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Use and Interpretation of LD Score Regression
LD Score regression distinguishes confounding from polygenicity in genome-wide association studies: https://sci-hub.bz/10.1038/ng.3211
- Po-Ru Loh, Nick Patterson, et al.


Both polygenicity (i.e. many small genetic effects) and confounding biases, such as cryptic relatedness and population stratification, can yield inflated distributions of test statistics in genome-wide association studies (GWAS). However, current methods cannot distinguish between inflation from bias and true signal from polygenicity. We have developed an approach that quantifies the contributions of each by examining the relationship between test statistics and linkage disequilibrium (LD). We term this approach LD Score regression. LD Score regression provides an upper bound on the contribution of confounding bias to the observed inflation in test statistics and can be used to estimate a more powerful correction factor than genomic control. We find strong evidence that polygenicity accounts for the majority of test statistic inflation in many GWAS of large sample size.

Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n3/extref/ng.3211-S1.pdf

An atlas of genetic correlations across human diseases
and traits: https://sci-hub.bz/10.1038/ng.3406


Supplementary Note: https://images.nature.com/original/nature-assets/ng/journal/v47/n11/extref/ng.3406-S1.pdf

ldsc is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
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november 2017 by nhaliday
Ancient Admixture in Human History
- Patterson, Reich et al., 2012
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.”
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november 2017 by nhaliday
The Same Old Story | West Hunter
People often reinterpret past events, recast them in terms of some contemporary ideology. When historians talk about the Monophysites in Byzantine times, they often suggest that those struggle are a mask for a kind of proto-nationalism. Maybe they were: and maybe nobody involved was thinking anything remotely like that. The Communists tried to come up with Marxist interpretations of ancient history, which led them to spend way too much time talking about Mazdakites in Sassanian Persia and the Zealots of Thessalonika . And Spartacus: but at least Spartacus was cool.

Then there are feminist versions of history. Let us never speak of them again.

Generally, this is all crap. But we could at least hope for something new along these lines: bullshit perhaps, but at least fresh bullshit. Obviously the reality underlying both the Punic Wars and the Crusades is the ancient struggle between EEF and ANE.
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november 2017 by nhaliday
Politics with Hidden Bases: Unearthing the Deep Roots of Party Systems
The research presented here uses a novel method to show that contemporary party systems may originate much further back than is usually assumed or might be expected—in reality many centuries. Using data on Ireland, a country with a political system that poses significant challenges to the universality of many political science theories, by identifying the ancestry of current party elites we find ethnic bases for the Irish party system arising from population movements that took place from the 12th century. Extensive Irish genealogical knowledge allows us to use surnames as a proxy for ethnic origin. Recent genetic analyses of Irish surnames corroborate Irish genealogical information. The results are particularly compelling given that Ireland is an extremely homogeneous society and therefore provides a tough case for our approach.
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november 2017 by nhaliday
Scotland’s many subcultures - Demos Quarterly
surname method

Turning to our analysis of the YouGov results, it was much to our surprise that the strongest majority support for independence was not among ‘pure’ historic Scots, but among people of Irish Catholic descent: with the latter being only 6 per cent net against independence, and historic Scots 16 per cent against. On the surface one might suppose this group would take its political lead from the Labour Party, for which it votes more consistently than any other group in Scotland.
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november 2017 by nhaliday
Caught in the act | West Hunter
The fossil record is sparse. Let me try to explain that. We have at most a few hundred Neanderthal skeletons, most in pretty poor shape. How many Neanderthals ever lived? I think their population varied in size quite a bit – lowest during glacial maxima, probably highest in interglacials. Their degree of genetic diversity suggests an effective population size of ~1000, but that would be dominated by the low points (harmonic average). So let’s say 50,000 on average, over their whole range (Europe, central Asia, the Levant, perhaps more). Say they were around for 300,000 years, with a generation time of 30 years – 10,000 generations, for a total of five hundred million Neanderthals over all time. So one in a million Neanderthals ends up in a museum: one every 20 generations. Low time resolution!

So if anatomically modern humans rapidly wiped out Neanderthals, we probably couldn’t tell. In much the same way, you don’t expect to find the remains of many dinosaurs killed by the Cretaceous meteor impact (at most one millionth of one generation, right?), or of Columbian mammoths killed by a wave of Amerindian hunters. Sometimes invaders leave a bigger footprint: a bunch of cities burning down with no rebuilding tells you something. But even when you know that population A completely replaced population B, it can be hard to prove that just how it happened. After all, population A could have all committed suicide just before B showed up. Stranger things have happened – but not often.
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september 2017 by nhaliday
Effective population size for advantageous mutations | West Hunter
So, with beneficial mutations, the effective population size is very different. Instead of being dominated by bottlenecks, it is more influenced by eras of large population size – more and more so as the selective advantage of the mutation increases. In the limit, if we imagine  mutations so advantageous that they spread  very rapidly, the effective population size approaches the population mean.
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august 2017 by nhaliday
Polygenic Adaptation has Impacted Multiple Anthropometric Traits | bioRxiv
By comparing these polygenic scores to a null distribution under genetic drift, we identify strong signals of selection for a suite of anthropometric traits including height, infant head circumference (IHC), hip circumference (HIP) and waist-to-hip ratio (WHR), as well as type 2 diabetes (T2D). In addition to the known north-south gradient of polygenic height scores within Europe, we find that natural selection has contributed to a gradient of decreasing polygenic height scores from West to East across Eurasia, and that this gradient is consistent with selection on height in ancient populations who have contributed ancestry broadly across Eurasia. We find that the signal of selection on HIP can largely be explained as a correlated response to selection on height. However, our signals in IHC and WC/WHR cannot, suggesting a response to selection along multiple axes of body shape variation. Our observation that IHC, WC, and WHR polygenic scores follow a strong latitudinal cline in Western Eurasia support the role of natural selection in establishing Bergmann's Rule in humans, and are consistent with thermoregulatory adaptation in response to latitudinal temperature variation.

study  bio  preprint  biodet  genetics  evolution  sapiens  pop-diff  embodied  recent-selection  survey  🌞  europe  asia  shift  GWAS  population-genetics  pop-structure  spearhead  environment  temperature  correlation  multi  hsu  scitariat  commentary 
july 2017 by nhaliday
Information Processing: Genetic variation in Han Chinese population
Largest component of genetic variation is a N-S cline (phenotypic N-S gradient discussed here). Variance accounted for by second (E-W) PC vector is much smaller and the Han population is fairly homogeneous in genetic terms: ...while we revealed East-to-West structure among the Han Chinese, the signal is relatively weak and very little structure is discernible beyond the second PC (p.24).

Neandertal ancestry does not vary significantly across provinces, consistent with admixture prior to the dispersal of modern Han Chinese.

My fellow officers informed me, that while the negotiation was going on, the ships were constantly crowded with all kinds of refreshments, and that when they were first boarded by the Chinese they received every attention from them that could be shown; and that the presents received by the different officers belonging to the embassy, were of immense value. That the natives of this part of China were of different complexions and manners from those in and near Canton; their colour being nearly white; and in their manners were much more free and candid; and that they were of a larger stature, and more athletic than the southern Chinese—they were much more sociable, and not so particular respecting their women being seen by the men. And were even fond of receiving the officers into their houses, when on shore, provided it could be done without the knowledge of the mandarins.

The study below discusses a psychological/cognitive/personality gradient between N and S China, possibly driven by a history of wheat vs rice cultivation.


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july 2017 by nhaliday
Caste system in India - Wikipedia
A recent series of research papers, by Reich et al. (2009), Metspalu et al. (2011), and Moorjani et al. (2013), make clear that India was peopled by two distinct groups who split genetically ca. 50,000 years ago,[81][82] which they called "Ancestral North Indians" (ANI) and "Ancestral South Indians" (ASI) respectively.[note 1] They found that the ANI genes are close to those of Middle Easterners, Central Asians and Europeans whereas the ASI genes are dissimilar to all other known populations outside India.[note 2][note 3] These two distinct groups, which had split ca. 50,000 years ago, formed the basis for the present population of India.[83]

According to Moorjani et al. these two groups mixed between 4,200 and 1,900 years ago (2200 BCE-100 CE), whereafter a shift to endogamy took place.[84] David Reich stated, "Prior to 4,200 years ago, there were unmixed groups in India. Sometime between 1,900 to 4,200 years ago, profound, pervasive convulsive mixture occurred, affecting every Indo-European and Dravidian group in India without exception.".[85] Following this mixture,

Strong endogamy must have applied since then (average gene flow less than 1 in 30 per generation) to prevent the genetic signatures of founder events from being erased by gene flow. Some historians have argued that "caste" in modern India is an "invention" of colonialism in the sense that it became more rigid under colonial rule. However, our results suggest that many current distinctions among groups are ancient and that strong endogamy must have shaped marriage patterns in India for thousands of years.[81]

Moorjani et al. discerned two waves of admixture in this period, with northern India showing later dates of admixture.[86] GaneshPrasad et al. (2013) studied "12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India." According to this study, southern India was already socially stratified 4,000 to 6,000 years ago, which is best explained by "the emergence of agricultural technology in South Asia." The study concludes that "The social stratification (in Tamil Nadu) was established 4,000 to 6,000 years ago and there was little admixture during the last 3,000 years, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area."[87]


A crucial factor is the collapse of the caste system over the last half century, a factor that undergirds many of the other reasons that the south has prospered — more stable governments, better infrastructure and a geographic position that gives it closer connections to the global economy.

“The breakdown of caste hierarchy has broken the traditional links between caste and profession, and released enormous entrepreneurial energies in the south,” said Ashutosh Varshney, a professor at Brown University who has studied the role of caste in southern India’s development. This breakdown, he said, goes a long way to explaining “why the south has taken such a lead over the north in the last three decades.”

Caste Is Stunting All of India’s Children: http://foreignpolicy.com/2017/09/15/caste-is-stunting-all-of-indias-children/
Fears of impurity continue to steer Indians away from toilets — and towards deadly fecal germs.

These Indian govt funded ads to encourage the wealthy but declining Parsi population to reproduce are quite extraordinary

India’s government has expanded a scheme offering payment incentives to Hindus who marry members of the country’s poorest and most oppressed caste, the Dalits.
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june 2017 by nhaliday
The story of modern human origins just got more complicated


The slow death of Out of Africa: http://dienekes.blogspot.com/2018/04/the-slow-death-of-out-of-africa.html
The significance of the discovery of modern humans in Arabia >85kya is that it provides a second spot (other than Israel) were modern humans existed outside Africa long before the alleged 60kya blitz out of the continent. We now have modern humans outside Africa in roughly two locations (Israel and Arabia), and three time slices (~175-85kya) in Misliya, Shkul/Qafzeh, and Al Wusta-1. It is no longer tenable to claim that these modern humans "died out" to make way for the alleged 60kya OoA event.
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june 2017 by nhaliday
Romanticizing the regressive – Brown Pundits
As far back as Herodotus Indian society seems to have been characterized by caste. Genetically the castes, and more precisely jatis, are very distinct. And their persistence on the Indian scene suggest some level of functional utility.


The connections between liberal Democratic Indian Americans and right-wing Hindu nationalism in India have been extensively discussed. That is not what I am getting at. Meet the Patels is not a political film, it is a personal one. There is no reason that Ravi should address political topics in the documentary, and much of what I am saying here would be implicit to any South Asian watching Meet the Patels. But to many Americans these darker realities would not be visible or implied in the cultural practices which Ravi admires.

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june 2017 by nhaliday
Genetics allows the dead to speak from the grave - The Unz Review
BOOKMARKIt is a running joke of mine on Twitter that the genetics of white people is one of those fertile areas of research that seems to never end. Is it a surprise that the ancient DNA field has first elucidated the nature of this obscure foggy continent, before rich histories of the untold billions of others? It’s funny, and yet these stories, true tales, do I think tell us a great deal about how modern human populations came to be in the last 10,000 years. The lessons of Europe can be generalized. We don’t have the rich stock of ancient DNA from China, the Middle East, or India. At least not enough to do population genomics, which requires larger sample sizes than a few. But, climate permitting, we may.


At about the same time the evidence for Neanderthal admixture came out, Luke Jostins posted results which showed that other human lineages were also undergoing encephalization, before their trajectory was cut short. That is, their brains were getting bigger before they went extinct. To me this suggested that the broader Homo lineage was undergoing a process of nearly inevitable change due to a series of evolutionary events very deep in our history, perhaps ancestral on the order of millions of years. Along with the evidence for admixture it made me reconsider my priors. Perhaps some Homo lineage was going to expand outward and do what we did, and perhaps it wasn’t inevitable that it was going to be us. Perhaps the Neanderthal Parallax scenario is not as fantastical as we might think?
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may 2017 by nhaliday

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