Self-reported ethnicity was an imperfect indicator of genetic ancestry, with 9% of individuals having >50% genetic ancestry from a lineage inconsistent with self-reported ethnicity. Limitations of self-reported ethnicity led to missed carriers in at-risk populations: for 10 ECS conditions, patients with intermediate genetic ancestry backgrounds—who did not self-report the associated ethnicity—had significantly elevated carrier risk. Finally, for 7 of the 16 conditions included in current screening guidelines, most carriers were not from the population the guideline aimed to serve.
It’s long been known that a certain percentage of people for various reasons give an ethnic background that doesn’t match their total genome. This is a problem because of the frequency of carriers varies by population. I first began to be curious about this issue 15 years ago. Today there is no excuse in my opinion for not genotyping if you are a hospital.
The wholesale costs of SNP-arrays are $25, and there are pretty simple turn-key ancestry inference algorithms. This doesn’t need to be an issue. This is 2020.
I have set up an account on Book Shop. Right now I put up a few history books. This is a better deal for me in regards to referrals than Amazon, though these are physical books only.
I haven’t been posting “Open Threads” as much because I’ve been busy. Sorry-not-sorry. Life happens. Though blogs are dead, my Brown Pundits blog is pulling in more than 200+ comments for each open thread. I wonder if people are tired of “discussing” on Twitter.
Behavioral genetics and cultural evolution have both revolutionized our understanding of human behavior, but largely independently of each other. Here we reconcile these two fields using a dual inheritance approach, which offers a more nuanced understanding of the interaction between genes and culture, and a resolution to several long-standing puzzles. For example, by neglecting how human environments are extensively shaped by cultural dynamics, behavioral genetic approaches systematically inflate heritability estimates and thereby overestimate the genetic basis of human behavior. A WEIRD gene problem obscures this inflation. Considering both genetic and cultural evolutionary forces, heritability scores become less a property of a trait and more a moving target that responds to cultural and social changes. Ignoring cultural evolutionary forces leads to an over-simplified model of gene-to-phenotype causality. When cumulative culture functionally overlaps with genes, genetic effects become masked, or even reversed, and the causal effect of an identified gene is confounded with features of the cultural environment, specific to a particular society at a particular time. This framework helps explain why it is easier to discover genes for deficiencies than genes for abilities. With this framework, we predict the ways in which heritability should differ between societies, between socioeconomic levels within some societies but not others, and over the life course. An integrated cultural evolutionary behavioral genetics cuts through the nature-nurture debate and elucidates controversial topics such as general intelligence.
I’m not sure that the modeling here really solved things too much, though it pushed the ball forward. But in any case, a cultural evolution framework clarifies and makes more precise what was always well understood from a quantitative and behavior genetic approach. Heritability is simply a population-level statistic that is always conditional on various environmental parameters. The heritability of height and intelligence likely are both higher in WEIRD environments because of cultural homogeneity. The homogeneity reduces the environmental factor and increases the impact of genetics on variation.
The authors take pains to distinguish their framework from gene-environmental interactions or gene-environment correlations. These two are widely explored in the behavior genetic literature. Rather, they suggest that cultural evolutionary pressures and characteristics over time modulate the effect size and direction of various SNPs on a trait. They suggest that cultural evolutionary modeling can help more easily explain the Flynn effect.
This preprint makes a lot more sense when you consider that the last author has written about the importance of theory in understanding and exploring scientific domains. I think the big theme of this preprint is basically to remove the environment from the domain of ad hoc noise residuals. In fact, they state this clearly, insofar as cultural variation is not simply ad hoc noise, but often exhibits directionality. In societies with more environmental variance on a trait, obviously the heritability will be lower, and vice versa. These are novel enough insights, though I’m not sure that one can say the problems were solved in their dual-inheritance modeling.
Update: I received the below from a friend who has a long critique of this preprint.
Reading Joe Henrich’s newest book I realized some things about my own life, which led me to a weird hypothesis: the WEIRDest people in the USA could very well be the children of Asian immigrant professionals in the 1970s and 1980s.
As I was growing up there was always a large cultural chasm between my parents and myself. I always attributed this to my personality, a natural individualist and liberal orientation in the broad sense. There were other children of these immigrants who were more traditionalist, after all. So there were natural dispositions that varied. At least that was my thought.
Without getting into personal details though, recently I found out that many of the young women I grew up within our family’s small Indian, Bangladeshi, and Pakistani, social circle are not married. Most are successful professionals. In many ways far more successful than me! (e.g., I’m thinking of a girl who graduated from Yale Law, for example). There were way too many professional unmarried women to think of this cohort as “traditionalist.”
My parents have plenty of non-Western values and preferences. But when they arrived in the United States in the early 1980s they were the only members of their whole families who lived in North America. I did not grow up with a rich and nourishing extended family network, because I had no one in my family outside of the nuclear family. To be frank I grew up a bit jealous of my friends who would visit their cousins since my cousins were simply vague names and faint memories. Growing up in a small town in eastern Oregon there was no one of my notional religion and hardly anyone of my race. There were families who were well known around town, and with hindsight, I assume that they would help their nieces and nephews with summer jobs and other such things. I could not, and never did, rely on such informal networks. I lacked such networks. All I could rely on were explicit and formally objective institutions and systems.
Finally, this individuality did not just apply to me. My parents moved themselves to a foreign country without any social or familial network. In various ways, over time they rebuilt something of a non-kin community, but it took literally decades. They didn’t just have shallow roots, they had no roots. Like me, they relied on explicit formal institutions and systems. That was all they had.
Obviously it is somewhat different for later generations. The immigrants of the 1970s and 1980s sponsored their relatives. And in the 1990s a massive wave of Asians into places like Silicon Valley allowed for the emergence of genuine enclaves in a fashion that wouldn’t be imaginable in previous generations. In many ways, the Indian American Zoomers are probably more Indian than the Indian American Gen-Xers.
Three months ago, early on in the quarantine, I purchased some Louisiana Brand Habanero Hot Sauce. In fact, I purchased 1 gallon. The reason was quarantine. I was clearly not going to go shopping for small batches, so I wanted a big one. And I wanted it to be hot, and have a simple and clean flavor. And Louisiana Brand Habanero was just that.
Now that three months have passed, I’m almost out. So I purchased some more. I will try other hot sauces, but this stuff really gets me 80-90% of the way there, and as long as we’re not really going shopping in person this seems best (I used to use Fuego, but it all seemed a bit precious).
Anyway, if The Fall of Romethe history book you should get, this is the hot sauce equivalent.
The police in China are collecting blood samples from men and boys from across the country to build a genetic map of its roughly 700 million males, giving the authorities a powerful new tool for their emerging high-tech surveillance state.
They have swept across the country since late 2017 to collect enough samples to build a vast DNA database, according to a new study published on Wednesday by the Australian Strategic Policy Institute, a research organization, based on documents also reviewed by The New York Times. With this database, the authorities would be able to track down a man’s male relatives using only that man’s blood, saliva or other genetic material.
An American company, Thermo Fisher, is helping: The Massachusetts company has sold testing kits to the Chinese police tailored to their specifications. American lawmakers have criticized Thermo Fisher for selling equipment to the Chinese authorities, but the company has defended its business.
I don’t have much to say, though you should read the piece. This is a vision of a particular future. I am obviously concerned, but I think I have to frankly “grade on a curve” here. The Chinese state already has an incredible amount of power and control over its citizens. The genetic angle is much more of a movement on the margins than a qualitative change in anything. Genes are not magic, but phone tracking is.
As for the involvement of American companies, I don’t know what to say. Have you stopped buying Chinese products?
The power of ancient DNA in terms of human evolution at this point is to a large extent the ability to understand the arc of human cultural history as reflected in our genealogies. Archaeologists have long attempted to infer aspects of social and cultural practice from material remains. Now, geneticists are getting into this game, with mixed results.
Today the Bradley lab in Ireland published a paper about the genetics of Neolithic Ireland (i.e., before the arrival of Bell Beakers ~2,500 BC). The first author is Lara Cassidy, who I interviewed last year. There is a reason this paper is in Nature.
Let me quote the abstract first:
…The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive…Although co-operative ideology has often been emphasized as a driver of megalith construction…the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy…Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites—specifically within polygynous and patrilineal royal families that are headed by god-king…We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.
There’s a lot of moving parts in this research, and the most interesting element isn’t the genetics, but the social structure that you can infer from the genetics. It seems entirely likely that the “Megalithic civilization” of Atlantic Europe was hierarchal. But this pretty much confirms it. As noted in the paper violations of first-order incest taboos as a cultural norm (as opposed to deviancy) are strongly associated with very stratified preliterate or semiliterate societies (with the possible exception of Zoroastrianism). Additionally, this research highlights that a set of individuals, likely paternally related, seem to be enriched in elite burials.
In a few circles, there are ideas that Neolithic Europeans were peaceful and matrilineal. The existence of stratification like this and the likelihood of ‘god-kings’ makes that very unlikely in Ireland. Though there was no doubt some variation in Neolithic Europe, the existence of “long-houses” in Germany from contemporary cultures is ominous. The matrilineal element is distinct. There are matrilineal societies that are quite warlike (e.g., the Nairs of Kerala or the Iroquois). But the possibility of common Y chromosomes suggests that this was a patrilineal society, which is, on the whole, more common anthropologically.
To me this is the most awesome part of the paper:
The Brú na Bóinne passage tombs appear in Medieval mythology that relates their construction to magical manipulations of the solar cycle by a tribe of gods, which has led to unresolved speculation about the durability of oral traditions across millennia…Although such longevity seems unlikely, our results strongly resonate with mythology that was first recorded in the eleventh century AD, in which a builder-king restarts the daily solar cycle by copulating with his sister…Fertae Chuile, a Middle Irish placename for the Dowth passage tomb (which neighbours Newgrange), is based on this lore, and can be translated as ‘Hill of Sin’ or ‘Hill of Incest’…
This is incredible. Unless you are set in your ways I think it is hard to deny that the medieval Irish were passing on a recollection in their myth from an encounter between Bell Beakers and the late descendants of the Newgrange people. In The Isles Norman Davies argues that the Irish, unlike the English and the British more generally (Brythonic), kept their own mythology, and so have a sense of their past in a way that is uncommon among Northern European peoples. The Irish legends imply that there were multiple waves of people, and it is assumed that the people who live in the great mounds are the Tuatha Dé Danann, who became ancient Irish demigods.
I suspect that the early Bell Beakers viewed the monuments of the Tuatha Dé Danann, the Newgrange people, like how some Americans view “Indian graveyards.” Even among modern people, there is superstition, so what can we expect from the ancients? The Greeks forgot their heritage and assumed that the cyclopean citadels of their ancestors were built by giants. No doubt agro-pastoralist Bell Beakers looked at the massive ruins, and perceived the work of the gods.
And we shouldn’t underestimate the ability of oral tradition to recall events for premodern people. Mount Mazama blew 7,700 years ago, but native people in the area have legends of that explosion. Australian Aboriginals have myths that clearly outline and detail landmarks that are now underwater due to rising sea levels. The point is that it’s plausible that facts that are 3,000 years old could persist down to Christian Ireland, and be recorded by priests.
There are lots more I could say about this paper in the details. They found an infant with Down syndrome! They show recent introgression of hunter-gatherer ancestry into some Neolithic individuals. Also, they show hunter-gatherer substructure (Irish hunter-gatherers do not have ancestry from Magdelanian populations, only Villabruna). But the biggest aspect here is that this paper now sets a standard for how you can synthesize ancient DNA with archaeology and mythology.
Even ten years ago a book arguing that Western prosperity might be due to the cultural and historical peculiarities of the Western Christian Church would be a bit “edgy”, insofar as economic differences between the “West and the rest” were often chalked up in mainstream elite circles as due to exploitation. In 2020 a book like this seems really out of place, especially with the current mood and its attitudes toward institutions associated with the West.
Ross Douthat: The Tom Cotton Op-Ed and the Cultural Revolution. Some of my academic friends dismiss the changes happening within their institution. I happen to know for a fact that many people are engaging in preference falsification and terrified that they’ll be targeted or denounced. Perhaps these people are paranoid, and the reigning grandees of justice are in fact tolerant and big-hearted souls, but they’re real people.
Archaeologists contend that it was our aptitude for symbolic, technological, and social behaviors that was central to Homo sapiens rapidly expanding across the majority of Earth’s continents during the Late Pleistocene. This expansion included movement into extreme environments and appears to have resulted in the displacement of numerous archaic human populations across the Old World. Tropical rainforests are thought to have been particularly challenging and, until recently, impenetrable by early H. sapiens. Here, we describe evidence for bow-and-arrow hunting toolkits alongside a complex symbolic repertoire from 48,000 years before present at the Sri Lankan site of Fa-Hien Lena—the earliest bow-and-arrow technology outside of Africa. As one of the oldest H. sapiens rainforest sites outside of Africa, this exceptional assemblage provides the first detailed insights into how our species met the extreme adaptive challenges that were encountered in Asia during global expansion.
The most interesting aspect of this is that it is pretty close (a few thousand years earlier) to the date for the arrival of modern humans in Europe. The admixture with Neanderthals seems to be about 10,000 years earlier than this date, while that with Denisovans around this date. Something happened around 50,000 years ago, as a group of modern humans in and around the Near East seem to have radiated rapidly all across Eurasia, and later Oceania.
I assume that modern(ish) humans were present in Southeast Asia, but most of the ancestry dates to this period and pulse. A decade ago I might posit some incredible biological change, but cultural innovations in the Holocene triggered massive demographic shifts. There’s no reason the same couldn’t apply to the Pleistocene.
For about ten years now there have been debates and discussions about the nature of Neanderthal admixture across Eurasia. How many admixture pulses were there? What is the relationship between admixture and selection? The fact is that West Eurasians have less Neanderthal admixture than East Eurasians. One explanation is that there was further admixture in East Eurasians. Another is dilution of Neanderthal admixture in West Eurasians due to later migration from Africans or Basal Eurasians (both of which lack Neanderthal admixture). But it could also be that the power of selection varies across Eurasia, with the lower population size of East Eurasians over the long-term resulting in less removal of Neanderthal ancestry from their genomes.
I think the main answer to the variation has to do with dilution. In particular, gene-flow from a very Basal Eurasian group into West Eurasians.
…We integrate recent maps of Neanderthal ancestry with well-powered association studies for more than 400 diverse traits to estimate heritability enrichment patterns in regions of the human genome tolerant of Neanderthal ancestry and in introgressed Neanderthal variants themselves. First, we find that variants in regions tolerant of Neanderthal ancestry are depleted of heritability for all traits considered, except skin and hair-related traits. Second, the introgressed variants remaining in modern Europeans are depleted of heritability for most traits; however, we discover that they are enriched for heritability of several traits with potential relevance to human adaptation to non-African environments, including hair and skin traits, autoimmunity, chronotype, bone density, lung capacity, and menopause age. To better understand the phenotypic consequences of these enrichments, we adapt recent methods to test for consistent directional effects of introgressed alleles, and we find directionality for several traits. Finally, we use a direction-of-effect-aware approach to highlight novel candidate introgressed variants that influence risk for disease…
The basic result seems to be that outside of a few characteristics, a lot of the Neanderthal variation is just not retained in the human genome. Traits like height, BMI, and EDU, are highly polygenic. So the genome-wide selection against Neanderthal alleles would be important.
There’s a lot of moving parts in this research, and the most interesting element isn’t the genetics, but the social structure that you can infer from the genetics. It seems entirely likely that the “Megalithic civilization” of Atlantic Europe was hierarchal. But this pretty much confirms it. As noted in the paper violations of first-order incest taboos as a cultural norm (as opposed to deviancy) are strongly associated with very stratified preliterate or semiliterate societies (with the possible exception of 
