'globe4' calculator

Patterson et al. (2012) recently published evidence for admixture in northern Europeans between a population resembling modern Sardinians (and the Neolithic Tyrolean Iceman, whose genome was published earlier this year), and, surprisingly Native Americans. The authors attribute the Amerindian-like ancestry element to a North Eurasian population that spawned Native Americans, and which also contributed ancestry to northern Europeans. They propose two possibilities for the origin of this admixture: (i) the Mesolithic Europeans resembled Amerindians, or (ii) there was an influx of Amerindian-like populations from the east during late prehistory. A palimpsest of these two processes may explain parts of the observed signal of admixture.

In a recent K=4 admixture experiment, I demonstrated that ADMIXTURE software produces an Amerindian ancestral component that closely tracks the signal of admixture using the D-statistic test. I have decided to make this test available for download and use with DIYDodecad.

The test has four ancestral populations:

• European
• Asian
• African
• Amerindian

It is important to remember that some of these components track different aspects of ancestry that is better resolved at higher resolution. There are also populations that "don't fit well" in this 4-partite scheme (e.g., certain African or Australasian populations).

For example, the Amerindian component of this test may indicate (i) real recent Native American ancestry, (ii) East Eurasian ancestry found in Siberia and East Asia, (iii) the common signal of admixture differentiating most European groups from Sardinians and Near Eastern Caucasoid groups. Similarly, the Asian component may indicate Australasian, South Asian, or East Eurasian ancestry. And, the European component tracks the ancestry of individuals from West Eurasia in general, although it reaches is maximum in Sardinians.

This test may, however, be useful to Old World individuals who want to get an idea about the signal of admixture discovered by Patterson et al., so I decided to make it available. For individuals who don't suspect recent Amerindian or Siberian/East Asian ancestry, and who don't belong to populations with recent such ancestry, the Amerindian component will most likely represent the aforementioned signal.

You need to extract the contents of the RAR file to the working directory of DIYDodecad. You use it by following exactly the instructions of the DIYDodecad README, but always type 'globe4' instead of 'dv3' in these instructions. You can consult the spreadsheet for proportions of the 4 components in different world populations.

Terms of use: 'globe4', including all files in the downloaded RAR file is free for non-commercial personal use. Commercial uses are forbidden. Contact me for non-personal uses of the calculator.

fastIBD analysis of Central/Eastern Europe

Please refer to the previous analysis on the Balkans/West Asia for more information about the interpretation of this type of analysis.

Clusters Galore


The Clusters Galore can be found in the spreadsheet. After inspection of the 23 clusters inferred with 21 dimensions, they could be described as:

1. Mordvin
2. East Slavic
3. Polish-Ukrainian
4. East Balkan
5. Vologda Russians
6. Lithuanian
7. Central European (combining many groups with small sample sizes)
8. A couple of related (?) individuals
9. Anatolian
10. Greek
11. Chuvash
12. Ossetian
13. A couple of related individuals
14. A couple of related individuals
15. Balkar
16. A couple of related individuals
17. Chechen
18. Kumyk
19. A couple of related individuals
20. Adygei
21. Lezgin #1 (main)
22. Lezgin #2
23. Lezgin #3

If you belong to a population with few other participants, you might end up latching onto a cluster dominated by a bigger group. This does not mean that your population is not distinctive, only that there are not enough samples to reveal its distinctiveness if it exists.

Inter-Population IBD

Results for Dodecad Participants

Results can be found in the spreadsheet.

If you have joined the Project, please consider leaving a comment in the Information about Project samples thread. That will help others make better sense of their results, e.g., if you find that you belong in the same cluster with some other individual, you might want to know something about their origins.

UPDATE: I have added the IBD sharing matrix.See here on how to use it.

Clusters Galore (fastIBD edition) for some northern European participants

You can find some new Clusters Galore results here (scroll down for spreadsheet link). The new methodology described in that post has made it possible to infer even finer-level population structure than "classical" Clusters Galore.

'eurasia7' calculator

This calculator was made with 196 different populations and 2,659 individuals, including 518 project participants. The following Dodecad populations do not have 5 individuals yet, so they are included in the OTHERS_D generic category:

Algerian_D, North_African_Jews_D, Slovenian_D, Mixed_Scandinavian_D, Danish_D, Moroccan_D, Tunisian_D, Serb_D, Austrian_D, Saudi_D, Pakistani_D, Tatar_Various_D, Palestinian_D, Greek_Italian_D, Romanian_D, Swiss_German_D, Szekler_D, Mandaean_D, Azeri_D, Czech_D, Georgian_D, Belgian_D, Latvian_D, Estonian_D, Bangladesh_D, Yemenese_D, Sri_Lanka_D, Hungarian_D, Basque_D, Udmurt_D, Egyptian_D

As always, I encourage people with 4 grandparents from the same country or ethnic group of Eurasia, North or East Africa to contact me (do not send data!) for possible inclusion in the Project. If I have overlooked any such individuals, drop me a line (my e-mail address is at the bottom of the blog). I usually start a new _D population whenever individuals with 4 grandparents from the same group are submitted, but I may have missed some.

Note that all individuals from the reference populations have also been included, including outliers; you should be aware of this when reading the population averages, and consult the Outliers tab in the v3 spreadsheet for some instances of outliers.

Due to image size restrictions in Picasa, the labels are not visible well. A large version of the above plot can be found in the download bundle.

The seven ancestral populations inferred at this level of resolution are:

• Sub_Saharan
• West_Asian
• Atlantic_Baltic
• East_Asian
• Southern
• South_Asian
• Siberian

As usual, you should take these names as useful labels, and interpret them in conjunction with the components' distribution in different populations, and their Fst distances, both of which can be found in the spreadsheet.

The table of Fst distances:

Below you can see a neighbor-joining tree based on inter-population Fst distances:

The first six dimensions of a multi-dimensional scaling of the same:

Calculator Files:

• The spreadsheet contains population averages, the table of Fst distances, and individual results for included Project participants.
• The download RAR file (Google Docs or Sendspace) contains all the files needed to run the calculator. You must download and install DIYDodecad 2.1 first. In order to run the calculator, you follow the instructions of the README file, but type 'eurasia7' instead of 'dv3'.

Terms of use: 'eurasia7', including all files in the downloaded RAR file is free for non-commercial personal use. Commercial uses are forbidden. Contact me for non-personal uses of the calculator.

Technical Details:

The calculator is built using allele frequencies of K=7 ancestral components inferred by ADMIXTURE 1.21 analysis of 2,659 individuals. Markers included in the source datasets, as well as the Family Finder and 23andMe (as of Oct 21) platforms were included. The marker set was thinned of markers with less than 99.5% genotype rate and less than 0.5% minor allele frequency. Linkage-disequilibrium based pruning was carried out with a window size of 250 SNPs, advanced by 25 SNPs and R-squared greater than 0.4. A total of 164,990 SNPs remained after these filtering steps.

All relevant populations available to me, and genotyped at a sufficient number of markers were included. Inclusion of the Kalash population resulted in a population-specific component at K=7, and hence their admixture components were inferred a posteriori. Their proportions are consistent with previous results, showing them to be a "West Asian" population (62.4%) with substantial "South Asian" admixture (37.1%), and near-complete absence of any other genetic components.

'euro7' calculator

I am releasing a new calculator for Europeans, including their immediate neighboring populations around the Black Sea (Caucasus and Anatolia). The calculator can be used with DIYDodecad

There are additional African and Far-Asian population controls, so, in principle, the calculator could be used by non-Europeans/Anatolians/Caucasians, although I would be less confident of their results. For example, people of South Asian ancestry may obtain a Far-Asian result if they use this calculator, due to the deep affinity of Ancestral South Indians with East Asians. Other West Eurasians and West Eurasian-admixed peoples, not from the studied regions (e.g., Arabians or East Africans) will have their West Eurasian components mapped onto the ones used in this calculator.

'euro7' uses 7 ancestral components:

• Caucasus
• Northwestern
• Northeastern
• Southeastern
• African
• Far_Asian
• Southwestern

These names represent 7 ancestral populations inferred by ADMIXTURE, and have been chosen based on the geographical regions where each of them achieves its maximum representation. You should always refer to A note of caution on admixture estimates, Interpretation of ADMIXTURE results: component sharing, as well as the average population values in the spreadsheet when interpreting your individual results.

The distribution of these 7 components can be seen in the barplot on the top left, and precise admixture proportions can be found in the spreadsheet. Note that additional samples have been used to infer these components, but as these come from Dodecad populations with less than 5 participants, I am not reporting average values for them, as per the usual project policy.

Here is the neighbor-joining tree based on the Fst divergences between the 7 ancestral components:
Instructions:

You can download the calculator RAR from here (Google docs; File->Download original), or here (sendspace).

You need to extract the contents of the RAR file to the working directory of DIYDodecad. You use it by following exactly the instructions of the DIYDodecad README, but always type 'euro7' instead of 'dv3' in these instructions.

Terms of use: 'euro7', including all files in the downloaded RAR file is free for non-commercial personal use. Commercial uses are forbidden. Contact me for non-personal uses of the calculator.

Calculators released by the Dodecad Project:

• bat
• africa9
• weac
• euro7

Fine-scale admixture in Europe (Dagestan/Basque/Sardinian components)

Wanting to see whether the Dagestan mystery would extend into Europe, I carried out an ADMIXTURE analysis including all my European populations. Once again, as this is done on only ~30k markers, a little noise on the low-level components is expected.

Admixture proportions can be found in the spreadsheet

Notably there is now both a Sardinian and a Basque centered cluster; the latter was formerly (in the standard K=10 analysis) split between "Southern European" and "Northern European". The Urkarah, Lezgin, and Stalskoe samples show the highest presence of the "blue" component, which I label, once again, Dagestan. Note, however, that you should not compare admixture proportions across ADMIXTURE runs for components that happen to be labeled the same (homonymous). Certainly "this" Dagestan is related to the "previous" Dagestan component, but do not assume they are identical.

Here is the Fst distance matrix between the 7 components:

Discussion

The most notable thing about this figure is the relative absence of the West Asian component in the periphery of Europe. The lowest values are seen in Basque, Sardinian, Orcadian, White Utahns, Lithuanians, Finns, and Scandinavians (in no particular order).

It is worthwhile to order the European populations in terms of their Dagestan component. Excluding the populations of the Caucasus, these are, in ascending order: Basque (0.7%), Sardinian, Cypriot, Belorussian, South Italian/Sicilian, Lithuanian, Tuscans, Portuguese, Greek (3.8%), Vologda Russian, Romanian, Finnish, Spaniards, North Italian, Dodecad Spaniards, Dodecad Russian, Chuvash, Hungarian, French (7.9%), German, Scandinavian, White Utahn, Orcadian (12.6%).

Interpreting this pattern is not easy, but it does seem that this component seems to have a V-like distribution, achieving its maximum in Caucasus and its environs, then undergoing a diminution, and achieving a secondary (lower) frequency mode in NW Europe.

The surprising appearance of the homonymous Dagestan component in India suggests a widespread presence of a common ancestry element. The West Asian element, by comparison seems to have a more normal /\-like distribution around its center in Anatolia-Caucasus-Iran region. It does reach the Atlantic coast, but is lacking in Scandinavia and Finland, and also in India itself.

This is just a piece of a broader puzzle, and the picture is not yet clear. However, we can tentatively say that whatever brought the "Dagestan" component to India was not a unidirectional process, but also brought a similar population element to western Europe.