Admixture plots

[Lemgrant]

Let's post here Admixture plots that researchers come up with by using the Admixture software (link1 (http://software.genetics.ucla.edu/admixture/), link2 (http://software.genetics.ucla.edu/admixture/admixture-manual.pdf))

https://i.imgur.com/ZNUG99O.jpg

https://digitalcommons.wayne.edu/cgi/viewcontent.cgi?article=1040&context=humbiol_preprints

https://www.researchgate.net/publication/264390976_No_Evidence_from_Genome-Wide_Data_of_a_Khazar_Origin_for_the_Ashkenazi_Jew s

https://i.imgur.com/VlNnvjF.png
https://i.imgur.com/WMhMoEg.png
https://i.imgur.com/1JHMNUA.png

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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0105090

https://i.imgur.com/fOuM2Cy.png
https://i.imgur.com/wPXfZeh.png

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https://www.researchgate.net/publication/327813522_Genes_reveal_traces_of_common_recent_dem ographic_history_for_most_of_the_Uralic-speaking_populations
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151024/

https://i.imgur.com/UNDC3Ub.png

[Lemgrant]

Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135820

ADMIXTURE plot (k = 6).
Ancestry proportions of 1,194 individuals as revealed by ADMIXTURE.
https://i.imgur.com/2559Sba.png

[michal3141]

Let's post here Admixture plots that researchers come up with by using the Admixture software (link1 (http://software.genetics.ucla.edu/admixture/), link2 (http://software.genetics.ucla.edu/admixture/admixture-manual.pdf))


I love these plots. Thanks Lemgrant!

[michal3141]

Btw these Poles with more Siberian/East Asian admixture than Ukrainians and Belarusians are probably from Estonian Poles dataset.

[Lucas]

Btw these Poles with more Siberian/East Asian admixture than Ukrainians and Belarusians are probably from Estonian Poles dataset.

Yes and conlusions from this study were biased.

[Lemgrant]

Yes and conlusions from this study were biased.

different studies show the same, so which one you are talking about?

[Peterski]

different studies show the same, so which one you are talking about?

He is talking about the Estonian Poles that different studies are using.

I uploaded them to GEDmatch from my "Poland Regions" account, see:

https://anthrogenica.com/showthread.php?16923-Inflanty-(Livonian)-Poles-on-GEDmatch

For example: Pagani 2016 sample Pole1 Kohtla-Järve - kit BD1045630

^^^
This Pole (from Pagani 2016 study) was born in Kohtla-Järve, Estonia:
(screenshot is from Supplementary Tables with details about samples)

https://i.imgur.com/XK0s3zH.png

[Lemgrant]

He is talking about the Estonian Poles that different studies are using.


I mean which study has biased conclusions.

[Voskos]

Crete https://wol-prod-cdn.literatumonline.com/cms/attachment/60507f8e-ad0e-4a6b-8736-0828e5636465/ahg12328-fig-0006-m.jpg

[Lemgrant]

Crete https://wol-prod-cdn.literatumonline.com/cms/attachment/60507f8e-ad0e-4a6b-8736-0828e5636465/ahg12328-fig-0006-m.jpg


Genetic history of the population of Crete

https://onlinelibrary.wiley.com/doi/full/10.1111/ahg.12328


ADMIXTURE analysis for the Cretans and the Andalusians, North Africans, Near Eastern populations, and the Venetians. Results are shown for K equal to four, five, and six hypothetical ancestral populations. (a) A possible shared component can be observed between the Andalusian and the Cretans, especially the western populations (Kissamos, Kandanos), especially for K equal to six. (b) The North African populations are genetically distinct from the Cretans, except for a small amount of shared ancestry between Tunisians and the Anoyia subpopulation for K equal to six. (c) A possible shared component can be observed between the Near East to the Cretans for K equal to four or five. (d) Cretans and the Venetian populations appear completely distinct with only very minor shared ancestry. We can also observe a possible shared component between the Italian populations and the Cretan subpopulations

[Voskos]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973929/

https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image% 20to%20zoom&p=PMC3&id=4973929_pone.0160614.g002.jpg

[Lemgrant]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4973929/

https://www.ncbi.nlm.nih.gov/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Click%20on%20image% 20to%20zoom&p=PMC3&id=4973929_pone.0160614.g002.jpg

Interesting!

[Lemgrant]

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[Lemgrant]

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[dududud]

Sardo are almost very pur in this (according the region).

[Lemgrant]

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[Lemgrant]

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[Leto]

https://www.researchgate.net/publication/332747456_The_genetic_history_of_admixture_across_ inner_Eurasia

[Mingle]

Yes and conlusions from this study were biased.

What conclusion did they make that you consider to be biased?

[Kaspias]

Subscribed, i will read the articles in my coffee time

[Lemgrant]

Revealing the impact of the Caucasus region on the genetic legacy of Romani people from genome-wide data
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0202890


Abstract
Romani people are a significant minority in Europe counting about 10 million individuals scattered throughout the continent. They are a migratory group originating from Northwestern India. Their exodus from India occurred approximately 1000–1500 years ago. The migration route of the Romani people was reconstructed with the help of cultural anthropology, linguistics and historical records. Their migration made them through Central Asia, Middle East and the Caucasus region, prior to the arriving into Europe. Yet the significance of these regions, especially of the Caucasus, in Roma ancestry was a rather neglected topic. Contribution of the Caucasus and further affected regions to the ancestry of Roma was investigated based on genome-wide autosomal marker data. 158 European Roma samples and 41 populations from the Caucasus region, from Middle East, Central Asia and from South Asia were considered in our tests. Population structure and ancestry analysis algorithms were applied to investigate the relationship of Roma with these populations. Identical by descent DNA segment analyses and admixture linkage disequilibrium based tests were also applied. Our results suggest that the Caucasus region plays also a significant role in the genetic legacy of Romani people besides the main sources, Europe and South Asia, previously investigated by other population genetic studies. The Middle East and Central Asia seems slightly less important but far from negligible in connection with the sources of Roma ancestry. Our results point out that the Caucasus region and altogether the area of the Caspian and Black Seas had a significant role in the migration of Romani people towards Europe and contributed significantly to the genetic legacy of Roma rival to the European and Indian main sources.

[Lemgrant]

The Genetics of Bene Israel from India Reveals Both Substantial Jewish and Indian Ancestry
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152056


Abstract
The Bene Israel Jewish community from West India is a unique population whose history before the 18th century remains largely unknown. Bene Israel members consider themselves as descendants of Jews, yet the identity of Jewish ancestors and their arrival time to India are unknown, with speculations on arrival time varying between the 8th century BCE and the 6th century CE. Here, we characterize the genetic history of Bene Israel by collecting and genotyping 18 Bene Israel individuals. Combining with 486 individuals from 41 other Jewish, Indian and Pakistani populations, and additional individuals from worldwide populations, we conducted comprehensive genome-wide analyses based on FST, principal component analysis, ADMIXTURE, identity-by-descent sharing, admixture linkage disequilibrium decay, haplotype sharing and allele sharing autocorrelation decay, as well as contrasted patterns between the X chromosome and the autosomes. The genetics of Bene Israel individuals resemble local Indian populations, while at the same time constituting a clearly separated and unique population in India. They are unique among Indian and Pakistani populations we analyzed in sharing considerable genetic ancestry with other Jewish populations. Putting together the results from all analyses point to Bene Israel being an admixed population with both Jewish and Indian ancestry, with the genetic contribution of each of these ancestral populations being substantial. The admixture took place in the last millennium, about 19–33 generations ago. It involved Middle-Eastern Jews and was sex-biased, with more male Jewish and local female contribution. It was followed by a population bottleneck and high endogamy, which can lead to increased prevalence of recessive diseases in this population. This study provides an example of how genetic analysis advances our knowledge of human history in cases where other disciplines lack the relevant data to do so.


ADMIXTURE analysis suggests Bene Israel members have Middle-Eastern ancestry


Identity-by-descent analysis suggest Bene Israel members are related to Jewish populations

[Lemgrant]

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[Lemgrant]

The time and place of European admixture in Ashkenazi Jewish history: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006644


Abstract
The Ashkenazi Jewish (AJ) population is important in genetics due to its high rate of Mendelian disorders. AJ appeared in Europe in the 10th century, and their ancestry is thought to comprise European (EU) and Middle-Eastern (ME) components. However, both the time and place of admixture are subject to debate. Here, we attempt to characterize the AJ admixture history using a careful application of new and existing methods on a large AJ sample. Our main approach was based on local ancestry inference, in which we first classified each AJ genomic segment as EU or ME, and then compared allele frequencies along the EU segments to those of different EU populations. The contribution of each EU source was also estimated using GLOBETROTTER and haplotype sharing. The time of admixture was inferred based on multiple statistics, including ME segment lengths, the total EU ancestry per chromosome, and the correlation of ancestries along the chromosome. The major source of EU ancestry in AJ was found to be Southern Europe (≈60–80% of EU ancestry), with the rest being likely Eastern European. The inferred admixture time was ≈30 generations ago, but multiple lines of evidence suggest that it represents an average over two or more events, pre- and post-dating the founder event experienced by AJ in late medieval times. The time of the pre-bottleneck admixture event, which was likely Southern European, was estimated to ≈25–50 generations ago.
https://i.imgur.com/KpBD2Zm.png


The ancestry of Identical-By-Descent (IBD) segments
A number of recent studies have shown that sharing of identical-by-descent (IBD) segments is abundant in the AJ population, and is likely due to a severe bottleneck around 30 generations ago [4, 7, 9, 15, 16]. An open question is the relative timing of the bottleneck and the European gene flow, with our current and past [9] point estimates dating admixture at around or slightly earlier than the bottleneck. Given that most IBD segments but the very long ones (e.g., of length >7cM) coalesce around the time of the bottleneck, we contrast three hypotheses. If admixture completely predated the bottleneck, then IBD segments should have the same EU/ME ancestry proportions as observed genome-wide. If European admixture completely post-dated the bottleneck, then IBD segments should show exclusive ME ancestry. If, on the other hand, European gene flow occurred both before and after the bottleneck, then IBD segments should show an elevated (though not exclusive) ME ancestry compared to the rest of the genome [41–43]. Further, IBD segments of different lengths shared between AJ and other populations could shed light on the geographic origin of each admixture event.

We detected long (>3cM) IBD segments using Germline [44] and Haploscore [45] (Methods). For segments shared within AJ individuals, we then computed the total amount of genetic material in IBD segments associated with each pair of diploid ancestries, namely, the fraction of SNPs in IBD segments where each of the two individuals sharing the segment has either homozygous EU ancestry, homozygous ME ancestry, or heterozygous ancestry. Clearly, errors in IBD segment detection and local ancestry inference could severely bias the conclusions of such an analysis. Fortunately, we could naturally account for these errors using the observed amount of genetic material in IBD segments shared between individuals labeled homozygous ME and homozygous EU, since the proportion of such segments is a direct measure of the noise level (Methods and S1 Text section 4).

Our results demonstrate an over-representation of Middle-Eastern IBD segments, consistent with two waves of gene flow. Specifically, we estimated the European fraction of the AJ ancestry at the bottleneck as 42%, less than the 53% observed genome-wide (Methods). The contribution of post-bottleneck European gene flow required to explain these figures is 19% of the AJ ancestry (Methods). Considering only segments of length between [3,7]cM (as longer segments may descend from ancestors even more recent than the bottleneck) slightly increased the inferred magnitude of post-bottleneck gene flow to 22%, or 23% when considering only segments between [3,4]cM.

Given a history of multiple admixture events, a natural question is the geographic source of each event. According to the documented AJ migration history, we speculated that the Southern-European gene flow was pre-bottleneck and that the Western/Eastern European contribution came later. Indeed, we note that the estimated proportion of ≈20% post-bottleneck replacement is close to our above estimate of ≈16% EU gene flow from sources other than Southern-EU as well as to TreeMix’s and Globetrotter’s results below (and perhaps also with our previous estimate of ≈15% EU ancestry based on AJ and Western European (CEU) data alone [46]). To test this hypothesis, we considered the European ancestry of IBD segments longer than 15cM, which are highly unlikely to predate the bottleneck. The proportion of AJ chromosomes with all regions masked but the >15cM IBD segments inferred by our geographic localization pipeline to be most likely Southern European decreased by 14.8% points compared to the genome-wide results. In contrast, the proportion of AJ chromosomes inferred to be most likely Eastern and Western European increased by 10.2 and 4.5% points, respectively. As a control, when we considered AJ individuals reduced to IBD segments of any length, there was no noticeable change.

We also considered IBD segments shared between AJ and other populations (Fig 5), and observed that the number of segments shared between AJ and Eastern Europeans was ≈6-fold higher than shared between AJ and Southern Europeans (consistent with [5]), with this ratio increasing to ≈60-fold for segments of more recent origin (length >7cM). Further, the number of segments shared with Eastern Europeans was ≈2-fold higher than with Western Europeans or the people of Iberia (P = 5∙10−3 for the difference, using permutations of the EU regional labels), pointing to Eastern Europe as the predominant source of recent gene flow.

https://i.imgur.com/vDCa3Gw.png

Fig 5. The number of IBD segments shared between Ashkenazi Jews (AJ) and other groups of populations.

IBD segments were detected by Germline and Haploscore, as explained in Methods. The population groups are as in Table 1. Note the different scale of panels (A) and (B) (segments of length between [3,7]cM and >7cM, respectively), and that sharing between AJ and either Southern Europeans or Middle Easterners completely vanishes for the longer (more recent) segments, indicating a relatively older divergence/gene flow. Also note that while sharing with Eastern Europeans is high compared to other groups, it is nevertheless a relatively rare event (≈0.04 segments per pair of individuals), in particular compared to sharing within AJ (≈3.4 segments per pair).

https://doi.org/10.1371/journal.pgen.1006644.g005

[marco]

Do I just upload my dna to progarm?

[Lemgrant]

Do I just upload my dna to progarm?

no

http://software.genetics.ucla.edu/admixture/admixture-manual.pdf

https://www.discovermagazine.com/the-sciences/analyzing-ancestry-with-admixture-step-by-step