Genome bloggers & Indian genomics
Dienekes, David, and Zack, have now integrated the insight from Reconstructing Indian History that the programs which infer population structure, such as STRUCTURE, frappe, and ADMIXTURE, can produce ancestral components which are themselves actually s…
Input determining output in ADMIXTURE
One reason I posted about how to run ADMIXTURE was so that the more readers themselves could become familiar with the biases of the program. That way they would get cautious about over-reading one particular set of results (the same goes for using PCA …
Eurasia, ADMIXTURE supervised & unsupervised
After yesterday’s post I thought it might be useful to see how running ADMIXTURE in different modes would impact the outcomes. Probably the major reason I wish more people would use this software is that they’d see that this program is jus…
Analyzing ancestry with ADMIXTURE, step by step
Over the past few months I was hoping more people would start doing what Zack Ajmal, Dienekes, and David, have been doing. There are public data sets, and open source software, so that anyone with nerdy inclination can explore their own questions out o…
Tea leaves and population substructure
Image credit: Wikimol
Over the past few months I’ve been encouraging people to pull down ADMIXTURE, and push the public data sets through it. Additionally, you can also convert your 23andMe raw file into pedigree format pretty easily and integ…
Eurasia + Mozabites + Papuans
I’m in a hurry right now, and won’t be posting much this week. But, I thought I’d dump some of the ADMIXTURE runs I have. This is one with 80,000 markers, and Eurasian populations, Papuans and Mozabites. I removed the New World and Af…
D.I.Y. population structure inference, part 1 of many
If you’ve been reading this weblog for a while you’ve seen many images like the one above. It comes from the 2008 paper Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation. The data set is from the Human Genome D…
Counting beans the proper way
Apropos of several of my recent posts, The New York Times has an interesting article up, Counting by Race Can Throw Off Some Numbers. Basically it outlines the difficulty of enumerating different racial and ethnic groups for different purposes in a mor…
Neandertal admixture, revisiting results after shaken priors
After 2010′s world-shaking revolutions in our understanding of modern human origins, the admixture of Eurasian hominins with neo-Africans, I assumed there was going to be a revisionist look at results which seemed to point to mixing between diffe…
ADMIXTURE vs. MDS, visualization is just visualization
Dienekes did another run of his data with K = 64. He posted a huge plot with the two largest dimensions of variation. He also posted an accompanying spreadsheet with the coordinates of where the Dodecad samples were. So I found my own position pretty q…
The genetic affinities of Ethiopians
In the open thread someone asked: “Any recent stuff on the genetics of Ethiopians.” That prompted me to look around, because I’m curious too. Poking around Wikipedia I couldn’t find anything recent. A lot of the studies are older uniparental lineage based works (NRY and mtDNA). Ethiopia is interesting because unlike almost all other Sub-Saharan […]
Ancestry in the Americas
The populations of the African Diaspora have a particular interest in the new genomics, and its relationship to ancestry. Unlike other post-Columbian Diasporas they have sketchy, at best, knowledge of the regions from which their ancestors arrived. This probably explains the popularity of Roots and Henry Louis Gates Jr.’s various genealogical projects which have utilized […]
The paradigm is dead, long live the paradigm!
Mitochondrial DNA and human evolution: Mitochondrial DNA from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DMAs stem from one woman who is postulated to have lived ab7out 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that […]
Eurogenes 500K SNP BioGeographicAncestry Project
Since I have been promoting the Dodecad Ancestry Project, it seems only fair to bring to your attention Eurogenes 500K SNP BioGeographicAncestry Project. The sample populations are a bit different from Dodecad, but again ADMIXTURE is the primary tool. But the author also makes recourse to other methodologies to explore more than simply population level […]
15 ancestral components to bind them all
Dienekes Pontikos keeps chugging along, and has cranked out a new bar plot from the ADMIXTURE program with 15 putative ancestral components. He has “69 populations, and 1,189 individuals in total.” Most of these were assembled from public data, but some of them are particular to the Dodecad Ancestry Project. He contends:
In comparison to the […]
What intra- & inter- population genetic variance tells us
The figure to the left is a composite merged from two different papers. One analyzes the patterns of genetic variation within African Americans, and the other the patterns within the East Turkic ethnic group, the Uyghurs. The bar plots show the ancestral element which is similar to two parent populations which resemble Europeans and Africans […]
History and Geography of Genes on a Desktop
In case you don’t know, Dienekes Pontikos has been posting a lot of analyses of available population genetic data sets with the ADMIXTURE program. You can find his myriad posts under the ADMIXTURE-experiments tag. Below is a bar plot he generated today. To follow up a debate which occurred last spring, it does seem from […]