My Origins Results......

[hfp43]

Harappa World And Native American

FWIW, Harappa World estimates 0.63% "American" and 0.70% "Beringian" for my Family Finder raw data. The sum of those is similar to my Native American results with Eurogenes K13 and MDLP World, and a bit higher than my NA results with Dodecad World9. MyOrigins shows no NA, even though my 33% French Canadian ancestry makes some detectable degree of NA highly likely.

[josh w.]

The lead author of the White Paper also developed Harrapa World. I suspect that MO might be derived from the Harrapa World program rather than be Harrapa World per se. Of course, they had to do a new data analysis for MO but within Harrapa World there have been new data analyses with changes in geographical regions..

Clarification. R Kahn has been involved with Harrapa World where his calculator is used. Since the information is private, I can only speculate.

[josh w.]

Clarification. R Kahn has been involved with Harrapa World where his calculator is used. Since the information is private, I can only speculate.

For example, does MO employ the calculator developed at Harrapa World.

[josh w.]

Yes, I also hope that the algorithms also respond to recent complaints about MO 'misses'.

To amplify on my last post. From the White Paper authorship, I might be incorrect but it appears that the Admixture pattern is computed by the Harrapa World program and then in a second step the best fit to the admixture pattern is estimated by an Oracle like program.

There is clearly a need for more data from MO. The admixture programs at Gedmatch show geographical area profiles for each reference group with new groups added all the time. 23&me is honest enough to post it's false positive and false negative rates.

[robe3b]

There is clearly a need for more data from MO. The admixture programs at Gedmatch show geographical area profiles for each reference group with new groups added all the time. 23&me is honest enough to post it's false positive and false negative rates.

The following has been extracted from the myOrigins paper by Razib Khan and Rui Hu:

We assembled a large number of candidate reference populations which were relatively unadmixed and sampled widely in terms of geography. From these we removed related or outlier individuals with the Plink software, utilizing identity-by-descent (IBD) analysis and visually inspecting multi-dimensional scaling plots (MDS). Further visualization established that the reference population sets were indeed genetically distinct from each other. We also ran Admixture and MDS with specific populations to asses if any individuals were outliers or exhibited notable gene flow from other reference groups, removing these. Admixture was run on an inter and intra-continental scale to establish a plausible number of K values utilizing the cross-validation method [Alexander2011]. After removing markers which were missing in more than 5 percent of loci and those with minor allele frequencies below 1 percent, the total intersection of SNPs across the pooled data set was 290,874. The final number of individuals in was 1,353.

I wonder how many "related or outlier individuals" were actually removed from the "large number of candidate reference populations which were relatively unadmixed and sampled widely in terms of geography".

[josh w.]

The following has been extracted from the myOrigins paper by Razib Khan and Rui Hu:

We assembled a large number of candidate reference populations which were relatively unadmixed and sampled widely in terms of geography. From these we removed related or outlier individuals with the Plink software, utilizing identity-by-descent (IBD) analysis and visually inspecting multi-dimensional scaling plots (MDS). Further visualization established that the reference population sets were indeed genetically distinct from each other. We also ran Admixture and MDS with specific populations to asses if any individuals were outliers or exhibited notable gene flow from other reference groups, removing these. Admixture was run on an inter and intra-continental scale to establish a plausible number of K values utilizing the cross-validation method [Alexander2011]. After removing markers which were missing in more than 5 percent of loci and those with minor allele frequencies below 1 percent, the total intersection of SNPs across the pooled data set was 290,874. The final number of individuals in was 1,353.



I wonder how many "related or outlier individuals" were actually removed from the "large number of candidate reference populations which were relatively unadmixed and sampled widely in terms of geography".

The unadmixed conclusion is surprising. There have been admixture studies of many of the reference group populations and they all show admixture, e.g. Diaspora Jews, Italians, Irish.

[josh w.]

The unadmixed conclusion is surprising. There have been admixture studies of many of the reference group populations and they all show admixture, e.g. Diaspora Jews, Italians, Irish.

The original statement is ambiguous. It says that the groups were selected because they were unadmixed. In other words, the lack of admixture within the groups was presumed rather than measured. On what basis was this presumption made, certainly not on prior research with the reference populations. Did they simply mean that the groups were homogeneous, even though the defining SNPs were selected from diverse (admixed) ancestry.

[josh w.]

The original statement is ambiguous. It says that the groups were selected because they were unadmixed. In other words, the lack of admixture within the groups was presumed rather than measured. On what basis was this presumption made, certainly not on prior research with the reference populations. Did they simply mean that the groups were homogeneous, even though the defining SNPs were selected from diverse (admixed) ancestry.

Or is the key 'relatively' unadmixed, e.g. 3 vs 6 source populations.

[Armando]

A friend from Puebla, Mexico, who is mostly of not entirely Indigenous, got these results. Population Finder 98.8% Native American-Maya. Origins results; New World-Bering Expansion 63%, East Asian-Asian Northeast 21%, European-North Circumpolar 10%, Central/South Asian-Eurasian Heartland 7%. All his ancestry is Mexican. Family oral tradition says Azteca.

Thus, the only remaining issue to be resolved is the sharp decrease in my Native American estimate (36.4%, according to PF, 31% as stated by myOrigins). Thanks for your help.

The sharp decrease in the Native American component has happened to all Latin Americans with Native American ancestry. Maya, Pima and Columbian reference populations were not included in myOrigins. They only used Karitiana and Surui as reference population for Native Americans.

Our Native American ancestry is now divided up mostly into, from most to least, New World-Bering Expansion and East Asian-Asian Northeast. European-North Circumpolar shows up at a very low percentage, mostly around 2-3%. Central/South Asian-Eurasian Heartland doesn't show up most of the time.

See section 6 Table of reference populations https://www.familytreedna.com/learn/...s-methodology/

The one thing I wonder is how Asians would have been affected if they had left Maya, Pima and Columbian as reference populations.

[Gary Fox]

Can I have the old Population Finder back please.....

Amen to that!

[PDHOTLEN]

Ahem! I got my results back from Ancestry.com today. And my origins percentages there are much different! From them I got the following: European = 98%, West Asia = 1%, and Asia = 1%. Europe is broken down to: Europe West = 33%, Scandinavia = 28%, Ireland = 17%, Great Britain = 14%, and traces in Europe = 6%. NOTICE THAT THERE IS NO NORTH MEDITERRANEAN/SOUTHERN EUROPE AT ALL!!! FTDNA gives me 20% Med/So. Eur. So I no longer think there was an NPE involving my maternal grandfather. However, as my father was 3/4 Norwegian, 28% seems a mite small.

[Svein]

However, as my father was 3/4 Norwegian, 28% seems a mite small.

Even if Norwegians have been in relative isolation, there are admixture from various groups. In myOrigins I have a large component from The British Isles (European Coastal Islands), even if I know of no such ancestry. It could be pretty old, perhaps going back to the vikings, who brought back Irish slaves.

Many Norwegians also have a Finnish component, such as my father and my maternal uncle in myOrigins. This and other admixture will have the "Scandinavian" % down.

[PDHOTLEN]

Ahem! I got my results back from Ancestry.com today. And my origins percentages there are much different! From them I got the following: European = 98%, West Asia = 1%, and Asia = 1%. Europe is broken down to: Europe West = 33%, Scandinavia = 28%, Ireland = 17%, Great Britain = 14%, and traces in Europe = 6%. NOTICE THAT THERE IS NO NORTH MEDITERRANEAN/SOUTHERN EUROPE AT ALL!!! FTDNA gives me 20% Med/So. Eur. So I no longer think there was an NPE involving my maternal grandfather. However, as my father was 3/4 Norwegian, 28% seems a mite small.

I looked at my Ancestry results a bit more. They break down that 6% traces in Europe to: Iberian Penn. = 4%, Italy/Greece = 1%, and Europe East at less than 1%. West Asia is 1% Caucasus, and Asia is less than 1% South Asia (where did that come from?). Welsh is lumped with Irish at Ancestry, and I know I have some Welsh in me.

[kiiski]

Even if Norwegians have been in relative isolation, there are admixture from various groups. In myOrigins I have a large component from The British Isles (European Coastal Islands), even if I know of no such ancestry. It could be pretty old, perhaps going back to the vikings, who brought back Irish slaves.

It's also possible that Scandinavian admixture in their British Isles reference population is causing it to overestimate British Isles ancestry in some Scandinavian customers. The MyOrigins components are estimates based on similarity and for most people it will be misleading to translate them to direct ancestral contributions - especially when dealing with populations that share much recent ancestry.

[PDHOTLEN]

I am still confused by the 20% Southern Europe that FTDNA gives me. Ancestry only gives me 4% Iberian and 1% Italy/Greece. Even that confuses me. FTDNA gives me 48% Scandinavian, while Ancestry only gives me 28% Scandi. And on and on. Anyway, I'm more interested in my family tree over the last few centuries than I am about ancient deep DNA.