Wednesday, October 31, 2012

'globe13' participant results

Project participant results for the globe13 calculator can be found in the spreadsheet. Population median results and Fst divergences are also included.

Below, you can see the first two dimensions of an MDS plot of the 13 components:

A neighbor-joining tree of the 13 components based on the Fst divergences:
I have also created a TreeMix plot using Palaeo_African as an outgroup, and allowing as many as 5 migration edges:
The actual tree is:


((West_African:0.00448794,(East_African:0.00506576,(((((East_Asian:0.0173284,Siberian:0.00732773):0.0027852,(Amerindian:0.026174,Arctic:0.0118342):0.00742092):0.0114738,Australasian:0.0488974):0.00266559,South_Asian:0.00734044):0.008089,(Southwest_Asian:0.00541405,((West_Asian:0.00620657,North_European:0.00657599):0.00311587,Mediterranean:0.00798949):0.00650328):0.0118925):0.0299627):0.00597674):0.00671186,Palaeo_African:0.0215931);
0.0640319 NA NA NA Palaeo_African:0.0215931 Australasian:0.0488974
0.270468 NA NA NA Australasian:0.0488974 East_Asian:0.0173284
0.185213 NA NA NA South_Asian:0.00734044 ((West_Asian:0.00620657,North_European:0.00657599):0.00311587,Mediterranean:0.00798949):0.00650328
0.129883 NA NA NA North_European:0.00657599 Amerindian:0.026174
0.138757 NA NA NA Arctic:0.0118342 (West_Asian:0.00620657,North_European:0.00657599):0.00311587

Monday, October 29, 2012

'globe13' calculator

The globe13 calculator is based on the K=13 analysis. It includes the following components:


  • Siberian
  • Amerindian
  • West_African
  • Palaeo_African
  • Southwest_Asian
  • East_Asian
  • Mediterranean
  • Australasian
  • Arctic
  • West_Asian
  • North_European
  • South_Asian
  • East_African

Fst divergences between ancestral components can be found here.

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 'globe13' instead of 'dv3' in these instructions. You can consult the spreadsheet for proportions of the 13 components in different world populations.

Terms of use: 'globe13', 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.

Tuesday, October 23, 2012

'globe10' calculator

As part of the on-going analysis of the world dataset, I am releasing the 'globe10' calculator, which is based on the K=10 analysis. This calculator includes the following ancestral components:
  • Amerindian
  • West_Asian
  • Australasian
  • Palaeo_African
  • Neo_African
  • Siberian
  • Southern
  • East_Asian
  • Atlantic_Baltic
  • South_Asian
The names may be the same as the ones from previous calculators released by the Project, but you should always consult the spreadsheet to see how they might differ. In this case, inclusion of Amerindian, Australasian populations, African hunter-gatherers, dealing with the Paniya issue, and inclusion of data of Schlebusch et al. (2012), and  Pagani et al. (2012), have all combined to change components in subtle ways, although their modalities remain largely unchanged, and hence so do the names.

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 'globe10' instead of 'dv3' in these instructions. You can consult the spreadsheet for proportions of the 10 components in different world populations.

Terms of use: 'globe10', 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.

Friday, October 19, 2012

'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.

Saturday, October 13, 2012

Geno 2.0 data request

If anyone has received results from the Geno 2.0 test of the Genographic Project and want to share it with me, feel free to send it at dodecad@gmail.com. I will not distribute it or share it with anyone. I want to see what SNPs are tested, what format the data is in, and what is its intersection with other available datasets. This way, I can update my DIYDodecad software so that Geno 2.0 testees can use the various calculators released by the project to get an alternative ancestry assessment.

In time, and if there is interest, I may release additional calculators that make use of the particular SNP set tested by Geno 2.0.