DIY admixture analysis
Dienekes Pontikos has just released DIY Dodecad, a DIY admixture analysis program. You can download the files yourself. It runs on both Linux and Windows. Since I already have tools in Linux I decided to try out the Windows version, and it seems to wor…
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…
Dodecad open for submissions
Since I know plenty of friends are getting, or just got, their V3 results, I thought I’d pass this on, Open-ended submission opportunity for 23andMe data (#2):
Who is eligible
Everyone who is of European, Asian, or North African ancestry and all …
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…
Me, myself, and Myanmar
I have spoken of my somewhat atypical, for a South Asian, genetic results before. Recently Dienekes performed some cluster analysis which confirmed the initial findings, while adding a little detail: I am DOD075. The Southeast Asian component is modal in Malays, while the East Asian component is modal in the North Chinese. Vietnamese and Cambodians […]
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 […]
Visualizing West Eurasia
Over at his blog Dienekes Pontikos has taken some public data sets and his own Dodecad samples and generated a massive MDS plot of West Eurasian populations. The MDS is fine as it goes. It illustrates clearly that when you visualize an individual on a plot defined by the two largest dimensions of variation in […]
Are Turks acculturated Armenians?
To the left you see a zoom in of a PCA which Dienekes produced for a post, Structure in West Asian Indo-European groups. The focus of the post is the peculiar genetic relationship of Kurds, an Iranian-speaking people, with Iranians proper, as well as Armenians (Indo-European) and Turks (not Indo-European). As you can see in […]
Some of the Indo-Europeans found?
School girls in Hunza, Pakistan A few days ago I observed that pseudonymous blogger Dienekes Pontikos seemed intent on throwing as much data and interpretation into the public domain via his Dodecad Ancestry Project as possible. What are the long term implications of this? I know that Dienekes has been cited in the academic literature, […]
“Genome blogging”
Nature profiles Dodecad, the Pickrell Affair, and the emergence of amateur genomicists in a new piece. Interestingly David of BGA is going to try and get something through peer review. In particular, the relationship of Assyrians and Jews. So we have Genomes Unzipped, Dodecad, and BGA. What next? Who next? I hope Dienekes doesn’t mind if […]
Re-visualizing European ancestry
I decided to take the Dodecad ADMIXTURE results at K = 10, and redo some of the bar plots, as well as some scatter plots relating the different ancestral components by population. Don’t try to pick out fine-grained details, see what jumps out in a gestalt fashion. I removed most of the non-European populations to […]
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 […]
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 […]
Assyrians & Finns in a worldwide genetic context
Dienekes is now allowing people to “out” themselves in terms of their ancestry on a comment thread over at the Dodecad Ancestry Project. One of the major purposes of the project has been to survey variation in under-sampled groups which could give us insights into human genetic history. Yesterday I pointed to an analysis of […]
My Dodecad results
A few days ago Dienekes opened up the Dodecad project to a wider range of Eurasians. I decided to send my 23andMe sample to Dienekes ASAP, and the results came back today. I’m DOD075. Dienekes also just put up an explanation of the 10 ancestral components he’s generating from ADMIXTURE (along with tree-like representations of […]
The Dodecad ancestry project
Dienekes Pontikos, Introducing the Dodecad ancestry project:
1) Project goals
The Dodecad ancestry project has two goals:
– To provide detailed ancestry analysis to individuals who have tested with 23andMe; other testing companies may be included in the future.
– To build samples of individuals for regions of the world (e.g. Greeks, Finns, Albanians, Southern Italians, etc.) currently under-represented […]