Angela
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It is presented here:
Tyler A. Joseph and Itsik Pe’er
"Inference of population structure from ancient dna"
https://www.biorxiv.org/content/biorxiv/early/2018/02/07/261131.full.pdf
The program is called "Dystruct".
"Abstract. Methods for inferring population structure from genetic information traditionally assumesamples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision ofthis paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference ofshared ancestry from data that include ancient DNA. By explicitly modeling population history andgenetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry fromancient and contemporary samples. Formally, we use a normal approximation of drift, which allows anovel, efficient algorithm for optimizing model parameters using stochastic variational inference. Weshow that Dystruct outperforms the state of the art when individuals are sampled over time, as iscommon in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to presentmodern samples as the mixtures of ancestral populations they really are, rather than the artifactualconverse of presenting ancestral samples as mixtures of contemporary groups.
I haven't tried to burrow into the math. If someone has, it would be great if you could give us some insights.
There don't seem to be any significant discrepancies between this new program and ADMIXTURE for SSA, Amerindian, East Asian, Austronesian etc., but when you get to Europe and the Middle East, and to some extent India there are indeed major differences.
From a very cursory overview, I'm quite ambivalent about any program that starts with so called "pure" populations. I don't think any population is "pure". I'm highly skeptical, for example, that the steppe people are "pure" more recent Kostenki types.
Anyway, this graph should point out the differences. I'd be interested in any reactions.
[/IMG]
Tyler A. Joseph and Itsik Pe’er
"Inference of population structure from ancient dna"
https://www.biorxiv.org/content/biorxiv/early/2018/02/07/261131.full.pdf
The program is called "Dystruct".
"Abstract. Methods for inferring population structure from genetic information traditionally assumesamples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision ofthis paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference ofshared ancestry from data that include ancient DNA. By explicitly modeling population history andgenetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry fromancient and contemporary samples. Formally, we use a normal approximation of drift, which allows anovel, efficient algorithm for optimizing model parameters using stochastic variational inference. Weshow that Dystruct outperforms the state of the art when individuals are sampled over time, as iscommon in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to presentmodern samples as the mixtures of ancestral populations they really are, rather than the artifactualconverse of presenting ancestral samples as mixtures of contemporary groups.
I haven't tried to burrow into the math. If someone has, it would be great if you could give us some insights.
There don't seem to be any significant discrepancies between this new program and ADMIXTURE for SSA, Amerindian, East Asian, Austronesian etc., but when you get to Europe and the Middle East, and to some extent India there are indeed major differences.
From a very cursory overview, I'm quite ambivalent about any program that starts with so called "pure" populations. I don't think any population is "pure". I'm highly skeptical, for example, that the steppe people are "pure" more recent Kostenki types.
Anyway, this graph should point out the differences. I'd be interested in any reactions.