Monthly Archives: September 2011

Interactive Tree Generation

Anyone know of any software to generate a javascript (or something) tree/dendrogram for the web which is interactive, i.e. branches can be expanded and collapsed and one can search for different nodes.

I want to use it to generate dendrograms including all Harappa participants and individual reference samples. So we are looking at more than 4,000 nodes on the tree.

Related Reading:

Admixture (Ref3 K=11) HRP0161-HRP0170

Here are the admixture results using Reference 3 for Harappa participants HRP0161 to HRP0170.

You can see the participant results in a spreadsheet as well as their ethnic breakdowns and the reference population results.

Here's our bar chart and table. Remember you can click on the legend or the table headers to sort.

If the above interactive charts are not working, here's a static bar graph.

HRP0161 is my mom.

HRP0169 is our first 100% Sri Lankan Tamil. Admixture results are close to the other non-Brahmin Tamils.

HRP0170 is a Haryana Jatt whose results match the other Haryana/UP Jatt.

Related Reading:

ANI/ASI Admixture Dating

Via Razib, here's an interesting abstract from the International Congress of Human Genetics by David Reich's group:

Estimating a date of mixture of ancestral South Asian populations.

Linguistic and genetic studies have shown that most Indian groups have ancestry from two genetically divergent populations, Ancestral North Indians (ANI) and Ancestral South Indians (ASI). However, the date of mixture still remains unknown. We analyze genome-wide data from about 60 South Asian groups using a newly developed method that utilizes information related to admixture linkage disequilibrium to estimate mixture dates. Our analyses suggest that major ANI-ASI mixture occurred in the ancestors of both northern and southern Indians 1,200-3,500 years ago, overlapping the time when Indo-European languages first began to be spoken in the subcontinent. These results suggest that this formative period of Indian history was accompanied by mixtures between two highly diverged populations, although our results do not rule other, older ANI-ASI admixture events. A cultural shift subsequently led to widespread endogamy, which decreased the rate of additional population mixtures.

I would be very interested in reading that paper. Also, I wonder how many new samples did they genotype beyond the ones in Reich et al' Reconstructing Indian Population History and if I could get my hands on the new data.

I have a feeling that ANI (Ancestral North Indian) captures a bunch of different migrations and conquests etc, so I am not sure if it can be equated to Indo-European language movement.

I wonder if I can use HAPMIX or StepPCO to get similar admixture dating.

Related Reading: