New alternative to ADMIXTURE?

[Angela]

It is presented here:

Tyler A. Joseph and Itsik Pe’er
"Inference of population structure from ancient dna"

https://www.biorxiv.org/content/bior...61131.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][/IMG]

[Johane Derite]

If i'm understanding this correctly, this new method is pointing to the Caucasus as having the most steppe(orange/kostenki) ancestry?

[Angela]

If i'm understanding this correctly, this new method is pointing to the Caucasus as having the most steppe(orange/kostenki) ancestry?

That's what it seems like to me, Johane. Thank you for making the graphs bigger for me, btw. :)

Oh, and look at the difference between Corded Ware and Bell Beaker using this. A lot of the change in the Copper Age would be resurgence of WHG, also, not steppe.

[Johane Derite]

Oh, and look at the difference between Corded Ware and Bell Beaker using this. A lot of the change in the Copper Age would be resurgence of WHG, also, not steppe.

Yeah a lot of the differences seem quite dramatic, I can't lie that I fully grasp it quite yet but it definitely seems like an interesting tool if it offers new points of view as
dramatic as this : D

[FIREYWOTAN]

Thanks for sharing a piece of another great opportunity uncover the mysteries of the moment.
The amazing part is that everytime a new reality is found there are usually so many questions that it makes us wonder. "Neanderthal Man" by Svante Paabo was all about the subtitle
"In Search Of Lost Genomes." Capturing Robert Shapiro"s "The Human Blueprint" or James D. Watson's "DNA The Story Of the Genetic Revolution" starts off at best as pie in the sky conclusion. Should a man be able to fly? I guess all I really want to share is how lucky we are to watch the secrets unfold.

[IronSide]

If i'm understanding this correctly, this new method is pointing to the Caucasus as having the most steppe(orange/kostenki) ancestry?

The Middle East has similar levels of Steppe to Europe.

I don't know what to make of this.

[Sile]

The Middle East has similar levels of Steppe to Europe.
I don't know what to make of this.

I cannot make anything out of this unless you tell me what each colour represents

[Falco]

The Middle East has similar levels of Steppe to Europe.

I don't know what to make of this.

Maybe it's conflating "Steppe" with "Caucasus" in the case of the Middle East?

[Angela]

There's more "Caucasus" than that in the Middle East. I think it's the "Steppe" part of Caucasus.

This is a "pure" component, according to them, a sort of hold over from Kostenki?

The colors change depending on whether you're looking at a or b, but it's easy to figure it out.

In b, which is all the ancient samples, if you look all the way to the left, the solid orange bar is Kostenki.

The grey is Mal'ta, and the brown is SHG, which again they see as a "pure" population, not a mix of WHG and EHG. In fact, the brown also equals Loschbour and Motala. The EHG don't exist here. In ADMIXTURE, they're showing steppe as a mixture of Mal'ta and European Hunter-Gatherer, plus a bit of Neolithic. However, in DYSTRUCT it's a "pure" population.

So, in the Middle East, we could think of it as ANE plus UHG in the terms we're more used to seeing it expressed?

In the modern populations section, I think they're showing Sardinians and Basque as having not "steppe". I could buy it about the Sardinians, if they're going by the isolated highland sample, but the Basque? Then what about their R1b? Of course, their Bell Beaker don't have much "steppe" either, so it could have disappeared by the time they got to Spain.

Ed. Grey actually may be Mal'ta plus Ust-Ishim, so something older than both of them.

[davef]

What's the really light blue that peaks in the Middle East ?

[IronSide]

What's the really light blue that peaks in the Middle East ?

It has to be Southwest Asian, aka the component that peaks in Natufians/Levantine farmers. you could see it overflowing to Africa, East African populations. it is a minor component in Europe, Caucasus and some populations in Asia.

[davef]

Thank you IronSide!

[Angela]

I wouldn't be so sure that there is an exact correspondence between any "cluster" here and a named "cluster" in ADMIXTURE analyses based on modern populations.

Every other group in Dystruct is different from what we would think, so this may be a slightly different formulation as well. I'd like to know if it's based on an ancient sample, and if so, which one. Natufians were different from Bronze Age Canaanites, for example. Modern day Levantines are different yet.

At any rate, ADMIXTURE finds much less of it in Europe.

It "is" found somewhere in Asia, interestingly, and I don't mean South Asia.

[IronSide]

Again the Middle East and Caucasus has more grey (Mal'ta ?) than Europe.

Is there any chance that this is all wrong ? what happened to the model before the discovery of Mal'ta that Europeans have an ancestry from a ghost population best modeled at the time to Native Americans ? and now Kostenki is more ancestral to Europe, hmmmm.

[Angela]

The grey might be a combination of Mal'ta and Ust-Ishm, so something older than either? It's the dominant cluster in South Asian genetics.

There's almost none of it in Europe according to this, I don't think.

[IronSide]

I am interested in David Reich's opinion on this.

[FIREYWOTAN]

Never a dull moment as one notion becomes and idea and before we known it there's a tree growing. The depth of each article seems beyond contradiction and yet in the blink of an eye it seems that were once again still trying to dig deeper. Frankly, that's what seems so enlightening but the passion of curiosity challenges us to reach new highs until were caught in the malstrom of another title wave.

[AdeoF]

Hmm the middle East is interesting since it's looks the European one. I think Dystruct is better for ancient admixture

[IronSide]

Hmm the middle East is interesting since it's looks the European one. I think Dystruct is better for ancient admixture

Two-thirds of the ancestry is common between them, even in ADMIXTURE, so no surprise there.

What surprises me is that Ust-Ishim and Ma'lta are now their own cluster (dominant in South Asia) separate from the Steppe, which is now like Kostenki ??

Basal Eurasian may not even be needed now because it was inferred that Ust-Ishim symmetrically shares alleles with East Asians and European hunter-gatherers, that means it takes a middle position between East Eurasians and West Eurasians, but it shares more allels with East Asians than Neolithic Europeans or modern Europeans, that means there was an ancestral group that split before East and West Eurasians themselves split. and it went to Europe, thus reducing the affinity to Ust-Ishim.

But now Ust-Ishim does have descendants in South Asia ...

[Wonomyro]

Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual
converse of presenting ancestral samples as mixtures of contemporary groups.

[MOESAN]

Here under, an interesting abstract thanks to MAJU of 'For what they were we are' blog -

February 14, 2018

Dystruct versus Admixture

Not really able yet to discern if this is an alternative way ahead for autosomal archaeogenetics or just another dead end. But it does seem interesting enough to mention here in any case.

It may be very important in the deciphering of the so-called "ANE" ghostly genetic influence.


Tyler A. Joseph & Itsik Pe'er. Inference of population structure from ancient DNA. bioRXiv 2018 (pre-pub). DOI:10.1101/261131

Methods for inferring population structure from genetic information traditionally assume samples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision of this paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference of shared ancestry from data that include ancient DNA. By explicitly modeling population history and genetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry from ancient and contemporary samples. Formally, we use a normal approximation of drift, which allows a novel, efficient algorithm for optimizing model parameters using stochastic variational inference. We show that Dystruct outperforms the state of the art when individuals are sampled over time, as is common in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of 92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual converse of presenting ancestral samples as mixtures of contemporary groups.

Still digesting this one but I do find very intriguing that they claim that Dystruct has much less time-entropy than ADMIXTURE (i.e. the relation between ancient and modern populations seems to be better identified) and that, using this method they get that the Samara (proto-Indoeuropean) population becomes much more clearly related to Kostenki-14 (a Gravettian hunter-gatherer from the Don area) and that the Paleo-Siberian "ANE" individuals form then their own distinct cluster with very limited impact in Europe (but much larger in parts of Asia (not labeled: South Asia?). This Kostenki-Samara "orange" component keeps influencing Western Indoeuropeans (Corded Ware, Unetice) but at markedly decreasing frequencies of "purity".


However the first admixture of Corded Ware is not with earlier farmers (mostly "green") but with some sort of late "hunter-gatherer" population ("brown" or "maroon" component. Only after the backlash of Bell Beaker, which in Central Europe appears as a mix of Neolithic peoples, Indoeuropeans and maybe even more of that mysterious extra HG element, we see some "return of the farmers", which clearly persists in Unetice.


In general, modern Europeans are (fig.5a, not shown here) quite "greener" than Unetice and some populations (I'm guessing Sardinians and Basques, no labels provided) have zero "orange" (IE) component, which ranges (my visual estimate) between 9% and 27% otherwise.

Fig.5-b (click to expand): Ancestry estimates for 92 ancient samples. The three leftmost samples are the Pleistocene hunter-gatherers. In Dystruct, late Neolithic samples and beyond present as a mixture of hunter-gatherers, Yamnaya steppe herders,and early Neolithic samples, matching supported historical migrations of steppe herders into Eastern and Western Europe.

Posted by Maju at Wednesday, February 14, 2018

[Angela]

Here under, an interesting abstract thanks to MAJU of 'For what they were we are' blog -

February 14, 2018

Dystruct versus Admixture


Not really able yet to discern if this is an alternative way ahead for autosomal archaeogenetics or just another dead end. But it does seem interesting enough to mention here in any case.

It may be very important in the deciphering of the so-called "ANE" ghostly genetic influence.


Tyler A. Joseph & Itsik Pe'er. Inference of population structure from ancient DNA. bioRXiv 2018 (pre-pub). DOI:10.1101/261131

Methods for inferring population structure from genetic information traditionally assume samples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision of this paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference of shared ancestry from data that include ancient DNA. By explicitly modeling population history and genetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry from ancient and contemporary samples. Formally, we use a normal approximation of drift, which allows a novel, efficient algorithm for optimizing model parameters using stochastic variational inference. We show that Dystruct outperforms the state of the art when individuals are sampled over time, as is common in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of 92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual converse of presenting ancestral samples as mixtures of contemporary groups.

Still digesting this one but I do find very intriguing that they claim that Dystruct has much less time-entropy than ADMIXTURE (i.e. the relation between ancient and modern populations seems to be better identified) and that, using this method they get that the Samara (proto-Indoeuropean) population becomes much more clearly related to Kostenki-14 (a Gravettian hunter-gatherer from the Don area) and that the Paleo-Siberian "ANE" individuals form then their own distinct cluster with very limited impact in Europe (but much larger in parts of Asia (not labeled: South Asia?). This Kostenki-Samara "orange" component keeps influencing Western Indoeuropeans (Corded Ware, Unetice) but at markedly decreasing frequencies of "purity".


However the first admixture of Corded Ware is not with earlier farmers (mostly "green") but with some sort of late "hunter-gatherer" population ("brown" or "maroon" component. Only after the backlash of Bell Beaker, which in Central Europe appears as a mix of Neolithic peoples, Indoeuropeans and maybe even more of that mysterious extra HG element, we see some "return of the farmers", which clearly persists in Unetice.


In general, modern Europeans are (fig.5a, not shown here) quite "greener" than Unetice and some populations (I'm guessing Sardinians and Basques, no labels provided) have zero "orange" (IE) component, which ranges (my visual estimate) between 9% and 27% otherwise.

Fig.5-b (click to expand): Ancestry estimates for 92 ancient samples. The three leftmost samples are the Pleistocene hunter-gatherers. In Dystruct, late Neolithic samples and beyond present as a mixture of hunter-gatherers, Yamnaya steppe herders,and early Neolithic samples, matching supported historical migrations of steppe herders into Eastern and Western Europe.

Posted by Maju at Wednesday, February 14, 2018

We already have a thread on the topic. I will combine the threads.