The genomic landscape of Brazil in 1950
A new whole-genome analysis out of Brazil has some interesting ancestry information. The preprint, Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil): As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still […]
The genomic landscape of Brazil in 1950
A new whole-genome analysis out of Brazil has some interesting ancestry information. The preprint, Whole-genome sequencing of 1,171 elderly admixed individuals from the largest Latin American metropolis (São Paulo, Brazil): As whole-genome sequencing (WGS) becomes the gold standard tool for studying population genomics and medical applications, data on diverse non-European and admixed individuals are still […]
Ancestry analysis quickstart
Over the years I have posted periodic tutorials on how to do some simple admixture analysis. Initially this was to foster the growth of “genome blogging”, but that’s basically dead along with blogging as a whole (Eurogenes being the primary exception here). But, unexpectedly it turns out a lot of baby-academics find my tutorials early […]
Indic civilization came to Southeast Asia because Indian people came to Southeast Asia. Lots of them
Reading Indonesia: Peoples and Histories. I selected it because unlike many books it wasn’t incredibly skewed to the early modern and postcolonial period. The author makes the interesting point that the Islamicization of western Indonesia and the rise of the great Javanese Hindu kingdom of Majapahit occurred around the same time. This, in contrast to […]
Tutorial to run supervised admixture analyses
ID Dai Gujrati Lithuanians Sardinian Tamil razib_23andMe 0.14 0.26 0.02 0.00 0.58 razib_ancestry 0.14 0.26 0.02 0.00 0.58 razib_ftdna 0.14 0.26 0.02 0.00 0.57 razib_daughter 0.05 0.14 0.29 0.18 0.34 razib_son 0.07 0.17 0.28 0.19 0.30 razib_son_2 0.06 0.19 0.29 0.19 0.27 razib_wife 0.00 0.07 0.55 0.38 0.00 This is a follow-up to my earlier […]
Tutorial to run PCA, Admixture, Treemix and pairwise Fst in one command
Today on Twitter I stated that “if the average person knew how to run PCA with plink and visualize with R they wouldn’t need to ask me anything.” What I meant by this is that the average person often asks me “Razib, is population X closer to population Y than Z?” To answer this sort […]
Black ancestry in white Americans of colonial background
I stumbled upon striking photographs of “white slaves” while reading The United States of the United Races: A Utopian History of Racial Mixing. The backstory here is that in the 19th century abolitionists realized that Northerners might be more horrified as to the nature of slavery if they could find children of mostly white ancestry, […]
Carving nature at its joints more realistically
If you are working on phylogenetic questions on a coarse evolutionary scale (that is, “macroevolutionary,” though I know some evolutionary geneticists will shoot me the evil eye for using that word) generating a tree of relationships is quite informative and relatively straightforward, since it has a comprehensible mapping onto to what really occurred in nature. […]
Why humans have so many pulse admixtures
The Blank Slate is one of my favorite books (though I’d say The Language Instinct is unjustly overshadowed by it). There is obviously a substantial biological basis in human behavior which is mediated by genetics. When The Blank Slate came out in the early 2000s one could envisage a situation in 2017 when empirically informed […]
Is Daniel MacArthur ‘desi’?
My initial inclination in this post was to discuss a recent ordering snafu which resulted in many of my friends being quite peeved at 23andMe. But browsing through their new ‘ancestry composition’ feature I thought I had to discuss it first, because of some nerd-level intrigue. Though I agree with many of Dienekes concerns about […]
Northern Europeans and Native Americans are not more closely related than previously thought
A new press release is circulating on the paper which I blogged a few months ago, Ancient Admixture in Human History. Unlike the paper, the title of the press release is misleading, and unfortunately I notice that people are circulating it, and probably misunderstanding what is going on. Here’s the title and first paragraph: Native […]
Northern Europeans and Native Americans are not more closely related than previously thought
A new press release is circulating on the paper which I blogged a few months ago, Ancient Admixture in Human History. Unlike the paper, the title of the press release is misleading, and unfortunately I notice that people are circulating it, and probably misunderstanding what is going on. Here’s the title and first paragraph: Native […]
Across the sea of grass: how Northern Europeans got to be ~10% Northeast Asian
The Pith: You’re Asian. Yes, you!
A conclusion to an important paper, Nick Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster, and David Reich:
In particular, we have presented ev…
The law of reversion to type as cultural illusion
A comment below:
Does the higher genetic diversity in sub-Saharan Africans explain why mixed children of blacks + other couples usually look more black than anything?
As in, the higher number of genetic characteristics overwhelms those of the other pa…
Out of who knows where
In The New York Times, DNA Turning Human Story Into a Tell-All: The tip of a girl’s 40,000-year-old pinky finger found in a cold Siberian cave, paired with faster and cheaper genetic sequencing technology, is helping scientists draw a surprisingly complex new picture of human origins. The new view is fast supplanting the traditional idea […]
Basque genetic distinctiveness (again)
With all the talk about Basques I decided to do my own analysis with Admixture. Dienekes gave me a copy of his IBS file, which has all the 1000 Genomes Spanish samples, including Basques. I merged it with the HGDP sample, which has French Basques (just “Basques” in the plots below) and French non-Basques. I […]
The sons of Adam: spirit, not blood
Hominin increase in cranial capacity, courtesy of Luke Jostins A few years ago a statistical geneticist at Cambridge’s Sanger Institute, Luke Jostins, posted the chart above using data from fossils on cranial capacity of hominins (the human lineage). As you can see there was a gradual increase in cranial capacity until ~250,000 years before the present, […]
D.I.Y. population structure analysis
I badger readers here to actually use all the analytic tools which researchers put out into public circulation, rather than just offering cheap opinions. Obviously it’s way more fun and informative to have discussions with someone who can check their own hunches by doing a few “runs” overnight. Secondly, if you have minimal technical skills […]
Genetic distinctiveness vs. genetic diversity
Meeting the Taino In the comments below a few days ago someone expressed concern at the diminishing of genetic diversity due to the disappearance of indigenous populations. My response was bascally that it depends. The issue here is whether that disappearance is due to assimilation, or extinction. If a given population is genetically absorbed into […]
Neandertal introgression and admixture
Ed Yong has a good good review of a new Neandertal introgression/admixture paper in PNAS. It’s not live on the web yet, so let me quote Ed: Even if the odds of successful interbreeding were just 5 percent, Neanderthal genes would make up the majo…