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You seem to work with these genomes on a daily basis. I am good an analyzing the data but I still need to work on “processing’ the data independently. My question to you or anyone. Sage you can jump in.
Looking at this new piece by Danial Shriner(edit by Cruiciani)…he is bucking the trend…but not completely .
I don’t understand why The Human Origins Reference Panel will give a different result compared to the other panels? My understanding was the reference panel was only used for "alignment" and any human panel should give similar or very similar results. It is remarkable that Natufians have so much more Sub-saharan DNA depending on the panel used?
-------------------- Quote: “Re-analysis of Whole Genome Sequence Data From 279 Ancient Eurasians Reveals Substantial Ancestral Heterogeneity Daniel Shriner*
Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, United States
Supervisedclustering or projection analysis is a staple technique in population genetic analysis. The utility of this technique depends critically on the reference panel. The most commonly used reference panel in the analysis of ancient DNA to date is based on the Human Origins array. We previously described a larger reference panel that captures more ancestries on the global level. Here, I reanalyzed DNA data from 279 ancient Eurasians using our reference panel. I found substantially more ancestral heterogeneity than has been reported. Reanalysis provides evidence against a resurgence of Western hunter-gatherer ancestry in the Middle to Late Neolithic and evidence for a common ancestor of farmers characterized?????????? by Western Asian ancestry, a transition of the spread of agriculture from demic to cultural diffusion, at least two migrations between the Pontic-Caspian steppes and Bronze Age Europe, and a sub-Saharan African component in Natufians that localizes to present-day**** southern ****Ethiopia.” ------------------
BTW WTF is Southern Ethiopia???
xyyman Member # 13597
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Remember Shriner is the same guy who REANALYZED work found SSA in Natufians
May be he is reading my work…xyyman. In this paper he is also critiquing “supervised” vs “Unsupervised” ancestry mapping!! It’s about sometime other than xxyman take them up on this….. lol!
xyyman Member # 13597
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So Danny Shriner is stating these European researchers have been bias all along and or falsifying data ...But he is "spinning" also. . But he is!!!!!! Why? “Characterized!! He is waffling. He is reluctant to use the word “origin” but wants to satisfy Eurocentric’s ..so he went with characterized meaning it can be found in the West Asians but it does not mean it originated there. He is playing it safe.
------------------------------------- Quote: “ with known ascertainment, for studies of human population genetics (Patterson et al., 2012). In the analysis of ancient DNA, the reference panel most widely used to date comprises <3,000 individuals genotyped using the Human Origins array Lazaridis et al., 2014; Günther et al., 2015; Mathieson et al., 2015; Cassidy et al., 2016 , although some data are not freely available. One consequence of use of a single reference panel is consistency within the ancient DNA field. Unfortunately, the labels for ancestries used in these paperslacks overlap with labels used by other researchers for ancestries in present-day peoples. Furthermore, none of the results in the ancient DNA papers has been replicated using a second reference panel. We previously combined completely public domain data to generate a reference panel comprising 5,966 individuals from 282 samples, “
“ancestor of farmers characterized?????????? by Western Asian ancestry”
In the Copper Age, Northern African ancestry increased while Arabian ancestry decreased, possibly indicating entry into Europe from northwest Africa rather than northeast Africa. The ratio of 5.4-fold more Southern European than Northern European ancestries and the presence of Northern African ancestry acquired from the Early Neolithic to the Copper Age Are inconsistent with a resurgence of peoples related to Western hunter-gatherers, given that Western hunter-gatherers had 1.6- fold more Northern European than Southern European ancestry and no Northern African ancestry. Instead, this ancestral profile is suggestive of an expansion of peoples from Southern Europe resembling those from the Remedello culture
The increase of Western Asian ancestry in the Bronze Age Levant and throughout Neolithic Western Asia is consistent with demic diffusion of agriculture via a **single** origin, with the original people characterized by Western Asian ancestry
Previously, no significant sharing of ancestral components with sub-Saharan African populations was found to accompany the presence of Y haplogroup E1b1b1b2 Lazaridis et al., 2016 E1b1b1b1a-M81, not E1b1b1b2-Z830, is presently common among Berbers in North Africa Arredi et al., 2004; Trombetta et al., 2015). E1b1b1b1a-M81 has a time to most recent common ancestor of only 2,300 (95% confidence interval [1900, 2700]) years before present Urasin, 2017 and therefore was not prevalent in Northern African ancestry during the Epipaleolithic. Ancestry shared by Omotic-speaking peoples is found predominantly in present-day southern Ethiopia and is associated with haplogroup E, thus revealing a plausible source. -------------------------
xyyman Member # 13597
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Elmaestro Member # 22566
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I actually don't work on genomes on a "daily" basis... I would like to, but money and shit.
Otherwise I've been extremely broke on time... do you have a link to the shriner article?
A short answer to the question in the OP... different alleles, different results. You can also develop a bias against more diverse pooling of people if you repeatedly analyze the same 1.3mil alleles.
For example the variants typically called in HOII or laz's 1240K dataset can give robust results showing clean distinctions between populations that grouped together due to low diversity (post bottle neck) but a different group of variants might better show similarities between radically different groups due to them being more frequently shared between said groups.
This is why Studies should typically try to include analysis of Homozygosity and Linkage, linkage disequibrium is a telling sign of migration or recent shared history, structural analysis and formal stats reflect similarity in variants between individuals.
If you switch your reference panel you are opening up the possibility that different groups might appear more affiliated because the alleles in question are now either more frequent or infrequent between populations.
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