PCA remains the swiss-army-knife to explore population structure
genotype-based methods? — Razib Khan (@razibkhan) November 15, 2017 I put up a poll without context yesterday to gauge people about what methods they preferred when it came to population genetic structure.* PCA came out on top by a plural majority. More explicitly model-based methods, such as Structure/Admixture, come in right behind them. Curiously, the […]
Population structure using haplotype data
The Pith: New software which gives you a more fine-grained understanding of relationships between populations and individuals. According to the reader survey >50 percent of you don’t know how to interpret PCA or model-based (e.g., ADMIXTURE) genetic plots, so I am a little hesitant to point to this new paper in PLoS Genetics, Inference of […]
How Chinese genetics is like Chinese food
Representatives of Szechuan and Shangdong cuisine
The Pith: The Han Chinese are genetically diverse, due to geographic scale of range, hybridization with other populations, and possibly local adaptation.
In the USA we often speak of “Chinese fo…
Africa in 12 ADMIXTURE chunks
Some have asked what the point is in poking around African population structure when Tishkoff et al. and Henn et al. have done such a good job in terms of coverage. First, it is nice to run your own analyses so you can slice & dice to your preferen…
A genomic map of human variation, where we’re at
Zack has started exploring the K’s of his merged data set for HAP. A commenter suggests that:
As you have begun interpreting the reference results, let me make a friendly warning: you have to keep in mind that most of the reference populations of…
“Asian” in all the right places
mtDNA haplogroup G1a2
The pith: In this post I examine the most recent results from 23andMe for my family in the context of familial and regional (Bengal) history. I also use these results to offer up a framework for the ethnognesis of the eastern Ben…
To classify humanity is not that hard
In my post below I quoted my interview L. L. Cavalli-Sforza because I think it gets to the heart of some confusions which have emerged since the finding that most variation on any given locus is found within populations, rather than between them. The standard figure is that 85% of genetic variance is within continental […]
Excavating the Neolithic genetic strata
After linking to Marnie Dunsmore’s blog on the Neolithic expansion, and reading Peter Bellwood’s First Farmers, I’ve been thinking a bit on how we might integrate some models of the rise and spread of agriculture with the new genomic findings. Bellwood’s thesis basically seems to be that the contemporary world pattern of expansive macro-language families […]