifests with individuals marrying after the birth of their first child, in some haste.