MOESAN
Elite member
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- Location
- Brittany
- Ethnic group
- more celtic
- Y-DNA haplogroup
- R1b - L21/S145*
- mtDNA haplogroup
- H3c
Dystruct vs admixture
Here under, an interesting abstract thanks to MAJU of 'For what they were we are' blog -
[h=2]February 14, 2018[/h] [h=3]Dystruct versus Admixture[/h]
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
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.
Posted by Maju at Wednesday, February 14, 2018
Here under, an interesting abstract thanks to MAJU of 'For what they were we are' blog -
[h=2]February 14, 2018[/h] [h=3]Dystruct versus Admixture[/h]
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
