The pregnancy wars

I don’t currently have time to read Emily Oster’s Expecting Better: Why the Conventional Pregnancy Wisdom Is Wrong and What YouReally Need to Know, but I am very excited that it came out. Having had a pregnant wife and becoming a parent has made it clear to me that much of ‘conventional wisdom’ in regards to both parenting and pregnancy are socially enforced norms which have marginal empirical grounding (this is clear when you look at the huge variation in cross-cultural expectations even in developing societies). So I’m glad that Oster is pushing this issue in a somewhat more rational and hard-headed fashion that has previously been the case (i.e., some of people who I think have good ideas about skepticism of the idea that every pregnancy is a medical emergency waiting to happen at any moment, also try to sell you on ‘alternative medicine’ more generally). It doesn’t help that she’s within the penumbra of University of Chicago’s academic celebrity.

But the reason I’m posting right now is that the book’s Amazon page is a case in point in regards to the intersection between pregnancy and the culture wars. Of 50 reviews as of this writing 20 give it five stars, 2 give it two stars, and 28 give it 1 star!

Indo-Aryans, Dravidians, and waves of admixture (migration?)

Citation: Genetic Evidence for Recent Population Mixture in India
Moorjani et al.

The Pith:In India 5,000 years ago there were the hunter-gathers. Then came the Dravidian farmers. Finally came the Indo-Aryan cattle herders.

There is a new paper out of the Reich lab, Genetic Evidence for Recent Population Mixture in India, which follows up on their seminal 2009 work, Reconstructing Indian Population History. I don’t have time right now to do justice to it, but as noted this morning in the press, it is “carefully and cautiously crafted.” Since I am not associated with the study, I do not have to be cautious and careful, so I will be frank in terms of what I think these results imply (note that confidence on many assertions below are modest). Though less crazy in a bald-faced sense than another recent result which came out of the Reich lab, this paper is arguably more explosive because of its historical and social valence in the Indian subcontinent. There has been a trend over the past few years of scholars in the humanities engaging in deconstruction and intellectual archaeology which overturns old historical orthodoxies, understandings, and leaves the historiography of a particular topic of study in a chaotic mess. From where I stand the Reich lab and its confederates are doing the same, but instead of attacking the past with cunning verbal sophistry (I’m looking at you postcolonial“theorists”), they are taking a sledge-hammer of statistical genetics and ripping apart paradigms woven together by innumerable threads. I am not sure that they even understand the depths of the havoc they’re going to unleash, but all the argumentation in the world will not stand up to science in the end, we know that.

Since the paper is not open access, let me give you the abstract first:

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Y, mtDNA, Adam, & Eve

For various reasons the idea of mitochondrial Eve and Y chromosomal Adam capture the public imagination. This frustrates many people, including me. I’ve gotten into the fatigue stage on this topic, but some sort of counter-attack is necessary against malignant memes. Even geneticists who don’t usually work with populations can get confused by the implications of mtDNA and Y chromosomal phylogenies. Melissa Wilson Sayres, who works on Y chromosomes, has a useful post (promised first of two) at Panda’s Thumb, Y and mtDNA are not Adam and Eve: Part 1. If you have friends/acquaintances who are confused by this issue, it might be a good place to start.

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Pigmentation, phylogeny, history, and adaptation

SLC45A2 rs16891982 frequency, Norton, Heather L., et al. “Genetic evidence for the convergent evolution of light skin in Europeans and East Asians.” Molecular biology and evolution 24.3 (2007): 710-722.

The above figure is from Norton et al.’s Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. It shows that rs16891982 on the SLC45A2 locus exhibits strong differentiation between Europe and the rest of the world. This is in contrast to SLC24A5, where the well known allele which differentiates Africans/East Asians from Europeans is found at very high frequencies across Western Eurasia (both my parents are homozygotes for the “European” variant; in fact SLC24A5’s derived variant is found at fractions on the order of ~50% in eastern and southern India). The ancestral allele on SLC24A5 is very difficult to find in Europeans, it is so close to fixation for the derived variant. In contrast SLC45A2‘s minor allele is segregating at appreciable frequencies in places like southern Spain, and the derived allele is not fixed even in Northern Europe.

I won’t review the literature on the genomics and evolution of human pigmentation at this point. Rather, I’ll just note that it seems most of the inter-population variation is controlled by a handful of genes. It’s a polygenic trait, but just. Second, a fair amount of evidence has emerged that some of the lightening derived variants have increased in frequency only very recently (e.g., on the order of ~10,000 years). Pigmentation is then a peculiar trait where the genetic underpinnings can give historical phylogenetic information because of the varied dates of differentiation and selective sweeps.

Below I’ve collated results from several studies on frequencies of SLC45A2. I invite readers to persue them. I will say two things. First, the frequency of the “European” variant in ~140 northern Ethiopians is 0%. This is peculiar for a population which may be on the order of ~50% West Eurasian. Second, the fraction of SLC45A2 derived variant in South Asians coincidentally tracks the “NE Euro” percentage in Zack Ajmal’s results.

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The Sports Gene, not as reductive as the title

Sports Illustrated writer David Epstein has a new book out, The Sports Gene: Inside the Science of Extraordinary Athletic Performance. The title strikes me as coarse and reductive, but I am aware that authors do not always have control over such things. I’ve corresponded with Epstein a bit over the past year, and he’s sent me some passages relating to human evolutionary genetics and paleoanthropology to me to make sure they don’t sound crazy. I haven’t had time to read the book, but judging from the interview I listened to on NPR it’s data rich and theory subtle. Though the title seems to imply that athleticism is a single gene trait where most of the variation in the population is due to genetic variation, Epstein denies this and instead presents the reality that athleticism is a complex trait which many dimensions, subject to numerous genetic and environment variables, and, interactions across those variables. That would make for a less sexy subtitle, but it would have had the attribute of being correct.

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Selection everlasting, suppositions no more

The Biometrician
I have alluded over the years to the early 20th century conflict between Mendelians, who were proto-geneticists, and the biometricians, who were classical Darwinians. As if in a Hegelian dialectic this clash of egos eventually lead to the synthesis which became population genetics. The historical process is outlined beautifully in Will Provine’s The Origins of Theoretical Population Genetics, but at the time it bore fruit in R. A. Fisher’s 1918 paper The Correlation between Relatives on the Supposition of Mendelian Inheritance. One might argue that though this publication ended the explicit debate and division, the reality is that the difference continued, not because of fundamental differences, but pragmatic ones. Classical population geneticists focused on single or two locus models to develop their intuitions about the trajectory of evolutionary processes. Quantitative geneticists refined their statistical techniques of inference on continuous characters whose heritable character was confirmed, but whose specific causal genetic elements remained mysterious.

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Mention Adam and Eve, and the press shall come

There were two papers in Science which came out on the Y chromosome, Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females and Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. I can recommend what Dienekes had to say, and I wasn’t going to comment until I saw this egregious piece in The New Scientist: Arabian flights: Early humans diverged in 150 years. Because of the title I did not initially think that this had anything to do with the Y chromosome, but it turns out that the piece uses the finding that three primary non-African haplogroups diverged in rapid succession from each other as the hook for the headline. In fact not only does the Y not offer definitive accounts of human history, it doesn’t even necessarily tell us about the history of men. It’s a marker, not a time machine. To repeat: the history of a specific genetic locus is not the history of a population. It has to be said.