Category: Population genetics
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If marrying cousins is so bad why does everyone want to marry their cousins?
The above figure illustrates the geographic distribution of the prevalence of people marrying people closely related to them. Mostly this involves cousin marriage. Most people know the urban legends around the debilities that occur due to cousin marriage, but traditionally the focus has been on rare recessive diseases (e.g., albinism). Now, a massive new study…
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Phenotype does not imply admixture
One of the questions I often get relate to whether “trait X comes from population Y and does that mean if one has trait X that one has more ancestry from population Y.” To give an illustration, I have had people ask “I have blue eyes, does that mean I am more ‘Western Hunter-Gather’ than…
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Extreme inbreeding is bad
If you read a book like Principles of Population Genetics, or know a little animal breeding, you know inbreeding has some serious consequences. The UK Biobank turns out to have about ~100 individuals who are the products of extreme inbreeding (EI). That is, they are the offspring of parent-child pairings or full-sibling pairings, as inferred…
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The genetic discovery of France
Finally, a deep drive into the population genetic structure of France, The Genetic History of France: …These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in…
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Uyghur genetics and Kenneth Kidd – going beneath the surface
The latest episode of NPR’s “Planet Money” was interesting to me and touched upon issues I’ve been thinking on a lot. Stuck In China’s Panopticon has a genetic angle. The Chinese government seems to be identifying and tracking Uyghurs with genetics. Or at least has the capability to do so. That is, in part, thanks…
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Population genetics + “deep learning”
Population genetics is many things, but a popular field that gets written up in Wired or the tech-press is usually not one of those things. It emerged out of Mendelian genetics in the early decades of the 20th-century, transforming elegant pedigrees in…
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Unleash the data kraken!
The Reich lab has just released a single resource of all downloadable genotypes of the world’s published ancient DNA data, including those from our pre-prints! Check it out, we’re pretty excited about it. https://t.co/PecuH07guy — Vagheesh Narasimhan (@vagheesh) April 4, 2019 The Reich lab has done a mitzvah and released a huge merged dataset of…
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The people of the Andaman Islands are not genetic fossils
So this is in the news, Police: American adventurer John Allen Chau killed by isolated Sentinelese tribe on Indian island. There is some talk about whether the guy was a Christian missionary or not, but that’s not really too relevant. Whether he believes in evolution or not (he was a graduate of a very conservative…
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Have we seen the face of Rama?
One of the problems with looking up pictures of the Kalash people of Pakistan is that photographers have a bias toward highlighting the most European-looking villagers. Let’s call this “Rudyard Kipling Lost White Races” syndrome. Therefore for your edification, I post the YouTube above which is probably more representative of what the Kalash look like.…
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It’s raining selective sweeps
A week ago a very cool new preprint came out, Identifying loci under positive selection in complex population histories. It’s something that you can’t even imagine just ten years ago. The authors basically figure out ways to identify deviations of markers from expected allele frequency given a null neutral evolutionary model. The method is put…
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The phylogenetic trees falling on the tundra
A massive new ancient DNA preprint just dropped, The population history of northeastern Siberia since the Pleistocene: …Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population…
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The post-neutral human genome (the Kern-Hahn era)
If you have any background in evolutionary biology you are probably aware of the controversy around the neutral theory of molecular evolution. Fundamentally a theoretical framework, and instrumentally a null hypothesis, it came to the foreground in the 1970s just as empirical molecular data in evolutionary was becoming a thing. At the same time that…
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The derived SNP that causes dry earwax was not found in all non-Africans
A new paper on Chinese genomics using hundreds of thousands of low-coverage data from NIPT screenings is making some waves. I’ll probably talk about the paper at some point. But I want to highlight the frequency of rs17822931 in Han Chinese. It’s pretty incredible how high it is. Because the derived variant SNP, which is…
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The population genetic structure of China (through noninvasive prenatal testing)
This week a big whole genome analysis of China was published in Cell, Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. The abstract: We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population…
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Chinese and Indian American population genetic structure
In Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past David Reich makes the observation that India is a nation of many different ethnicities, while China is dominated by a single ethnicity, the Han. This is obviously true, more or less. Even today the vast majority…
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Nomads, cosmopolitan predators, and peasants, xenophobic producers
Ten years ago when I read Peter Heather’s Empires and Barbarians, its thesis that the migrations and conquests of the post-Roman period were at least in part folk wanderings, where men, women, and children swarmed into the collapsing Empire en masse, was somewhat edgy. Today Heather’s model has to a large extent been validated. The recent…
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How related should you expect relatives to be?
Like many Americans in the year 2018 I’ve got a whole pedigree plugged into personal genomic services. I’m talking from grandchild to grandparent to great-aunt/uncles. A non-trivial pedigree. So we as a family look closely at these patterns, and we’re not surprised at this point to see really high correlations in some cases compared to what…
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David Burbridge’s 10 questions for A. W. F. Edwards In 2006
A few years ago I watched a documentary about the rise of American-influenced rock music in Britain in the 1960s. At some point, one of the Beatles, probably Paul McCartney, or otherwise Eric Clapton, was quoted as saying that they wanted to introduce Americans to “their famous people.” Though patronizing and probably wrong, what they…
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My interview of James F. Crow in 2006
Since the death of L. L. Cavalli-Sforza I’ve been thinking about the great scientists who have passed on. Last fall, I mentioned that Mel Green had died. There was a marginal personal connection there. I had the privilege to talk to Green at length about sundry issues, often nonscientific. He was someone who been doing science…
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Local ancestry deconvolution made simpler (?)
I’ve been waiting for a local ancestry deconvolution method to come out of Simon Myers’ group for a few years. Well, I think we’re there, Fine-scale Inference of Ancestry Segments without Prior Knowledge of Admixing Groups. Here’s the abstract: We present an algorithm for inferring ancestry segments and characterizing admixture events, which involve an arbitrary…