Tag Archives: armenia

HarappaWorld Tweaks

Posted by on May 29, 2012 18 comments

First of all, I wanted to draw your attention to the fact that I am using weighted means for population averages for HarappaWorld instead of just averaging all samples' results. The weighting gives less importance to outliers. I find this to be a better solution than a simple average or median. A median removes all outliers but it also rejects a lot of information.

An example of the weighted mean effect can be seen in the Behar et al Armenian samples. Four of the samples have higher NE European percentages than the rest. As you can see in the table below, the weighting makes their impact on the population results low.

Mean Weighted Mean
Ethnicity armenian armenian armenian armenian
Dataset behar yunusbayev behar yunusbayev
N 19 16 19 16
S Indian 0.37% 0.52% 0.41% 0.52%
Baloch 16.57% 17.73% 17.07% 17.65%
Caucasian 54.35% 56.43% 57.29% 56.61%
NE Euro 8.96% 2.98% 5.35% 2.95%
SE Asian 0.10% 0.12% 0.10% 0.13%
Siberian 0.49% 0.09% 0.29% 0.09%
NE Asian 0.14% 0.08% 0.16% 0.09%
Papuan 0.28% 0.27% 0.26% 0.27%
American 0.19% 0.18% 0.22% 0.18%
Beringian 0.26% 0.19% 0.23% 0.20%
Mediterranean 8.46% 8.37% 8.21% 8.40%
SW Asian 9.81% 13.03% 10.40% 12.91%
San 0.00% 0.00% 0.00% 0.00%
E African 0.02% 0.00% 0.01% 0.00%
Pygmy 0.00% 0.00% 0.00% 0.00%
W African 0.00% 0.00% 0.00% 0.00%

Another example is the Somali samples in Reich et al data. There is one sample (out of 6) who seems to be eastern Bantu. Let's compare the unweighted mean and weighted mean for Somalis in Reich et al and Harappa participants.

Mean Weighted Mean
Ethnicity somali somali somali somali
Dataset harappa reich harappa reich
N 2 6 2 6
S Indian 0.00% 1.62% 0.00% 1.49%
Baloch 0.00% 0.00% 0.00% 0.00%
Caucasian 2.76% 0.00% 2.76% 0.00%
NE Euro 0.00% 0.11% 0.00% 0.04%
SE Asian 0.27% 0.05% 0.27% 0.06%
Siberian 0.00% 0.04% 0.00% 0.05%
NE Asian 0.00% 0.41% 0.00% 0.46%
Papuan 0.26% 0.10% 0.26% 0.11%
American 0.14% 0.17% 0.14% 0.19%
Beringian 0.23% 0.33% 0.23% 0.38%
Mediterranean 2.12% 3.25% 2.12% 3.65%
SW Asian 31.73% 24.48% 31.73% 27.33%
San 1.96% 1.48% 1.96% 1.37%
E African 60.37% 56.75% 60.37% 60.13%
Pygmy 0.15% 1.78% 0.15% 1.23%
W African 0.00% 9.43% 0.00% 3.51%

Also, I have divided Singapore Indians into 4 groups (actually 3 groups and 1 outlier) since they are so heterogeneous. Here are the weighted mean admixture proportions for all Singapore Indians and the four subgroups.

Ethnicity singapore-indian singapore-indian-1 singapore-indian-2 singapore-indian-3 singapore-indian-4
Dataset sgvp sgvp sgvp sgvp sgvp
N 83 31 41 10 1
S Indian 53.57% 61.95% 50.39% 33.68% 27.81%
Baloch 33.97% 30.24% 36.00% 40.72% 14.27%
Caucasian 3.55% 1.92% 4.03% 9.32% 4.53%
NE Euro 2.93% 0.08% 3.89% 9.84% 35.38%
SE Asian 1.31% 1.30% 1.23% 0.63% 1.20%
Siberian 0.45% 0.47% 0.44% 0.43% 1.19%
NE Asian 0.92% 0.91% 0.80% 1.19% 3.26%
Papuan 0.72% 1.09% 0.50% 0.35% 0.62%
American 0.42% 0.35% 0.44% 0.69% 1.29%
Beringian 0.56% 0.38% 0.65% 0.76% 0.00%
Mediterranean 0.67% 0.40% 0.72% 1.33% 10.38%
SW Asian 0.90% 0.86% 0.87% 1.05% 0.06%
San 0.01% 0.00% 0.01% 0.00% 0.00%
E African 0.03% 0.02% 0.04% 0.00% 0.00%
Pygmy 0.00% 0.00% 0.00% 0.00% 0.00%
W African 0.01% 0.01% 0.00% 0.00% 0.00%

I have updated the spreadsheet as well as HarappaWorld Oracle.

Participation Changes

Posted by on May 16, 2012 5 comments

Now that I have DIY HarappaWorld out, I am changing the participation requirements a little bit with somewhat different requirements for South Asians compared to other regions.

If you have any real ancestry from a South Asian origin, you are eligible to participate. Partial South Asian ancestry is okay. The list of countries of origin I count as South Asian are as follows:

  • Afghanistan
  • Bangladesh
  • Bhutan
  • India
  • Maldives
  • Nepal
  • Pakistan
  • Sri Lanka

Note that 2-3% South Asian from Dr. McDonald's BGA or Dodecad Project does not count as South Asian ancestry.

If you have all four of your grandparents from one of the following countries or regions, you can also send me your data.

  • Burma
  • Tibet
  • Uyghur from Xinjiang, China
  • Tajikistan
  • Kyrgyzstan
  • Kazakhstan
  • Uzbekistan
  • Turkmenistan
  • Iran
  • Turkey
  • Azerbaijan
  • Armenia
  • Georgia
  • North Caucasian Federal District, Russia
  • Iraq
  • Syria
  • Lebanon
  • Jordan

Relatives will only be accepted when they are a better replacement for current participants. For example, replacing a participant by his/her parents or his maternal uncle and paternal aunt gets us two unrelated participants (assuming, of course, that the two sides of the family are not related by blood). Another example could be if a participant is of partial South Asian ancestry and they get replaced by a relative who has more South Asian ancestry.

Everyone else can use DIY HarappaWorld. It's fairly easy to use on both Windows and Linux. The only hard part right now is that you have to install R to standardize your genome file. I might look into creating an executable for that to make it easier.

Finally, please be honest.