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 […]
Running your own analyses
For the technically inclined people here: Tutorial To Run PCA, Admixture, Treemix And Pairwise Fst In One Command.
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 […]
The fault in our parameters
Of the books, I own Elements of Evolutionary Genetics is one I consult frequently because of its range and comprehensiveness. The authors, Brian Charlesworth and Deborah Charleswencyclopedican encyclopediac knowledge of the literature. To truly understand the evolutionary process in all its texture and nuance it is important to absorb a fair amount of theory, and Elements […]
Burmese are a bit Bengali
About ten years ago I read the book The River of Lost Footsteps: Histories of Burma. Though I have read books where Burma figures prominently (e.g., Strange Parallels), this is the only history of Burma I have read. The author is Burmese, and provide something much more than a travelogue, as might have been the […]
Soft & hard selection vs. soft & hard sweeps
When I was talking to Matt Hahn I made a pretty stupid semantic flub, confusing “soft selection” with “soft sweeps.” Matt pointed out that soft/hard selection were terms more appropriate to quantitative genetics rather than population genomics. His viewpoint is defensible, though going back into the literature on soft/selection, e.g., Soft and hard selection revisited, […]
The mutation accumulation controversy continues….
Every few years I check to see if the great mutation accumulation controversy has resolved itself. I don’t know if anyone calls it that, but that’s what I think of it as. There are two major issues that matter here: mutation rates are a critical parameter in evolutionary models, and, mutation accumulation over time matters […]
The peoples of the Maghreb have some Pleistocene roots
The Maghreb is an important and interesting place. In the history of Western civilization, the tension between Carthage, the ancient port city based out of modern-day Tunisia, and Rome, is one of the more dramatic and tragic rivalries that has resonances down through the ages. Read Adrian Goldsworthy’s chapter on the Battle of Cannae in […]
Are Turks Armenians under the hood?
Benedict Anderson’s Imagined Communities: Reflections on the Origin and Spread of Nationalism is one of those books I haven’t read, but should. In contrast, I have read Azar Gat’s Nations, which is a book-length counterpoint to Imagined Communities. To take a stylized and extreme caricature, Imagined Communities posits nations to be recent social and historical constructions, while Nations sees […]
Genetic distances across Eurasia
I feel that for whatever reason that over the past few years that many people have started to exhibit weak intuitions about the magnitude of between population differences on this weblog. Two suggestions for why this might occur. * First, the proliferation of PCA plots with individuals can make it hard to discern averages * […]
How South Asian populations relate to each other
Since people asking me about this, and I’m running the South Asian Genotype Project, I thought I would post two non-PCA visualizations of how various South Asian groups relate to each other (along with a few outgroups). The radial plot above is a neighbor-joining tree visualized from pairwise Fst statistics (basically a proxy for genetic […]
Island demes in an empty world
As you probably know a new ancient genome paper was published last week in Nature, Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. There is at least one other involving Willerslev in the works for what it’s worth. Carl Zimmer has a good write-up in The New York Times, while Greg Cochran […]
Natural selection in humans (OK, 375,000 British people)
The above figure is from Evidence of directional and stabilizing selection in contemporary humans. I’ll be entirely honest with you: I don’t read every UK Biobank paper, but I do read those where Peter Visscher is a co-author. It’s in PNAS, and a draft which is not open access. But it’s a pretty interesting […]
A genetic map of the world
The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow. […]
A genetic map of the world
The above map is from a new preprint on the patterns of genetic variation as a function of geography for humans, Genetic landscapes reveal how human genetic diversity aligns with geography. The authors assemble an incredibly large dataset to generate these figures. The orange zones are “troughs” of gene flow. Basically barriers to gene flow. […]
Visualizing intra-European phylogenetic distances
In L. L. Cavalli-Sforza’s The History and Geography of Human Genes he used between population group genetic distances, as measured in FST values, to generate a series of visualizations, which then allowed him to infer historical processes. Basically the way it works is that you look at genetic variation, and see how much of […]
Visualizing intra-European phylogenetic distances
In L. L. Cavalli-Sforza’s The History and Geography of Human Genes he used between population group genetic distances, as measured in FST values, to generate a series of visualizations, which then allowed him to infer historical processes. Basically the way it works is that you look at genetic variation, and see how much of […]
The Saxon Panmixia
One reason I quite like Norman Davies’ book The Isles is that it is a history of Britain and Ireland which explicitly aims to not privilege the story of the English inordinately. As the most powerful and numerous people of the British Isles the English loom large, but in the period between Gildas and Bede […]
The Saxon Panmixia
One reason I quite like Norman Davies’ book The Isles is that it is a history of Britain and Ireland which explicitly aims to not privilege the story of the English inordinately. As the most powerful and numerous people of the British Isles the English loom large, but in the period between Gildas and Bede […]
Soft selection for gentleness in Puerto Rican African Honeybees
When I was a kid “killer bees” were a major pop culture thing. There were movies about the bees, and we would get updates about their march northward in the news. They were a cautionary tale of our species’ hubris. Today we have a little bit more perspective. These bees were actually just African […]